CONGEN manual                                              February 1981
CONGEN manual                                              February 1981


                           Table of Contents
                           Table of Contents
                           Table of Contents
                           Table of Contents





Section                                                             Page




I.    INTRODUCTION            .  .  .  .  .  .  .  .  .  .  .  .  .  . 2

    I.A    Basic CONGEN Concepts .  .  .  .  .  .  .  .  .  .  .  .  . 2

    I.B    Normal Sequence of Commands .  .  .  .  .  .  .  .  .  .  . 8

    I.C    How to Start CONGEN   .  .  .  .  .  .  .  .  .  .  .  .   10


II.   Sample CONGEN Session   .  .  .  .  .  .  .  .  .  .  .  .  .   12


III.  CONGEN Input            .  .  .  .  .  .  .  .  .  .  .  .  .   31


IV.   CONGEN Commands         .  .  .  .  .  .  .  .  .  .  .  .  .   34

    IV.A   Glossary of CONGEN Commands .  .  .  .  .  .  .  .  .  .   35

    IV.B   DEFINE and Subcommands   .  .  .  .  .  .  .  .  .  .  .   38

         IV.B.1  Glossary of DEFINE Subcommands .  .  .  .  .  .  .   40

         IV.B.2  DEFINE TERMTYPE .  .  .  .  .  .  .  .  .  .  .  .   41

         IV.B.3  DEFINE MOLFORM  .  .  .  .  .  .  .  .  .  .  .  .   43

         IV.B.4  DEFINE ATOM  .  .  .  .  .  .  .  .  .  .  .  .  .   46

         IV.B.5  DEFINE AROMATICS   .  .  .  .  .  .  .  .  .  .  .   48

         IV.B.6  DEFINE SUBSTRUCTURE   .  .  .  .  .  .  .  .  .  .   51

              IV.B.6.a  Introduction to Editstruc  .  .  .  .  .  .   54

              IV.B.6.b  Glossary of Editstruc Commands   .  .  .  .   57

              IV.B.6.c  SHOW  .  .  .  .  .  .  .  .  .  .  .  .  .   60

              IV.B.6.d  DRAW  .  .  .  .  .  .  .  .  .  .  .  .  .   61

              IV.B.6.e  GET   .  .  .  .  .  .  .  .  .  .  .  .  .   64



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CONGEN manual                                              February 1981


              IV.B.6.f  CHAIN .  .  .  .  .  .  .  .  .  .  .  .  .   67

              IV.B.6.g  RING  .  .  .  .  .  .  .  .  .  .  .  .  .   69

              IV.B.6.h  BRANCH   .  .  .  .  .  .  .  .  .  .  .  .   72

              IV.B.6.i  LINK  .  .  .  .  .  .  .  .  .  .  .  .  .   74

              IV.B.6.j  JOIN  .  .  .  .  .  .  .  .  .  .  .  .  .   78

              IV.B.6.k  BORD  .  .  .  .  .  .  .  .  .  .  .  .  .   80

              IV.B.6.l  UNJOIN   .  .  .  .  .  .  .  .  .  .  .  .   83

              IV.B.6.m  ATNAME   .  .  .  .  .  .  .  .  .  .  .  .   86

              IV.B.6.n  HRANGE   .  .  .  .  .  .  .  .  .  .  .  .   91

              IV.B.6.o  FREEV .  .  .  .  .  .  .  .  .  .  .  .  .   94

              IV.B.6.p  TAG   .  .  .  .  .  .  .  .  .  .  .  .  .   98

              IV.B.6.q  LNODE .  .  .  .  .  .  .  .  .  .  .  .  .  101

              IV.B.6.r  ARTYPE   .  .  .  .  .  .  .  .  .  .  .  .  104

              IV.B.6.s  ERASE .  .  .  .  .  .  .  .  .  .  .  .  .  107

              IV.B.6.t  DONE  .  .  .  .  .  .  .  .  .  .  .  .  .  113

              IV.B.6.u  HALT  .  .  .  .  .  .  .  .  .  .  .  .  .  114

    IV.C   FIX and Subcommands   .  .  .  .  .  .  .  .  .  .  .  .  116

    IV.D   SEARCH and Subcommands   .  .  .  .  .  .  .  .  .  .  .  123

         IV.D.1  SEARCH <library name> .  .  .  .  .  .  .  .  .  .  124

         IV.D.2  SEARCH MYLIB <file name> .  .  .  .  .  .  .  .  .  127

    IV.E   GENERATE           .  .  .  .  .  .  .  .  .  .  .  .  .  129

         IV.E.1  Superatom Input .  .  .  .  .  .  .  .  .  .  .  .  134

         IV.E.2  Constraint Input   .  .  .  .  .  .  .  .  .  .  .  139

              IV.E.2.a  Glossary of Constraint Types  .  .  .  .  .  141

              IV.E.2.b  Substructure Constraints   .  .  .  .  .  .  142

              IV.E.2.c  Proton Constraints   .  .  .  .  .  .  .  .  145

              IV.E.2.d  Ring Constraints  .  .  .  .  .  .  .  .  .  147



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CONGEN manual                                              February 1981


              IV.E.2.e  Loop Constraints  .  .  .  .  .  .  .  .  .  152

              IV.E.2.f  Partial Constraint   .  .  .  .  .  .  .  .  154

    IV.F   PRUNE              .  .  .  .  .  .  .  .  .  .  .  .  .  156

    IV.G   IMBED              .  .  .  .  .  .  .  .  .  .  .  .  .  160

         IV.G.1  Superatom Input .  .  .  .  .  .  .  .  .  .  .  .  167

         IV.G.2  Constraint Input   .  .  .  .  .  .  .  .  .  .  .  172

    IV.H   AROMATIZE          .  .  .  .  .  .  .  .  .  .  .  .  .  173

    IV.I   DRAW               .  .  .  .  .  .  .  .  .  .  .  .  .  179

    IV.J   SHOW and Subcommands  .  .  .  .  .  .  .  .  .  .  .  .  188

         IV.J.1  Glossary of SHOW Subcommands   .  .  .  .  .  .  .  189

         IV.J.2  SHOW CTABLE  .  .  .  .  .  .  .  .  .  .  .  .  .  190

         IV.J.3  SHOW STATUS  .  .  .  .  .  .  .  .  .  .  .  .  .  193

         IV.J.4  SHOW HISTORY .  .  .  .  .  .  .  .  .  .  .  .  .  194

         IV.J.5  SHOW AROMATICS  .  .  .  .  .  .  .  .  .  .  .  .  195

         IV.J.6  SHOW LIBRARY .  .  .  .  .  .  .  .  .  .  .  .  .  196

    IV.K   FORGET             .  .  .  .  .  .  .  .  .  .  .  .  .  200

    IV.L   SAVE               .  .  .  .  .  .  .  .  .  .  .  .  .  203

    IV.M   RESTORE            .  .  .  .  .  .  .  .  .  .  .  .  .  205

    IV.N   SURVEY             .  .  .  .  .  .  .  .  .  .  .  .  .  207

         IV.N.1  SURVEY First Sample Session .  .  .  .  .  .  .  .  209

         IV.N.2  SURVEY Subcommand Mode   .  .  .  .  .  .  .  .  .  212

              IV.N.2.a  Glossary of SURVEY Subcommands   .  .  .  .  214

              IV.N.2.b  SELECT Command Format   .  .  .  .  .  .  .  215

         IV.N.3  SURVEY Second Sample Session   .  .  .  .  .  .  .  216

    IV.O   STEREO and Subcommands   .  .  .  .  .  .  .  .  .  .  .  221

         IV.O.1  Glossary of STEREO Subcommands .  .  .  .  .  .  .  222

         IV.O.2  STEREO Sample Session .  .  .  .  .  .  .  .  .  .  223



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CONGEN manual                                              February 1981


    IV.P   EXIT               .  .  .  .  .  .  .  .  .  .  .  .  .  229


V.    Substructures in CONGEN .  .  .  .  .  .  .  .  .  .  .  .  .  230

    V.A    Superatoms         .  .  .  .  .  .  .  .  .  .  .  .  .  233

    V.B    Substructures as Constraints   .  .  .  .  .  .  .  .  .  235


VI.   Structure Generation in CONGEN   .  .  .  .  .  .  .  .  .  .  237


VII.  Constraints in CONGEN   .  .  .  .  .  .  .  .  .  .  .  .  .  239


VIII. Imbedding in CONGEN     .  .  .  .  .  .  .  .  .  .  .  .  .  246


IX.   Aromaticity in CONGEN   .  .  .  .  .  .  .  .  .  .  .  .  .  248


X.    Tagging in CONGEN       .  .  .  .  .  .  .  .  .  .  .  .  .  250


XI.   Link Nodes in CONGEN    .  .  .  .  .  .  .  .  .  .  .  .  .  253


    Index                     .  .  .  .  .  .  .  .  .  .  .  .  .  255



























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CONGEN manual                                              February 1981


                         **********
                         *        *
                         * CONGEN *
                         *        *
                         **********



                USER'S MANUAL - DRAFT VERSION
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ughout  the  document  we  have  accompanied  explanation of
various commands with detailed examples of actual input to and responses
from CONGEN to commands and error conditions.  Depending on the printing
medium used to reproduce the document, the input which would be typed by
you in all the examples is indicated in bold face type or is underlined.
Output by the program is in normal text.  In most cases, the input is in
lower case type while the output by CONGEN is in upper case.  This helps
differentiate the  two and  makes the document  easier to  read.  CONGEN
will  accept input  in  either upper  or  lower case,  however.   In the
examples we have frequently added  blank lines between lines of  text as
another way of making the document easier to read.












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CONGEN manual                                              February 1981


        I    INTRODUCTION
             INTRODUCTION
             INTRODUCTION
             INTRODUCTION

                        ****************
                        *              *
                        * INTRODUCTION *
                        *              *
                        ****************




        I.A    Basic CONGEN Concepts
               Basic CONGEN Concepts
               Basic CONGEN Concepts
               Basic CONGEN Concepts

                *************************
                *                       *
                * Basic CONGEN Concepts *
                *                       *
                *************************


        The CONGEN program (CONstrained structure GENerator) is designed
to  aid  the  structural  chemist  in  arriving  at  a  set  of possible
structures  ("candidates")  for  an  unknown  compound  based  upon your
analysis of spectroscopic and chemical data.  It is assumed that through
this analysis that  you have determined  the molecular formula  and have
drawn  a  number  of  conclusions  about  the  presence  or  absence  of
substructural features in the unknown molecule.  The assistance provided
by  CONGEN is  to discover,  using a  structure generator,  all  ways of
combining  the atoms  of the  molecular formula  into  complete chemical
structures which  are consistent  with these  conclusions.  We  refer to
these conclusions as constraints  because within the program  they serve
                     constraints
                     constraints
                     constraints
to restrict, or constrain, the structure generator to  produce (usually)
only a  tiny fraction  of the  vast number  of structural  isomers which
could possibly be built from the atoms of the molecular formula.

        Constraints  are  of  two  general  types,  referred  to  in the
subsequent discussion as  required and forbidden.   Required constraints
                          required     forbidden
                          required     forbidden
                          required     forbidden
are features which are believed to be present in the  unknown structure,
and which thus are required  to be present in the  generated candidates.
For example, spectral  data may indicate  the presence of  certain well-
characterized functional groupings such as amides or phenyl rings,  or a
sequence of spin-decoupling NMR experiments may have allowed the chemist
to  "map out"  the detailed  structure of  one or  more portions  of the
unknown.  Forbidden constraints are features whose presence can be ruled
out on the basis of  either available data or general  considerations of
chemical stability.  For example, spectra obtained from the  unknown may
lack certain  characteristic features which  would have been  present if
certain functional groups such as ketones or cyclopropyl  rings occurred
in  the  molecule.  Also,  CONGEN  does  not have  a  built-in  sense of
chemical stability,  and will produce  highly strained ring  systems and
other unstable  groupings such as  cyclobutadienes and  peroxides unless
these  possibilities are  expressly  ruled out.   It may  seem  that the




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CONGEN manual                                              February 1981


number of these  unstable substructures could  be enormous, but  for any
given CONGEN  problem, it  is usually  necessary to  specify only  a few
which might arise when all other constraints are satisfied.

        Of course, there must be some way for you chemist to communicate
to the program the  constraints which are applicable to  your particular
problem.  Standard chemical nomenclature provides a means  of expressing
some  features, but  it  is usually  not precise  enough  or unambiguous
enough to allow  you to express especially  complex or subtle  pieces of
structural information.   Thus, while a  "library" is provided  of terms
describing common functional groups,  it is necessary also to  provide a
more general method of defining terms to be used in a  particular CONGEN
problem.  The Editstruc  subprogram supplies this extended  language, in
which the  chemist can build  substructures of arbitrary  complexity and
associate with them names  of his own choosing.  In  Editstruc, commands
are  available to  construct rings  and chains  of atoms,  to  join them
together in  any chosen  fashion, to define  bond multiplicities  and to
associate properties with  atoms such as  atom name, number  of hydrogen
atoms  and  aromaticity.  The  library  of  terms is  simply  a  file of
commonly  used Editstruc  structures, with  chemically  meaningful names
like METHYL and HYDROXYL.
     METHYL     HYDROXYL
     METHYL     HYDROXYL
     METHYL     HYDROXYL

        In order to communicate your problem to CONGEN, you in principle
need only a means of defining the molecular formula, a means of defining
terms  not contained  in the  library and  a means  of  specifying which
substructures  are   required  constraints   and  which   are  forbidden
constraints.  However, because of the way in which CONGEN approaches the
structure  generation problem,  there are  some additional  and somewhat
artificial  concepts  which  need  to be  learned  if  you  are  to make
efficient  use of  the  program.  The  central  new concept  is  that of
Superatoms, which are polyatomic fragments (e.g., a benzene  ring) which
Superatoms
Superatoms
Superatoms
are used as "building  blocks" in much the  same way as are  atoms.  The
advantage  of  using  Superatoms  for  structure  generation  is  easily
understood; if a given substructure  is known to be present, it  is much
more  efficient   to  use  that   substructure  as  a   building  block,
incorporating it a priori  into the structures, rather than  to generate
                 a priori
                 a priori
                 a priori
using  only  the  molecular formula,  constantly  testing  the resulting
structures for the presence of the desired substructure.  Superatoms are
conceptually  quite close  to required  constraints, with  the exception
that Superatoms are  not allowed to  overlap one another  while required
constraints may overlap arbitrarily.  For example, naphthalene cannot be
built from  two benzene  ring Superatoms,  but it  would survive  a test
requiring the presence of  two benzene ring substructures.  Part  of the
current DENDRAL research is  devoted to exploring ways of  removing this
distinction between Superatoms  and required constraints  without giving
up the efficiencies provided by the Superatom concept.

        A further  artificiality is  introduced by  the specific  way in
which CONGEN deals with Superatoms.  The structure  generation algorithm
is not capable of dealing directly with these polyatomic  fragments, but
can  only  construct  structures  out  of  single  "atoms"  of specified
valences.   What  actually happens,  then,  is that  the  Superatoms are




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CONGEN manual                                              February 1981


initially "collapsed" and considered to be just single atoms, with "atom
names" supplied by you and with  "valences" equal to the sum of  all the
available bonding sites in  the fragment.  For example, suppose  you had
used  Editstruc to  define the  term R6  to be  a cyclohexane  ring with
                                     R6
                                     R6
                                     R6
twelve  valences left  "free" to  bond to  other atoms.   If R6  is then
                                                             R6
                                                             R6
                                                             R6
specified as a Superatom, CONGEN  will initially take R6 to be  a single
                                                      R6
                                                      R6
                                                      R6
atom of  valence twelve.  If  the molecular formula  were C8H16  in this
case, there would  also be two carbons  and 16 hydrogens to  be combined
with R6. Only two structures, 1
     R6.                      1
     R6.                      1
     R6.                      1

                  C-R6-C           R6-C-C

                     1                2
                     1                2
                     1                2
                     1                2
and 2, would result from this generation.  (Note that the hydrogen atoms
    2
    2
    2
are "suppressed" in these drawings;  the number of hydrogens on  an atom
is inferred from its valence together with the number of neighbors shown
in  the  drawing.)  Now,  structure  2  represents  only  one  molecule,
                                     2
                                     2
                                     2
ethylcyclohexane, because there is only one way to place an  ethyl group
on the six-membered ring.  However, 1 really represents  four structural
                                    1
                                    1
                                    1
isomers because  the methyl groups  may be attached  around the  ring to
give   1,1-,  1,2-,   1,3-  or   1,4-dimethylcyclohexane.    (There  are
configurational stereochemical isomers  possible for each of  1,2-, 1,3-
and  1,4-dimethylcyclohexane.   These  isomers  can  be  constructed and
examined in a  final step after imbedding,  using the STEREO  command in
                                                      STEREO
                                                      STEREO
                                                      STEREO
CONGEN.)

        Before the structure generation problem is finished,  of course,
the  Superatoms must  be  re-expanded, and  there is  a  special process
called imbedding  to accomplish this.   The imbedder  accepts structures
       imbedding
       imbedding
       imbedding
such  as 1  and  2 and  determines all  unique  ways in  which  this re-
         1       2
         1       2
         1       2
expansion can take place.  In this simple example, we have used only one
Superatom, but the typical CONGEN problem has several.  Structures which
contain  unimbedded Superatoms  are called  intermediate  structures, as
                                            intermediate  structures
                                            intermediate  structures
                                            intermediate  structures
opposed to final structures in which all Superatoms have been expanded.
           final structures
           final structures
           final structures

        It would be  possible for CONGEN  to carry out  these imbeddings
automatically so that you were never aware that a separate procedure was
being invoked.  But intermediate structures usually contain a great deal
of  chemically meaningful  information, and  it is  usually  possible to
phrase constraints which can be applied to these structures  even before
the imbeddings are done. Suppose, for example, that you have defined one
term BZ to represent a benzene ring and another term KET to  represent a
     BZ                                              KET
     BZ                                              KET
     BZ                                              KET
ketone (C=O) functionality, and  have specified these to  be Superatoms.
        C=O
        C=O
        C=O
If  you also  have  information, say  from  a UV  spectrum,  telling you
whether or not the ketone  is conjugated with the benzene ring,  you may
be  able  to  say  something  about  the  presence  or  absence  of  the
"substructure" BZ-KET in intermediate structures.  For this  example, as
               BZ-KET
               BZ-KET
               BZ-KET
for most CONGEN problems,  it is very useful  to give you access  to the
intermediate  structures and  to allow  you control  over  the imbedding
process (i.e., the  decision of which Superatoms  are to be  imbedded at
which  points  in  the  session).   In  this  way,  you  are  given many
opportunities  during  the  session  to  examine,  and  perhaps  further




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CONGEN manual                                              February 1981


constrain, the  generation problem.  But  with this  greater flexibility
comes  an increased  responsibility  to consider  carefully  the precise
phrasing of constraints, keeping in mind that when CONGEN  applies these
constraints to intermediate  structures, it "thinks" the  Superatoms are
just ordinary atoms with odd names and peculiar valences.   For example,
in the BZ-KET case above, you  might wish to specify that the  ketone is
       BZ-KET
       BZ-KET
       BZ-KET
in fact conjugated with the  benzene ring.  The temptation is  to phrase
this  constraint  as the  required  substructure C'-C=O  (where  C' here
                                                 C'-C=O          C'
                                                 C'-C=O          C'
                                                 C'-C=O          C'
represents an aromatic carbon  atom).  Although this is  the appropriate
phrasing of the constraint for final structures, it will  not accomplish
the  desired  effect for  the  intermediate structures  in  which  C' is
                                                                   C'
                                                                   C'
                                                                   C'
"hidden"  within BZ  and C=O  is "hidden"  within KET.   The appropriate
                 BZ      C=O                      KET
                 BZ      C=O                      KET
                 BZ      C=O                      KET
phrasing is to require the presence of the two-atom  substructure BZ-KET
                                                                  BZ-KET
                                                                  BZ-KET
                                                                  BZ-KET
in  the intermediate  structures.   Thus, when  applied  to intermediate
structures, constraints  must usually be  translated to account  for the
fact  that  many  details  of  the  structures  are  hidden  within  the
Superatoms, and will not be directly accessible until the Superatoms are
imbedded.

        There  are  two  somewhat  unexpected  features  of intermediate
structures which deserve special mention.  First, a multiple  bond which
appears  in such  a structure  does not  necessarily represent  a "real"
multiple bond.  Consider, for example, the Superatom R6 (mentioned above
                                                     R6
                                                     R6
                                                     R6
- a cyclohexane ring with twelve free valences) in a  generation problem
for which  the molecular  formula is  C8H14.  One  possible intermediate
structure is 3, in which the "double bond" C=R6
             3                             C=R6
             3                             C=R6
             3                             C=R6

                      C=R6-C

                        3
                        3
                        3
                        3
appears.  This should be interpreted as meaning that there are two bonds
from that carbon to atoms within  R6, but that the two bonds may  or may
                                  R6
                                  R6
                                  R6
not be "split apart" into  two single bonds.  If given structure  3, the
                                                                  3
                                                                  3
                                                                  3
imbedder  would  produce twelve  final  structures some  of  which would
contain multiple bonds  (for example, 4 and  5) and some of  which would
                                      4      5
                                      4      5
                                      4      5
not (for example, 6 and 7).  If you
                  6     7
                  6     7
                  6     7




















                                   5
CONGEN manual                                              February 1981


         C-C           C-C         C-C         C-C
        /   \         /   \       /   \       / \ \
     C=C     C     C=C     C     C     C     C   C C-C
        \   /         \   /      |\   /       \  |/
         C-C           C-C       C-C-C         C-C
        /                 \        |
       C                   C       C

          4             5           6           7
          4             5           6           7
          4             5           6           7
          4             5           6           7

knew that there  were no double bonds  in this unknown, you  might think
that 3 should be eliminated as an intermediate structure, but clearly it
     3
     3
     3
should not be.  The appropriate  time for testing for multiple  bonds is
during (or after) the imbedding of R6 in this case.
                                   R6
                                   R6
                                   R6

        A  second  feature  of  intermediate  structures  is  even  more
unusual:  there may  be  bonds which  connect a  Superatom  with itself.
These  self-bonds  are  called  internal  bonds  or  loops  and  have no
                                internal  bonds      loops
                                internal  bonds      loops
                                internal  bonds      loops
counterpart  in final  structures.  Internal  bonds in  a  Superatom, or
intra-superatom  bonds,   are  interpreted   as  bonds   which  directly
interconnect two free valences  within the Superatom.  For  example, the
intermediate  structure  8, in  which  the symbol  "i"  stands  for "one
                         8
                         8
                         8
internal

                          C-R6-C
                            |
                            i

                            8
                            8
                            8
                            8

bond",  is  one  which  would be  produced  by  the  generator  from the
molecular  formula  C8H14  and  the  Superatom  R6.   This  structure is
                                                R6
                                                R6
                                                R6
interpreted to mean that there are two methyl groups attached to  R6 and
                                                                  R6
                                                                  R6
                                                                  R6
that in  addition there is  a bond connecting  two of the  free valences
within R6.  The imbedder recognizes these loops, and part of its task is
       R6
       R6
       R6
to find all unique ways of forming such interconnections while imbedding
the  Superatom.   Among the  structures  produced by  the  imbedder from
structure 8 would be structures 9-11.  In some cases you
          8                     9 11
          8                     9 11
          8                     9 11

                C              C-C                      C
                |              |/ \                    /
            C-C-C-C            C   C-C            C-C-C
            | | |               \  |              | | |
            C-C-C                C-C              C-C-C
                                 |                     \
                                 C                      C

              9                  10                 11
              9                  10                 11
              9                  10                 11
              9                  10                 11

have information  which restricts the  possible distributions  of loops,
and there is a special type of constraint for expressing restrictions of
this kind.




                                   6
CONGEN manual                                              February 1981


        To  the  chemist who  is  interested in  experimenting  with the
CONGEN program,  the concepts  outlined above  must be  well understood.
The interested reader  who wishes to get  a better understanding  of the
concepts and see their application to sample problems is referred to the
following publications:

        1) R. E. Carhart, D. H. Smith, H. Brown and C. Djerassi,  J. Am.
                                                                  J. Am.
                                                                  J. Am.
                                                                  J. Am.
Chem. Soc., 97, 5755 (1975).
Chem. Soc.  97
Chem. Soc.  97
Chem. Soc.  97

        2)  C. J.  Cheer, D.  H. Smith,  C. Djerassi,  B. Tursch,  J. C.
Braekman and D. Daloze, Tetrahedron, 32, 1807 (1976).
                        Tetrahedron  32
                        Tetrahedron  32
                        Tetrahedron  32

        These publications deal with an older version of CONGEN  but the
concepts  and  procedures are  quite  similar to  those  of  the current
version.









































                                   7
CONGEN manual                                              February 1981


        I.B    Normal Sequence of Commands
               Normal Sequence of Commands
               Normal Sequence of Commands
               Normal Sequence of Commands

                *******************************
                *                             *
                * Normal Sequence of Commands *
                *                             *
                *******************************


        The  normal  sequence  of commands  for  analyzing  a structural
problem is presented in this section.  However, commands for any problem
may be issued in any order; we present here a generally useful sequence.
CONGEN  will  respond with  appropriate  error messages  if  you  try to
perform a task in the program which makes no sense at the point  you try
it.

        1) Define to CONGEN  all relevant "chemistry" for  your problem.
This  includes the  molecular formula,  names and  valences of  new atom
types, and  names and  definitions of  substructures inferred  from your
data, to  be used as  Superatoms to construct  structural isomers  or as
constraints to force CONGEN  to construct just the structural  types you
desire.  There  are two  mechanisms for  defining such  information, the
CONGEN  commands  DEFINE  and  SEARCH,  the  latter  used   to  retrieve
                  DEFINE       SEARCH
                  DEFINE       SEARCH
                  DEFINE       SEARCH
predefined substructures from files. Also, the CONGEN command FIX may be
                                                              FIX
                                                              FIX
                                                              FIX
used to correct erroneous definitions.  See:

        DEFINE       Section IV.B
        DEFINE
        DEFINE
        DEFINE
        SEARCH       Section IV.D
        SEARCH
        SEARCH
        SEARCH
        FIX          Section IV.C
        FIX
        FIX
        FIX


        2)  Generate intermediate  structures using  the  CONGEN command
GENERATE.   This  command encompasses  specification  of  Superatoms and
GENERATE
GENERATE
GENERATE
constraints. See:

        GENERATE     Section IV.E
        GENERATE
        GENERATE
        GENERATE


        3) Save your results  on a named file  at this point and  at any
other point where significant computations have been carried  out, using
the CONGEN command SAVE.  See:
                   SAVE
                   SAVE
                   SAVE

        SAVE         Section IV.L
        SAVE
        SAVE
        SAVE


        4) Draw a selection of the generated structures using the CONGEN
command  DRAW.   Use the  CONGEN  commands PRUNE  or  FORGET  to discard
         DRAW                              PRUNE      FORGET
         DRAW                              PRUNE      FORGET
         DRAW                              PRUNE      FORGET
unwanted structures.  See:

        DRAW         Section IV.I
        DRAW
        DRAW
        DRAW
        PRUNE        Section IV.F
        PRUNE
        PRUNE
        PRUNE
        FORGET       Section IV.K
        FORGET
        FORGET
        FORGET




                                   8
CONGEN manual                                              February 1981


        5)  Use  the  CONGEN  command  IMBED  to  expand  Superatoms  in
                                       IMBED
                                       IMBED
                                       IMBED
intermediate structures back to  their complete form.  This may  be done
in one or more steps,  each involving a sequence IMBED, DRAW,  PRUNE and
                                                 IMBED  DRAW   PRUNE
                                                 IMBED  DRAW   PRUNE
                                                 IMBED  DRAW   PRUNE
SAVE, where appropriate.  See:
SAVE
SAVE
SAVE

        IMBED        Section IV.G
        IMBED
        IMBED
        IMBED


        6) At any  point, but usually after  GENERATE or IMBED,  use the
                                             GENERATE    IMBED
                                             GENERATE    IMBED
                                             GENERATE    IMBED
AROMATIZE  command  (in  problems  where  aromaticity  is  relevant)  to
AROMATIZE
AROMATIZE
AROMATIZE
introduce or modify the concept of aromaticity. See:

        AROMATIZE    Section IV.H
        AROMATIZE
        AROMATIZE
        AROMATIZE


        7)  At  any  point,  but  usually  only  when   complete,  final
structures are in  hand, use the CONGEN  commands SURVEY, to  peruse the
                                                  SURVEY
                                                  SURVEY
                                                  SURVEY
list   of   structures,   and   STEREO,   to   explore   configurational
                                STEREO
                                STEREO
                                STEREO
stereochemical isomers of one or more structures or substructures.  See:

        SURVEY       Section IV.N
        SURVEY
        SURVEY
        SURVEY
        STEREO       Section IV.O
        STEREO
        STEREO
        STEREO


        8) Use the CONGEN command  SHOW to get a summary of  the current
                                   SHOW
                                   SHOW
                                   SHOW
status of you problem.  Use the CONGEN command EXIT, saving your session
                                               EXIT
                                               EXIT
                                               EXIT
if you have not already done so, to terminate your session at  any point
in the above  sequence.  Use the CONGEN  command RESTORE to  recover any
                                                 RESTORE
                                                 RESTORE
                                                 RESTORE
problem  at  the point  at  which you  exited  in order  to  continue an
uncompleted problem.  See:

        SHOW         Section IV.J
        SHOW
        SHOW
        SHOW
        EXIT         Section IV.P
        EXIT
        EXIT
        EXIT
        RESTORE      Section IV.M
        RESTORE
        RESTORE
        RESTORE






















                                   9
CONGEN manual                                              February 1981


        I.C    How to Start CONGEN
               How to Start CONGEN
               How to Start CONGEN
               How to Start CONGEN

                       ************************
                       *                      *
                       * How to Start CONGEN  *
                       *                      *
                       ************************


        The  following  describes  the commands  required  to  start the
CONGEN  program once  you have  completed the  log-in procedures  on the
computer system you are using.

@congen                 If logged in at SUMEX as GUEST
 congen
 congen
 congen

                or

@<carhart>congen        If logged in at SUMEX on another account
 <carhart>congen
 <carhart>congen
 <carhart>congen

                or

@ru congen              If using CONGEN on another DEC PDP-10 or -20
 ru congen
 ru congen
 ru congen
                          operating a standard DEC operating system.
                or        Note that an "extension" may be necessary,
                          e.g., run congen.sav, depending on the
                                run congen.sav
                                run congen.sav
                                run congen.sav
@run congen               extension given to the program name when
 run congen
 run congen
 run congen
                          CONGEN was loaded onto the system.

WELCOME TO CONGEN VERSION VI            CONGEN responds

CONGEN IS A PROGRAM FOR COMPUTER-ASSISTED STRUCTURE ELUCIDATION
DEVELOPED WITH NIH SUPPORT BY THE DENDRAL GROUP AT STANFORD

                                        CONGEN queries

DO YOU WANT TO RECORD YOUR SESSION?:yes
                                    yes
                                    yes
                                    yes

                        You will accumulate a complete record of your
                          CONGEN session for future reference, a
                          "laboratory notebook" entry, if you will.
                          This recording also will help all of us
                          determine causes of any problems which arise
                          during use of CONGEN.  The recording file is
                          saved in a repository on SUMEX.  If you are
                          using CONGEN on a TOPS-10 machine, the EXIT
                                                                 EXIT
                                                                 EXIT
                                                                 EXIT
                          command (Section IV.P) will ask you for the
                          file name in which to save the recording

PLEASE TYPE YOUR NAME:john doe - compound w - August 30,1979, 10 AM
                      john doe - compound w - August 30,1979, 10 AM
                      john doe - compound w - August 30,1979, 10 AM
                      john doe - compound w - August 30,1979, 10 AM

                        Any text up to 79 characters without blanks,
                          maximum 95 characters.  This is not used for
                          a file name, only a heading for the recording



                                   10
CONGEN manual                                              February 1981


                          file

                or

DO YOU WANT TO RECORD YOUR SESSION?:no
                                    no
                                    no
                                    no

                        There is seldom reason to answer no

#?                      CONGEN symbol "#" - ready to accept input;
 ?
 ?
 ?
                          type ? for help on options

GENERATE IMBED PRUNE DRAW DEFINE FIX SHOW FORGET     CONGEN replies
SEARCH SAVE RESTORE EXIT SURVEY STEREO AROMATIZE

                ******************************









































                                   11
CONGEN manual                                              February 1981


        II    Sample CONGEN Session
              Sample CONGEN Session
              Sample CONGEN Session
              Sample CONGEN Session

                *************************
                *                       *
                * Sample CONGEN Session  *
                *                       *
                *************************


        The following  is an  annotated typescript  of a  CONGEN session
which parallels  the structure elucidation  problem described  by Cheer,
et. al (C. J. Cheer, D. H. Smith, C. Djerassi, B. Tursch, J. C. Braekman
and D. Daloze, Tetrahedron, 32, 1807 (1976)) of [+]-Palustrol.   Much of
               Tetrahedron  32
               Tetrahedron  32
               Tetrahedron  32
the  typescript consists  of  messages printed  by the  program  for the
user's  information, and  only a  small fraction  is typed  by  the user
himself.  To  help distinguish  the latter from  the former,  the user's
input appears underlined or in  bold face, depending on the  medium used
for  reproduction  of  the  document.   At  the  end  of  each  line  of
information provided by  the user, he has  also typed a  carriage return
which  is not  explicitly  represented but  which is  needed  before the
program  begins its  interpretation of  the typed  instructions  on that
line.   Annotations are  offset  from the  left margin  and  are written
primarily in lower case type.

        First, the user starts  CONGEN.  The program types  # indicating
its readiness to accept commands.  The user types ? to see a  summary of
his options.

@CONGEN                         A greeting from CONGEN will precede the
 CONGEN
 CONGEN
 CONGEN
                                  CONGEN # prompt
#?
 ?
 ?
 ?
GENERATE IMBED PRUNE DRAW DEFINE FIX SHOW FORGET
SEARCH SAVE RESTORE EXIT SURVEY STEREO AROMATIZE


        A  CONGEN  session typically  begins  with a  definition  of the
molecular formula.  Here, the user types ? to see an explanation of what
input is expected. DEFINE MOLFORM could also be typed on one line.
                   DEFINE MOLFORM
                   DEFINE MOLFORM
                   DEFINE MOLFORM

#DEFINE
 DEFINE
 DEFINE
 DEFINE
DEFINITION TYPE:?
                ?
                ?
                ?
ATOM SUBSTRUCTURE AROMATICS MOLFORM TERMTYPE
DEFINITION TYPE:MOLFORM
                MOLFORM
                MOLFORM
                MOLFORM
MOLECULAR FORMULA:?
                  ?
                  ?
                  ?
A LIST OF ATOM NAMES AND QUANTITIES (ONES MAY BE OMITTED), SEPARATED
BY BLANKS OR COMMAS (E.G., C 4 H 5 BR)
MOLECULAR FORMULA:C 15 H 26 O
                  C 15 H 26 O
                  C 15 H 26 O
                  C 15 H 26 O
MOLECULAR FORMULA DEFINED


        Now the user  wishes to define  the substructures which  will be
needed later  on, starting  with a  substructure called  (arbitrarily) A




                                   12
CONGEN manual                                              February 1981


which will  be a  Superatom, one  of the  inferred substructures  of the
unknown compound.  Note that the user anticipates the prompt "DEFINITION
TYPE:" and includes  the response "SUBSTRUCTURE"  as part of  the DEFINE
                                   SUBSTRUCTURE                   DEFINE
                                   SUBSTRUCTURE                   DEFINE
                                   SUBSTRUCTURE                   DEFINE
command.  Seeing that the information has already been  supplied, CONGEN
does not  type out that  prompt.  All commands  can be extended  in this
way, e.g.,  DEFINE SUBSTRUCTURE A  will obviate any  additional prompts.
            DEFINE SUBSTRUCTURE A
            DEFINE SUBSTRUCTURE A
            DEFINE SUBSTRUCTURE A
Unambiguous short forms of keywords such as DEFINE also work, e.  g., DE
                                            DEFINE                    DE
                                            DEFINE                    DE
                                            DEFINE                    DE
S A.
S A
S A
S A

#DEFINE SUBSTRUCTURE
 DEFINE SUBSTRUCTURE
 DEFINE SUBSTRUCTURE
 DEFINE SUBSTRUCTURE
NAME:?
     ?
     ?
     ?
A NAME (OTHER THAN X OR H) WHICH HAS
NOT PREVIOUSLY BEEN DEFINED
NAME:A
     A
     A
     A
(NEW SUBSTRUCTURE)


        The >  prompt indicates that  the structure editor  Editstruc is
ready to accept commands.  After looking at the options, the user begins
by building a ring of  three carbon atoms, drawing it in  numbered form,
placing a one-carbon branch  onto atom 1 and drawing  again.  Extensions
and short forms work here also, e. g., RING 3, DRAW N.
                                       RING 3, DRAW N
                                       RING 3, DRAW N
                                       RING 3, DRAW N

>?
 ?
 ?
 ?
CHAIN  RING   BRANCH LINK   JOIN   BORD
ATNAME HRANGE FREEV  TAG    LNODE  ARTYPE
UNJOIN ERASE  SHOW   DRAW   GET    DONE   HALT
>RING
 RING
 RING
 RING
RING SIZE:?
          ?
          ?
          ?
AN INTEGER GREATER THAN ZERO
RING SIZE:3
          3
          3
          3
>DRAW
 DRAW
 DRAW
 DRAW
TYPE OF DRAWING:?
                ?
                ?
                ?
NUMBERED ATNAMED
TYPE OF DRAWING:NUMBERED
                NUMBERED
                NUMBERED
                NUMBERED

SUBSTRUCTURE A:

2-3
 \|
  1

>BRANCH
 BRANCH
 BRANCH
 BRANCH
FROM ATOM:1
          1
          1
          1
LENGTH OF BRANCH:1
                 1
                 1
                 1
>DRAW NUMBERED
 DRAW NUMBERED
 DRAW NUMBERED
 DRAW NUMBERED

SUBSTRUCTURE A:

4-1-3
   \|
    2




                                   13
CONGEN manual                                              February 1981


        The  user is  now familiar  with the  BRANCH command  and "types
                                              BRANCH
                                              BRANCH
                                              BRANCH
ahead"  the responses  to  its prompts.   In the  second  BRANCH command
                                                          BRANCH
                                                          BRANCH
                                                          BRANCH
below, he supplies  two sets of responses  to these prompts on  the same
line.   Editstruc  will interpret  "BRANCH  2  1 3  1"  as  two separate
                                    BRANCH  2  1 3  1
                                    BRANCH  2  1 3  1
                                    BRANCH  2  1 3  1
commands, "BRANCH 2 1" followed by "BRANCH 3 1".  All Editstruc commands
           BRANCH 2 1               BRANCH 3 1
           BRANCH 2 1               BRANCH 3 1
           BRANCH 2 1               BRANCH 3 1
may be given multiple sets of responses in this fashion.

>BRANCH 1 1
 BRANCH 1 1
 BRANCH 1 1
 BRANCH 1 1
>BRANCH 2 1 3 1
 BRANCH 2 1 3 1
 BRANCH 2 1 3 1
 BRANCH 2 1 3 1
>DRAW NUMBERED
 DRAW NUMBERED
 DRAW NUMBERED
 DRAW NUMBERED

SUBSTRUCTURE A:

4     7
 \   /
  1-3
 / \|
5   2
     \
      6



        The  HRANGE command  is  used to  associate with  each  atom the
             HRANGE
             HRANGE
             HRANGE
appropriate  number of  hydrogens.  In  this case,  the number  is known
precisely for each  atom, but in general  any range consistent  with the
valences of the atoms may be used.

>HRANGE
 HRANGE
 HRANGE
 HRANGE
ATOM:4
     4
     4
     4
MINIMUM NUMBER OF H'S:3
                      3
                      3
                      3
MAXIMUM NUMBER OF H'S:3
                      3
                      3
                      3
>HRANGE 5 3 3 6 1 1 7 2 2 2 1 1 3 1 1 1 0 0
 HRANGE 5 3 3 6 1 1 7 2 2 2 1 1 3 1 1 1 0 0
 HRANGE 5 3 3 6 1 1 7 2 2 2 1 1 3 1 1 1 0 0
 HRANGE 5 3 3 6 1 1 7 2 2 2 1 1 3 1 1 1 0 0
>DRAW ATNAMED
 DRAW ATNAMED
 DRAW ATNAMED
 DRAW ATNAMED

SUBSTRUCTURE A:(HRANGES NOT INDICATED)

C     C
 \   /
  C-C
 / \|
C   C
     \
      C



        The drawings  do not  show HRANGE values,  but the  SHOW command
                                   HRANGE                   SHOW
                                   HRANGE                   SHOW
                                   HRANGE                   SHOW
presents all information about the structure in tabular form.

>SHOW
 SHOW
 SHOW
 SHOW
SUBSTRUCTURE A
ATOM  TYPE NEIGHBORS    HRANGE



                                   14
CONGEN manual                                              February 1981


  1     C    5  4  3  2  0-0
  2     C    6  3  1     1-1
  3     C    7  1  2     1-1
  4     C    1           3-3
  5     C    1           3-3
  6     C    2           1-1
  7     C    3           2-2


        Note that two valences on atom  6, and one on atom 7,  have been
left "free"; the sum of all neighbors (including hydrogen atoms) is less
than the valence on  each of these atoms.   Because A is not  a complete
                                                    A
                                                    A
                                                    A
structure,  but only  a piece  of a  structure, such  free  valences are
needed by  CONGEN to identify  the sites in  the substructure  which are
available  for  forming additional  bonds  to other  parts  of completed
structures.  The HRANGE on each  of these atoms has been  specified with
                 HRANGE
                 HRANGE
                 HRANGE
the maximum number of hydrogens equal to the minimum number, so  none of
the free valences in A will be allowed to bond to hydrogen.  There is an
                     A
                     A
                     A
alternative and sometimes simpler way of specifying free  valences using
the FREEV command.  Instead of the above HRANGE commands, the user could
    FREEV                                HRANGE
    FREEV                                HRANGE
    FREEV                                HRANGE
have used the command  "FREEV 6 2 7  1" and the substructure  would have
                        FREEV 6 2 7  1
                        FREEV 6 2 7  1
                        FREEV 6 2 7  1
had  the  same  meaning.   However, there  are  several  rules  (see the
definition of substructure HEP, below) concerning the  interpretation of
                           HEP
                           HEP
                           HEP
FREEV which need  to be kept  in mind.  HRANGE  is the simpler  and more
FREEV                                   HRANGE
FREEV                                   HRANGE
FREEV                                   HRANGE
general command, though it is sometimes more cumbersome than FREEV.
                                                             FREEV
                                                             FREEV
                                                             FREEV

        Satisfied that the substructure is accurately defined,  the user
leaves  Editstruc with  the DONE  command.  Following  this,  he defines
                            DONE
                            DONE
                            DONE
other  terms B,  ETH, CH3,  CH2 and  CH, all  of which  will be  used as
             B   ETH  CH3   CH2      CH
             B   ETH  CH3   CH2      CH
             B   ETH  CH3   CH2      CH
Superatoms.

>DONE
 DONE
 DONE
 DONE
A DEFINED
#DEFINE SUBSTRUCTURE B
 DEFINE SUBSTRUCTURE B
 DEFINE SUBSTRUCTURE B
 DEFINE SUBSTRUCTURE B
(NEW SUBSTRUCTURE)
>CHAIN
 CHAIN
 CHAIN
 CHAIN
CHAIN LENGTH:2
             2
             2
             2
>ATNAME
 ATNAME
 ATNAME
 ATNAME
ATOM:1
     1
     1
     1
ATOM NAME:O
          O
          O
          O
>HRANGE 1 1 1 2 0 0
 HRANGE 1 1 1 2 0 0
 HRANGE 1 1 1 2 0 0
 HRANGE 1 1 1 2 0 0
>DRAW ATNAMED
 DRAW ATNAMED
 DRAW ATNAMED
 DRAW ATNAMED

SUBSTRUCTURE B:(HRANGES NOT INDICATED)

O-C

>SHOW
 SHOW
 SHOW
 SHOW
SUBSTRUCTURE B
ATOM  TYPE NEIGHBORS HRANGE
  1     O    2        1-1
  2     C    1        0-0
>DONE
 DONE
 DONE
 DONE



                                   15
CONGEN manual                                              February 1981


B DEFINED
#DEFINE SUBSTRUCTURE ETH
 DEFINE SUBSTRUCTURE ETH
 DEFINE SUBSTRUCTURE ETH
 DEFINE SUBSTRUCTURE ETH
(NEW SUBSTRUCTURE)
>CHAIN 2
 CHAIN 2
 CHAIN 2
 CHAIN 2
>HRANGE 1 3 3 2 1 1
 HRANGE 1 3 3 2 1 1
 HRANGE 1 3 3 2 1 1
 HRANGE 1 3 3 2 1 1
>DONE
 DONE
 DONE
 DONE
ETH DEFINED


        The user  also wants  to specify  methyl, methylene  and methine
groups as Superatoms.  Suspecting that these common groups are contained
in the general library (GENLIB), he SHOWs the contents of  that library.
                        GENLIB      SHOW
                        GENLIB      SHOW
                        GENLIB      SHOW
Note that there are many synonymous entries (e. g., ETHYL, ET  and C2H5)
                                                    ETHYL  ET      C2H5
                                                    ETHYL  ET      C2H5
                                                    ETHYL  ET      C2H5
in the library.  Seeing the  desired terms CH, CH2 and CH3  he retrieves
                                           CH  CH2     CH3
                                           CH  CH2     CH3
                                           CH  CH2     CH3
their definitions with SEARCH.  The effect is exactly the same as  if he
                       SEARCH
                       SEARCH
                       SEARCH
had DEFINEd these substructures.
    DEFINEd
    DEFINEd
    DEFINEd

#SHOW LIBRARY GENLIB
 SHOW LIBRARY GENLIB
 SHOW LIBRARY GENLIB
 SHOW LIBRARY GENLIB
THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

***** Note - the SHOW command now outputs a number for each entry *****
                 SHOW
                 SHOW
                 SHOW
*****          See Section IV.J.6, SHOW LIBRARY command        *****
                                   SHOW LIBRARY
                                   SHOW LIBRARY
                                   SHOW LIBRARY

METHYL ME MET CH3 ETHYL ET C2H5 PROPYL PRO PR ISOPROPYL I-PROPYL IPR C1
C2 CH2 C3 CH C4 PRIMARYC SECONDARYC TERTIARYC QUATERNARYC HO OH HYDROXY
HYDROXYL SH THIO THIOL NH2 N1 PRIMARYN NH N2 SECONDARYN N3 TERTIARYN
PRIMARYOH SECONDARYOH TERTIARYOH KET KETO CO ALD PHENYL BENZYL PH
PRIMARYCH3 SECONDARYCH3 TERTIARYCH3 METHYLENE METHINE C=C DB H2C=C
CH2=C CH2=CH CH=CH
#SEARCH GENLIB CH CH2 CH3
 SEARCH GENLIB CH CH2 CH3
 SEARCH GENLIB CH CH2 CH3
 SEARCH GENLIB CH CH2 CH3
CH, CH2 AND CH3 DEFINED


        The user now defines substructure  MET, which will be used  as a
                                           MET
                                           MET
                                           MET
forbidden substructure during the structure generation.  Notice  the way
the  user  "steps  through"  the  prompts  of  the  ATNAME  command when
                                                    ATNAME
                                                    ATNAME
                                                    ATNAME
specifying the "polyname" (CH2 B ETH).
                           CH2 B ETH
                           CH2 B ETH
                           CH2 B ETH

#DEFINE SUBSTRUCTURE MET 
 DEFINE SUBSTRUCTURE MET 
 DEFINE SUBSTRUCTURE MET 
 DEFINE SUBSTRUCTURE MET 
(NEW SUBSTRUCTURE)
>CHAIN 2
 CHAIN 2
 CHAIN 2
 CHAIN 2
>ATNAME 1
 ATNAME 1
 ATNAME 1
 ATNAME 1
ATOM NAME:?
          ?
          ?
          ?
AN ATOM NAME, OR A LEFT PARENTHESIS TO BEGIN A POLYNAME
ATOM NAME:(
          (
          (
          (
(POLY)ATOM NAME:CH2
                CH2
                CH2
                CH2
(POLY)ATOM NAME:B
                B
                B
                B
(POLY)ATOM NAME:EHT
                EHT
                EHT
                EHT
(POLY)ATOM NAME:?
                ?
                ?
                ?
AN ATOM NAME, OR A RIGHT PARENTHESIS OR CARRIAGE RETURN
TO INDICATE THAT THE POLYNAME IS COMPLETE
(POLY)ATOM NAME:)
                )
                )
                )
>SHOW
 SHOW
 SHOW
 SHOW



                                   16
CONGEN manual                                              February 1981


SUBSTRUCTURE MET
ATOM  TYPE NEIGHBORS POLYNAME
  1   POLY   2        (CH2 B EHT)
  2     C    1


        Seeing that he has made an error (by typing EHT instead of ETH),
                                                    EHT
                                                    EHT
                                                    EHT
the  user erases  the name  and specifies  it again.   This time,  he is
familiar with the ATNAME prompts and supplies all the information as the
                  ATNAME
                  ATNAME
                  ATNAME
single "name" (CH2 B ETH).
               CH2 B ETH
               CH2 B ETH
               CH2 B ETH

>ERASE
 ERASE
 ERASE
 ERASE
WHAT TO ERASE:?
              ?
              ?
              ?
ATNAME HRANGE FREEV TAG LNODE ATOM
WHAT TO ERASE:ATNAME
              ATNAME
              ATNAME
              ATNAME
WHICH ATOM?:1
            1
            1
            1
>ATNAME 1 (CH2 B ETH) 2 CH3
 ATNAME 1 (CH2 B ETH) 2 CH3
 ATNAME 1 (CH2 B ETH) 2 CH3
 ATNAME 1 (CH2 B ETH) 2 CH3
>SHOW
 SHOW
 SHOW
 SHOW
SUBSTRUCTURE MET
ATOM  TYPE NEIGHBORS POLYNAME
  1   POLY   2        (CH2 B ETH)
  2   CH3    1
>DONE
 DONE
 DONE
 DONE
MET DEFINED


        All terms needed for  structure generation are now  defined, and
the user issues the GENERATE command.  CONGEN first requests information
                    GENERATE
                    GENERATE
                    GENERATE
about Superatoms, then requests constraints.

#GENERATE
 GENERATE
 GENERATE
 GENERATE
SUPERATOM:A
          A
          A
          A
RANGE OF OCCURRENCES:1
                     1
                     1
                     1
I WAS EXPECTING A WORD
RANGE OF OCCURRENCES:?
                     ?
                     ?
                     ?
PLEASE GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
AT LEAST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL
RANGE OF OCCURRENCES:AT LEAST 1
                     AT LEAST 1
                     AT LEAST 1
                     AT LEAST 1


        The response "AT  LEAST X" here will  cause CONGEN to  include X
                      AT  LEAST X                                      X
                      AT  LEAST X                                      X
                      AT  LEAST X                                      X
Superatoms of the specified type in the intermediate structure, but will
not prohibit the construction of additional substructures of  that type.
For example, if CH3 is used as a Superatom and there are three hydrogens
                CH3
                CH3
                CH3
and  one carbon  available during  generation, the  "AT LEAST  X" option
                                                     AT LEAST  X
                                                     AT LEAST  X
                                                     AT LEAST  X
would allow  the construction  of structures in  which these  atoms were
combined into an additional methyl group (note, however, that  any extra
methyl  groups produced  in this  way would  appear in  the intermediate
structures as  primary carbon  atoms -C, not  as Superatoms  -CH3).  The
                                     -C                      -CH3
                                     -C                      -CH3
                                     -C                      -CH3
"EXACTLY  X" option  is similar,  but prohibits  such extra  copies from
 EXACTLY  X
 EXACTLY  X
 EXACTLY  X




                                   17
CONGEN manual                                              February 1981


being constructed.  The "RANGE X TO Y" option causes the program  to use
                         RANGE X TO Y
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                E GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
NONE     AT LEAST X     AT MOST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL
RANGE OF OCCURRENCES:NONE
                     NONE
                     NONE
                     NONE


        Note  that there  are several  ways of  specifying  the quantity
here.  The options have their usual English meanings; "NONE"  means that
                                                       NONE
                                                       NONE
                                                       NONE
the feature is to be completely avoided, "RANGE X TO Y" means that every
                                          RANGE X TO Y
                                          RANGE X TO Y
                                          RANGE X TO Y
intermediate structure  is to contain  not less than  X nor more  than Y
                                                      X                Y
                                                      X                Y
                                                      X                Y
occurrences  of the  feature,  and the  other options  have  the obvious
meanings.

CONSTRAINT:RING
           RING
           RING
           RING
RING SIZE:2
          2
          2
          2
RANGE OF OCCURRENCES:NONE
                     NONE
                     NONE
                     NONE
CONSTRAINT:RING 3, EXACTLY 1
           RING 3, EXACTLY 1
           RING 3, EXACTLY 1
           RING 3, EXACTLY 1


        The RING constraints are expressed in terms of final structures,
            RING
            RING
            RING




                                   18
CONGEN manual                                              February 1981


not  intermediate structures.   CONGEN does  the  constraint translation
internally  to find  the correct  expression of  these  constraints when
applied to intermediate structures.  One of our goals is to  extend this
automatic constraint translation to the SUBSTRUCTURE constraints, but at
                                        SUBSTRUCTURE
                                        SUBSTRUCTURE
                                        SUBSTRUCTURE
present that remains an unsolved  problem.  Note that the "ring  size" 2
is a generic way of referring to multiple bonds; each multiple bond in a
final  structure counts  as one  "two-membered ring"  regardless  of its
multiplicity.

CONSTRAINT:LOOP
           LOOP
           LOOP
           LOOP
SUPERATOM:A
          A
          A
          A
RANGE OF OCCURRENCES:NONE
                     NONE
                     NONE
                     NONE


        The LOOP constraint  allows the user  to restrict the  number of
            LOOP
            LOOP
            LOOP
internal  bonds  which CONGEN  allocates  to each  Superatom  (these are
represented  as  "loops" -  bonds  which interconnect  a  Superatom with
itself - in intermediate structures, hence the name LOOP).  In this case
                                                    LOOP
                                                    LOOP
                                                    LOOP
it is  possible to interconnect  atoms 6  and 7 of  Superatom A  with an
                                                              A
                                                              A
                                                              A
internal bond (see above), but the user does not want to  consider those
possibilities.

CONSTRAINT:


        Again,  a simple  carriage return  typed at  this  point informs
CONGEN that there are no further constraints.  The  structure generation
commences at this point, and the program prints one dot (".")  each time
it has built an  additional structure.  Approximately every  two minutes
(if the structure generation takes that long) CONGEN will issue a report
of the number of structures obtained so far, and a rough (!) estimate of
the percentage completion of the problem.

........................................................................
........................................................................
.................................
177 STRUCTURES WERE GENERATED


        The user now draws some of the intermediate structures to see if
he has overlooked some important constraints.  Some of the  drawings are
presented in an unusually large format to prevent crowding of the three-
character atom names.  The drawing portion of the program is  limited to
three characters at most for each atom - any Superatom names longer than
this will appear truncated to the first three characters.

#DRAW
 DRAW
 DRAW
 DRAW
TYPE OF DRAWING:?
                ?
                ?
                ?
NUMBERED ATNAMED
TYPE OF DRAWING:ATNAMED
                ATNAMED
                ATNAMED
                ATNAMED
ITEMS TO BE DRAWN:?
                  ?
                  ?
                  ?
PLEASE TYPE ONE OR MORE ENTRIES IN ANY OF THE FOLLOWING FORMS:
    THE NAME OF A DEFINED SUBSTRUCTURE



                                   19
CONGEN manual                                              February 1981


OR: AN INTEGER N, INDICATING THE NTH STRUCTURE IN YOUR CURRENT LIST
OR: A PAIR OF INTEGERS IN PARENTHESES, E.G. (1 10); (M N) INDICATES A
    RANGE OF THE MTH THROUGH THE NTH STRUCTURES IN YOUR CURRENT LIST
OR: A # FOLLOWED BY AN INTEGER (E.G. #3) INDICATING THE STRUCTURE WHICH
    IS 'ATTACHED' TO THE INDEX N (THIS INDEX IS PRINTED IN DRAWINGS)
OR: A PAIR (#M #N) INDICATING A THE RANGE OF STRUCTURES ASSOCIATED WITH
    INDICES M THROUGH N
ITEMS TO BE DRAWN:(2 4) 7
                  (2 4) 7
                  (2 4) 7
                  (2 4) 7

#2:

            CH2---CH----CH2
            /     /      |
           /     /       |
          /     /        |
         /     /         |
        /     /          |
CH3----A-----B          CH2
              \         /
               \       /
                \     /
                 \   /
                  \ /
                  ETH
































                                   20
CONGEN manual                                              February 1981


#3:

            CH2----A----CH2
            /     /      |
           /     /       |
          /     /        |
         /     /         |
        /     /          |
CH3---CH-----B          CH2
              \         /
               \       /
                \     /
                 \   /
                  \ /
                  ETH


#4:
     C
 B=A-H
 |   2\  C
ETH   CH-H
  \C C/  3
   H-H
   2 2

#7:

CH2----A-===-B
 |            \
 |             \
 |              \
 |               \
 |                \
ETH               CH----CH3
  \               /
   \             /
    \           /
     \         /
      \       /
      CH2---CH2


        At this point  the user chooses  to imbed the  methyl, methylene
and methine Superatoms. These are especially simple imbeddings, one-for-
one substitutions  of atoms C  for Superatoms CH3,  CH2 and CH,  and the
                            C                 CH3   CH2     CH
                            C                 CH3   CH2     CH
                            C                 CH3   CH2     CH
overall number of structures  does not change.  Because no  new chemical
features will be introduced during these imbeddings, it is not necessary
for the user to specify any constraints.  It is often more  efficient to
imbed more complex Superatoms first if there are  associated constraints
                                    if
                                    if
                                    if
which  will  reduce  the  number  of  structures,  leaving   the  simple
imbeddings to  be done  on a  smaller set  of structures  at the  end As




                                   21
CONGEN manual                                              February 1981


CONGEN begins to consider each starting structure, it prints a "#" mark,
and for each new structure produced, it prints a "." mark.

#IMBED
 IMBED
 IMBED
 IMBED
SUPERATOM:CH3
          CH3
          CH3
          CH3
NUMBER TO BE IMBEDDED:1
                      1
                      1
                      1
SUPERATOM:CH2
          CH2
          CH2
          CH2
NUMBER TO BE IMBEDDED:3
                      3
                      3
                      3
SUPERATOM:CH
          CH
          CH
          CH
NUMBER TO BE IMBEDDED:1
                      1
                      1
                      1
SUPERATOM:
THE 'EXPANDED' FORMULA IS C 5 A 1 B 1 ETH 1 H 10
CONSTRAINT:
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
TRANSFERRING STRUCTURES TO FILE...
177 STRUCTURES WERE OBTAINED


        Now ETH and B will be imbedded.  Again, the result is a one-for-
            ETH     B
            ETH     B
            ETH     B
one substitution of substructures for Superatoms, because each Superatom
has only one atom to  which bonds may be formed.  Again,  no constraints
are needed.   The number of  structures decreases during  this imbedding
because some previously unrecognized duplication (e.g., structures 4 and
7  in  the  above  drawings)  is perceived  once  all  CH,  CH3  and ETH
                                                       CH   CH3      ETH
                                                       CH   CH3      ETH
                                                       CH   CH3      ETH
Superatoms have been  imbedded.  The program indicates  these duplicates
by  printing  a "D"  mark  rather than  a  "." mark  for  each redundant
structure, then discarding the duplicate rather than including it in the
list of structures.

#IMBED
 IMBED
 IMBED
 IMBED
SUPERATOM:ETH
          ETH
          ETH
          ETH
NUMBER TO BE IMBEDDED:1
                      1
                      1
                      1
SUPERATOM:B
          B
          B
          B
NUMBER TO BE IMBEDDED:1
                      1
                      1
                      1
SUPERATOM:
THE 'EXPANDED' FORMULA IS O 1 C 8 A 1 H 15
CONSTRAINT:
#.#.#.#.#.#.#D#.#.#D#D#.#.#.#.#.#.#.#.#.#D#.#.#D#D#.#.#.#.#.#.#.#.#D#.#.
#.#D#D#D#D#.#.#.#.#.#.#D#D#.#.#.#.#D#D#D#.#D#D#.#.#.#.#.#.#.#D#.#.#.#.#.
#.#.#D#D#.#.#.#D#.#D#.#.#D#D#D#.#.#D#D#.#.#.#.#.#D#.#.#D#.#.#.#.#.#.#.#.
#.#.#D#.#.#.#.#.#D#.#D#.#.#D#D#D#.#D#.#D#.#.#.#.#D#.#.#.#.#D#.#.#.#.#.#.
#.#.#D#D#.#.#.#D#.#D#.#D#D#.#.#.#D#D#D#.#.#.#.#.#.#D#.#.#.#D#D#.#D
TRANSFERRING STRUCTURES TO FILE...
124 STRUCTURES WERE OBTAINED


        Finally,  A  is  imbedded.  This  is  a  more  complex imbedding
                  A
                  A
                  A
because  there  are  several  (up  to  three)  ways  of   permuting  the




                                   22
CONGEN manual                                              February 1981


attachments to the "atom" A among the free valences in  the substructure
                          A
                          A
                          A
A.   Also,  this imbedding  may  introduce new  double  bonds  or three-
A
A
A
membered rings.  For example, in structure #4 in the drawings  above the
"double bond"  B=A can  be expanded during  the imbedding  of A  to form
               B=A                                            A
               B=A                                            A
               B=A                                            A
either a double  bond or a five-membered  ring.  Because of this,  it is
necessary to specify the ring-size constraints once again.

#IMBED
 IMBED
 IMBED
 IMBED
SUPERATOM:A
          A
          A
          A
NUMBER TO BE IMBEDDED:1
                      1
                      1
                      1
SUPERATOM:
THE 'EXPANDED' FORMULA IS O 1 C 15 H 26
CONSTRAINT:RING 2, NONE
           RING 2, NONE
           RING 2, NONE
           RING 2, NONE
CONSTRAINT:RING 3, EXACTLY 1
           RING 3, EXACTLY 1
           RING 3, EXACTLY 1
           RING 3, EXACTLY 1
CONSTRAINT:
#.#...#...#.#.#.#...#.#...#.#.#...#.#..#.#..#.#.#..#..#.#..#.#...#...#.#
.#...#..#...#...#..#..#...#..#.#..#.#...#...#..#.#.#...#...#..#...#...#.
#...#...#..#...#...#...#..#..#..#..#...#...#...#...#..#...#.#...#...#..#
.#...#...#..#...#...#.#.#...#...#...#...#...#...#...#...#...#...#...#.#.
#.#..#.#.#.#...#.#...#.#...#...#...#...#..#...#...#.#...#..#..#..#...#..
.#...#...#.#...#.#...#...#..#..#..#.
TRANSFERRING STRUCTURES TO FILE...
272 STRUCTURES WERE OBTAINED
#DRAW ATNAMED (1 3)
 DRAW ATNAMED (1 3)
 DRAW ATNAMED (1 3)
 DRAW ATNAMED (1 3)

#1:
C    O    C-C
 \   |   /   \
  C--C--C     C
 /   |   \   /|
C    |    \ / |
 \   |     C--C-C
  C--C        |
      \       C
       C

#2:
C    O  C      C
 \   |  |     /
  C--C--C--C-C
  |  |     |/ \
  C  C     C   C
   \ |\   /
    \| C-C
     C

#3:
             C
            /
    C   C--C
   / \ /   |
  C   C    |
  |   |    C



                                   23
CONGEN manual                                              February 1981


  |   |    |\
  C---C--C-C-C-C
 /    |      |
C     O      C


        These are now final structures (i.e., no Superatoms remain to be
imbedded).   Additional  information   about  the  environment   of  the
cyclopropyl  ring  became  available,  allowing  the  definition  of the
following substructure, arbitrarily called HEP, which is required  to be
                                           HEP
                                           HEP
                                           HEP
present.

#DEFINE SUBSTRUCTURE HEP
 DEFINE SUBSTRUCTURE HEP
 DEFINE SUBSTRUCTURE HEP
 DEFINE SUBSTRUCTURE HEP
(NEW SUBSTRUCTURE)
>RING 3
 RING 3
 RING 3
 RING 3
>BRANCH 1 1 1 1 2 1 3 3
 BRANCH 1 1 1 1 2 1 3 3
 BRANCH 1 1 1 1 2 1 3 3
 BRANCH 1 1 1 1 2 1 3 3
>DRAW NUMBERED
 DRAW NUMBERED
 DRAW NUMBERED
 DRAW NUMBERED

SUBSTRUCTURE HEP:

  4
  |
5-1-3-7-8-9
  |/
  2
  |
  6


        It can be cumbersome to use the HRANGE command to  identify free
                                        HRANGE
                                        HRANGE
                                        HRANGE
valences in large substructures  because one needs to specify  the range
for  every atom.   The  FREEV command  offers an  alternative  and often
                        FREEV
                        FREEV
                        FREEV
simpler route.  When FREEV is used, there are several  assumptions about
                     FREEV
                     FREEV
                     FREEV
HRANGE which are made implicitly by the program.  First, any  atom which
HRANGE
HRANGE
HRANGE
does  NOT bear  one of  these  special free  valences is  assumed  to be
"saturated" with  hydrogen atoms,  so that no  additional bonds  to that
atom may be  formed.  Secondly, a specified  free valence is  assumed to
bond only to  non-hydrogen atoms (i.e.,  an atom bearing  specified free
valences is implicitly given an HRANGE with the minimum number  equal to
                                HRANGE
                                HRANGE
                                HRANGE
the maximum number) unless this assumption is explicitly overridden by a
separate  HRANGE associated  with  the corresponding  atom.   Atoms with
          HRANGE
          HRANGE
          HRANGE
"polynames" or the name X ( a special symbol meaning "any atom")  can be
                        X
                        X
                        X
given specified  free valences with  FREEV, but no  implicit assumptions
                                     FREEV
                                     FREEV
                                     FREEV
are  ever  made  about  the  HRANGE  on  such  atoms.   This  means that
                             HRANGE
                             HRANGE
                             HRANGE
effectively the free valences are  ignored on such atoms and  any number
of connections can be made to them.  However, this specification of free
valences does "saturate"  other atoms just as  noted above and  no bonds
can be made to such atoms.

***** Note - this behavior can lead to unexpected results.        *****
***** Avoid placing free valences on X or POLYNAME atoms.         *****





                                   24
CONGEN manual                                              February 1981


The FREEV command below accomplishes the same effect as would the longer
    FREEV
    FREEV
    FREEV
command:

        HRANGE 1 0 0 2 1 1 3 1 1 4 3 3 5 3 3 6 2 2 7 1 1 8 1 1 9 3 3
        HRANGE 1 0 0 2 1 1 3 1 1 4 3 3 5 3 3 6 2 2 7 1 1 8 1 1 9 3 3
        HRANGE 1 0 0 2 1 1 3 1 1 4 3 3 5 3 3 6 2 2 7 1 1 8 1 1 9 3 3
        HRANGE 1 0 0 2 1 1 3 1 1 4 3 3 5 3 3 6 2 2 7 1 1 8 1 1 9 3 3

>FREEV 6 1 7 1 8 1
 FREEV 6 1 7 1 8 1
 FREEV 6 1 7 1 8 1
 FREEV 6 1 7 1 8 1
>DRAW ATNAMED
 DRAW ATNAMED
 DRAW ATNAMED
 DRAW ATNAMED

SUBSTRUCTURE HEP:

         C
   \     |
    C--C-C-C
   /    \|
 -C      C
  |       \
  C        C
            \


        Note that the special free valences inserted by FREEV  are drawn
                                                        FREEV
                                                        FREEV
                                                        FREEV
as single bonds with one end left "open".  Now, PRUNE with constraints.
                                                PRUNE
                                                PRUNE
                                                PRUNE

>DONE
 DONE
 DONE
 DONE
HEP DEFINED
#PRUNE
 PRUNE
 PRUNE
 PRUNE
CONSTRAINT:SUBSTRUCTURE HEP, AT LEAST 1
           SUBSTRUCTURE HEP, AT LEAST 1
           SUBSTRUCTURE HEP, AT LEAST 1
           SUBSTRUCTURE HEP, AT LEAST 1
CONSTRAINT:
*******************.*.**.**.*.******************************...****...**
****************..*.*..***.*.**..*****.....*.***************.*.*..****..
..*..*.*....*.*....*******........******.*....********..*.******.*..***.
*.***..**.****....*..**************.*..*...****......***
88 STRUCTURES SURVIVED PRUNING


        At this point, the  user has dramatically reduced the  number of
structural  possibilities,  but there  are  still too  many  to consider
individually by manual inspection.  The SAVE command allows him  to save
                                        SAVE
                                        SAVE
                                        SAVE
on file all of his structures and all other information he has given the
program  during  this  session.   The file  name  he  chooses  here will
identify this particular file so that he can restore it at a later date.

#SAVE
 SAVE
 SAVE
 SAVE
FILE NAME:?
          ?
          ?
          ?
A WORD OF THE FORM XXXXXX.YYY WHERE XXXXXX IS A 'NAME' OF
FROM ONE TO SIX LETTERS AND/OR DIGITS AND WHERE YYY IS AN
OPTIONAL 'EXTENSION' OF FROM ONE TO THREE LETTERS AND/OR DIGITS.
THE '.' MAY BE OMITTED IF THE EXTENSION IS OMITTED
FILE NAME:CASE1.SV
          CASE1.SV
          CASE1.SV
          CASE1.SV
SAVED ON CASE1.SV


#EXIT
 EXIT
 EXIT
 EXIT



                                   25
CONGEN manual                                              February 1981


DO YOU WANT TO SAVE YOUR SESSION ON FILE?:NO
                                          NO
                                          NO
                                          NO

        Since the user has just  saved his session, he does not  need to
save it again at this point.

EXIT.
^C
@


        At  a  later  time,  the  user  returns  with   more  structural
information in the form of the required substructure PEN  defined below.
                                                     PEN
                                                     PEN
                                                     PEN
Also, he previously  had forgotten to test  for the presence  of exactly
two ETH substructures after imbedding ETH, CH and CH3.  He  restores the
    ETH                               ETH  CH     CH3
    ETH                               ETH  CH     CH3
    ETH                               ETH  CH     CH3
saved session, defines PEN and prunes with both PEN and ETH.
                       PEN                      PEN     ETH
                       PEN                      PEN     ETH
                       PEN                      PEN     ETH

        This session demonstrates  highly abbreviated input as  it might
be  typed by  a very  experienced user.   Short forms  are used  for the
keywords, and  in many  places the  semicolon (;)  is used  to terminate
variable-length responses (e.  g., input following an  Editstruc command
or the  responses to the  SUPERATOM: prompts following  GENERATE).  This
                                                        GENERATE
                                                        GENERATE
                                                        GENERATE
allows the user greater flexibility in "typing ahead" his information.

@CONGEN                         A greeting from CONGEN will precede the
 CONGEN
 CONGEN
 CONGEN
                                  CONGEN # prompt
#RESTORE CASE1.SV
 RESTORE CASE1.SV
 RESTORE CASE1.SV
 RESTORE CASE1.SV
CASE1.SV RESTORED
#DE S PEN
 DE S PEN
 DE S PEN
 DE S PEN
(NEW SUBSTRUCTURE)

        For example, the following command is equivalent to the several
lines:
                CHAIN 4
                CHAIN 4
                CHAIN 4
                CHAIN 4
                BRANCH 2 1 2 1
                BRANCH 2 1 2 1
                BRANCH 2 1 2 1
                BRANCH 2 1 2 1
                ATNAME 1 O
                ATNAME 1 O
                ATNAME 1 O
                ATNAME 1 O
                DRAW NUMBERED
                DRAW NUMBERED
                DRAW NUMBERED
                DRAW NUMBERED

>C 4;B 2 1 2 1;A 1 O;D N
 C 4;B 2 1 2 1;A 1 O;D N
 C 4;B 2 1 2 1;A 1 O;D N
 C 4;B 2 1 2 1;A 1 O;D N
I TAKE B TO MEAN BRANCH
I TAKE D TO MEAN DRAW

SUBSTRUCTURE PEN:
NON-C ATOMS: 1->O

  5
  |
1-2-3-4
  |
  6

>F 3 1 5 1 6 2;D A
 F 3 1 5 1 6 2;D A
 F 3 1 5 1 6 2;D A
 F 3 1 5 1 6 2;D A
I TAKE D TO MEAN DRAW




                                   26
CONGEN manual                                              February 1981


SUBSTRUCTURE PEN:

     O
     |   /
 -C--C--C
     |   \
     |
     C
    / \
   C

>DONE
 DONE
 DONE
 DONE
PEN DEFINED


        The following two commands are interpreted respectively as

        PRUNE SUBSTRUCTURE PEN AT LEAST 1; and
        PRUNE SUBSTRUCTURE PEN AT LEAST 1
        PRUNE SUBSTRUCTURE PEN AT LEAST 1
        PRUNE SUBSTRUCTURE PEN AT LEAST 1

        PRUNE  SUBSTRUCTURE   ETH  EXACTLY   TWO;  with   the  semicolon
        PRUNE  SUBSTRUCTURE   ETH  EXACTLY   TWO
        PRUNE  SUBSTRUCTURE   ETH  EXACTLY   TWO
        PRUNE  SUBSTRUCTURE   ETH  EXACTLY   TWO
terminating the list of constraints in each case.

#P S PEN L 1;
 P S PEN L 1;
 P S PEN L 1;
 P S PEN L 1;
.*...*...*****************************************************.*.....***
*.*..****....*..
22 STRUCTURES SURVIVED PRUNING
#P S ETH E 2;
 P S ETH E 2;
 P S ETH E 2;
 P S ETH E 2;
..........*.......*...
20 STRUCTURES SURVIVED PRUNING
#SA CASE1.SV2
 SA CASE1.SV2
 SA CASE1.SV2
 SA CASE1.SV2
SAVED ON CASE1.SV2


        Having saved these  twenty structures for future  reference, the
user now  decides to see  which of the  structures satisfy  the isoprene
rule.  Though he has no hard evidence to indicate that the unknown is an
isoprenoid structure, he has the  structures safely on file and  can now
experiment a  bit.  The  use of the  '?' below  shows him  the available
libraries and the SEARCH command enables him to restore  the appropriate
                  SEARCH
                  SEARCH
                  SEARCH
substructure.  One of the  four surviving structures (#209 below)  is in
fact the correct structure for the unknown.

#S L ?
 S L ?
 S L ?
 S L ?
I TAKE S TO MEAN SHOW
GENLIB ISOLIB BMTERP BSTERP TSTERP AMNACD SURVLIB MYLIB
LIBRARY TO BE SHOWN:I
                    I
                    I
                    I
THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:
2-HT 2-IRR 3-HT-HT 3-IRR 4-HT-HT-HT 4-IRR

*** Note - the output of SHOW LIBRARY now numbers each substructure ***
                         SHOW LIBRARY
                         SHOW LIBRARY
                         SHOW LIBRARY

#SE I 3-HT-HT
 SE I 3-HT-HT
 SE I 3-HT-HT
 SE I 3-HT-HT
3-HT-HT DEFINED



                                   27
CONGEN manual                                              February 1981


#P S 3-HT-HT L 1;
 P S 3-HT-HT L 1;
 P S 3-HT-HT L 1;
 P S 3-HT-HT L 1;
*.*.***.***.********
4 STRUCTURES SURVIVED PRUNING
#D A(1 4)
 D A(1 4)
 D A(1 4)
 D A(1 4)
I TAKE D TO MEAN DRAW


#25:
   O
    \  C
     C-|--C       -
    / \|   \
C--C   C    C
   |    \   |\   C
   |     \  | \ /
   C      C-C--C
    \    /      \
     C--C        C

#30:
C--C        C
|   \      / \
|    C----C   C
C    |   /|   |\   C
 \   |  / |   | \ /
  C--|-C--|---C--C     -    -
 /   C    O       \
C                  C

#209:
        C
       /
   C--C
  /   |
 /    |
C     C
 \   / \     C
  \ /   \   /
 O-C     C-C
   |     |/ \
   C     C   C
  / \   /
 C   C-C

#223:
   C
    \
     C--C--C
    /       \
O--C         C
   |\        |\   C
   | \       | \ /
   |  C-C----C--C



                                   28
CONGEN manual                                              February 1981


   C  |/         \
    \ /           C      |
     C|
      |
      C



        Now, during the GENERATE  of the previous session, the  user had
                        GENERATE
                        GENERATE
                        GENERATE
limited  the number  of "loops"  on Superatom  A to  NONE  because those
                                               A     NONE
                                               A     NONE
                                               A     NONE
structural   possibilities  seemed   most  likely   to  him.    But  for
thoroughness, he now considers those structures in which A has one loop.
                                                         A
                                                         A
                                                         A
(It  cannot  have two  or  more loops  because  it has  only  three free
valences.) Note that  with the abbreviated inputs,  the user is  able to
carry out  the entire  case with just  five lines  of typed  input.  The
single resulting structure can be ruled out on the basis of NMR evidence
because some coupling  should have been  seen between the  methylene and
methine protons attached to carbons neighboring the three-membered ring.

#G A L 1 B E 1 CH3 E 1 CH2 E 3 CH E 1 ETH L 1;
 G A L 1 B E 1 CH3 E 1 CH2 E 3 CH E 1 ETH L 1;
 G A L 1 B E 1 CH3 E 1 CH2 E 3 CH E 1 ETH L 1;
 G A L 1 B E 1 CH3 E 1 CH2 E 3 CH E 1 ETH L 1;

S MET N R 2 N R 3 E 1 L A L 1;       (this line was broken in two
S MET N R 2 N R 3 E 1 L A L 1;
S MET N R 2 N R 3 E 1 L A L 1;
S MET N R 2 N R 3 E 1 L A L 1;
                                         parts to fit on page)
'COLLAPSED' FORMULA IS A 1 B 1 CH3 1 CH2 3 CH 1 ETH 1
.................................
33 STRUCTURES WERE GENERATED
#I CH3 1 CH2 3 CH 1;;
 I CH3 1 CH2 3 CH 1;;
 I CH3 1 CH2 3 CH 1;;
 I CH3 1 CH2 3 CH 1;;
THE 'EXPANDED' FORMULA IS C 5 A 1 B 1 ETH 1 H 10
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
TRANSFERRING STRUCTURES TO FILE...
33 STRUCTURES WERE OBTAINED
#I ETH 1 B 1;;
 I ETH 1 B 1;;
 I ETH 1 B 1;;
 I ETH 1 B 1;;
THE 'EXPANDED' FORMULA IS O 1 C 8 A 1 H 15
#.#.#.#D#.#.#.#D#D#.#.#D#.#.#.#.#D#.#D#D#D#D#.#D#.#.#.#D#D#.#.#D#D
TRANSFERRING STRUCTURES TO FILE...
19 STRUCTURES WERE OBTAINED
#I A 1; R 2 N R 3 E 1;
 I A 1; R 2 N R 3 E 1;
 I A 1; R 2 N R 3 E 1;
 I A 1; R 2 N R 3 E 1;
THE 'EXPANDED' FORMULA IS O 1 C 15 H 26
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
TRANSFERRING STRUCTURES TO FILE...
19 STRUCTURES WERE OBTAINED
#P S HEP L 1 S PEN L 1;
 P S HEP L 1 S PEN L 1;
 P S HEP L 1 S PEN L 1;
 P S HEP L 1 S PEN L 1;
******************.
1 STRUCTURE SURVIVED PRUNING
#D A 1
 D A 1
 D A 1
 D A 1
I TAKE D TO MEAN DRAW

#19:
      C    C  O C
     / \   |  |/ \
    C   C--C--C   \
   / \ /      |    C
C-C---C       |   /



                                   29
CONGEN manual                                              February 1981


  |           C--C
  C          /
            C

#E N
 E N
 E N
 E N

EXIT.
^C
@

                ******************************













































                                   30
CONGEN manual                                              February 1981


        III    CONGEN Input
               CONGEN Input
               CONGEN Input
               CONGEN Input

                ****************
                *              *
                * CONGEN Input *
                *              *
                ****************


        CONGEN does  not always  prompt you with  a textual  message for
what it expects might be the next command because for most  problems the
precise  sequence of  commands is  unpredictable.  Unless  very specific
information is  required, CONGEN provides  a simple "prompt,"  usually a
single  character, indicating  that it  is ready  to accept  input.  The
prompt you see  depends on the portion  of the program you  are actually
using (see below).

        Every input to  CONGEN is terminated  with a carriage  return to
indicate to CONGEN  that you have  finished what you  wish to type  on a
line.

        When  you begin  CONGEN, and  after completion  of  every CONGEN
command except  EXIT (see  Section IV.A,  Glossary of  CONGEN Commands),
                EXIT
                EXIT
                EXIT
the prompt you see is the number, or pound, sign, #.  At this  point you
may request help by typing a question mark, or issue any CONGEN command.

        In  Editstruc  (see  Glossary  of  Editstruc  Commands,  Section
IV.B.6.b),  you are  given  the ">"  prompt indicating  CONGEN  is ready
to accept  input.  In  SURVEY (see  SURVEY, Section  IV.N you  are given
                       SURVEY       SURVEY
                       SURVEY       SURVEY
                       SURVEY       SURVEY
the  "->" prompt  and  in STEREO  (see Glossary  of  STEREO Subcommands,
                          STEREO                     STEREO
                          STEREO                     STEREO
                          STEREO                     STEREO
Section IV.O.1),  you are  given the  "ST>" prompt.   At this  point you
can ask for help with the question mark, or issue any relevant command.

        At  other places  within  various commands,  CONGEN  prompts you
explicitly for  what it  needs, with a  text string,  usually terminated
with a colon.  At this point you may issue a question mark for  help, or
respond with the requested information.

        Every time  you respond  with a question  mark for  help, CONGEN
provides you with  some guidance on what  it expects, and  reprompts you
again with the same  symbol or text string  to remind you about  what it
needs.

        CONGEN has  a very  tolerant mechanism  for accepting  input and
detecting errors.  The points discussed in the subsequent paragraphs are
illustrated liberally in the  Sample CONGEN Session, Section II,  and in
example input for individual commands throughout the document.

        Some prompts require only a single command while  others require
a  command  and  additional information  on  numbers,  or  ranges, i.e.,
several "arguments"  to use mathematical  jargon.  CONGEN allows  you to
type only part of  a command requiring several arguments,  processes the




                                   31
CONGEN manual                                              February 1981


partial command and requests whatever additional information it needs to
complete the  command.  In this  way you can  "step through"  a command,
supplying arguments one at a time, at each step asking for help  on what
is expected next.  As you become familiar with a particular command, all
information to complete that command can be typed on one line.

        If part or all of a command requiring arguments is typed  on one
line, either the  space character or the  comma can be used  to separate
the portions of the command from one another.

        If any part of a  command requiring arguments is detected  to be
in error, the error  and any parts of  the line following the  error are
erased by CONGEN  and you are prompted  again for the  specific argument
that was in error.  You must then make a correct input and  complete the
rest of  the line (which  was erased).  You  can, however,  complete the
entire command on the same  line on which you type the  correct argument
if you wish, by typing the remaining input after the argument.  Remember
that CONGEN will have processed and executed all parts of the command up
to the error, properly.

        All commands can be extended where appropriate, for example, the
Editstruc commands where you may wish to create several chains  or rings
or branches without having to retype the CHAIN, RING, etc.   string over
                                         CHAIN  RING
                                         CHAIN  RING
                                         CHAIN  RING
and over again.

        For the experienced  user of CONGEN, several  different commands
can be  typed on one  line.  The semi-colon  (;) character may  be typed
after any command  that may be of  variable length (e.g.,  in Editstruc,
Superatom  and  constraints  prompt  sequences  in  GENERATE  and IMBED)
                                                    GENERATE      IMBED
                                                    GENERATE      IMBED
                                                    GENERATE      IMBED
followed by another command on the same line, and so forth.   The Sample
CONGEN Session, Section II, illustrates several such  command sequences.
There  is  a  limit  of  95  to  the  number  of  characters,  and thus,
indirectly, to the  number of commands which  can be input in  this way.
CONGEN will reprompt for missing  parts of the last command it  was able
to process if this limit is exceeded.  You must retype all  input beyond
the limit - it will have been lost.

        Every CONGEN command can be abbreviated, in most cases down to a
single character,  to save  the experience  user a  lot of  typing.  Any
abbreviation  is all  right as  long  as it  is unambiguous.   If  it is
ambiguous, CONGEN will  select the most  frequently used command  as the
one it thinks you  want (if you did not  want this command see  the next
paragraph).  This acceptance  of abbreviations  does not  hold  true for
arguments such as substructure,  file and atom names.  These  names must
be typed completely, as  you wish them to  read or exactly as  they were
first used.

        If you type the wrong command, a carriage return response to the
subsequent prompt will allow you  to exit from the command.   Of course,
if what you typed was a complete command, with all  necessary arguments,
                        complete
                        complete
                        complete
then the command will be processed by CONGEN.  If, however,  the command
required several arguments which  you did not type, the  carriage return




                                   32
CONGEN manual                                              February 1981


response  should eventually  get you  back to  where you  can  issue the
desired  command.  Note  that this  is not  the case  in  commands where
carriage return is  a legal response  to terminate the  command sequence
and continue computation, for example in Superatom and  constraint input
to GENERATE.  If you are  really in trouble in such a  command sequence,
   GENERATE
   GENERATE
   GENERATE
and subsequent carriage returns are accepted by CONGEN as the  signal to
continue  a  long  computation,  such  as  in  GENERATE,  see  the  next
                                               GENERATE
                                               GENERATE
                                               GENERATE
paragraph.

        Interruption  of  CONGEN.   Any  computation  can  be terminated
        Interruption  of  CONGEN
        Interruption  of  CONGEN
        Interruption  of  CONGEN
(abort, interrupt) by  typing control (cntrl  key on most  terminals) in
conjunction (at the same time) as C, or control-C.  This causes  an exit
from CONGEN back to the monitor of your computer system, at  which point
you can restart CONGEN (see How to Start CONGEN, Section I.C).  You will
be put  back in CONGEN  at the point  immediately before you  issued the
command which was aborted, and no aspect of your session will be lost.

        Exit from CONGEN. Do not,  repeat DO NOT exit CONGEN at  the end
        Exit from CONGEN. Do not
        Exit from CONGEN. Do not
        Exit from CONGEN. Do not
of your session with a  control-C.  Use the EXIT command.  If  you leave
                                            EXIT
                                            EXIT
                                            EXIT
with  control-C and  subsequently  run another  program or  log  off the
computer system, your  recording file will be  lost and you will  not be
able to restart CONGEN at the  point you left your session.  If  you had
not saved anytime  during your session  (CONGEN command SAVE),  all your
                                                        SAVE
                                                        SAVE
                                                        SAVE
results, as  far as the  computer is concerned,  will be lost.   What is
even worse is that several temporary files used by CONGEN are not erased
unless you exit normally (with the EXIT command).  If control-C  is used
                                   EXIT
                                   EXIT
                                   EXIT
by mistake, there  is a finite chance  that a later session  with CONGEN
will  reference  those files,  which  are named  according  to  your job
number.  If you need  to delete such files,  they are all named  with an
extension "CG," in other words, in the form 0nnXXX.CG, where 0nn is your
job number, and XXX may  be a variety of characters including  REC, TOP,
STR.  You  will need  to use  whatever command  is available  under your
operating  system  to  delete  the  files,  e.g.,  on  TENEX,  the SUMEX
operating system, the DELETE command.

                ******************************




















                                   33
CONGEN manual                                              February 1981


        IV    CONGEN Commands
              CONGEN Commands
              CONGEN Commands
              CONGEN Commands

                *******************
                *                 *
                * CONGEN Commands *
                *                 *
                *******************


        This section covers all  of the CONGEN commands  in considerable
detail,  beginning  with   a  Glossary  and  continuing   with  separate
subsections for each command.

                ******************************

        ***** Use of CONGEN Commands *****
              Use of CONGEN Commands
              Use of CONGEN Commands
              Use of CONGEN Commands


        The available  commands in CONGEN  can be summarized  by issuing
the  question mark  response to  the CONGEN  # prompt:  Each  command is
summarized in  the following  Glossary, Section  IV.A, and  discussed in
detail in subsequent sections.

#?                              Ask for help
 ?
 ?
 ?

GENERATE IMBED PRUNE DRAW DEFINE FIX SHOW FORGET        CONGEN replies
SEARCH SAVE RESTORE EXIT SURVEY STEREO AROMATIZE

#                               Ready for next CONGEN command

                ******************************

























                                   34
CONGEN manual                                              February 1981


        IV.A    Glossary of CONGEN Commands
                Glossary of CONGEN Commands
                Glossary of CONGEN Commands
                Glossary of CONGEN Commands

                *******************************
                *                             *
                * Glossary of CONGEN Commands *
                *                             *
                *******************************


        The following is a list and brief description of CONGEN commands
which can be issued when you have the "#" prompt from  CONGEN indicating
that the program is ready to accept input.  Any command can be issued at
any time.   If a particular  command is inconsistent  at the time  it is
given to CONGEN, the program will provide appropriate error messages.

        Terminate commands with a carriage return, the signal  to CONGEN
that you have finished typing a line.

        See  Section  III,  CONGEN Input,  for  special  instructions on
abbreviating  commands,  extending  commands  where  repetitive  use  is
appropriate, and placing several different commands on one line.

CONGEN   Short
Command  Form*                          Function
-------  -----     ---------------------------------------------------

DEFINE    DE  To define to CONGEN the chemical context of a
DEFINE
DEFINE
DEFINE
                 structural problem, including:
                     a) the characteristics of your computer terminal
                        so that subsequent typed drawings will be
                        legible; or
                     b) the molecular formula; or
                     c) the name and valence of atoms other than
                        C, N, O, X and H; or
                     d) selection of substructural templates for
                        specifying aromaticity; or
                     e) the name and Editstruc definition of a new
                        substructure;
                 All such definitions may be saved (see SAVE command,
                                                        SAVE
                                                        SAVE
                                                        SAVE
                   Section IV.L) and restored (see RESTORE command
                                                   RESTORE
                                                   RESTORE
                                                   RESTORE
                   Section IV.M) later to avoid redefinition of
                   commonly used chemistry.

FIX       F   To alter a definition previously created using DEFINE.
FIX                                                          DEFINE
FIX                                                          DEFINE
FIX                                                          DEFINE

SEARCH    SE  To retrieve selected substructures from a library file.
SEARCH
SEARCH
SEARCH

GENERATE  G   To generate (intermediate) structures using the
GENERATE
GENERATE
GENERATE
                 molecular formula and specified Superatoms and
                 constraints.

PRUNE     P   To discard from the current list of structures all
PRUNE
PRUNE
PRUNE
                 those which do not satisfy specified constraints.



                                   35
CONGEN manual                                              February 1981


IMBED     I   To imbed (re-expand) selected Superatoms in
IMBED
IMBED
IMBED
                 intermediate structures, using specified constraints.

AROMATIZE A   To convert existing structures to their aromatic
AROMATIZE
AROMATIZE
AROMATIZE
                 counterparts by considering the special electronic
                 resonances of aromatic systems as specified in part
                 by the DEFINE AROMATICS command.  Only one of two
                        DEFINE AROMATICS
                        DEFINE AROMATICS
                        DEFINE AROMATICS
                 or more possible Kekule forms is retained.

DRAW      D   To print, on your computer terminal, drawings of
DRAW
DRAW
DRAW
                 selected structures or substructures.

SHOW      S   To show you any of the following:
SHOW
SHOW
SHOW
                     a) a tabular representation ("connection table") of
                        selected structures or substructures; or
                     b) a summary of the current status of your session;
                        or
                     c) a history of your session (not implemented
                        9/79); or
                     d) aromaticity (not implemented 9/79); or
                     e) the contents, by substructure name, of any
                        substructure library.

FORGET    F   To forget, by deletion, the definition of selected
FORGET
FORGET
FORGET
                 atoms or substructures, or to delete specified
                 structures from the list of structures.

SAVE      SA  To store on a specified file all information about the
SAVE
SAVE
SAVE
                 current session.

RESTORE   R   To retrieve from a specified file all information
RESTORE
RESTORE
RESTORE
                 about a previous session.

SURVEY    SU  To test all structures in the current list of structures
SURVEY
SURVEY
SURVEY
                 against substructures stored in a specified library
                 file, to report the occurrence of those substructures
                 and to select structures with specified combinations
                 of substructural features.

STEREO    ST  To generate stereoisomers of selected structures or
STEREO
STEREO
STEREO
                 substructures, to examine the stereochemical
                 symmetry group for equivalent atoms and to view
                 configurations about selected atoms.

EXIT      EX  To erase all information about the current session
EXIT
EXIT
EXIT
                 and leave CONGEN.

*  As with all input to CONGEN, any command may be abbreviated
   to any extent, including mere specification of the first letter
   of the command.  If the letters specified are not unique (e.g.,
   the letter s alone could stand for the commands SHOW, SEARCH, SAVE,
              s                                    SHOW  SEARCH  SAVE
              s                                    SHOW  SEARCH  SAVE
              s                                    SHOW  SEARCH  SAVE
   SURVEY or STEREO, while an sh would suffice for the command show) the
   SURVEY    STEREO           sh                               show
   SURVEY    STEREO           sh                               show
   SURVEY    STEREO           sh                               show
   program will either prompt you again or select automatically the



                                   36
CONGEN manual                                              February 1981


   most frequently used command beginning with those letters.
   The short form shown is the shortest abbreviation which will be
   interpreted correctly.

                ******************************

        Each of these commands is described in detail in the following
sections:

CONGEN
Command         Described in
-------         ------------
DEFINE          Section IV.B
DEFINE
DEFINE
DEFINE
FIX             Section IV.C
FIX
FIX
FIX
SEARCH          Section IV.D
SEARCH
SEARCH
SEARCH
GENERATE        Section IV.E
GENERATE
GENERATE
GENERATE
PRUNE           Section IV.F
PRUNE
PRUNE
PRUNE
IMBED           Section IV.G
IMBED
IMBED
IMBED
AROMATIZE       Section IV.H
AROMATIZE
AROMATIZE
AROMATIZE
DRAW            Section IV.I
DRAW
DRAW
DRAW
SHOW            Section IV.J
SHOW
SHOW
SHOW
FORGET          Section IV.K
FORGET
FORGET
FORGET
SAVE            Section IV.L
SAVE
SAVE
SAVE
RESTORE         Section IV.M
RESTORE
RESTORE
RESTORE
SURVEY          Section IV.N
SURVEY
SURVEY
SURVEY
STEREO          Section IV.O
STEREO
STEREO
STEREO
EXIT            Section IV.P
EXIT
EXIT
EXIT





























                                   37
CONGEN manual                                              February 1981


        IV.B    DEFINE and Subcommands
                DEFINE and Subcommands
                DEFINE and Subcommands
                DEFINE and Subcommands

                *************************
                *                       *
                * CONGEN Command DEFINE *
                *                       *
                *************************


        The DEFINE  command is  used to define  to CONGEN  all requisite
            DEFINE
            DEFINE
            DEFINE
structural  information to  be  used during  the course  of  your CONGEN
session, whether the problem  is one of structure elucidation  or isomer
generation  performed  for  any  other  purpose.   CONGEN   begins  with
knowledge only  of the chemical  atoms C,  H, N and  O and  their normal
valences.   All other  structural information  must be  supplied  to the
            All
            All
            All
program.  Although commonly used structural information may  be provided
to CONGEN via  restoring a file resulting  from a previous  session (see
CONGEN  command  RESTORE, Section  IV.M),  or by  searching  one  of the
                 RESTORE
                 RESTORE
                 RESTORE
substructure libraries for previously defined substructures  (see CONGEN
command SEARCH,  Section IV.D),  most problems will  require use  of the
        SEARCH
        SEARCH
        SEARCH
DEFINE command to specify new atoms, substructures and so forth.
DEFINE
DEFINE
DEFINE

        The structure of the  CONGEN program (see Section  I.B) requires
that  all  substructural information  (substructures  and  aromatics) be
defined before carrying out the next step in the procedure  of structure
        before
        before
        before
generation  where the  information is  required, i.e.,  GENERATE, IMBED,
                                                        GENERATE  IMBED
                                                        GENERATE  IMBED
                                                        GENERATE  IMBED
PRUNE, STEREO and SURVEY.  None of these five commands will allow you to
PRUNE  STEREO     SURVEY
PRUNE  STEREO     SURVEY
PRUNE  STEREO     SURVEY
define new  substructures or change  the definition of  aromaticity from
within the commands themselves.

        The following sections describe in detail the use of  the CONGEN
command DEFINE.  The  section begins with  a glossary of  subcommands, a
        DEFINE
        DEFINE
        DEFINE
description  of  general  use  of the  command,  then  continues  with a
description of  each of  the subcommands including  examples of  use and
error conditions.

        The  last  subcommand,  SUBSTRUCTURE,  (see  Section  IV.B.6) is
                                SUBSTRUCTURE
                                SUBSTRUCTURE
                                SUBSTRUCTURE
documented at length because it involves use of another set  of commands
contained within the structure editor Editstruc.  The  DEFINE subcommand
                                      Editstruc        DEFINE
                                      Editstruc        DEFINE
                                      Editstruc        DEFINE
SUBSTRUCTURE,  followed  by  substructure  name  and   definition  using
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE
Editstruc, will  be one of  the most frequently  used commands  for most
structural problems  because of  the wide  variety of  new substructures
encountered in new problems.

        The DEFINE command can be issued to CONGEN any time  during your
            DEFINE
            DEFINE
            DEFINE
session when CONGEN requests a new command with the #  prompt.  However,
remember  that  all  necessary structural  information  must  be defined
before using it  in the next step  in your CONGEN session,  e.g., CONGEN
before
before
before
commands GENERATE (see Section IV.E or IMBED (see Section IV.G.
         GENERATE                      IMBED
         GENERATE                      IMBED
         GENERATE                      IMBED

                *****************************

        ***** Use of the DEFINE command in CONGEN *****
              Use of the DEFINE command in CONGEN
              Use of the DEFINE command in CONGEN
              Use of the DEFINE command in CONGEN



                                   38
CONGEN manual                                              February 1981


        Here is a brief example illustrating only the request  to CONGEN
that you wish to define something:

#define                         Issue the DEFINE command to CONGEN
 define                                   DEFINE
 define                                   DEFINE
 define                                   DEFINE

DEFINITION TYPE:?               Request help to see selections
                ?
                ?
                ?

ATOM SUBSTRUCTURE AROMATICS MOLFORM TERMTYPE    Here are the choices

DEFINITION TYPE:atom            Make a selection, e.g., ATOM
                atom                                    ATOM
                atom                                    ATOM
                atom                                    ATOM

        or

#define atom                    All on one line
 define atom
 define atom
 define atom

        or

#define a                       One line, short form for ATOM subcommand
 define a                                                ATOM
 define a                                                ATOM
 define a                                                ATOM

                ******************************

        Subsequent sections discuss the use of each of the DEFINE
                                                           DEFINE
                                                           DEFINE
                                                           DEFINE
subcommands:

        TERMTYPE           Section IV.B.2
        TERMTYPE
        TERMTYPE
        TERMTYPE
        MOLFORM            Section IV.B.3
        MOLFORM
        MOLFORM
        MOLFORM
        ATOM               Section IV.B.4
        ATOM
        ATOM
        ATOM
        AROMATICS          Section IV.B.5
        AROMATICS
        AROMATICS
        AROMATICS
        SUBSTRUCTURE       Section IV.B.6
        SUBSTRUCTURE
        SUBSTRUCTURE
        SUBSTRUCTURE

                ******************************

























                                   39
CONGEN manual                                              February 1981


        IV.B.1    Glossary of DEFINE Subcommands
                  Glossary of DEFINE Subcommands
                  Glossary of DEFINE Subcommands
                  Glossary of DEFINE Subcommands

                **********************************
                *                                *
                * Glossary of DEFINE Subcommands *
                *                                *
                **********************************


        See  Section  III,  CONGEN Input,  for  special  instructions on
abbreviating  commands,  extending  commands  where  repetitive  use  is
appropriate, and placing several different commands on the same line.

        Any subcommand may be issued at any time; inconsistent use  of a
subcommand will result in error messages from the program.

        Terminate all commands with  a carriage return as the  signal to
CONGEN that you have finished typing a line of input.

DEFINE       Short
DEFINE       Short
DEFINE       Short
DEFINE       Short
Subcommand   Form*                Function
Subcommand   Form                 Function
Subcommand   Form                 Function
Subcommand   Form                 Function
----------   -----   -----------------------------------------------

TERMTYPE     T       To specify to CONGEN a number code for computer
TERMTYPE
TERMTYPE
TERMTYPE
                        terminal output so that structure drawings will
                        be typed correctly. (See Section IV.B.2).

MOLFORM      M       To define to CONGEN the molecular formula of the
MOLFORM
MOLFORM
MOLFORM
                        structural problem. (See Section IV.B.3).

ATOM         A       To define to CONGEN the names and valences of
ATOM
ATOM
ATOM
                        new atoms (not restricted to names in the
                                   not
                                   not
                                   not
                        periodic table).  Atoms C, N, O and H are
                        predefined; X is reserved.
                                    X
                                    X
                                    X
                        (See Section IV.B.4).

AROMATICS    AR      To define your concept of aromaticity via
AROMATICS
AROMATICS
AROMATICS
                        selection of substructural templates you
                        choose to be aromatic. (See Section IV.B.5).

SUBSTRUCTURE S       To define, using Editstruc, names and identities
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE
                        of substructures to be used in subsequent
                        structure generation with constraints. (See
                        Section IV.B.6)

*  Any unambiguous abbreviation of any DEFINE subcommand may be
                                       DEFINE
                                       DEFINE
                                       DEFINE
   used.  The short form given is the shortest abbreviation which
   will be correctly interpreted.

                *****************************






                                   40
CONGEN manual                                              February 1981


        IV.B.2    DEFINE TERMTYPE
                  DEFINE TERMTYPE
                  DEFINE TERMTYPE
                  DEFINE TERMTYPE

                ******************************
                *                            *
                * DEFINE Subcommand TERMTYPE *
                *                            *
                ******************************


        The DEFINE subcommand TERMTYPE  is used to select a  number code
            DEFINE            TERMTYPE
            DEFINE            TERMTYPE
            DEFINE            TERMTYPE
so  that subsequent  structure drawings  on your  computer  terminal are
typed correctly.

                ******************************

        ******* Use of the DEFINE subcommand TERMTYPE *******
                Use of the DEFINE subcommand TERMTYPE
                Use of the DEFINE subcommand TERMTYPE
                Use of the DEFINE subcommand TERMTYPE

#define termtype                On one line
 define termtype
 define termtype
 define termtype

OLD TERMINAL TYPE IS 1          CONGEN replies

NEW TERMINAL TYPE:?             Ask for help to see choices
                  ?
                  ?
                  ?

SELECT THE NUMBER CORRESPONDING TO THE DRAWING BELOW WHICH LOOKS
MOST LIKE TETRAHEDRANE:
1     C
     /|\
    C--|-C
     \|/
      C                         CONGEN types all this on your
                                  terminal
2     C
     /!\
    C---C      !
     \!/
      C

NEW TERMINAL TYPE:2             CONGEN prompts again and you
                  2
                  2
                  2
                                  reply
THE TERMINAL TYPE HAS BEEN RESET TO 2

        or

#define termtype 2              All on one line
 define termtype 2
 define termtype 2
 define termtype 2
OLD TERMINAL TYPE IS 1
THE TERMINAL TYPE HAS BEEN RESET TO 2   CONGEN replies

#                               Back to CONGEN for next command

                ******************************

        ***** Examples of input errors and CONGEN responses *****
              Examples of input errors and CONGEN responses
              Examples of input errors and CONGEN responses
              Examples of input errors and CONGEN responses




                                   41
CONGEN manual                                              February 1981


#define termtype                Ask to define termtype
 define termtype
 define termtype
 define termtype
OLD TERMINAL TYPE IS 1
NEW TERMINAL TYPE:0             Illegal response
                  0
                  0
                  0
I DON'T UNDERSTAND - TYPE ? FOR HELP
NEW TERMINAL TYPE:3             Another illegal response
                  3
                  3
                  3
I DON'T UNDERSTAND - TYPE ? FOR HELP
NEW TERMINAL TYPE:?             Request help
                  ?
                  ?
                  ?

SELECT THE NUMBER CORRESPONDING TO THE DRAWING BELOW WHICH LOOKS
MOST LIKE TETRAHEDRANE:
1     C
     /|\
    C--|-C
     \|/
      C

2     C
     /!\
    C---C      !
     \!/
      C
NEW TERMINAL TYPE:2             A legal response
                  2
                  2
                  2
THE TERMINAL TYPE HAS BEEN RESET TO 2   CONGEN replies
#                               Return to CONGEN for next command

                ******************************






























                                   42
CONGEN manual                                              February 1981


        IV.B.3    DEFINE MOLFORM
                  DEFINE MOLFORM
                  DEFINE MOLFORM
                  DEFINE MOLFORM

                *****************************
                *                           *
                * DEFINE Subcommand MOLFORM *
                *                           *
                *****************************


        The  molecular  formula  (MOLFORM)  for  the  structural problem
                                  MOLFORM
                                  MOLFORM
                                  MOLFORM
analyzed by CONGEN  must be specified  prior to structure  generation by
issuing the  DEFINE MOLFORM command.   The CONGEN command  GENERATE (see
             DEFINE MOLFORM                                GENERATE
             DEFINE MOLFORM                                GENERATE
             DEFINE MOLFORM                                GENERATE
Section  IV.E)  will   prompt  you  for  it   if  it  was   not  defined
previously.  Generally,  definition of the  molecular formula  should be
done early in a CONGEN session, as illustrated below.

        Every CONGEN  problem must have  an explicit  molecular formula.
                              must
                              must
                              must
Structural problems  where the  molecular formula  is unknown  cannot be
analyzed by CONGEN.  However, if  the molecular formula of a  portion of
the molecule can be inferred in some way, then it may still  be possible
to utilize CONGEN  using a dummy atom  name, e.g., ZZ,  with appropriate
valence, to  represent the  rest of the  molecule.  For  example, assume
that mass spectrometry or  chemical degradation yielded evidence  for an
intact (i.e.,  connected) substructure of  formula C10H17O2  attached to
the rest  of a larger  molecule of unknown  molecular formula  through a
single  covalent bond.   The atom  ZZ,  with a  valence of  one,  can be
defined to  represent the rest  of the molecule  (using the  DEFINE ATOM
                                                             DEFINE ATOM
                                                             DEFINE ATOM
                                                             DEFINE ATOM
command,   Section   IV.B.4),   resulting   in   a   molecular   formula
C10H17O2ZZ input to CONGEN.  If the substructure(s) of known  formula is
connected  to the  larger structure  with two  or more  bonds,  then the
valence of the new atom, e.g., ZZ, must be specified accordingly.

        If  there  are  two  or  more  possibilities  for  the molecular
formula, each possibility must be treated as a separate CONGEN problem.

                ******************************

        ******* Use of the DEFINE subcommand MOLFORM *******
                Use of the DEFINE subcommand MOLFORM
                Use of the DEFINE subcommand MOLFORM
                Use of the DEFINE subcommand MOLFORM

#define molform                 On one line
 define molform
 define molform
 define molform

MOLECULAR FORMULA:?             Request help
                  ?
                  ?
                  ?

A LIST OF ATOM NAMES AND QUANTITIES (ONES MAY BE OMITTED), SEPARATED
BY BLANKS OR COMMAS (E.G., C 4 H 5 BR)  CONGEN replies

MOLECULAR FORMULA:c 20 h 36 n 2 o 4     Specify molecular formula
                  c 20 h 36 n 2 o 4
                  c 20 h 36 n 2 o 4
                  c 20 h 36 n 2 o 4

MOLECULAR FORMULA DEFINED       CONGEN replies

                or

#define molform c 20 h 36 n 2 o 4       All on one line
 define molform c 20 h 36 n 2 o 4
 define molform c 20 h 36 n 2 o 4
 define molform c 20 h 36 n 2 o 4



                                   43
CONGEN manual                                              February 1981


MOLECULAR FORMULA DEFINED       CONGEN replies

#                               Ready for next CONGEN command

                *****************************

        If an atom (or atoms) is used which has not been defined, CONGEN
will request its valence and define the atom.  For example:

#define molform c 5 h 8 cl br   New atoms cl and br
 define molform c 5 h 8 cl br
 define molform c 5 h 8 cl br
 define molform c 5 h 8 cl br
DEFINING ATOM CL...
VALENCE:1                       Specify the valence of cl
        1
        1
        1
CL DEFINED
DEFINING ATOM BR...
VALENCE:1                       Specify the valence of br
        1
        1
        1
MOLECULAR FORMULA DEFINED
#                               Ready for next CONGEN command


                ******************************

        ******** Error conditions and CONGEN replies ********
                 Error conditions and CONGEN replies
                 Error conditions and CONGEN replies
                 Error conditions and CONGEN replies

        1) Molecular formula already defined:

#define molform                 Try to redefine
 define molform
 define molform
 define molform

THE MOLECULAR FORMULA IS ALREADY DEFINED.  PLEASE USE THE
FIX COMMAND IF YOU WANT TO CHANGE IT.   CONGEN replies

#                               Ready for next CONGEN command

        2) Implicit violation of chemical valence:

#define molform
 define molform
 define molform
 define molform

MOLECULAR FORMULA:c 20 h 36 n 1 o 4     An illegal molecular formula
                  c 20 h 36 n 1 o 4
                  c 20 h 36 n 1 o 4
                  c 20 h 36 n 1 o 4

THAT FORMULA IMPLIES AN UNPAIRED ELECTRON ON SOME ATOM

MOLECULAR FORMULA:              CONGEN replies and reprompts

        3) Illegal input:

#define molform 6 6             Can't use integer names
 define molform 6 6
 define molform 6 6
 define molform 6 6
I WAS EXPECTING A WORD          CONGEN replies and erases
ERASING ...6 6                    illegal name and rest of line
MOLECULAR FORMULA:              CONGEN reprompts

        4) Mistyping:

#define molform c 20 h 35 n1o4          Oops - interpreted as one atom
 define molform c 20 h 35 n1o4
 define molform c 20 h 35 n1o4
 define molform c 20 h 35 n1o4
DEFINING ATOM N1O4...                     of type N1O4
                                                  N1O4
                                                  N1O4
                                                  N1O4



                                   44
CONGEN manual                                              February 1981


VALENCE:                                Carriage return results in
MOLECULAR FORMULA:c 20 h 35 n 1 o 4       reprompting
                  c 20 h 35 n 1 o 4
                  c 20 h 35 n 1 o 4
                  c 20 h 35 n 1 o 4
MOLECULAR FORMULA DEFINED
#                               Ready for next CONGEN command

                ******************************


















































                                   45
CONGEN manual                                              February 1981


        IV.B.4    DEFINE ATOM
                  DEFINE ATOM
                  DEFINE ATOM
                  DEFINE ATOM

                **************************
                *                        *
                * DEFINE Subcommand ATOM *
                *                        *
                **************************


        All atoms other than C, N, O, H and the reserved name X  must be
                                                              X
                                                              X
                                                              X
defined  to  CONGEN and  have  their valence  specified  using  the ATOM
                                                                    ATOM
                                                                    ATOM
                                                                    ATOM
subcommand,  i.e.,  DEFINE  ATOM.   Use  of  an  undefined  atom  in the
                    DEFINE  ATOM
                    DEFINE  ATOM
                    DEFINE  ATOM
molecular formula will result in automatic prompting for the  valence of
that atom, as  indicated under the  DEFINE MOLFORM command  (see Section
                                    DEFINE MOLFORM
                                    DEFINE MOLFORM
                                    DEFINE MOLFORM
IV.B.3.

        An  atom can  possess only  a single  valence.  If  one  atom is
present in a molecule in  different valence states, a unique  symbol and
valence  must be  used for  each different  state, e.g.,  S2 and  S4 for
bivalent and tetravalent sulfur, respectively.

                ******************************

        ********** Use of the DEFINE subcommand ATOM **********
                   Use of the DEFINE subcommand ATOM
                   Use of the DEFINE subcommand ATOM
                   Use of the DEFINE subcommand ATOM

#define atom                    On one line
 define atom
 define atom
 define atom

NAME:?                          Ask for help
     ?
     ?
     ?

A NAME (OTHER THAN X OR H) WHICH HAS
NOT PREVIOUSLY BEEN DEFINED     CONGEN replies and

NAME:si                           reprompts
     si
     si
     si

VALENCE:4                       Specify valence
        4
        4
        4

        or

#define atom si 4               All on one line
 define atom si 4
 define atom si 4
 define atom si 4

        or

#define atom si 4 cl 1 br 1     Several atoms and valences on
 define atom si 4 cl 1 br 1
 define atom si 4 cl 1 br 1
 define atom si 4 cl 1 br 1
                                  one line

#                               Ready for next CONGEN command

                ******************************

        ******* Error conditions and CONGEN replies ********
                Error conditions and CONGEN replies
                Error conditions and CONGEN replies
                Error conditions and CONGEN replies

        1) Attempt to define atoms X or H:




                                   46
CONGEN manual                                              February 1981


#define atom x                  Attempt to define atom X
 define atom x
 define atom x
 define atom x

THE NAMES X AND H HAVE SPECIAL MEANINGS AND CAN'T BE USED HERE

NAME:h                          CONGEN reprompts; atom H tried
     h
     h
     h

THE NAMES X AND H HAVE SPECIAL MEANINGS AND CAN'T BE USED HERE

NAME:                           CONGEN reprompts - carriage
                                  return gets back to CONGEN #
#                                 prompt

        2) Attempt to define an existing substructure as an atom:

#define atom xyz                XYZ is an existing substructure
 define atom xyz                XYZ
 define atom xyz                XYZ
 define atom xyz                XYZ

XYZ IS ALREADY DEFINED AS A SUBSTRUCTURE AND CAN'T BE USED HERE
ERASING ...XYZ
                                CONGEN replies and prompts
NAME:                             for another name

        3) Illegal input:

#define atom r
 define atom r
 define atom r
 define atom r
VALENCE:?                       Ask for help
        ?
        ?
        ?
AN INTEGER GREATER THAN ZERO    CONGEN replies
VALENCE:-1                      Illegal valence
        -1
        -1
        -1
THIS QUANTITY SHOULD BE GREATER THAN ZERO       CONGEN replies
VALENCE:q                       Another illegal valence
        q
        q
        q
I WAS EXPECTING A NUMBER        CONGEN replies
VALENCE:2                       Finally, a legal valence
        2
        2
        2
R DEFINED
#                               Ready for next CONGEN command

        4) Attempt to define an existing atom, e.g., R:

#define atom r                  Atom R previously defined
 define atom r
 define atom r
 define atom r
R IS ALREADY DEFINED AS AN ATOM AND CAN'T BE USED HERE
ERASING ...R                    CONGEN replies, erases illegal
NAME:                             input and reprompts for name

                ******************************














                                   47
CONGEN manual                                              February 1981


        IV.B.5    DEFINE AROMATICS
                  DEFINE AROMATICS
                  DEFINE AROMATICS
                  DEFINE AROMATICS

                *******************************
                *                             *
                * DEFINE Subcommand AROMATICS *
                *                             *
                *******************************


        CONGEN  is  equipped  to  treat  aromaticity.   A  definition of
AROMATICS is carried out via the DEFINE AROMATICS command.  A discussion
AROMATICS                        DEFINE AROMATICS
AROMATICS                        DEFINE AROMATICS
AROMATICS                        DEFINE AROMATICS
of the  various ways  in which  aromaticity is  specified to  CONGEN and
handled  in  the various  functions,  e.g., GENERATE,  IMBED,  PRUNE, is
                                            GENERATE   IMBED   PRUNE
                                            GENERATE   IMBED   PRUNE
                                            GENERATE   IMBED   PRUNE
included in  Aromaticity, Section IX.   Briefly, aromaticity  is treated
via a template-based procedure which you begin by selecting from  a menu
of templates those systems which  you wish to be viewed as  aromatic, as
described below.   Obviously, templates which  are not relevant  to your
structural problem, because your  structures are non-aromatic or  do not
contain relevant heteroatoms, need not be selected.

        Selection of  a particular template,  e.g., benzene,  will allow
CONGEN  to  recognize the  aromatic  nature of  all  polycyclic aromatic
systems comprised of  edge-fused six-membered rings,  e.g., naphthalene,
anthracene, benzpyrene.  Selection of templates in addition  to benzene,
e.g., pyridine, will  allow CONGEN to  recognize the aromatic  nature of
polycyclic aromatic ring systems comprised of one or more of each of the
template ring systems.

        If  templates  are  defined,  aromaticity  is  considered during
GENERATE for atoms "visible" to CONGEN at that point, i.e.,  those atoms
GENERATE
GENERATE
GENERATE
not  hidden  within  unimbedded  Superatoms.   Subsequent  to  structure
generation,  the  AROMATIZE  command,  Section  IV.H  or  imbedding (see
                  AROMATIZE
                  AROMATIZE
                  AROMATIZE
IMBED,  Section  IV.G)   will  convert  structures  to   their  aromatic
IMBED
IMBED
IMBED
counterparts  using  the  templates selected  as  illustrated  below and
remove any  resonance duplicates remaining  from GENERATE.  Only  one of
                                                 GENERATE
                                                 GENERATE
                                                 GENERATE
two  or more  possible Kekule  forms is  retained for  a  given aromatic
system during the conversion to aromatic systems.

        The  sequence  described  below represents  the  first  stage of
treatment of aromaticity -  specification to CONGEN of the  templates to
be considered aromatic.  CONGEN begins with no templates defined.
                                            no
                                            no
                                            no

                ******************************

        ******** Use of the DEFINE subcommand AROMATICS ********
                 Use of the DEFINE subcommand AROMATICS
                 Use of the DEFINE subcommand AROMATICS
                 Use of the DEFINE subcommand AROMATICS

#define
 define
 define
 define
DEFINITION TYPE:aromatics       Ask to define aromatics
                aromatics
                aromatics
                aromatics

TEMPLATES TO BE CONSIDERED AROMATIC:?   Ask for help
                                    ?
                                    ?
                                    ?

EITHER THE WORD NONE, OR ONE OR MORE SELECTIONS FROM THE FOLLOWING
LIST OF NAMES (SPECIAL ABBREVIATIONS ARE IN PARENTHESES):



                                   48
CONGEN manual                                              February 1981


BENZENE PYRIDINE(PD) PYRIMIDINE(PM) FURAN
PYRROLE(PR) THIOPHENE IMIDAZOLE AZULENE         CONGEN replies

TEMPLATES TO BE CONSIDERED AROMATIC:benzene azulene     Select two
                                    benzene azulene
                                    benzene azulene
                                    benzene azulene

AROMATICS DEFINED               CONGEN replies

        or

#define aromatics b a           All on one line - short form
 define aromatics b a
 define aromatics b a
 define aromatics b a

AROMATICS DEFINED

#                               Ready for next CONGEN command

                ******************************

        ******** Error conditions and CONGEN replies ********
                 Error conditions and CONGEN replies
                 Error conditions and CONGEN replies
                 Error conditions and CONGEN replies

        1) Aromatics already defined:

#define aromatics               Aromatics previously defined
 define aromatics
 define aromatics
 define aromatics

AROMATICS ARE ALREADY DEFINED - PLEASE USE THE FIX COMMAND
TO CHANGE THEM.                 CONGEN replies and returns to
                                  CONGEN # prompt
#                               Ready for next CONGEN command

        2) Illegal input:

#define aromatics 4             An integer is illegal
 define aromatics 4
 define aromatics 4
 define aromatics 4

I WAS EXPECTING A WORD          CONGEN replies and
ERASING ...4                      erases illegal input and
TEMPLATES TO BE CONSIDERED AROMATIC:      prompts for templates

                or

#define aromatics aw            AW is not a legal reply
 define aromatics aw
 define aromatics aw
 define aromatics aw

AW IS NOT AN EXPECTED KEYWORD HERE      CONGEN replies and
TEMPLATES TO BE CONSIDERED AROMATIC:      reprompts for templates

        3) Structures already constructed without defining aromaticity:

#def aromatics pyridine         Structures built without defining
 def aromatics pyridine
 def aromatics pyridine
 def aromatics pyridine
                                  aromatics - CONGEN replies

OK, BUT YOUR STRUCTURES WILL NOT REFLECT ANY CHANGES IN AROMATICS
UNTIL YOU AROMATIZE (OR IMBED) THEM.
SHALL I PROCEED ANYWAY?:y       If you answer no, back to CONGEN
                        y
                        y
                        y
                                  prompt
TEMPLATES TO BE CONSIDERED AROMATIC:    Ready for input



                                   49
CONGEN manual                                              February 1981


                ******************************























































                                   50
CONGEN manual                                              February 1981


        IV.B.6    DEFINE SUBSTRUCTURE
                  DEFINE SUBSTRUCTURE
                  DEFINE SUBSTRUCTURE
                  DEFINE SUBSTRUCTURE

                **********************************
                *                                *
                * DEFINE Subcommand SUBSTRUCTURE *
                *                                *
                **********************************


        All  substructural  information  about  a   structural  problem,
besides  that  retrieved  from files  of  substructures  (CONGEN command
SEARCH,  Section  IV.D)  or  restored  from  a  previous  run  of CONGEN
SEARCH
SEARCH
SEARCH
(CONGEN  command  RESTORE, Section  IV.M),  is specified  to  CONGEN via
                  RESTORE
                  RESTORE
                  RESTORE
the DEFINE  SUBSTRUCTURE command.  The  subcommand SUBSTRUCTURE  must be
    DEFINE  SUBSTRUCTURE                           SUBSTRUCTURE
    DEFINE  SUBSTRUCTURE                           SUBSTRUCTURE
    DEFINE  SUBSTRUCTURE                           SUBSTRUCTURE
used to define all substructural information for later use  in GENERATE,
                                                               GENERATE
                                                               GENERATE
                                                               GENERATE
IMBED,  PRUNE,  SURVEY  and  STEREO.   CONGEN  begins  with  no built-in
IMBED   PRUNE   SURVEY       STEREO                          no
IMBED   PRUNE   SURVEY       STEREO                          no
IMBED   PRUNE   SURVEY       STEREO                          no
substructures.  Although common substructures are available in a library
(See CONGEN  commands SHOW  LIBRARY (Section  IV.J) and  SEARCH <library
                      SHOW  LIBRARY                      SEARCH
                      SHOW  LIBRARY                      SEARCH
                      SHOW  LIBRARY                      SEARCH
name>  (Section   IV.D))  most  problems   require  definition   of  new
substructures to be used in structure generation or constraints.

        Any name may be used for a substructure, as long as it is not an
integer or the reserved names X and H, and has not been  used previously
in your CONGEN session as an atom or substructure name.  The name can be
many characters in length.  Long  names may be a problem for  the simple
reasons that  whenever the name  is used elsewhere  in CONGEN  the whole
name must be typed correctly, character for character, and substructures
used  as  Superatoms  (see  Substructures  in  CONGEN,  Section  V) will
appear in drawings  with only the first  three characters of  their name
showing.

        The   DEFINE  SUBSTRUCTURE   command  must   be  used   for  all
              DEFINE  SUBSTRUCTURE
              DEFINE  SUBSTRUCTURE
              DEFINE  SUBSTRUCTURE
substructures, ranging in complexity from simple groups such  as methyl,
ethyl, hydroxyl (all  of which, however,  are predefined in  the library
GENLIB if you wish to access  them in that way) up to  large, polyatomic
GENLIB
GENLIB
GENLIB
groups.

        The subcommand SUBSTRUCTURE is analogous to the  ATOM subcommand
                       SUBSTRUCTURE                      ATOM
                       SUBSTRUCTURE                      ATOM
                       SUBSTRUCTURE                      ATOM
in that each substructure, like each atom, is given a unique  name.  For
atoms,  however, you  need specify  only the  valence, for  which CONGEN
prompts you  directly (see  DEFINE ATOM  command, Section  IV.B.4).  For
                            DEFINE ATOM
                            DEFINE ATOM
                            DEFINE ATOM
substructures  you  generally must  supply  considerable  information to
CONGEN on the precise definition of the substructure.  For  this reason,
use  of  the  DEFINE  SUBSTRUCTURE  command  calls  into  operation  the
              DEFINE  SUBSTRUCTURE
              DEFINE  SUBSTRUCTURE
              DEFINE  SUBSTRUCTURE
structure  editing  functions  which  comprise  the  subprogram  we call
Editstruc, for  substructure definition  and manipulation.   Rather than
Editstruc
Editstruc
Editstruc
refer  to  the  various  commands in  Editstruc  as  subcommands  of the
SUBSTRUCTURE  subcommand,  we will  simply  refer to  them  as Editstruc
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE
commands.

        There  are   several  conventions   about  the   definition  and
subsequent use of substructures in CONGEN which you should  know.  These




                                   51
CONGEN manual                                              February 1981


are  summarized  in  Section  V,  Substructures  in   CONGEN.   Briefly,
substructures  eventually  used  as  Superatoms  (see  Section  V.A)  in
generating structures can possess no tags, aromatic designations or link
nodes, or atom names which are themselves names of  other substructures.
Substructures are  assumed to have  all available bonding  sites (unused
valences, i.e., those not connected to non-hydrogen neighbors)  free for
connection to a larger structure, unless: 1) hydrogen  ranges, specified
via the HRANGE command, below, limit the number of other connections; or
        HRANGE
        HRANGE
        HRANGE
2) free valences, specified via  the FREEV command, below, are  used any
                                     FREEV
                                     FREEV
                                     FREEV
place in the substructure, at which point all other unused  valences are
assumed to be saturated with hydrogen atoms.

        CONGEN works in hydrogen-suppressed format.  Hydrogen atoms need
not be  specified (in fact  you cannot explicitly  use a  hydrogen atom)
other than implicitly through the HRANGE command.  Hydrogen atoms do not
                                  HRANGE
                                  HRANGE
                                  HRANGE
appear in  drawings; the  number must  be interpreted  based on  how the
substructure  was defined.   As a  simple example,  the definition  of a
chain of atoms  of length one, that  atom named O, represents  either an
ether oxygen or an hydroxyl group unless the hydrogen range is specified
as exactly zero or exactly 1, respectively.

                ******************************

        ******** Use of DEFINE subcommand SUBSTRUCTURE ********
                 Use of DEFINE subcommand SUBSTRUCTURE
                 Use of DEFINE subcommand SUBSTRUCTURE
                 Use of DEFINE subcommand SUBSTRUCTURE

#define substructure            Substructure definition
 define substructure
 define substructure
 define substructure

NAME:?                          Ask for help
     ?
     ?
     ?

A NAME (OTHER THAN X OR H) WHICH HAS
NOT PREVIOUSLY BEEN DEFINED     CONGEN replies and
NAME:xyz                          reprompts for name, e.g., XYZ
     xyz                                                    XYZ
     xyz                                                    XYZ
     xyz                                                    XYZ

(NEW SUBSTRUCTURE)              CONGEN checks it - a new name

>                               Ready for Editstruc command

        or

#define substructure XYZ        All on one line
 define substructure XYZ
 define substructure XYZ
 define substructure XYZ

(NEW SUBSTRUCTURE)              CONGEN replies

>?                              Ready for Editstruc command, ask for
 ?
 ?
 ?
                                  help.  CONGEN replies
CHAIN  RING   BRANCH LINK  JOIN   BORD
ATNAME HRANGE FREEV  TAG   LNODE  ARTYPE
UNJOIN ERASE  SHOW   DRAW  GET    DONE   HALT

>                               Ready for next Editstruc command

                ******************************




                                   52
CONGEN manual                                              February 1981


        ******** Error conditions and CONGEN replies ********

        1) Name already exists as an atom or a substructure name:

#define substructure c          Attempt to redefine Carbon
 define substructure c
 define substructure c
 define substructure c

C IS ALREADY DEFINED AS AN ATOM AND CAN'T BE USED HERE
ERASING ...C                        CONGEN replies and
NAME:                                 reprompts for name

        or

#define substructure xyz            Assume XYZ defined previously
 define substructure xyz                   XYZ
 define substructure xyz                   XYZ
 define substructure xyz                   XYZ

XYZ IS ALREADY DEFINED AS A SUBSTRUCTURE AND CAN'T BE USED HERE
ERASING ...XYZ                      CONGEN replies and
NAME:                                 reprompts for name

        2) Illegal input:

#define substructure 42             Can't use an integer
 define substructure 42
 define substructure 42
 define substructure 42

I WAS EXPECTING A WORD              CONGEN replies and
NAME:                                 reprompts for name

                ******************************






























                                   53
CONGEN manual                                              February 1981


        IV.B.6.a    Introduction to Editstruc
                    Introduction to Editstruc
                    Introduction to Editstruc
                    Introduction to Editstruc

                *****************************
                *                           *
                * Introduction to Editstruc *
                *                           *
                *****************************


        Editstruc  is  the  "structure editor"  invoked  by  issuing the
DEFINE SUBSTRUCTURE <name> command to CONGEN.  It has a set  of commands
DEFINE SUBSTRUCTURE
DEFINE SUBSTRUCTURE
DEFINE SUBSTRUCTURE
for   defining   arbitrarily   complex   (within   CONGEN's  topological
representation of  structure) substructures  for use  in other  parts of
CONGEN, namely GENERATE, IMBED, SURVEY and STEREO.
               GENERATE  IMBED  SURVEY     STEREO
               GENERATE  IMBED  SURVEY     STEREO
               GENERATE  IMBED  SURVEY     STEREO

        Editstruc's commands consist of a set of  structure manipulation
commands  which allow  specification  of chains  and rings  of  atoms by
length and size, respectively, together with a variety of commands which
create branches, modify bond orders and modify atom properties.  A given
substructure may  be constructed  using these commands  in a  variety of
ways,  all of  which can  yield eventually  the same  substructure.  Any
command can be issued at  any time.  CONGEN will reply  with appropriate
error  messages  if  a  given  command  makes  no  sense.   For  further
information on  substructure representation and  use within  CONGEN, see
Section V.

        There  are  many  errors  which  can  be  made  in   defining  a
substructure using  Editstruc.  The most  common errors  involve valence
violations, either  explicit or implicit  due to association  of illegal
numbers of  free valences or  nonsensical hydrogen ranges  to particular
atoms.  Atom  names can  be used which  have not  yet been  defined.  We
stress that Editstruc  itself provides no  error checking to  catch such
            Editstruc  itself provides no  error checking
            Editstruc  itself provides no  error checking
            Editstruc  itself provides no  error checking
errors.  A reason for  this is that some  errors can only be  noted when
the substructure  is actually  used, for  example, an  attempt to  use a
substructure which has tags or  link nodes as a Superatom.   Because any
given  substructure may  be used  as a  Superatom or  a  constraint (see
Section  V),  or both,  we  cannot easily  determine  some  errors until
actual  use  of the  substructure  is attempted.   Therefore,  all error
                                                               all
                                                               all
                                                               all
checking is deferred until such  use.  Common errors and how  to recover
from them  are summarized in  the sections on  error conditions  for the
CONGEN  commands  GENERATE  (Section  IV.E),  PRUNE  (Section  IV.F) and
                  GENERATE                    PRUNE
                  GENERATE                    PRUNE
                  GENERATE                    PRUNE
IMBED (Section IV.G);  it is within these  commands that errors  will be
IMBED
IMBED
IMBED
detected and described to you.

        The description of the commands which follows is organized  in a
particular way.  Commands which allow you to "view" the  substructure as
you  build  it  up are  presented  first  so that  the  effects  of each
structure building command can be visualized in the  examples presented.
Commands used to create  and connect atoms are presented  next, followed
by  commands to  modify  atom properties  and finally  commands  to exit
Editstruc.

                ******************************



                                   54
CONGEN manual                                              February 1981


        ***** Default assumptions on atom and bond properties *****
              Default assumptions on atom and bond properties
              Default assumptions on atom and bond properties
              Default assumptions on atom and bond properties

        The following are the defaults for atom and bond properties.

        1) *** Atom properties ***
               Atom properties
               Atom properties
               Atom properties

                a) Atom names - all atoms created (e.g., via the
        CHAIN or RING commands) are assumed to be carbon atoms;
        CHAIN    RING
        CHAIN    RING
        CHAIN    RING
        The ATNAME command is used to specify another atom type.
            ATNAME
            ATNAME
            ATNAME
        The concepts of variable and "any" atom type exist, but such
        types must be stated explicitly by naming an atom or atoms
        with "polynames" for variable, but specified, type, or with
        type X, representing any type.
             X
             X
             X

                b) Hydrogen ranges - assumed to be "any" (up to
        the maximum unused valence of an atom) unless explicitly
        restricted using the HRANGE command, or unless free valences
                             HRANGE
                             HRANGE
                             HRANGE
        are used on any atom in the substructure at which point
                    any
                    any
                    any
        all other unused valences are assumed to be saturated with
        hydrogen atoms;

                c) Free valences - free valences, i.e., bonds with
        an unspecified terminus, do not exist explicitly unless
        placed by the FREEV command.  Bonding sites always exist
                      FREEV
                      FREEV
                      FREEV
        implicitly unless FREEV is used.  See Hydrogen ranges, above.
                          FREEV
                          FREEV
                          FREEV

                d) Tags - no atom is tagged unless a tag is placed
        by the TAG command;
               TAG
               TAG
               TAG

                e) Link nodes - no atom is a link node unless
        explicitly stated by the LNODE command;
                                 LNODE
                                 LNODE
                                 LNODE

                f) Aromatic type - all atoms created are assumed to
        be either aromatic or non-aromatic unless specified by
           either
           either
           either
        the ARTYPE command.
            ARTYPE
            ARTYPE
            ARTYPE

        2) *** Bond properties ***
               Bond properties
               Bond properties
               Bond properties

                a) Bond orders - all bonds created (e.g., by the CHAIN
                                                                 CHAIN
                                                                 CHAIN
                                                                 CHAIN
        or RING commands) are assumed to be single bonds; the JOIN,
           RING                                               JOIN
           RING                                               JOIN
           RING                                               JOIN
        BORD or UNJOIN commands must be used to modify bond orders.
        BORD    UNJOIN
        BORD    UNJOIN
        BORD    UNJOIN
        CONGEN will not modify bond orders during computations unless
        the bond order has been given the special type ANY.
                                                       ANY
                                                       ANY
                                                       ANY

                ******************************

          *** Substructure Numbering Conventions ***
              Substructure Numbering Conventions
              Substructure Numbering Conventions
              Substructure Numbering Conventions


        Every  atom created  for a  substructure is  assigned  a number,
beginning with  the integer one  and continuing by  numbering additional
atoms  consecutively as  they are  created.  The  numbering  sequence is




                                   55
CONGEN manual                                              February 1981


quite logical:  chains created are  numbered from one  end to  the other
beginning  with  the  next  available  integer;  rings  are  numbered in
sequence  around the  ring.  Because  most Editstruc  commands  refer to
atoms by  their number,  you can make  your definition  of substructures
more efficient by keeping  the numbering convention in mind.   Thus, you
can modify  and add  to substructures without  the necessity  of drawing
each intermediate result.  Of  course, you must check your  final result
                                           must
                                           must
                                           must
to ensure that no mistakes  have been made.  For example, if  you wanted
to define a  substructure corresponding to 2,3-dimethylpentane,  you can
create a chain of five carbon atoms and place a branch of length  one on
each of atoms two and  three knowing that CONGEN had numbered  the chain
according to the above convention.

        The  actual  numbering  of  a  substructure  is   irrelevant  to
                                                          irrelevant
                                                          irrelevant
                                                          irrelevant
subsequent computations.  If  there is a choice  as to where to  place a
branch, or which atom should  be named other than carbon, any  choice is
all  right,  assuming  that  eventually  you  define   the  substructure
correctly.

                ******************************




































                                   56
CONGEN manual                                              February 1981


        IV.B.6.b    Glossary of Editstruc Commands
                    Glossary of Editstruc Commands
                    Glossary of Editstruc Commands
                    Glossary of Editstruc Commands

                **********************************
                *                                *
                * Glossary of Editstruc Commands *
                *                                *
                **********************************


        All commands are terminated with a carriage return as the signal
to CONGEN that you have finished your line of input.

        See  Section  III,  CONGEN Input,  for  special  instructions on
abbreviating  commands,  extending  commands  where  repetitive  use  is
appropriate, and placing several different commands on the same line.

Editstruc Short
Command   Form*                         Function
--------- ----- --------------------------------------------------------

        ********** Substructure display commands **********
                   Substructure display commands
                   Substructure display commands
                   Substructure display commands

SHOW        S   To present a tabular representation ("connection table")
SHOW
SHOW
SHOW
                of the current substructure, including all atom and bond
                properties.

DRAW        D   To print a drawing of the substructure on your terminal
DRAW
DRAW
DRAW
                with either atom names (ATNAMED) or atom numbers
                                        ATNAMED
                                        ATNAMED
                                        ATNAMED
                (NUMBERED).
                 NUMBERED
                 NUMBERED
                 NUMBERED

        ********** Substructure creation commands **********
                   Substructure creation commands
                   Substructure creation commands
                   Substructure creation commands

GET         G   To retrieve the complete definition of a previously
GET
GET
GET
                created substructure for modification to a definition
                of the new substructure. Very useful when creating
                several, closely related substructures.

CHAIN       C   To create a chain of carbon atoms of specified length.
CHAIN
CHAIN
CHAIN
                The chain can be of length one. The chain is not con-
                nected to previously created atoms in the substructure.

RING        R   To create a ring of carbon atoms of specified size. The
RING
RING
RING
                ring can be of size two (C=C). The ring is not con-
                nected to previously created atoms in the substructure.

BRANCH      B   To create a chain of carbon atoms of specified length
BRANCH
BRANCH
BRANCH
                and connect one end of it to a designated, previously
                created atom.

LINK        L   To create a chain of specified length and attach each
LINK
LINK
LINK
                end to previously created atoms.  Spiro centers are
                created by attaching both ends to the same atom.




                                   57
CONGEN manual                                              February 1981


        ****** Substructure atom and bond property commands ******
               Substructure atom and bond property commands
               Substructure atom and bond property commands
               Substructure atom and bond property commands

JOIN        J   To increase the bond order between specified atoms by
JOIN
JOIN
JOIN
                one.  Can be used to connect previously disconnected
                atoms.

UNJOIN      U   To decrease the bond order between specified atoms by
UNJOIN
UNJOIN
UNJOIN
                one. Can be used to disconnect previously connected
                atoms.

BORD        BO  To set the bond order between two specified atoms
BORD
BORD
BORD
                to a selected value, e.g., two for double bond, three
                for triple, etc. A bond order of ANY may also be
                                                 ANY
                                                 ANY
                                                 ANY
                specified.

ATNAME      A   To assign a specified name to a specified atom.  The
ATNAME
ATNAME
ATNAME
                name may have the special designation X for any
                                                      X
                                                      X
                                                      X
                non-hydrogen atom, or the name may be a "polyname"
                which represents a set of specified names.

HRANGE      H   To assign a specified range (minimum to maximum, min.
HRANGE
HRANGE
HRANGE
                may equal max.) of hydrogen atoms to a specified atom.

FREEV       F   To assign a specified number of bonding sites, or "free
FREEV
FREEV
FREEV
                valences" to a specified atom. This influences CONGEN's
                assumptions about hydrogen ranges - see Section V,
                Substructures in CONGEN.

TAG         T   To assign a tag to a specified atom. A tag is used in
TAG
TAG
TAG
                special ways to count substructural features and is
                useful for certain NMR constraints, for example.  See
                Section X, Tagging in CONGEN.

LNODE       LN  To specify an atom as a "link node," a chain of atoms
LNODE
LNODE
LNODE
                of specified (min. to max.) range of lengths. See
                Section XI, Link Nodes in CONGEN.

ARTYPE      AR  To specify the aromatic type of an atom, either
ARTYPE
ARTYPE
ARTYPE
                aromatic or non-aromatic.  See Section IX,
                Aromaticity in CONGEN.

 ****** Command to modify existing substructural characteristics ******
        Command to modify existing substructural characteristics
        Command to modify existing substructural characteristics
        Command to modify existing substructural characteristics

ERASE       E   To erase previously created atoms, associated bonds and
ERASE
ERASE
ERASE
                their properties. Generally used to correct errors in
                original specifications.

        ********** Commands to exit Editstruc **********

DONE        DO  To exit Editstruc, thereby permanently defining or
DONE
DONE
DONE
                redefining the substructure.

HALT        H   To exit Editstruc without defining or redefining the
HALT                              without defining or redefining
HALT                              without defining or redefining
HALT                              without defining or redefining



                                   58
CONGEN manual                                              February 1981


                substructure.  This is usually an "oops" exit when
                you wish the current Editstruc session had never begun.

                ******************************

        For detailed descriptions of the function and use of each
command, see the following Sections:

        Command         Section
        -------         -------
        SHOW          Section IV.B.6.c
        SHOW
        SHOW
        SHOW
        DRAW          Section IV.B.6.d
        DRAW
        DRAW
        DRAW
        GET           Section IV.B.6.e
        GET
        GET
        GET
        CHAIN         Section IV.B.6.f
        CHAIN
        CHAIN
        CHAIN
        RING          Section IV.B.6.g
        RING
        RING
        RING
        BRANCH        Section IV.B.6.h
        BRANCH
        BRANCH
        BRANCH
        LINK          Section IV.B.6.i
        LINK
        LINK
        LINK
        JOIN          Section IV.B.6.j
        JOIN
        JOIN
        JOIN
        BORD          Section IV.B.6.k
        BORD
        BORD
        BORD
        UNJOIN        Section IV.B.6.l
        UNJOIN
        UNJOIN
        UNJOIN
        ATNAME        Section IV.B.6.m
        ATNAME
        ATNAME
        ATNAME
        HRANGE        Section IV.B.6.n
        HRANGE
        HRANGE
        HRANGE
        FREEV         Section IV.B.6.o
        FREEV
        FREEV
        FREEV
        TAG           Section IV.B.6.p
        TAG
        TAG
        TAG
        LNODE         Section IV.B.6.q
        LNODE
        LNODE
        LNODE
        ARTYPE        Section IV.B.6.r
        ARTYPE
        ARTYPE
        ARTYPE
        ERASE         Section IV.B.6.s
        ERASE
        ERASE
        ERASE
        DONE          Section IV.B.6.t
        DONE
        DONE
        DONE
        HALT          Section IV.B.6.u
        HALT
        HALT
        HALT

                ******************************

























                                   59
CONGEN manual                                              February 1981


        IV.B.6.c    SHOW
                    SHOW
                    SHOW
                    SHOW

                **************************
                *                        *
                * Editstruc Command SHOW *
                *                        *
                **************************


        The SHOW command is used to present to you a tabular description
            SHOW
            SHOW
            SHOW
of   the  structural   characteristics  of   your   substructure.   This
description is referred to  as a connection table, because  it specifies
the interconnections of each atom in the substructure. The  SHOW command
                                                            SHOW
                                                            SHOW
                                                            SHOW
also  summarizes atom  and bond  properties in  the table  itself  or in
additional text output with the table.  Some of these properties are not
                                                                     not
                                                                     not
                                                                     not
presented  with substructure  drawings  (see the  DRAW  command, Section
                                                  DRAW
                                                  DRAW
                                                  DRAW
IV.B.6.d);  the  SHOW command  must  be  used to  verify  that  all such
                 SHOW
                 SHOW
                 SHOW
properties, in particular hydrogen  ranges, aromatic types and  ANY bond
                                                                ANY
                                                                ANY
                                                                ANY
orders, have been assigned properly.

        As an example of the use of the SHOW command  and interpretation
                                        SHOW
                                        SHOW
                                        SHOW
of the tabular output, assume that Editstruc had previously been used to
specify a substructure (given the name, arbitrarily,  XYZ) corresponding
                                                      XYZ
                                                      XYZ
                                                      XYZ
to  a   decalin  ring  system   (two  edge-fused,   six-membered  rings)
substituted at C-3 with  an hydroxyl group.  For  illustrative purposes,
assume that C-1 had been tagged, C-4 had received one free  valence, C-2
was declared to be a link  node and C-3 was declared to  be non-aromatic
(all  performed  using   Editstruc  commands  described   in  subsequent
sections).  The connection table  output obtained from the  SHOW command
                                                            SHOW
                                                            SHOW
                                                            SHOW
would appear as follows:

                ******************************

        ***** Use of Editstruc command SHOW *****
              Use of Editstruc command SHOW
              Use of Editstruc command SHOW
              Use of Editstruc command SHOW

>show                           Issue SHOW command to Editstruc
 show                                 SHOW
 show                                 SHOW
 show                                 SHOW

SUBSTRUCTURE XYZ:               Name given to substructure

ATOM# TYPE NEIGHBORS HRANGE LNODE ARTYPE       Connection table

  1*    C   10  2                         Atom 1 tagged
  2     C    3  1           1-2           Atom 2 an lnode, length 1-2
  3     C   11  4  2              NON-AR  Atom 3 non-aromatic
  4     C    5  3 FV                      Atom 4, one free valence
  5     C   10  6  4
  6     C    7  5
  7     C    8  6
  8     C    9  7
  9     C   10  8
 10     C    5  1  9
 11     O    3        1-1                 Atom 11, an oxygen, with
                                              hydrogen range 1-1.



                                   60
CONGEN manual                                              February 1981


TAGGED ATOMS ARE INDICATED BY A *

>                               Ready for next Editstruc command

                ******************************

        The list of neighbors in the connection table is  interpreted as
follows.  In the above table, atom  1 is a carbon atom (and  is tagged),
connected to  atoms 10  and 2,  atom 2 is  an lnode  of length  1-2, all
carbon atoms, connected to atoms 1 and 3, and so forth.   Multiple bonds
appear as multiple entries in the neighbors list.  Thus, if there were a
double bond between C-6 and  C-7, the neighbors list for C-6  would read
"7 7 5" and that for C-7 "8 6 6" (order of entries unimportant).

                ******************************



        IV.B.6.d    DRAW
                    DRAW
                    DRAW
                    DRAW

                **************************
                *                        *
                * Editstruc Command DRAW *
                *                        *
                **************************


        The DRAW command is used to produce drawings of the substructure
            DRAW
            DRAW
            DRAW
you  are defining.   It  should be  used  in conjunction  with  the SHOW
                                                                    SHOW
                                                                    SHOW
                                                                    SHOW
command (Section IV.B.6.c) to  visualize all relevant details  about the
substructure.   The  command  can  be  issued  at  any  time  during the
definition of a substructure;  we recommend frequent use of  the command
at least  until you  feel confident  in your  ability to  define complex
substructures with few errors.

        Certain features  of the  drawings are governed  by the  type of
terminal you possess.  See Section IV.B.2, the DEFINE  TERMTYPE command,
                                               DEFINE  TERMTYPE
                                               DEFINE  TERMTYPE
                                               DEFINE  TERMTYPE
for  instructions  in  how  to choose  the  drawing  format  for certain
structural features.  There is  no capability in this version  of CONGEN
for  support  of  graphics terminals;  only  teletype  drawings  will be
produced.  For information on  the algorithm used for drawing,  see R.E.
Carhart, J. Chem. Inf. Comp. Sci., 16, 82 (1976).
         J. Chem. Inf. Comp. Sci.  16
         J. Chem. Inf. Comp. Sci.  16
         J. Chem. Inf. Comp. Sci.  16

        There are  certain rules followed  by the drawing  program which
are important in interpretation of the drawings:

        1) the program will allow bonds to cross in the  typed drawings,
but  atom  names or  numbers  are not  allowed  to  overlap.  Therefore,
although atom names may be placed in spaces adjacent to one  another, no
part of any atom name will be "hidden" from view;

        2) the program  is restricted to 50  or fewer atoms.  Every free
valence counts also as one atom;



                                   61
CONGEN manual                                              February 1981


        3) the program will use only the first three characters  of atom
names longer than three characters.  This may make some atoms  appear to
be equivalent when they are  not, if similar, long atom names  have been
used;

        4) single bonds are  indicated by one or more  hyphen characters
(for horizontally  oriented bonds),  and slashes  and vertical  bars (or
exclamation  marks)  for   angled  and  vertical   bonds,  respectively.
Multiple bonds  are indicated by  one (or more)  characters of  a single
type, independent of of  the orientation of the bond.   These characters
are:

                =  double bond
                #  triple bond
                *  quadruple bond
                &  quintuple bond
                $  sextuple bond

(Bond orders higher than six are  not drawn and will result in  an error
message "SOME ATOM TOO CROWDED  - CANNOT DRAW ***" message  from CONGEN.
The SHOW command must be used to visualize such large bond orders.)
    SHOW
    SHOW
    SHOW

        5) Drawings may be produced with either atom names  (ATNAMED) or
                                                             ATNAMED
                                                             ATNAMED
                                                             ATNAMED
their   corresponding  numbers   (NUMBERED).   The   latter   option  is
                                  NUMBERED
                                  NUMBERED
                                  NUMBERED
particularly  useful  when  using  Editstruc,  because  all substructure
modification commands refer to atom numbers.

                ******************************

        **** Use of the DRAW command in Editstruc ****
             Use of the DRAW command in Editstruc
             Use of the DRAW command in Editstruc
             Use of the DRAW command in Editstruc


        Assume  that  the  decalin  ring  system  (two  edge-fused, six-
membered  rings),  substituted with  an  oxygen atom  at  C-3,  has been
defined  previously  using Editstruc  commands  described  in subsequent
sections, namely  RING 10;  JOIN 5  10; BRANCH  3 1;  ATNAME 11  O.  The
                  RING 10;  JOIN 5  10; BRANCH  3 1;  ATNAME 11  O
                  RING 10;  JOIN 5  10; BRANCH  3 1;  ATNAME 11  O
                  RING 10;  JOIN 5  10; BRANCH  3 1;  ATNAME 11  O
following indicates how the DRAW command is used:
                            DRAW
                            DRAW
                            DRAW

>draw                           Issue the DRAW command to Editstruc
 draw                                     DRAW
 draw                                     DRAW
 draw                                     DRAW

TYPE OF DRAWING:?               Ask for help
                ?
                ?
                ?

NUMBERED ATNAMED                Options: atom numbers or names

TYPE OF DRAWING:atnamed         Select drawing with atom names
                atnamed
                atnamed
                atnamed

SUBSTRUCTURE XYZ:               CONGEN draws the substructure XYZ
                                                              XYZ
                                                              XYZ
                                                              XYZ

        C-C
       /  |
    C-C   C
   /  |  /
O-C   C-C



                                   62
CONGEN manual                                              February 1981


  |  /
  C-C

>draw numbered                  Request drawing with atom numbers
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:
NON-C ATOMS: 11->O              CONGEN tells what atoms are non-carbon

         6-7
        /  |
     4-5   8
    /  |  /
11-3  10-9
   |  /
   2-1

>draw a n                       Short form, extended command for both
 draw a n
 draw a n
 draw a n
                                  types of drawings
SUBSTRUCTURE XYZ:

        C-C
       /  |
    C-C   C
   /  |  /
O-C   C-C
  |  /
  C-C

SUBSTRUCTURE XYZ:
NON-C ATOMS: 11->O

         6-7
        /  |
     4-5   8
    /  |  /
11-3  10-9
   |  /
   2-1


        Assume that subsequent commands associated hydrogen  ranges (see
HRANGE,  Section  IV.B.6.n)  and  aromatic  types  (see  ARTYPE, Section
HRANGE                                                   ARTYPE
HRANGE                                                   ARTYPE
HRANGE                                                   ARTYPE
IV.B.6.r)  with one  or more  atoms,  and that  atom 1  has  been tagged
(see TAG,  Section IV.B.6.p) and  atom 8 has  been declared a  link node
     TAG
     TAG
     TAG
(see  LNODE, Section  IV.B.6.q).   The following  ATNAMED  drawing would
      LNODE                                       ATNAMED
      LNODE                                       ATNAMED
      LNODE                                       ATNAMED
result:

>draw a                         Ask to draw
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:(ARTYPES AND HRANGES NOT INDICATED)
TAGGED ATOMS ARE INDICATED BY AN ATTACHED *
LNODES ARE INDICATED BY AN ATTACHED @




                                   63
CONGEN manual                                              February 1981


        *
        |                       Note that DRAW does not indicate arom-
                                          DRAW
                                          DRAW
                                          DRAW
        C                         atic or hydrogen range information.
       / \                        Tags appear as "*" and link nodes as
    C-C   C                       "@" signs.  The SHOW command provides
                                                  SHOW
                                                  SHOW
                                                  SHOW
   /  |   |                       additional information
@-C   C   C-O
  |  / \ /
  C-C   C

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Substructure not yet defined:

>draw a                         Ask to draw before creating any atoms
 draw a
 draw a
 draw a
SUBSTRUCTURE XYZ:               CONGEN replies and returns to Editstruc
THERE IS NO STRUCTURE TO DRAW     prompt
>

        2) Use of an integer or characters other than those for
ATNAMED or NUMBERED drawings:
ATNAMED    NUMBERED
ATNAMED    NUMBERED
ATNAMED    NUMBERED

>draw 10                        Ask to draw an integer
 draw 10
 draw 10
 draw 10
I WAS EXPECTING A WORD          CONGEN replies, and erases integer and
ERASING ...10                     reprompts
TYPE OF DRAWING:?               Ask for help
                ?
                ?
                ?
NUMBERED ATNAMED                CONGEN replies and
TYPE OF DRAWING:                  reprompts

>draw t                         Illegal character
 draw t
 draw t
 draw t
T IS NOT AN EXPECTED KEYWORD HERE       CONGEN replies and
ERASING ...T                              erases character and
TYPE OF DRAWING:                          reprompts

                ******************************


        IV.B.6.e    GET
                    GET
                    GET
                    GET

                *************************
                *                       *
                * Editstruc Command GET *
                *                       *
                *************************


        The  GET  command  is  used  to  retrieve  the  definition  of a
             GET
             GET
             GET
previously  defined  substructure.   It  is  particularly   useful  when
defining a number of closely related substructures, because you  can use
a previous  definition as  a foundation  on which  to build  the related




                                   64
CONGEN manual                                              February 1981


substructure, without  having to begin  again from scratch.   Of course,
the  substructure  which  is   retrieved  must  exist  as  one   of  the
substructures  in  your current  CONGEN  session, i.e.,  must  have been
defined  with Editstruc  in your  current session,  or restored  from an
earlier  session  (see  the CONGEN  command  RESTORE,  Section  IV.M) or
                                             RESTORE
                                             RESTORE
                                             RESTORE
restored  from  an existing  library  of substructures  (see  the CONGEN
command SEARCH, Section IV.D).
        SEARCH
        SEARCH
        SEARCH

                *****************************

        ***** Use of the GET command in Editstruc *****
              Use of the GET command in Editstruc
              Use of the GET command in Editstruc
              Use of the GET command in Editstruc


        Assume that  the substructure XYZ  has been  defined previously,
                                      XYZ
                                      XYZ
                                      XYZ
and that you  wish to define a  substructure named PDQ which  is closely
                                                   PDQ
                                                   PDQ
                                                   PDQ
related to XYZ.  You ask to define PDQ and enter Editstruc:
           XYZ                     PDQ
           XYZ                     PDQ
           XYZ                     PDQ

B
  define sub pdq               Define PDQ
  define sub pdq                      PDQ
  define sub pdq                      PDQ
  define sub pdq                      PDQ
(NEW SUBSTRUCTURE)                 A new name

>draw a                         Ask to draw
 draw a
 draw a
 draw a

SUBSTRUCTURE PDQ:               Not defined yet
THERE IS NO STRUCTURE TO DRAW

>get                            Issue GET command
 get                                  GET
 get                                  GET
 get                                  GET

DEFINED NAME:?                  Ask for help
             ?
             ?
             ?
THE NAME OF A DEFINED
SUBSTRUCTURE                    CONGEN replies and
DEFINED NAME:xyz                  reprompts.  Answer XYZ as the name
             xyz                                     XYZ
             xyz                                     XYZ
             xyz                                     XYZ
                                  of the previously defined substructure

>show                           CONGEN retrieves the definition of XYZ
 show                                                              XYZ
 show                                                              XYZ
 show                                                              XYZ
                                  which is then shown and drawn
SUBSTRUCTURE PDQ:

ATOM# TYPE NEIGHBORS
  1     C   10  2
  2     C    3  1
  3     C   11  4  2
  4     C    5  3
  5     C   10  6  4
  6     C    7  5
  7     C    8  6
  8     C    9  7
  9     C   10  8
 10     C    5  1  9
 11     O    3

>draw a n
 draw a n
 draw a n
 draw a n




                                   65
CONGEN manual                                              February 1981


SUBSTRUCTURE PDQ:

        C-C
       /  |
    C-C   C
   /  |  /
O-C   C-C
  |  /
  C-C

SUBSTRUCTURE PDQ:
NON-C ATOMS: 11->O

         6-7
        /  |
     4-5   8
    /  |  /
11-3  10-9
   |  /
   2-1

>                               Editstruc prompt - ready for commands
                                  to modify definition to yield the
                                  desired substructure XYZ
                                                       XYZ
                                                       XYZ
                                                       XYZ

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Attempt to GET an integer:
                      GET
                      GET
                      GET

>get 3                          An integer is illegal
 get 3
 get 3
 get 3
I WAS EXPECTING A WORD          CONGEN replies and
ERASING ...3                      erases and
DEFINED NAME:?                    reprompts. Ask for help
             ?
             ?
             ?
THE NAME OF A DEFINED           CONGEN replies
SUBSTRUCTURE                      and
DEFINED NAME:                     reprompts.

        2) Attempt to GET an undefined substructure:
                      GET
                      GET
                      GET

>get re                         Assume RE undefined
 get re                                RE
 get re                                RE
 get re                                RE
                                  CONGEN replies

I DON'T BELIEVE YOU HAVE DEFINED A SUBSTRUCTURE CALLED RE.

>                                 and returns to Editstruc prompt

                ******************************







                                   66
CONGEN manual                                              February 1981


        IV.B.6.f    CHAIN
                    CHAIN
                    CHAIN
                    CHAIN

                ***************************
                *                         *
                * Editstruc Command CHAIN *
                *                         *
                ***************************


        The CHAIN  command is used  to create a  chain of  carbon atoms,
            CHAIN
            CHAIN
            CHAIN
connected by single bonds, of specified length.

        If other atoms  already exist as  part of the  substructure, the
chain  is  not  connected  to  one  of  the  existing  atoms.   Thus,  a
           not
           not
           not
disconnected  substructure results.   Disconnected substructures  can be
drawn with no difficulty,  and utilized in constraints  (see Constraints
in   CONGEN,   Section   VII)   if   desired.    However,   disconnected
substructures  cannot be  used  as Superatoms  (see  Superatoms, Section
V.A).

                ******************************

        ***** Use of the CHAIN command in Editstruc *****
              Use of the CHAIN command in Editstruc
              Use of the CHAIN command in Editstruc
              Use of the CHAIN command in Editstruc


        Assume that you are defining the substructure XYZ, and  no other
                                                      XYZ
                                                      XYZ
                                                      XYZ
atoms have been previously created:

>chain                          Issue the CHAIN command
 chain                                    CHAIN
 chain                                    CHAIN
 chain                                    CHAIN

CHAIN LENGTH:?                  Ask for help
             ?
             ?
             ?

AN INTEGER GREATER THAN ZERO    CONGEN replies and

CHAIN LENGTH:10                   reprompts.  Ask for length of 10 atoms
             10
             10
             10

>draw a                         CONGEN gives Editstruc prompt.  Ask to
 draw a
 draw a
 draw a
                                  Draw the result

SUBSTRUCTURE XYZ:               CONGEN replies with the drawing

C
 \
  C
   \
    C-C-C-C-C-C-C-C

>                               Return to Editstruc prompt

        The CHAIN command can be used to create single atoms.  Assume
            CHAIN
            CHAIN
            CHAIN
no other atoms have been previously defined:

>chain 1                        On one line, ask for a single atom
 chain 1
 chain 1
 chain 1



                                   67
CONGEN manual                                              February 1981


                                  chain
>draw a                         Ask to draw the result
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:

C                               The result, a single carbon atom.

>                               Return to Editstruc prompt

        The CHAIN command can be extended to produce multiple,
            CHAIN
            CHAIN
            CHAIN
disconnected chains.  Assume no atoms have been defined previously:

>chain 3 6                      Ask for chains of length 3 and 6
 chain 3 6
 chain 3 6
 chain 3 6

>draw n                         Ask to draw the result with atom
 draw n
 draw n
 draw n
                                  numbers
SUBSTRUCTURE XYZ:               CONGEN replies

1-2-3

4-5-6-7-8-9

>                               Return to Editstruc prompt

                ******************************

        ***** Error conditions and CONGEN replies ] *****
              Error conditions and CONGEN replies 
              Error conditions and CONGEN replies 
              Error conditions and CONGEN replies 

        1) Illegal input:

>chain g                        Characters illegal
 chain g
 chain g
 chain g
I WAS EXPECTING A NUMBER        CONGEN replies and
CHAIN LENGTH:                     reprompts

>chain -45                      Illegal negative integer
 chain -45
 chain -45
 chain -45
THIS QUANTITY SHOULD BE GREATER THAN ZERO       CONGEN replies and
CHAIN LENGTH:                                     reprompts

        2) Length too large

>chain 89                       Length too large
 chain 89
 chain 89
 chain 89

NOTE: I'M ALMOST OUT OF LIST SPACE      CONGEN replies with warning
>                               Better control-C and restart CONGEN

>chain 232                      Length much too large
 chain 232
 chain 232
 chain 232

SORRY, I'LL HAVE TO STOP; I'VE RUN OUT OF LIST SPACE
                                CONGEN replies and exits from itself.
             or                   You must run CONGEN again.  You will
                                  have lost the current definition, but
NOT ENOUGH ROOM FOR THAT          retained all previous work.




                                   68
CONGEN manual                                              February 1981


                ******************************


        IV.B.6.g    RING
                    RING
                    RING
                    RING

                **************************
                *                        *
                * Editstruc Command RING *
                *                        *
                **************************


        The  RING command  is used  to create  a ring  of  carbon atoms,
             RING
             RING
             RING
connected with single bonds, of specified size.

        If other atoms  exist in the substructure,  the new ring  is not
connected to  them.  Thus, disconnected  substructures will  result (see
the description  of the Editstruc  command CHAIN, Section  IV.B.6.f, for
                                           CHAIN
                                           CHAIN
                                           CHAIN
additional information on disconnected substructures).

                *****************************

        ***** Use of the RING command in Editstruc *****
              Use of the RING command in Editstruc
              Use of the RING command in Editstruc
              Use of the RING command in Editstruc


        Assume that you have requested to define the  substructure named
XYZ and that no atoms have been created previously:
XYZ
XYZ
XYZ

>ring                           Issue RING command
 ring                                 RING
 ring                                 RING
 ring                                 RING

RING SIZE:?                     Ask for help
          ?
          ?
          ?

AN INTEGER GREATER THAN ZERO    CONGEN replies and

RING SIZE:2                       reprompts. Answer ring size 2
          2
          2
          2
                                  (a simple way of creating a
                                  double bond).

>draw a                         Ask to draw the result
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:

C=C

>                               Return to Editstruc for next command

        More conventionally, a real ring (assume no other atoms exist):

>ring 3                         On one line
 ring 3
 ring 3
 ring 3

>draw a                         Ask to draw the result
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:



                                   69
CONGEN manual                                              February 1981


C-C
 \|
  C

>                               Return to Editstruc for next command

        Several disconnected rings (assume no atoms previously defined):

>ring 5 6 7                     On one line
 ring 5 6 7
 ring 5 6 7
 ring 5 6 7

>draw a                         Ask to draw the result
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:               CONGEN replies

  C-C
 /  |
C   C
 \ /
  C

  C-C
 /   \
C     C
 \   /
  C-C































                                   70
CONGEN manual                                              February 1981


   C
  /|
 / C
C   \
|    C
C    |
 \   C
  \ /
   C

>                               Return to Editstruc for next command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Illegal input:

>ring 5 t 7                     On one line, letter t illegal
 ring 5 t 7
 ring 5 t 7
 ring 5 t 7
I WAS EXPECTING A NUMBER        CONGEN replies and
ERASING ...T 7                    erases last part of line and
RING SIZE:                        reprompts for another ring size(s)
                                Note that a carriage return response
>draw a                           followed by a request to draw
 draw a
 draw a
 draw a
                                  illustrates that the first part of
SUBSTRUCTURE XYZ:                 the command, i.e., RING 5, was
                                                     RING 5
                                                     RING 5
                                                     RING 5
                                  processed correctly
  C-C
 /  |
C   C
 \ /
  C

>                               Return to Editstruc for next command

>ring -8                        Negative ring sizes illegal
 ring -8
 ring -8
 ring -8
THIS QUANTITY SHOULD BE GREATER THAN ZERO       CONGEN replies and
RING SIZE:                                        reprompts

        2) Very large ring sizes:

>ring 89                        A very large ring
 ring 89
 ring 89
 ring 89
NOTE: I'M ALMOST OUT OF LIST SPACE    CONGEN complains - it's best
                                  to HALT (see Editstruc command HALT,
                                     HALT                        HALT
                                     HALT                        HALT
                                     HALT                        HALT
                                  Section IV.B.6.u) or control-C,
                                  restart
>ring 248                       A much-too-large ring
 ring 248
 ring 248
 ring 248

SORRY, I'LL HAVE TO STOP; I'VE RUN OUT OF LIST SPACE
                                CONGEN exits from itself - you must
            or                    run the program again.  You will
                                  have lost the current definition, but
NOT ENOUGH ROOM FOR THAT          everything else in your session will



                                   71
CONGEN manual                                              February 1981


                                  be all right.


                ******************************


        IV.B.6.h    BRANCH
                    BRANCH
                    BRANCH
                    BRANCH

                ****************************
                *                          *
                * Editstruc Command BRANCH *
                *                          *
                ****************************


        The BRANCH command  is used to create  a chain of  carbon atoms,
            BRANCH
            BRANCH
            BRANCH
connected  by single  bonds, of  specified length,  and to  connect that
chain to an existing atom in the substructure, again with a single bond.
In order to  use the command,  the atoms which  are to be  branched must
have been created previously (e.g., by the Editstruc commands CHAIN (see
                                                              CHAIN
                                                              CHAIN
                                                              CHAIN
Section IV.B.6.f) or RING (see Section IV.B.6.g)).
                     RING
                     RING
                     RING

        The   BRANCH  command   is  particularly   useful   in  creating
              BRANCH
              BRANCH
              BRANCH
substituents on existing chains and/or rings of atoms.

                ******************************

        ***** Use of the BRANCH command in Editstruc *****
              Use of the BRANCH command in Editstruc
              Use of the BRANCH command in Editstruc
              Use of the BRANCH command in Editstruc


        Because  the  branch  command  requires  the  presence  of atoms
created in previous commands, let us first create a chain of five carbon
atoms.  Again, assume the name of the substructure is XYZ:
                                                      XYZ
                                                      XYZ
                                                      XYZ

>chain 5                        Create a chain of 5 carbons
 chain 5
 chain 5
 chain 5

>draw a n                       Draw, both named and numbered
 draw a n
 draw a n
 draw a n

SUBSTRUCTURE XYZ:               CONGEN draws both

C-C-C-C-C

SUBSTRUCTURE XYZ:

1-2-3-4-5

>branch                         Issue the BRANCH command
 branch                                   BRANCH
 branch                                   BRANCH
 branch                                   BRANCH

FROM ATOM:?                     Ask for help
          ?
          ?
          ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

FROM ATOM:2                       reprompts - choose atom 2
          2
          2
          2



                                   72
CONGEN manual                                              February 1981


LENGTH OF BRANCH:?              CONGEN asks for length, you ask for help
                 ?
                 ?
                 ?

AN INTEGER GREATER THAN ZERO    CONGEN replies and

LENGTH OF BRANCH:2                reprompts - you choose length 2
                 2
                 2
                 2

>draw a n                       Ask to draw, both named and numbered
 draw a n
 draw a n
 draw a n

SUBSTRUCTURE XYZ:               CONGEN draws both

          C
         /
        C
       /
C-C-C-C
      |
      C

SUBSTRUCTURE XYZ:

          7
         /
        6
       /
5-4-3-2
      |
      1

>                               Ready for next Editstruc command


        The BRANCH command, like all CONGEN commands, can be extended to
            BRANCH
            BRANCH
            BRANCH
perform successive operations without having to issue separate commands.
Thus, to place additional branches on the above structure:

>branch 3 1 6 1 4 3             Branch atoms 3 and 6, length 1, and
 branch 3 1 6 1 4 3
 branch 3 1 6 1 4 3
 branch 3 1 6 1 4 3
                                  atom 4 length 3, all on one line.
>draw n                         Draw the result, with atom numbers
 draw n
 draw n
 draw n


















                                   73
CONGEN manual                                              February 1981


SUBSTRUCTURE XYZ:

  1    8    5
   \   |   /
    2--3--4
   /       \
9-6        10
  |          \
  7          11
               \
                12

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Attempt to branch from a non-existing atom:

>branch 16 1                    Atom 16 doesn't exist
 branch 16 1
 branch 16 1
 branch 16 1
THERE IS NO ATOM NUMBERED 16    CONGEN replies and
ERASING ...16 1                   erases rest of input line and
FROM ATOM:                        reprompts for another number

        2) Illegal atom number or length:

>branch me 3                    ME is not an atom number
 branch me 3                    ME
 branch me 3                    ME
 branch me 3                    ME
I WAS EXPECTING A NUMBER        CONGEN replies and
ERASING ...ME 3                   erases rest of input line and
FROM ATOM:                        reprompts for another number

>branch 6 -3                    Negative integer illegal
 branch 6 -3
 branch 6 -3
 branch 6 -3
THIS QUANTITY SHOULD BE GREATER THAN ZERO       CONGEN replies and
ERASING ...-3                                     erases the -3 and
LENGTH OF BRANCH:                                 reprompts for length

                ******************************


        IV.B.6.i    LINK
                    LINK
                    LINK
                    LINK

                **************************
                *                        *
                * Editstruc Command LINK *
                *                        *
                **************************


        The LINK command creates  a chain of carbon atoms,  connected by
            LINK
            LINK
            LINK
single bonds,  of specified  length and attaches  each end  to specified
atoms, again  with single  bonds.  In order  to use  LINK, the  atoms to
                                                     LINK
                                                     LINK
                                                     LINK




                                   74
CONGEN manual                                              February 1981


which  the chain  will be  attached must  have been  defined previously,
e.g.,  using  the CHAIN  (see  Section IV.B.6.f)  or  RING  (see Section
                  CHAIN                               RING
                  CHAIN                               RING
                  CHAIN                               RING
IV.B.6.g) commands in Editstruc.

        If the  atom to  which the ends  of the  chain are  connected is
specified to be the same for both ends, a spiro center is the result.

        The LINK command can be used in a variety of ways.  For example,
            LINK
            LINK
            LINK
it can  be used  to connect  two previously  disconnected pieces  of the
substructure, as a simple method for specifying bridges  in bridged-ring
systems, for creating spiro centers, and so forth.

                ******************************

        ***** Use of the LINK command in Editstruc *****
              Use of the LINK command in Editstruc
              Use of the LINK command in Editstruc
              Use of the LINK command in Editstruc


        Assume  that  you  have  requested  to  CONGEN  to   define  the
substructure XYZ.  In  order to use LINK,  atoms which are to  be linked
             XYZ                    LINK
             XYZ                    LINK
             XYZ                    LINK
must already  exist, so the  first illustrative step  is to  create some
atoms:

>chain 3 3                      Create two 3-carbon chains
 chain 3 3
 chain 3 3
 chain 3 3

>draw n                         Draw them, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

1-2-3

4-5-6

>link                           Issue the LINK command
 link                                     LINK
 link                                     LINK
 link                                     LINK

FROM ATOM:?                     CONGEN replies - ask for help
          ?
          ?
          ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

FROM ATOM:1                       reprompts - answer atom 1
          1
          1
          1

TO ATOM:4                       Atom 1 to be linked to atom 4
        4
        4
        4

LENGTH OF LINK:?                Ask for help
               ?
               ?
               ?

AN INTEGER GREATER THAN ZERO    CONGEN replies and

LENGTH OF LINK:1                  reprompts - answer length 1
               1
               1
               1

>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:               CONGEN replies

  2-1-7-4-5                     Note that the new atom 7 has been



                                   75
CONGEN manual                                              February 1981


 /         \                      placed between atoms 1 and 4, as
3           6                     requested

>                               Ready for next Editstruc command

>link 3 6                       Next command - on one line, both atoms
 link 3 6
 link 3 6
 link 3 6
                                  to which the link is affixed
LENGTH OF LINK:2                CONGEN now needs only the length
               2
               2
               2

>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:               Note that this link has formed a ring
                                  by inserting the two new atoms,
  2-1----7                        numbered 8 and 9, between atoms 3
 /       |                        and 6, as requested
3        |
|        4
8       /
 \     /
  9-6-5

>link 1 3 1                     Ready for next command - another link,
 link 1 3 1
 link 1 3 1
 link 1 3 1
                                  all on one line
>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:               Note that the last link formed a 6,1,1
                                  bridged ring system
 1---7-4
 |\     \
10 2     5
  \|     |
   3     6
    \   /
     8-9

>                               Ready for next Editstruc command


        Assume that you  wish to create  a spiro-fused 6,6  ring system.
Here  is one  way  to do  it, assuming  again  that you  are  defining a
substructure named XYZ and have just begun the definition:
                   XYZ
                   XYZ
                   XYZ

>ring 6                         Create a ring of 6 atoms
 ring 6
 ring 6
 ring 6

>draw n                         Draw the result, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

  2-3
 /   \
1     4
 \   /
  6-5



                                   76
CONGEN manual                                              February 1981


>link 1 1 5                     Form the spiro ring by linking both
 link 1 1 5
 link 1 1 5
 link 1 1 5
                                  ends of a 5 carbon chain to atom 1
>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

  5-6   7-8
 /   \ /   \
4     1     9
 \   / \   /
  3-2  11-10

>                               Ready for next Editstruc  command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Attempt to link to a non-existent atom:

>link 6 7 4                     Assume atom 7 does not exist
 link 6 7 4
 link 6 7 4
 link 6 7 4

THERE IS NO ATOM NUMBERED 7     CONGEN replies and
ERASING ...7 4                    erases and reprompts
TO ATOM:                          for atom to which 6 is linked

        2) Illegal input:

>link 5 6 a                     All letters illegal
 link 5 6 a
 link 5 6 a
 link 5 6 a
I WAS EXPECTING A NUMBER        CONGEN replies and
ERASING ...A                      erases offending letter and
LENGTH OF LINK:                   reprompts for correct length

>link 5 6 -2                    All negative integers (or zero) illegal
 link 5 6 -2
 link 5 6 -2
 link 5 6 -2
THIS QUANTITY SHOULD BE GREATER THAN ZERO       CONGEN replies and
ERASING ...-2                                     erases illegal input
LENGTH OF LINK:                                   and reprompts

                ******************************

















                                   77
CONGEN manual                                              February 1981


        IV.B.6.j    JOIN
                    JOIN
                    JOIN
                    JOIN

                **************************
                *                        *
                * Editstruc Command JOIN *
                *                        *
                **************************


        The  JOIN command  is used  to increase  the bond  order between
             JOIN
             JOIN
             JOIN
existing atoms  by one, i.e.,  it forms an  additional bond  between the
existing
existing
existing
atoms.  If they are disconnected, JOIN connects them with a single bond.
                                  JOIN
                                  JOIN
                                  JOIN
If  they are  already connected,  JOIN places  an  additional connection
                                  JOIN
                                  JOIN
                                  JOIN
between them.

        The  Editstruc  command   BORD  for  bond  order   (see  Section
                                  BORD
                                  BORD
                                  BORD
IV.B.6.k)  can  be used  to  perform similar  bond  order modifications.
The   Editstruc   command   UNJOIN  (see   Section   IV.B.6.l)   is  the
                            UNJOIN
                            UNJOIN
                            UNJOIN
counterpart of JOIN and is used to decrease bond orders by one.
               JOIN
               JOIN
               JOIN

                ******************************

        ***** Use of the JOIN command in Editstruc *****
              Use of the JOIN command in Editstruc
              Use of the JOIN command in Editstruc
              Use of the JOIN command in Editstruc


        Assume  that you  are defining  a substructure  named  XYZ.  The
                                                               XYZ
                                                               XYZ
                                                               XYZ
atoms  to be  joined must  already exist,  so first  we create  some for
illustrating use of JOIN:
                    JOIN
                    JOIN
                    JOIN

>chain 6                        Create a chain of 6 carbons
 chain 6
 chain 6
 chain 6

>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

1-2-3-4-5-6

>join                           Issue the JOIN command
 join                                     JOIN
 join                                     JOIN
 join                                     JOIN

FIRST ATOM:?                    CONGEN replies - ask for help
           ?
           ?
           ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

FIRST ATOM:1                      reprompts for first atom - specify 1
           1
           1
           1

SECOND ATOM:?                   CONGEN replies - ask for help
            ?
            ?
            ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

SECOND ATOM:6                     reprompts - ask to join to atom 6
            6
            6
            6

>draw n                         Draw the result
 draw n
 draw n
 draw n




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SUBSTRUCTURE XYZ:

  2-3
 /   \
1     4
 \   /
  6-5

>join 1                         Partly on one line
 join 1
 join 1
 join 1

SECOND ATOM:2                   CONGEN prompts for second atom - atom 2
            2
            2
            2

>join 3 4                       All on one line
 join 3 4
 join 3 4
 join 3 4

>draw n                         Draw the result of the last two joins
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:               CONGEN replies - note double bonds
                                  between atoms 1 and 2, 3 and 4 as
  2-3                             requested
 =   =
1     4
 \   /
  6-5

>branch 4 2                     Now, sprout a branch
 branch 4 2
 branch 4 2
 branch 4 2

>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:               CONGEN replies

      3-2
     =   =
8-7-4     1
     \   /
      5-6

>join 7 8 7 8 5 6               Join atom 7 to 8 twice, and atom 5 to 6
 join 7 8 7 8 5 6
 join 7 8 7 8 5 6
 join 7 8 7 8 5 6

>draw n                         Draw the result
 draw n
 draw n
 draw n

















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SUBSTRUCTURE XYZ:

      3-2
     =   =
8#7-4     1                     Note the # symbol for triple bonds
     \   /
      5=6

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>join 6 12                      Assume atom 12 does not exist
 join 6 12
 join 6 12
 join 6 12
THERE IS NO ATOM NUMBERED 12    CONGEN replies and
ERASING ...12                     erases bad atom number and
SECOND ATOM:                      reprompts for second atom

        2) Illegal input:

>join 4 t                       Can't use letters
 join 4 t
 join 4 t
 join 4 t
I WAS EXPECTING A NUMBER        CONGEN replies and
ERASING ...T                      erases offending letter and
SECOND ATOM:                      reprompts for second atom

>join 4 -1                      Can't use integers zero or less
 join 4 -1
 join 4 -1
 join 4 -1
THIS QUANTITY SHOULD BE GREATER THAN ZERO       CONGEN replies and
ERASING ...-1                                     erases the -1 and
SECOND ATOM:                                      reprompts

        3) Attempt to join an atom to itself:

>join 2 2                       Nonsense request
 join 2 2
 join 2 2
 join 2 2
ATOM 2 CAN'T BE JOINED TO ITSELF         CONGEN replies, erases both
                                                                both
                                                                both
                                                                both
FIRST ATOM:                                numbers and prompts for first

                ******************************


        IV.B.6.k    BORD
                    BORD
                    BORD
                    BORD

                **************************
                *                        *
                * Editstruc Command BORD *
                *                        *
                **************************


        The  BORD   command  (short  for   bond  order)   represents  an
             BORD
             BORD
             BORD




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alternative to  the Editstruc commands  JOIN (see Section  IV.B.6.j) and
                                        JOIN
                                        JOIN
                                        JOIN
UNJOIN  (see Section  IV.B.6.l) for  establishing bond  orders,  or bond
UNJOIN
UNJOIN
UNJOIN
multiplicities, between atoms.  The BORD command allows you  to specify,
                                    BORD
                                    BORD
                                    BORD
by an integer value, the bond order between a pair of atoms.   The atoms
referred   to  must   have  been   defined  previously.    Integer  bond
multiplicities  have  their  expected meaning.   A  bond  order  of zero
implies no  connection, one a  single bond, two  a double bond,  three a
triple bond, and so forth.

        In addition, the BORD  command recognizes a special  bond order,
                         BORD
                         BORD
                         BORD
called ANY.  The designation of ANY to a bond order means that  the pair
       ANY                      ANY
       ANY                      ANY
       ANY                      ANY
of atoms may  be connected by  a bond of  any order. Thus,  ANY includes
                                                            ANY
                                                            ANY
                                                            ANY
bond orders  1, 2,  3, ....  n.  Designation of  a bond  as an  ANY bond
                                                                ANY
                                                                ANY
                                                                ANY
causes Editstruc to set the bond order to one, primarily for  clarity in
drawings, and to associate with this bond a special marker indicating to
CONGEN that the bond may have any order.

        Such  variable  bond  orders are  important  in  Superatoms (see
Section  V.A) if  the process  of structure  generation may  lead  to an
increase in the  bond order between two  atoms already connected  in the
Superatom.   They are  also important  in constraints  if one  wishes to
check only that certain pairs of atoms are connected, independent of the
multiplicity of the bond connecting them.

                ******************************

        ***** Use of the BORD command in Editstruc *****
              Use of the BORD command in Editstruc
              Use of the BORD command in Editstruc
              Use of the BORD command in Editstruc


        The BORD command  assumes that the  atoms for which  bond orders
            BORD
            BORD
            BORD
are  to be  specified already  exist.  Assume  that you  are  defining a
substructure  named  XYZ.   Here  is an  illustration  of  how  the same
                     XYZ
                     XYZ
                     XYZ
substructure used as one of the illustrations for the  Editstruc command
JOIN  (see Section  IV.B.6.j) can  be  built with  the aid  of  the BORD
JOIN                                                                BORD
JOIN                                                                BORD
JOIN                                                                BORD
command.  First, create the necessary atoms:

>chain 6                        Specify a 6 carbon chain
 chain 6
 chain 6
 chain 6

>branch 4 2                     Create the two carbon branch
 branch 4 2
 branch 4 2
 branch 4 2

>draw n                         Draw the result, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:               CONGEN replies

          8
         /
        7
       /
1-2-3-4
      |
      5
      |
      6



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>bord                           Issue the BORD command
 bord                                     BORD
 bord                                     BORD
 bord                                     BORD

FIRST ATOM:?                    Ask for help
           ?
           ?
           ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

FIRST ATOM:1                      reprompts for first atom - reply 1
           1
           1
           1

SECOND ATOM:6                   Request for second atom - reply 6
            6
            6
            6

BOND ORDER:?                    Ask for help
           ?
           ?
           ?

A NON-NEGATIVE INTEGER, OR THE WORD 'ANY'       CONGEN replies and

BOND ORDER:1                      reprompts for bond order - reply 1
           1
           1
           1

>bord 1 2                       Partly on one line
 bord 1 2
 bord 1 2
 bord 1 2

BOND ORDER:2                    CONGEN prompts for missing information
           2
           2
           2

>bord 3 4 2                     All on one line
 bord 3 4 2
 bord 3 4 2
 bord 3 4 2

>draw n                         Draw the result, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:               CONGEN replies

  6-5
 /   \
1     4-7-8
 =   =
  2-3

>bord 7 8 any                   Illustrate use of ANY bond order
 bord 7 8 any                                     ANY
 bord 7 8 any                                     ANY
 bord 7 8 any                                     ANY

>draw n                         Draw the result, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:
BOND 8-7 IS OF TYPE 'ANY'       Note that the ANY bond designation
                                              ANY
                                              ANY
                                              ANY
                                  appears in the heading, but not in
  6-5                             the drawing
 /   \
1     4-7-8
 =   =
  2-3

>show                           Also, show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS           Note that the 7,8 bond appears in the
  1     C    2  2  6              connection table as a single bond -
  2     C    1  1  3              the ANY bond designation appears in
                                      ANY
                                      ANY
                                      ANY
  3     C    4  4  2              the footing of the table



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  4     C    3  3  7  5
  5     C    6  4               Note also that multiple bonds are
  6     C    1  5                 designated by multiple entries in
  7     C    8  4                 the neighbors list, e.g., for atom 1,
  8     C    7                    neighbors 2 2 6
BOND 8-7 IS OF TYPE 'ANY'

>bord 7 8 3 5 6 2               Two commands on one line - reset 7,8
 bord 7 8 3 5 6 2
 bord 7 8 3 5 6 2
 bord 7 8 3 5 6 2
                                  bond order from any to triple
>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

  6=5
 /   \
1     4-7#8
 =   =
  2-3

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>bord 8 10 2                    Atom 10 does not exist
 bord 8 10 2
 bord 8 10 2
 bord 8 10 2
THERE IS NO ATOM NUMBERED 10    CONGEN replies and
ERASING ...10 2                   erases atom 10 and rest of input line
SECOND ATOM:                      and reprompts for second atom number

        2) Illegal input:

>bord 1 6 double                BORD requires integer or ANY bond orders
 bord 1 6 double                BORD                     ANY
 bord 1 6 double                BORD                     ANY
 bord 1 6 double                BORD                     ANY
DOUBLE ISN'T AN EXPECTED RESPONSE HERE  CONGEN replies and
ERASING ...DOUBLE                         erases illegal characters and
BOND ORDER:                               reprompts for bond order

>bord 2 r 4                     BORD needs an atom number
 bord 2 r 4                     BORD
 bord 2 r 4                     BORD
 bord 2 r 4                     BORD
I WAS EXPECTING A NUMBER        CONGEN replies and erases
ERASING ...R 4                    the character R and rest of line
                                                R
                                                R
                                                R
SECOND ATOM:                      and reprompts for missing input

                ******************************


        IV.B.6.l    UNJOIN
                    UNJOIN
                    UNJOIN
                    UNJOIN

                ****************************
                *                          *
                * Editstruc Command UNJOIN *
                *                          *



                                   83
CONGEN manual                                              February 1981


                ****************************


        The UNJOIN command is  the counterpart of the  Editstruc command
            UNJOIN
            UNJOIN
            UNJOIN
JOIN (see  Section IV.B.6.j).   It is  used to  decrease the  bond order
JOIN
JOIN
JOIN
between  pairs  of  specified,  existing atoms.   It  can  be  used, for
example, to reduce a triple bond to a double, or to disconnect two atoms
previously connected by a single bond.

                ******************************

        ***** Use of the UNJOIN command in Editstruc *****
              Use of the UNJOIN command in Editstruc
              Use of the UNJOIN command in Editstruc
              Use of the UNJOIN command in Editstruc


        In  order  to use  the  UNJOIN command,  you  must  have already
                                UNJOIN
                                UNJOIN
                                UNJOIN
created the bonds (and their associated atoms) which you wish to UNJOIN.
                                                                 UNJOIN
                                                                 UNJOIN
                                                                 UNJOIN
Assume  that you  have  created the  substructure, named  XYZ,  used for
                                                          XYZ
                                                          XYZ
                                                          XYZ
illustration for the Editstruc commands JOIN (see Section  IV.B.6.j) and
                                        JOIN
                                        JOIN
                                        JOIN
BORD (see Section IV.B.6.k).  It is drawn again here:
BORD
BORD
BORD

>draw n                         Draw, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

  6=5
 /   \
1     4-7#8
 =   =
  2-3

>unjoin                         Issue the UNJOIN command
 unjoin                                   UNJOIN
 unjoin                                   UNJOIN
 unjoin                                   UNJOIN

FIRST ATOM:?                    Ask for help
           ?
           ?
           ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

FIRST ATOM:7                      reprompts for first atom - reply 7
           7
           7
           7

SECOND ATOM:8                   Number of second atom
            8
            8
            8

>draw n                         Draw the result, numbered
 draw n
 draw n
 draw n















                                   84
CONGEN manual                                              February 1981


SUBSTRUCTURE XYZ:

  6=5
 /   \
1     4-7=8
 =   =
  2-3

>unjoin 7 8                     On one line, unjoin 7 and 8 again
 unjoin 7 8
 unjoin 7 8
 unjoin 7 8

>draw n                         Draw the result, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

  6=5
 /   \
1     4-7-8
 =   =
  2-3

>un 1 2 3 4 5 6 1 6             Short form, several unjoins on one line
 un 1 2 3 4 5 6 1 6
 un 1 2 3 4 5 6 1 6
 un 1 2 3 4 5 6 1 6

>draw n                         Draw the result, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:

          8
         /
        7
       /
1-2-3-4
      |
      5
      |
      6

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>unjoin 8 10                    Atom 10 does not exist
 unjoin 8 10
 unjoin 8 10
 unjoin 8 10
THERE IS NO ATOM NUMBERED 10    CONGEN replies and
ERASING ...10                     erases the atom number and
SECOND ATOM:                      reprompts for missing input

        2) Atoms not connected:

>unjoin 1 3                     Atoms 1 and 3 are not connected
 unjoin 1 3
 unjoin 1 3
 unjoin 1 3
ATOM 1 AND ATOM 3 AREN'T CONNECTED      CONGEN replies and



                                   85
CONGEN manual                                              February 1981


FIRST ATOM:                               reprompts for first atom

        3) Illegal input:

>unjoin 1 two                   The characters are illegal
 unjoin 1 two
 unjoin 1 two
 unjoin 1 two
I WAS EXPECTING A NUMBER        CONGEN replies and
ERASING ...TWO                    erases characters and
SECOND ATOM:                      reprompts for missing input

                ******************************


        IV.B.6.m    ATNAME
                    ATNAME
                    ATNAME
                    ATNAME

                ****************************
                *                          *
                * Editstruc Command ATNAME *
                *                          *
                ****************************


        The  ATNAME  command  is  used  to  associate  atom  names  with
             ATNAME
             ATNAME
             ATNAME
specified atoms.  All atoms created by the Editstruc commands CHAIN (see
                                                              CHAIN
                                                              CHAIN
                                                              CHAIN
Section  IV.B.6.f),  RING  (see Section  IV.B.6.g),  and  so  forth, are
                     RING
                     RING
                     RING
created as carbon atoms.  The ATNAME command is used to rename specified
                              ATNAME
                              ATNAME
                              ATNAME
atoms to be other atoms such as oxygen, nitrogen and so forth (or it may
be used to change the name back to carbon).

        The ATNAME  command is  used by referring  to specific  atoms by
            ATNAME
            ATNAME
            ATNAME
number; such atoms must have been created previously.

        There are  no restrictions  to the names  used for  atoms except
that they cannot be integers or the reserved name H.  The name  used may
be a chemical atom name, or an arbitrary name used by you to represent a
special atom type, or an arbitrary name used by you, that name being the
name of a Superatom which will  be defined at some point in  your CONGEN
session.  CONGEN's  method  for  structure  representation  (see Section
V,  Substructures   in  CONGEN)  and   generation  (see   Section  IV.E,
Section I.A)  permits the use  of names of  other substructures  as atom
names in  your current substructure.   This convention has  meaning only
                                       This convention has  meaning only
                                       This convention has  meaning only
                                       This convention has  meaning only
when  defining   substructures  to  be   used  as  constraints   -  such
when  defining   substructures  to  be   used  as  constraints   -  such
when  defining   substructures  to  be   used  as  constraints   -  such
when  defining   substructures  to  be   used  as  constraints   -  such
substructures may have atom  names which are the names  of substructures
substructures may have atom  names which are the names  of substructures
substructures may have atom  names which are the names  of substructures
substructures may have atom  names which are the names  of substructures
used as Superatoms.  You cannot use names of other substructures as atom
used as Superatoms
used as Superatoms
used as Superatoms
names in substructures  destined to be used  as Superatoms - this  is an
error condition which CONGEN will discover during the input phase of the
CONGEN command GENERATE (see Section IV.E).
               GENERATE
               GENERATE
               GENERATE

        Additional flexibility is provided by allowing atoms names to be
of specified,  variable type,  called polynames, or  of type  "any", for
                                      polynames
                                      polynames
                                      polynames
which the special atom name X is reserved.  A polyname is a set  of atom
                            X
                            X
                            X
names which might be associated with a particular atom.  For  example, a
specified atom in your substructure might  be either an N or an  O; this




                                   86
CONGEN manual                                              February 1981


atom can be given the polyname (N O), where the parentheses are required
to inform CONGEN that the atom name enclosed is a polyname.  The  name X
                                                                       X
                                                                       X
                                                                       X
given to a specified atom means that atom can be of any name.  Polynames
                                                    any        Polynames
                                                    any        Polynames
                                                    any        Polynames
and the name X cannot be used in substructures which will  be Superatoms
and the name X
and the name X
and the name X
(see Section V.A, Superatoms).

                ******************************

        ***** Use of the ATNAME command in Editstruc *****
              Use of the ATNAME command in Editstruc
              Use of the ATNAME command in Editstruc
              Use of the ATNAME command in Editstruc


        The ATNAME command can only be used to associate atom names with
            ATNAME
            ATNAME
            ATNAME
existing atoms.   Therefore, as  an illustration,  we first  create some
atoms, assuming we are defining a substructure named XYZ.
                                                     XYZ
                                                     XYZ
                                                     XYZ

>ring 6                         Create a six-membered ring
 ring 6
 ring 6
 ring 6

>draw a                         Draw it, atnamed
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:

  C-C
 /   \
C     C
 \   /
  C-C

>atname                         Issue the ATNAME command
 atname                                   ATNAME
 atname                                   ATNAME
 atname                                   ATNAME

ATOM:?                          Ask for help
     ?
     ?
     ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

ATOM:1                            reprompts for atom number - reply 1
     1
     1
     1

ATOM NAME:?                     Request for name - ask for help
          ?
          ?
          ?

AN ATOM NAME, OR A LEFT PARENTHESIS TO BEGIN A POLYNAME
                                CONGEN replies and
ATOM NAME:o                       reprompts for name - reply O
          o                                                  O
          o                                                  O
          o                                                  O

>draw atnamed                   Draw the result
 draw atnamed
 draw atnamed
 draw atnamed














                                   87
CONGEN manual                                              February 1981


SUBSTRUCTURE XYZ:

  C-C
 /   \
O     C
 \   /
  C-C

>atname 2                       Partly on one line
 atname 2
 atname 2
 atname 2

ATOM NAME:o                     CONGEN prompts for missing input
          o
          o
          o

>draw atnamed                   Draw the result
 draw atnamed
 draw atnamed
 draw atnamed

SUBSTRUCTURE XYZ:               Note that numbered drawings are not
                                  requested - remember the Editstruc
  O-C                             numbering conventions (see
 /   \                            Section IV.B.6.a)
O     C
 \   /
  C-C

>atname 3 n                     All on one line
 atname 3 n
 atname 3 n
 atname 3 n

>atname 4 s 5 si                Two commands on one line
 atname 4 s 5 si
 atname 4 s 5 si
 atname 4 s 5 si

>draw atnamed                   Draw the result
 draw atnamed
 draw atnamed
 draw atnamed

SUBSTRUCTURE XYZ:

  O-N
 /   \
O     S
 \   /
  C-SI

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS           Note the new atom types appear as their
  1     O    6  2                 names in the TYPE column
                                               TYPE
                                               TYPE
                                               TYPE
  2     O    3  1
  3     N    4  2
  4     S    5  3
  5    SI    6  4
  6     C    1  5

>atname 3 c 5 c                 Change atoms 3 and 5 back to carbon
 atname 3 c 5 c
 atname 3 c 5 c
 atname 3 c 5 c

>draw a                         Draw the result
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:



                                   88
CONGEN manual                                              February 1981


  O-C
 /   \
O     S
 \   /
  C-C

>atname 6                       Begin naming atom 6 as a polyname
 atname 6
 atname 6
 atname 6

ATOM NAME:?                     Ask for help as a reminder
          ?
          ?
          ?

AN ATOM NAME, OR A LEFT PARENTHESIS TO BEGIN A POLYNAME

ATOM NAME:(                     Begin stepping through the command
          (
          (
          (

(POLY)ATOM NAME:c n o           Associate C, N and O with the name of
                c n o
                c n o
                c n o
                                     atom 6

(POLY)ATOM NAME:?               Ask for more help
                ?
                ?
                ?

AN ATOM NAME, OR A RIGHT PARENTHESIS OR CARRIAGE RETURN
TO INDICATE THAT THE POLYNAME IS COMPLETE
                                CONGEN replies that additional names
                                  can be added or the polyname can be
                                  terminated with a closing parenthesis
(POLY)ATOM NAME:)               Reprompt for name - reply with ) to
                )
                )
                )
                                  finish name
>draw atnamed                   Draw the result
 draw atnamed
 draw atnamed
 draw atnamed

SUBSTRUCTURE XYZ:
POLYATOMS: P1->(C N O)          Note that polyatom names are given
                                  special names for the drawings - the
  O-C                             special name is shown in the heading
 /   \                            for the structure drawing
O     S
 \   /
 P1-C

>atname 3 (c n o s p) 5 x       Another polyname, all on one line, also
 atname 3 (c n o s p) 5 x
 atname 3 (c n o s p) 5 x
 atname 3 (c n o s p) 5 x
                                  with association of the "any" name X
                                                                     X
                                                                     X
                                                                     X
                                  designation for the name of atom 5
>draw atnamed                   Draw the result, atnamed
 draw atnamed
 draw atnamed
 draw atnamed















                                   89
CONGEN manual                                              February 1981


SUBSTRUCTURE XYZ:
POLYATOMS: P2->(C N O S P), P1->(C N O)         Note - two designators
                                                  for two polynames
  O-P2
 /   \
O     S                         Note - atom 5 appears with name X, for
 \   /                            type "any"
 P1-X

>show                           Use the SHOW command to see result
 show                                   SHOW
 show                                   SHOW
 show                                   SHOW

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS POLYNAME
  1     O    6  2
  2     O    3  1
  3   POLY   4  2     (C N O S P)       Polynames appear as type "POLY"
  4     S    5  3                         with the actual name given in
  5     X    6  4                         a separate column. "Any" atom
  6   POLY   1  5     (C N O)             type X simply appears as an
                                               X
                                               X
                                               X
                                          atom named X
                                                     X
                                                     X
                                                     X

>                               Ready for next Editstruc command

                ********************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>atname 8 s                     Atom 8 doesn't exist
 atname 8 s
 atname 8 s
 atname 8 s
THERE IS NO ATOM NUMBERED 8     CONGEN replies and
ERASING ...8 S                    erases number and rest of input line
ATOM:                             and reprompts for missing input

        2) Illegal input:

>atname three b                 Characters illegal
 atname three b
 atname three b
 atname three b
I WAS EXPECTING A NUMBER        CONGEN replies and erases
ERASING ...THREE B                characters and rest of input line
ATOM:                             and reprompts for missing information

>atname -2 r                    Negative integers illegal
 atname -2 r
 atname -2 r
 atname -2 r
THERE IS NO ATOM NUMBERED -2
ERASING ...-2 R
ATOM:

>atname 3 ()                    No polyname given
 atname 3 ()
 atname 3 ()
 atname 3 ()
I WAS EXPECTING A WORD          CONGEN replies and
ERASING ...)                      erases right parenthesis and
(POLY)ATOM NAME:                  reprompts for missing polyname

>atname 3 (c n o (              Illegal termination of polyname
 atname 3 (c n o (
 atname 3 (c n o (
 atname 3 (c n o (



                                   90
CONGEN manual                                              February 1981


I WAS EXPECTING A WORD OR A RIGHT PARENTHESIS
ERASING ...(                    CONGEN erases illegal character and re-
(POLY)ATOM NAME:                  quests more name or legal termination

                ******************************


        IV.B.6.n    HRANGE
                    HRANGE
                    HRANGE
                    HRANGE

                ****************************
                *                          *
                * Editstruc Command HRANGE *
                *                          *
                ****************************


        The  HRANGE command  allows you  to assign  a range  of hydrogen
             HRANGE
             HRANGE
             HRANGE
atoms  to  a  particular  atom.  As  discussed  in  the  introduction to
Editstruc (see Section  IV.B.6.a), the default  value for the  number of
hydrogen  atoms associated  with any  atom is  any number,  ranging from
                                               any
                                               any
                                               any
(valence of atom minus the number of non-hydrogen neighbors) to (valence
of atom).  In order to  identify particular carbons, or any  other atom,
as  particular  groups,  e.g.,  methyl,  methine,  hydroxyl,  the HRANGE
                                                                  HRANGE
                                                                  HRANGE
                                                                  HRANGE
command  must be  used to  associate the  relevant hydrogen  ranges with
specified atoms.

        Hydrogen atom ranges have  both minimum (min) and  maximum (max)
values. Thus, if min =  max, an exact number of hydrogens  is associated
with an atom, e.g., min = max  = 3 to designate a carbon with  a single,
non-hydrogen neighbor,  as a methyl  group.  If min  < max, then  a true
range is associated with a specified atom. You can associate a max value
of ANY number of hydrogens with an atom.
   ANY
   ANY
   ANY

        Specification  of  hydrogen  ranges for  all  atoms  in  a large
substructure can be tedious.   As an alternative, the  Editstruc command
FREEV  (see  Section  IV.B.6.o)  can  be  used  to   designate  specific
FREEV
FREEV
FREEV
bonding sites (free valences) in the substructure (bonding sites to non-
                                                                    non-
                                                                    non-
                                                                    non-
hydrogen neighbors) where it may be connected within a  larger complete,
hydrogen
hydrogen
hydrogen
structure.  Use of one or  more free valences changes the  default value
for  the hydrogen  range of  atoms which  do not  bear free  valences to
exactly  the  number   required  to  saturate  the   unfilled  valences.
exactly  the  number   required  to  saturate  the   unfilled  valences
exactly  the  number   required  to  saturate  the   unfilled  valences
exactly  the  number   required  to  saturate  the   unfilled  valences
Generally  speaking,  if  there  are  many  possible  bonding  sites for
connection  of the  substructure  within a  larger structure  it  may be
easier to specify  the few remaining hranges.   If there are  many atoms
which  cannot participate  such connections,  the FREEV  command  may be
                                                  FREEV
                                                  FREEV
                                                  FREEV
easier to specify the few remaining sites for connection.

        Hydrogen  ranges  can  only  be  associated  with  atoms created
previously by, e.g., the Editstruc commands CHAIN (see Section IV.B.6.f)
                                            CHAIN
                                            CHAIN
                                            CHAIN
or RING (see Section IV.B.6.g).
   RING
   RING
   RING

                ******************************




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        ***** Use of the HRANGE command in Editstruc *****
              Use of the HRANGE command in Editstruc
              Use of the HRANGE command in Editstruc
              Use of the HRANGE command in Editstruc


        Assume that a substructure  named XYZ is being  defined.  First,
                                          XYZ
                                          XYZ
                                          XYZ
we need to create the atoms to which we will associate hydrogen ranges:

>ring 6                         A six-membered ring
 ring 6
 ring 6
 ring 6

>branch 1 3                     Branch at atom 1, length 3
 branch 1 3
 branch 1 3
 branch 1 3

>join 7 9                       Connect atom 7 to 9
 join 7 9
 join 7 9
 join 7 9

>draw numbered                  Draw the result
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:

  5--6      8
 /    \    /|
4      1--7-9
 \    /
  3--2

>hrange                         Issue the HRANGE command
 hrange                                   HRANGE
 hrange                                   HRANGE
 hrange                                   HRANGE

ATOM:?                          Ask for help
     ?
     ?
     ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

ATOM:1                            reprompts for atom number - reply 1
     1
     1
     1

MINIMUM NUMBER OF H'S:?         Ask for help
                      ?
                      ?
                      ?

A NON-NEGATIVE INTEGER          CONGEN replies with allowed values

MINIMUM NUMBER OF H'S:0           and reprompts for min - reply 0
                      0
                      0
                      0

MAXIMUM NUMBER OF H'S:?         Ask for help
                      ?
                      ?
                      ?

A NON-NEGATIVE INTEGER, OR THE WORD 'ANY'       CONGEN replies and

MAXIMUM NUMBER OF H'S:1           reprompts for max - reply 1
                      1
                      1
                      1
                                Note that this allows atom 1 to be
                                either quaternary or tertiary
                                either
                                either
                                either

>hrange 5                       Partly on one line
 hrange 5
 hrange 5
 hrange 5

MINIMUM NUMBER OF H'S:1         CONGEN prompts for missing input
                      1
                      1
                      1

MAXIMUM NUMBER OF H'S:2
                      2
                      2
                      2

>hrange 4 1                     More on one line
 hrange 4 1
 hrange 4 1
 hrange 4 1

MAXIMUM NUMBER OF H'S:2         CONGEN prompts for missing input
                      2
                      2
                      2



                                   92
CONGEN manual                                              February 1981


>hrange 3 1 2                   All on one line
 hrange 3 1 2
 hrange 3 1 2
 hrange 3 1 2

>hrange 2 2 2 8 2 2 9 1 2       Several on one line
 hrange 2 2 2 8 2 2 9 1 2
 hrange 2 2 2 8 2 2 9 1 2
 hrange 2 2 2 8 2 2 9 1 2

>draw atnamed                   Draw the result, atnamed
 draw atnamed
 draw atnamed
 draw atnamed

SUBSTRUCTURE XYZ:(HRANGES NOT INDICATED)

  C--C      C                   Note that hydrogen ranges are not
                                                              not
                                                              not
                                                              not
 /    \    /|                     indicated in the drawing, but the
C      C--C-C                     header message indicates some have
 \    /                           been specified
  C--C

>show                           The SHOW command summarizes all hrange
 show                               SHOW
 show                               SHOW
 show                               SHOW
                                  information
SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS HRANGE
  1     C    7  6  2  0-1
  2     C    3  1     2-2
  3     C    4  2     1-2
  4     C    5  3     1-2
  5     C    6  4     1-2
  6     C    1  5
  7     C    9  1  8
  8     C    9  7     2-2
  9     C    7  8     1-2

>hrange 6 0 any                 Illustrate use of ANY as max
 hrange 6 0 any                                   ANY
 hrange 6 0 any                                   ANY
 hrange 6 0 any                                   ANY

>hrange 2 1 any                 Modify hrange on atom 2
 hrange 2 1 any
 hrange 2 1 any
 hrange 2 1 any

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS HRANGE
  1     C    7  6  2  0-1
  2     C    3  1     1-ANY     Now, ANY appears for the max on atoms
  3     C    4  2     1-2         2 and 6
  4     C    5  3     1-2
  5     C    6  4     1-2
  6     C    1  5     0-ANY
  7     C    9  1  8
  8     C    9  7     2-2
  9     C    7  8     1-2

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies



                                   93
CONGEN manual                                              February 1981


        1) Non-existent atom:

>hrange 7 1 2                   Assume atom 7 does not exist
 hrange 7 1 2
 hrange 7 1 2
 hrange 7 1 2
THERE IS NO ATOM NUMBERED 7     CONGEN replies and
ERASING ...7 1 2                  erases 7 and rest of input line and
ATOM:                             reprompts for atom number

        2) Min > max (detected as an error condition and corrected!):
                      detected as an error condition and corrected!)
                      detected as an error condition and corrected!)
                      detected as an error condition and corrected!)

>ring 3                         Assume a 3-membered ring created
 ring 3
 ring 3
 ring 3
>hrange 1 2 0                   Note that min > max
 hrange 1 2 0
 hrange 1 2 0
 hrange 1 2 0
>show                           Command accepted, show result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS HRANGE
  1     C    3  2     0-2       Note that min and max reversed so
                                                      reversed
                                                      reversed
                                                      reversed
  2     C    3  1                 that min < max
  3     C    1  2

>                               Ready for next Editstruc command

        3) Illegal input:

>hrange 2 one three             Characters not allowed
 hrange 2 one three
 hrange 2 one three
 hrange 2 one three
I WAS EXPECTING A NUMBER        CONGEN replies and
ERASING ...ONE THREE              erases offending characters and
MINIMUM NUMBER OF H'S:            reprompts for missing input

>hrange 1 -1 0                  Negative integers not allowed
 hrange 1 -1 0
 hrange 1 -1 0
 hrange 1 -1 0
THIS QUANTITY SHOULD NOT BE NEGATIVE
ERASING ...-1 0
MINIMUM NUMBER OF H'S:          Reprompt for missing input

                ******************************


        IV.B.6.o    FREEV
                    FREEV
                    FREEV
                    FREEV

                ***************************
                *                         *
                * Editstruc Command FREEV *
                *                         *
                ***************************


        The FREEV command is used to associate free valences, or bonding
            FREEV
            FREEV
            FREEV
sites,  with specified  atoms.  The  free valences  represent  points of
connection of the specified  atom to non-hydrogen atoms external  to the
substructure.  A  more detailed  description of the  meaning and  use of
free valences is in Section V, Substructures in CONGEN.





                                   94
CONGEN manual                                              February 1981


        The  FREEV  command  represents  an  alternative  to  the HRANGE
             FREEV                                                HRANGE
             FREEV                                                HRANGE
             FREEV                                                HRANGE
command for  designation of  bonding sites.  This  is explained  in more
detail in the description  of the Editstruc command HRANGE  (see Section
                                                    HRANGE
                                                    HRANGE
                                                    HRANGE
IV.B.6.n).  One important point - assignment of any free valences to any
atom changes  the default setting  for the hydrogen  range on  atoms not
bearing explicitly-placed free valences.  Normally the default is  ANY -
                                                                   ANY
                                                                   ANY
                                                                   ANY
use of the FREEV command  changes the default to "saturated",  i.e., all
           FREEV
           FREEV
           FREEV
unused valences on atoms without free valences are assumed to  be filled
with hydrogen atoms and no bonding sites are available on such atoms.

        Hydrogen ranges can  be used on  atoms bearing free  valences as
long as the  range does not  force only hydrogen  atoms to be  bonded to
                             force
                             force
                             force
such atoms.  For example, a  carbon atom bearing four free  valences can
have a hydrogen range of 0-2, but not 2-4.  The latter range would force
at least two hydrogens on  the carbon.  CONGEN detects this as  an error
condition and reports it to you during input to GENERATE.
                                                GENERATE
                                                GENERATE
                                                GENERATE

        Although free valences can be associated with atoms named "X" or
                                                                   X
                                                                   X
                                                                   X
with  polynames (see  Editstruc command  ATNAME, Section  IV.B.6.m), the
                                         ATNAME
                                         ATNAME
                                         ATNAME
free valences will be ignored and  any number of bonds can be  formed to
such  atoms.   If  free  valences  are  present  on  other  atoms  in  a
substructure with  X or  polynamed atoms,  the hydrogen  range on  X and
                   X                                               X
                   X                                               X
                   X                                               X
polynamed atoms will be 0-ANY unless  only one of the atom types  in the
                                      only one
                                      only one
                                      only one
polyname matches atom types in the molecular formula, in which  case the
normal default pertains (the atom will be "saturated" with hydrogens).

        If  any free  valences  exist, hydrogen  ranges  associated with
atoms  which  do  not  bear  free  valences  will  be  ignored  when the
substructure  is  used  during GENERATE  (see  CONGEN  command GENERATE,
                               GENERATE                        GENERATE
                               GENERATE                        GENERATE
                               GENERATE                        GENERATE
Section IV.E).

        The change in the default value for hydrogen ranges is simply to
make it easier to define large substructures which possess only  a small
number of bonding sites.

        Atoms for which  free valences will  be assigned must  have been
created previously, e.g., by  the Editstruc commands CHAIN  (see Section
                                                     CHAIN
                                                     CHAIN
                                                     CHAIN
IV.B.6.f) or RING (see Section IV.B.6.g).
             RING
             RING
             RING

                ******************************

        ***** Use of the FREEV command in Editstruc *****
              Use of the FREEV command in Editstruc
              Use of the FREEV command in Editstruc
              Use of the FREEV command in Editstruc


        Assume you are defining a substructure named XYZ.  First, create
                                                     XYZ
                                                     XYZ
                                                     XYZ
some atoms for subsequent illustration of the freev command:

>ring 6                         Create a six-membered ring
 ring 6
 ring 6
 ring 6

>branch 1 2 4 1                 Place branches on atoms 1 and 4
 branch 1 2 4 1
 branch 1 2 4 1
 branch 1 2 4 1

>draw numbered                  Draw the result, numbered
 draw numbered
 draw numbered
 draw numbered




                                   95
CONGEN manual                                              February 1981


SUBSTRUCTURE XYZ:

      6-5
     /   \
8-7-1     4-9
     \   /
      2-3

>freev                          Issue the FREEV command
 freev                                    FREEV
 freev                                    FREEV
 freev                                    FREEV

ATOM:?                          Ask for help
     ?
     ?
     ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

ATOM:5                            reprompts for atom number - reply 5
     5
     5
     5

FREE VALENCE:?                  CONGEN asks for free valence - ask for
             ?
             ?
             ?
                                  help
A NON-NEGATIVE INTEGER          CONGEN replies and

FREE VALENCE:2                    reprompts for free valence - reply 2
             2
             2
             2

>draw numbered                  Draw the result, numbered
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:


          |
       6--5-                    Note that free valences are drawn as
      /   |                       bonds with an unspecified terminus
     /    |
8-7-1     4
     \   / \
      2-3   9

>freev 6                        Partly on one line
 freev 6
 freev 6
 freev 6

FREE VALENCE:1                  CONGEN prompts for missing input
             1
             1
             1

>freev 9 1                      All on one line
 freev 9 1
 freev 9 1
 freev 9 1

>freev 2 1 3 2 8 2              Several on one line
 freev 2 1 3 2 8 2
 freev 2 1 3 2 8 2
 freev 2 1 3 2 8 2

>draw numbered                  Draw the result, numbered
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:


               |
          \    |
           2---3--
          /    |
 \       /     |



                                   96
CONGEN manual                                              February 1981


  8--7--1      |
  |      \ /   4--9--
  |       6   /
           \ /
            5
           / \

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS           Note that free valences appear in
  1     C    7  6  2              the connection table as entries "FV"
  2     C    3  1 FV              in the neighbors list, one entry
  3     C    4  2 FV FV           for each free valence
  4     C    9  5  3
  5     C    6  4 FV FV
  6     C    1  5 FV
  7     C    1  8
  8     C    7 FV FV
  9     C    4 FV

>freev 3 1 5 0                  Use the FREEV command to alter the
 freev 3 1 5 0                          FREEV
 freev 3 1 5 0                          FREEV
 freev 3 1 5 0                          FREEV
                                  number of previously assigned FV's
>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS
  1     C    7  6  2
  2     C    3  1 FV
  3     C    4  2 FV            Free valences on atoms 3 and 5 have
  4     C    9  5  3              been changed as requested
  5     C    6  4
  6     C    1  5 FV
  7     C    1  8
  8     C    7 FV FV
  9     C    4 FV

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>freev 10 1                     Assume atom 10 does not exist
 freev 10 1
 freev 10 1
 freev 10 1
THERE IS NO ATOM NUMBERED 10    CONGEN replies and
ERASING ...10 1                   erases bad input and
ATOM:                             reprompts for a new atom number

        2) Atom too crowded to DRAW (see also Editstruc command
                               DRAW
                               DRAW
                               DRAW



                                   97
CONGEN manual                                              February 1981


DRAW, Section IV.B.6.d):
DRAW
DRAW
DRAW

>freev 5 8                      Perhaps a typographical error
 freev 5 8
 freev 5 8
 freev 5 8
>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS
  1     C    7  6  2
  2     C    3  1 FV
  3     C    4  2 FV
  4     C    9  5  3
  5     C    6  4 FV FV FV FV FV FV FV FV
  6     C    1  5 FV
  7     C    1  8
  8     C    7 FV FV
  9     C    4 FV

>draw atnamed                   Try to draw
 draw atnamed
 draw atnamed
 draw atnamed
SUBSTRUCTURE XYZ:
CAN'T DRAW - SOME ATOM IS TOO CROWDED           CONGEN complains
>                               Ready for next Editstruc command

        3) Illegal input:

>freev 1 r                      Can't use integers
 freev 1 r
 freev 1 r
 freev 1 r
I WAS EXPECTING A NUMBER        CONGEN replies
ERASING ...R
FREE VALENCE:                   Reprompt for integer free valence

>freev 2 -1                     Negative numbers illegal
 freev 2 -1
 freev 2 -1
 freev 2 -1
THIS QUANTITY SHOULD NOT BE NEGATIVE    CONGEN replies
ERASING ...-1
FREE VALENCE:                   Reprompt for positive integer free
                                  valence

                ******************************


        IV.B.6.p    TAG
                    TAG
                    TAG
                    TAG

                *************************
                *                       *
                * Editstruc Command TAG *
                *                       *
                *************************


        The TAG command  is used to associate  a "tag" with  a specified
            TAG
            TAG
            TAG
atom.   These tags  have  special meaning  in CONGEN.   They  change the
method  by  which  occurrences of  substructures  are  counted  when the
substructures  are  encountered  in  structures  during  application  of




                                   98
CONGEN manual                                              February 1981


constraints.   This is  discussed  in detail  in Section  X,  Tagging in
CONGEN. Tags are particularly useful  when the number of a  certain type
of atom in a  given substructural environment must be  determined, e.g.,
the number of vinyl methyl groups (from 1H NMR) or the number of carbons
on double or aromatic bonds (from 13C NMR).  Certain constraints of this
type cannot  be stated  using the usual  language of  constraints unless
tags are used.

        Tags should not be used in substructures destined to be  used as
Superatoms.

***** Note (9/79) - Such use is accepted by CONGEN, but makes no   *****
***** sense.  Please avoid it - there is no reason for such tags.  *****


        Although multiple tags are allowed, you will find the concept of
tagging sufficiently  complex that we  suggest use of  a single  tag per
substructure;   under  ordinary   circumstances  multiple   tags   in  a
substructure are not required.

        An  atom to  which a  tag  is to  be associated  must  have been
created previously, e.g., by  the Editstruc commands CHAIN  (see Section
                                                     CHAIN
                                                     CHAIN
                                                     CHAIN
IV.B.6.f) or RING (see Section IV.B.6.g).
             RING
             RING
             RING

                ******************************

        ***** Use of the TAG command in Editstruc *****
              Use of the TAG command in Editstruc
              Use of the TAG command in Editstruc
              Use of the TAG command in Editstruc


        Assume that  a substructure,  named XYZ,  is being  defined.  In
                                            XYZ
                                            XYZ
                                            XYZ
order to illustrate  use of the TAG  command, we must first  create some
                                TAG
                                TAG
                                TAG
atoms:

>ring 6                         Create a six-membered ring
 ring 6
 ring 6
 ring 6

>join 1 2                       Create a double bond
 join 1 2
 join 1 2
 join 1 2

>branch 1 1                     Branch at atom 1, length 1
 branch 1 1
 branch 1 1
 branch 1 1

>draw numbered                  Draw the result, numbered
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:

  5-6
 /   \
4     1-7
 \   =
  3-2

>tag                            Issue the TAG command
 tag                                      TAG
 tag                                      TAG
 tag                                      TAG

ATOM:?                          Ask for help
     ?
     ?
     ?




                                   99
CONGEN manual                                              February 1981


THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

ATOM:2                           reprompts for the atom number - reply 2
     2
     2
     2

>draw numbered                  Draw the result, numbered
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:
TAGGED ATOMS ARE INDICATED BY AN ATTACHED *

  7                             Note the tag is represented by an
   \                              asterisk
    1-6
   =   \
*-2     5
   \   /
    3-4

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS
  1     C    7  6  2  2
  2*    C    3  1  1            Note the tag is placed adjacent to the
  3     C    4  2                 atom number in the connection table
  4     C    5  3                 and the existence of tags is noted in
  5     C    6  4                 the footing
  6     C    1  5
  7     C    1
TAGGED ATOMS ARE INDICATED BY A *

>                               Ready for next Editstruc command

                *******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>tag 8                          Assume atom 8 does not exist
 tag 8
 tag 8
 tag 8
THERE IS NO ATOM NUMBERED 8     CONGEN replies and
ERASING ...8                      erases atom number and
ATOM:                             reprompts for new number

        2) Illegal input:

>tag -2                         Negative integers not allowed
 tag -2
 tag -2
 tag -2
THERE IS NO ATOM NUMBERED -2    CONGEN replies and
ERASING ...-2                     erases and
ATOM:                             reprompts
>tag eight                      Characters not allowed
 tag eight
 tag eight
 tag eight
I WAS EXPECTING A NUMBER        CONGEN replies and
ERASING ...EIGHT                  erases and



                                  100
CONGEN manual                                              February 1981


ATOM:                             reprompts

                ******************************


        IV.B.6.q    LNODE
                    LNODE
                    LNODE
                    LNODE

                ***************************
                *                         *
                * Editstruc Command LNODE *
                *                         *
                ***************************


        The LNODE command is  to associate the special property  of link
            LNODE
            LNODE
            LNODE
node  to  a  specified  atom.  This  property  is  used  to  represent a
designated atom  as a  variable (minimum,  or min,  to maximum,  or max)
length  path  of  atoms,  of   length  min  to  max.   Details   of  the
interpretation and use  of link nodes are  included in Section  XI, Link
Nodes in CONGEN.

        The LNODE  command is of  particular utility  when substructural
            LNODE
            LNODE
            LNODE
constraints expressing ring or chain membership of certain atoms must be
made, independent of the size of the ring or length of the chain.

        There are many details of use of link nodes which  are important
for  full  utilization  of  the  LNODE  command  (see  Section  XI, Link
                                 LNODE
                                 LNODE
                                 LNODE
Nodes).  However,  there are certain  important considerations  which we
summarize here.  Link nodes may not have minimum length zero.  All atoms
in the variable length path (which may be part of a ring or a chain) are
of the atom type given by the specified atom termed the link node.  Link
nodes have no meaning in substructures used as Superatoms -  CONGEN will
detect this as an error condition.

        The atom to which the  property of link node is  associated must
have been created previously, e.g., by the Editstruc commands CHAIN (see
                                                              CHAIN
                                                              CHAIN
                                                              CHAIN
Section IV.B.6.f) or RING (see Section IV.B.6.g).
                     RING
                     RING
                     RING

                ******************************

        ***** Use of the LNODE command in Editstruc *****
              Use of the LNODE command in Editstruc
              Use of the LNODE command in Editstruc
              Use of the LNODE command in Editstruc


        Assume  that you  are defining  a substructure,  named  XYZ.  In
                                                                XYZ
                                                                XYZ
                                                                XYZ
order to  use the  LNODE command  you must  have previously  created the
                   LNODE
                   LNODE
                   LNODE
atom(s) which  you wish  to designate  as link  nodes.  First,  begin by
creating some atoms for illustration:

>ring 6;link 1 4 1              Two commands on one line to create the
 ring 6;link 1 4 1
 ring 6;link 1 4 1
 ring 6;link 1 4 1
                                  bicyclo - 2.2.1 ring system
>draw numbered                  Draw the result, numbered
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:



                                  101
CONGEN manual                                              February 1981


2--1--6
|  |  |
|  7  |
|  |  |
3--4--5

>lnode                          Issue the LNODE command
 lnode                                    LNODE
 lnode                                    LNODE
 lnode                                    LNODE

ATOM:?                          Ask for help
     ?
     ?
     ?

THE NUMBER OF AN EXISTING ATOM          CONGEN replies and

ATOM:7                            reprompts for atom number - reply 7
     7
     7
     7

MINIMUM LENGTH:?                Ask for help
               ?
               ?
               ?

AN INTEGER GREATER THAN ZERO    CONGEN replies and

MINIMUM LENGTH:1                  reprompts for min
               1
               1
               1

MAXIMUM LENGTH:3                Prompt for max - reply 3
               3
               3
               3

>draw atnamed                   Draw the result
 draw atnamed
 draw atnamed
 draw atnamed

SUBSTRUCTURE XYZ:
LNODES ARE INDICATED BY AN ATTACHED @

       C                        Note the additional information in
      / \                         the header to the drawing
     C   C
    /|  /
@--C--|-C
     C |
      \|
       C

>draw numbered                  Draw with numbers
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:
LNODES ARE INDICATED BY AN ATTACHED @

       5
      / \
     4   6
    /|  /
@--7--|-1
     3 |
      \|
       2

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:



                                  102
CONGEN manual                                              February 1981


ATOM# TYPE NEIGHBORS LNODE     Note that this substructure now
  1     C    7  6  2              represents bicyclo-2.2.1, -2.2.2
  2     C    3  1                 and -2.2.3 systems (all carbon atoms)
  3     C    4  2                 because the path length represented
  4     C    7  5  3              by the lnode is 1, 2 or 3 atoms long
  5     C    6  4
  6     C    1  5               Note that link nodes have a separate
  7     C    4  1    1-3          column and the min-max is placed there

>lnode 6 3 5                    On one line
 lnode 6 3 5
 lnode 6 3 5
 lnode 6 3 5
>lnode 2 1 2 3 8 10             Two more, on one line
 lnode 2 1 2 3 8 10
 lnode 2 1 2 3 8 10
 lnode 2 1 2 3 8 10

>draw numbered                  Draw the result
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:
LNODES ARE INDICATED BY AN ATTACHED @

@
 \
  3--4-5
  | /  |
@--|7   6
  | \ / \
  2--1   @
  |
  @

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS LNODE
  1     C    7  6  2
  2     C    3  1    1-2
  3     C    4  2    8-10
  4     C    7  5  3
  5     C    6  4
  6     C    1  5    3-5
  7     C    4  1    1-3

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>lnode 5 1 4                    Assume atom 5 does not exist
 lnode 5 1 4
 lnode 5 1 4
 lnode 5 1 4
THERE IS NO ATOM NUMBERED 5     CONGEN replies and
ERASING ...5 1 4                  erases and
ATOM:                             reprompts




                                  103
CONGEN manual                                              February 1981


        2) Min > max (detected as an error condition and corrected):
                      detected as an error condition and corrected
                      detected as an error condition and corrected
                      detected as an error condition and corrected

>ring 3                         Create a 3-membered ring as an example
 ring 3
 ring 3
 ring 3
>lnode 3 4 1                    Note min > max
 lnode 3 4 1
 lnode 3 4 1
 lnode 3 4 1
>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS LNODE
  1     C    3  2
  2     C    3  1
  3     C    1  2    1-4        Note min and max reversed!!

        3) Illegal input:

>lnode 2 1 two                  Characters not allowed
 lnode 2 1 two
 lnode 2 1 two
 lnode 2 1 two
TWO ISN'T AN EXPECTED RESPONSE HERE     CONGEN replies and
ERASING ...TWO                            erases and
MAXIMUM LENGTH:                           reprompts for missing input

>lnode r 1 2                    Same pattern as above...
 lnode r 1 2
 lnode r 1 2
 lnode r 1 2
I WAS EXPECTING A NUMBER
ERASING ...R 1 2
ATOM:

                ******************************


        IV.B.6.r    ARTYPE
                    ARTYPE
                    ARTYPE
                    ARTYPE

                ****************************
                *                          *
                * Editstruc Command ARTYPE *
                *                          *
                ****************************


        The ARTYPE  command is  used to  assign the  aromatic type  of a
            ARTYPE
            ARTYPE
            ARTYPE
specified atom.   CONGEN represents aromaticity  essentially as  an atom
property  (see  Section  IX,  Aromaticity  in  CONGEN)  but  detects the
aromatic nature of structures by recognizing the requisite atom and bond
distributions  in  such  systems.   In  Editstruc  you  are  allowed  to
designate the aromatic nature of atoms only, not bonds.

        To ensure  proper use  of substructures  with aromatic  atoms in
CONGEN,  you  should review  the  section on  aromaticity  (Section IX).
One  important  thing  to  keep in  mind  is  that  CONGEN  searches for
substructures  in complete  structures (by  graph-matching,  see Section
VII,  during application  of constraints)  based on  both atom  and bond
properties.  If  you specify an  aromatic substructure using  ARTYPE for
                                                              ARTYPE
                                                              ARTYPE
                                                              ARTYPE
appropriate atoms and place alternating double and single bonds  for one
                  and
                  and
                  and
of  two  or  more  possible Kekule  structures,  you  may  mis-apply the




                                  104
CONGEN manual                                              February 1981


constraint,  because  CONGEN  keeps  only  one  of  the  possible Kekule
structures once structures have been aromatized.  Use bond orders of ANY
                                                                     ANY
                                                                     ANY
                                                                     ANY
(see Editstruc command BORD, Section IV.B.6.k) for such substructures.
                       BORD
                       BORD
                       BORD

        The default  specification of aromatic  type is  either.  Unless
                                                         either
                                                         either
                                                         either
you  specifically designate  an atom  to be  aromatic,  or non-aromatic,
CONGEN will assume that it may be of either type.

        The ARTYPE command can only be used to refer to atoms previously
            ARTYPE
            ARTYPE
            ARTYPE
created  during definition  of your  substructure, e.g.,  by use  of the
Editstruc commands  CHAIN (see  Section IV.B.6.f)  or RING  (see Section
                    CHAIN                             RING
                    CHAIN                             RING
                    CHAIN                             RING
IV.B.6.g).

        The aromatic  nature of  atoms in  substructures destined  to be
used  as Superatoms  must not,  by convention,  be  specified.  Aromatic
                          not
                          not
                          not
types  can  be  assigned to  substructures  used  as  constraints during
GENERATE if  appropriate, i.e.,  if any  defined aromatic  templates are
GENERATE
GENERATE
GENERATE
pertinent.  Such constraints only apply  to atoms which are not  part of
unimbedded  Superatoms.  Although  it  is somewhat  artificial  to leave
atoms in,  e.g., a  recognizable benzene  ring with  ARTYPE unspecified,
                                                     ARTYPE
                                                     ARTYPE
                                                     ARTYPE
CONGEN will perceive  such aromaticity later  in your session,  based on
your  definition  of   aromaticity  (See  the  CONGEN   command  DEFINE,
                                                                 DEFINE
                                                                 DEFINE
                                                                 DEFINE
subcommand AROMATICS, Section IV.B.5), and use of the AROMATIZE (Section
           AROMATICS                                  AROMATIZE
           AROMATICS                                  AROMATIZE
           AROMATICS                                  AROMATIZE
IV.H) and IMBED (Section IV.G) commands.
          IMBED
          IMBED
          IMBED

                ******************************

        ***** Use of the ARTYPE command in Editstruc *****
              Use of the ARTYPE command in Editstruc
              Use of the ARTYPE command in Editstruc
              Use of the ARTYPE command in Editstruc


        Assume  that you  are defining  a substructure,  named  XYZ.  In
                                                                XYZ
                                                                XYZ
                                                                XYZ
order to assign aromatic types to atoms, you must first have created the
desired substructure, for example:

>chain 2                        Define a substructure which can be
 chain 2
 chain 2
 chain 2
>atname 2 o                       used to represent phenolic hydroxyl
 atname 2 o
 atname 2 o
 atname 2 o
>hrange 2 1 1                     groups
 hrange 2 1 1
 hrange 2 1 1
 hrange 2 1 1

>draw atnamed                   Draw the result before specifying
 draw atnamed
 draw atnamed
 draw atnamed
                                  ARTYPE
                                  ARTYPE
                                  ARTYPE
                                  ARTYPE

SUBSTRUCTURE XYZ:(HRANGES NOT INDICATED)

C-O

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS HRANGE
  1     C    2
  2     O    1        1-1




                                  105
CONGEN manual                                              February 1981


>artype                         Issue the ARTYPE command
 artype                                   ARTYPE
 artype                                   ARTYPE
 artype                                   ARTYPE

ATOM:?                          Ask for help
     ?
     ?
     ?

THE NUMBER OF AN EXISTING ATOM  CONGEN replies and

ATOM:1                            reprompts for atom number - reply 1 -
     1
     1
     1
                                  remember, it's the carbon that is
                                  aromatic, not the oxygen
AROMATIC OR NON-AROMATIC:?      Ask for help
                         ?
                         ?
                         ?

AROMATIC NON-AROMATIC           One of two choices - abbreviations
                                  possible (e.g., A or N)
                                                  A    N
                                                  A    N
                                                  A    N

AROMATIC OR NON-AROMATIC:aromatic       Select aromatic
                         aromatic
                         aromatic
                         aromatic

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS HRANGE ARTYPE     Note the new column in the
  1     C    2               AROM         connection table for
  2     O    1        1-1                 artype

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>artype 6 n                     Assume atom 6 does not exist
 artype 6 n
 artype 6 n
 artype 6 n
THERE IS NO ATOM NUMBERED 6     CONGEN replies and
ERASING ...6 N                    erases and
ATOM:                             reprompts

        2) Illegal input:

>artype two a                   Characters illegal
 artype two a
 artype two a
 artype two a
I WAS EXPECTING A NUMBER
ERASING ...TWO A
ATOM:

>artype 2 h                     H not an aromatic type
 artype 2 h
 artype 2 h
 artype 2 h
H IS NOT AN EXPECTED KEYWORD HERE
ERASING ...H
AROMATIC OR NON-AROMATIC:       Reprompt for allowed aromatic types

>artype 2 -4                    Negative integers not allowed
 artype 2 -4
 artype 2 -4
 artype 2 -4
I WAS EXPECTING A WORD
ERASING ...-4
AROMATIC OR NON-AROMATIC:       Reprompt



                                  106
CONGEN manual                                              February 1981


                ******************************


        IV.B.6.s    ERASE
                    ERASE
                    ERASE
                    ERASE

                ***************************
                *                         *
                * Editstruc Command ERASE *
                *                         *
                ***************************


        The ERASE  command is  designed to make  it possible  to correct
            ERASE
            ERASE
            ERASE
errors made in  creation of atoms  or specification of  atom properties.
(Bond properties  can be corrected  using the Editstruc  commands UNJOIN
                                                                  UNJOIN
                                                                  UNJOIN
                                                                  UNJOIN
(see Section  IV.B.6.l) or BORD  (see Section IV.B.6.k)).   Certain atom
                           BORD
                           BORD
                           BORD
properties, such as free valences (see Editstruc command  FREEV, Section
                                                          FREEV
                                                          FREEV
                                                          FREEV
IV.B.6.o) can  be corrected simply  by respecifying the  correct number.
However, ERASE  provides a  general correction  procedure, and  makes it
         ERASE
         ERASE
         ERASE
possible to erase items which can be removed in no other way.

        In order to use the  ERASE command there must be  a substructure
                             ERASE
                             ERASE
                             ERASE
with  items  to  be   erased.   Presumably  you  have  created   such  a
substructure using other Editstruc commands.

                ******************************

        ***** Use of the ERASE command in Editstruc *****
              Use of the ERASE command in Editstruc
              Use of the ERASE command in Editstruc
              Use of the ERASE command in Editstruc


        Assume that you  have created a complicated  substructure, named
XYZ, and noticed  that you have made  many errors in  specifying various
XYZ
XYZ
XYZ
properties of that substructure.  First,  here is an example to  be used
as illustration:

>draw n                         Draw it, numbered
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:(ARTYPES AND HRANGES NOT INDICATED)
NON-C ATOMS: 1->O, 6->S, 8->N, 12->O
TAGGED ATOMS ARE INDICATED BY AN ATTACHED *
LNODES ARE INDICATED BY AN ATTACHED @

          *
          |  |
  @       1--2-
   \     /   |
    9---10   |
   /    |    3
*-8     5   / \
   \   / \ /  12
    7-6   4     \
    |     |     13
                  \



                                  107
CONGEN manual                                              February 1981


>draw a                         Draw it, atnamed
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:(ARTYPES AND HRANGES NOT INDICATED)
TAGGED ATOMS ARE INDICATED BY AN ATTACHED *
LNODES ARE INDICATED BY AN ATTACHED @

          *
          |  |
  @       O--C-
   \     /   |
    C---C    |
   /    |    C
*-N     C   / \
   \   / \ /   O
    C-S   C     \
    |     |      C
                  \


>show                           Show it
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS    HRANGE LNODE ARTYPE
  1*    O   10  2        2-2
  2     C    3  1 FV FV              NON-AR
  3     C   12  4  2                  AROM
  4     C    5  3 FV
  5     C   10  6  4                 NON-AR
  6     S    7  5
  7     C    8  6 FV
  8*    N    9  7
  9     C   10  8              2-4
 10     C    5  1  9
 12     O    3 13        2-2
 13     C   12 FV        2-3
TAGGED ATOMS ARE INDICATED BY A *

>erase                          Issue the ERASE command
 erase                                    ERASE
 erase                                    ERASE
 erase                                    ERASE

WHAT TO ERASE:?                 Ask for help
              ?
              ?
              ?

ATNAME HRANGE FREEV TAG LNODE ARTYPE ATOM       CONGEN replies with
                                                  items which can be
                                                  erased

                ***** ERASE ATNAME command *****
                      ERASE ATNAME command
                      ERASE ATNAME command
                      ERASE ATNAME command

        The ERASE ATNAME command replaces the current name associated
            ERASE ATNAME
            ERASE ATNAME
            ERASE ATNAME
with a specified atom with the name C for carbon.  If the atom is
already carbon, no change results.

WHAT TO ERASE:atname            Select ATNAME
              atname                   ATNAME
              atname                   ATNAME
              atname                   ATNAME



                                  108
CONGEN manual                                              February 1981


WHICH ATOM?:?                   Ask for help
            ?
            ?
            ?

THE NUMBER OF AN EXISTING ATOM, OR THE WORD 'ALL'       CONGEN replies

WHICH ATOM?:1                   Select atom 1
            1
            1
            1

>erase atname 6 8 12            On one line, three more atoms
 erase atname 6 8 12
 erase atname 6 8 12
 erase atname 6 8 12

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS    HRANGE LNODE ARTYPE    Note that atoms 1,6,8
  1*    C   10  2        2-2                      and 12 are now carbon
  2     C    3  1 FV FV              NON-AR
  3     C   12  4  2                  AROM
  4     C    5  3 FV
  5     C   10  6  4                 NON-AR
  6     C    7  5
  7     C    8  6 FV
  8*    C    9  7
  9     C   10  8              2-4
 10     C    5  1  9
 12     C    3 13        2-2
 13     C   12 FV        2-3
TAGGED ATOMS ARE INDICATED BY A *

                ***** ERASE HRANGE command *****
                      ERASE HRANGE command
                      ERASE HRANGE command
                      ERASE HRANGE command

        The ERASE HRANGE command removes any hydrogen ranges from a
            ERASE HRANGE
            ERASE HRANGE
            ERASE HRANGE
specified atom; the hydrogen range thus reverts to the default value.

>erase hrange                   Ask to erase HRANGE
 erase hrange                                HRANGE
 erase hrange                                HRANGE
 erase hrange                                HRANGE

WHICH ATOM?:?                   Ask for help
            ?
            ?
            ?

THE NUMBER OF AN EXISTING ATOM, OR THE WORD 'ALL'       CONGEN replies

WHICH ATOM?:1 12                Specify two atoms on one line
            1 12
            1 12
            1 12

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS    HRANGE LNODE ARTYPE    Note that hranges on
  1*    C   10  2                                 atoms 1 and 12 are
  2     C    3  1 FV FV              NON-AR       erased
  3     C   12  4  2                  AROM
  4     C    5  3 FV
  5     C   10  6  4                 NON-AR
  6     C    7  5
  7     C    8  6 FV
  8*    C    9  7



                                  109
CONGEN manual                                              February 1981


  9     C   10  8              2-4
 10     C    5  1  9
 12     C    3 13
 13     C   12 FV        2-3
TAGGED ATOMS ARE INDICATED BY A *

                ***** ERASE FREEV command *****
                      ERASE FREEV command
                      ERASE FREEV command
                      ERASE FREEV command

        The ERASE FREEV command removes any free valences associated
            ERASE FREEV
            ERASE FREEV
            ERASE FREEV
with a specified atom.

>erase freev                    Issue command
 erase freev
 erase freev
 erase freev

WHICH ATOM?:2                   Select atom 2
            2
            2
            2

>erase freev 4 7                On one line, both atoms 4 and 7
 erase freev 4 7
 erase freev 4 7
 erase freev 4 7

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS HRANGE LNODE ARTYPE       Note that atoms 2, 4 and
  1*    C   10  2                                 7 have no free valence
  2     C    3  1                 NON-AR
  3     C   12  4  2               AROM
  4     C    5  3
  5     C   10  6  4              NON-AR
  6     C    7  5
  7     C    8  6
  8*    C    9  7
  9     C   10  8           2-4
 10     C    5  1  9
 12     C    3 13
 13     C   12 FV     2-3
TAGGED ATOMS ARE INDICATED BY A *

                ***** ERASE TAG command *****
                      ERASE TAG command
                      ERASE TAG command
                      ERASE TAG command

>erase tag                      Issue command
 erase tag
 erase tag
 erase tag

WHICH ATOM?:all                 Select all atoms
            all                        all
            all                        all
            all                        all

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS HRANGE LNODE ARTYPE       Note all tags gone
  1     C   10  2
  2     C    3  1                 NON-AR
  3     C   12  4  2               AROM
  4     C    5  3
  5     C   10  6  4              NON-AR
  6     C    7  5



                                  110
CONGEN manual                                              February 1981


  7     C    8  6
  8     C    9  7
  9     C   10  8           2-4
 10     C    5  1  9
 12     C    3 13
 13     C   12 FV     2-3

                ***** ERASE ARTYPE command *****
                      ERASE ARTYPE command
                      ERASE ARTYPE command
                      ERASE ARTYPE command

>erase artype 3 5               On one line
 erase artype 3 5
 erase artype 3 5
 erase artype 3 5

                ***** ERASE LNODE command *****
                      ERASE LNODE command
                      ERASE LNODE command
                      ERASE LNODE command

>erase lnode 9                  On one line
 erase lnode 9
 erase lnode 9
 erase lnode 9

>show                           Show the result of last two commands
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM  TYPE NEIGHBORS HRANGE ARTYPE      Note 3 and 5 have no artype
  1     C   10  2                         and the lnode at 9 is gone
  2     C    3  1           NON-AR        (together with the column)
  3     C   12  4  2
  4     C    5  3
  5     C   10  6  4
  6     C    7  5
  7     C    8  6
  8     C    9  7
  9     C   10  8
 10     C    5  1  9
 12     C    3 13
 13     C   12 FV     2-3

                ***** ERASE ATOM command *****
                      ERASE ATOM command
                      ERASE ATOM command
                      ERASE ATOM command

        The ERASE ATOM command removes the specified atom or atoms from
            ERASE ATOM
            ERASE ATOM
            ERASE ATOM
the connection table of the substructure and makes the appropriate
modifications to the neighbors list of any remaining atoms to which the
deleted atoms were connected.  The connection table is not renumbered
                                                       not
                                                       not
                                                       not
even if gaps in the numbering of the substructure result.

>erase atom 13                  On one line
 erase atom 13
 erase atom 13
 erase atom 13

>show                           Show the result
 show
 show
 show

SUBSTRUCTURE XYZ:

ATOM# TYPE NEIGHBORS ARTYPE    Note that atom 13, together with all
  1     C   10  2                 its connections to other atoms and
  2     C    3  1    NON-AR       its properties are gone, as is the
  3     C   12  4  2              HRANGE column now that no atoms
                                  HRANGE
                                  HRANGE
                                  HRANGE
  4     C    5  3                 have specified hranges
  5     C   10  6  4



                                  111
CONGEN manual                                              February 1981


  6     C    7  5
  7     C    8  6
  8     C    9  7
  9     C   10  8
 10     C    5  1  9
 12     C    3

>draw n                         Draw the result
 draw n
 draw n
 draw n

SUBSTRUCTURE XYZ:(ARTYPES NOT INDICATED)

         6-7
        /  |
     4-5   8
    /  |  /
12-3  10-9
   |  /
   2-1

>erase atom 5 6                 On one line, erase two more atoms
 erase atom 5 6
 erase atom 5 6
 erase atom 5 6

>draw numbered                  Draw the result
 draw numbered
 draw numbered
 draw numbered

SUBSTRUCTURE XYZ:(ARTYPES NOT INDICATED)

              4
             /
7-8-9-1-1-2-3
      0      \
              12

>                               Ready for next Editstruc command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Non-existent atom:

>erase atom 5                   Assume no atom 5
 erase atom 5
 erase atom 5
 erase atom 5
THERE IS NO ATOM NUMBERED 5     CONGEN replies and
ERASING ...5                      erases atom number and
WHICH ATOM?:                      reprompts for atom

        2) Non-existent property:

>erase lnode 3                  Assume that none of the following
 erase lnode 3
 erase lnode 3
 erase lnode 3
>erase artype 4                   properties exist on the indicated
 erase artype 4
 erase artype 4
 erase artype 4
>erase atname 10                  atoms - no error message!
 erase atname 10                          no error message!
 erase atname 10                          no error message!
 erase atname 10                          no error message!
>erase hrange 8
 erase hrange 8
 erase hrange 8
 erase hrange 8
>erase freev 9
 erase freev 9
 erase freev 9
 erase freev 9

        3) Illegal input:



                                  112
CONGEN manual                                              February 1981


>erase hydrogen 2               The word hydrogen is not an item
 erase hydrogen 2
 erase hydrogen 2
 erase hydrogen 2
HYDROGEN IS NOT AN EXPECTED KEYWORD HERE        CONGEN replies and
ERASING ...HYDROGEN 2                             erases and
WHAT TO ERASE:                                    reprompts for item

>erase atom 5                   Non-existent atom
 erase atom 5
 erase atom 5
 erase atom 5
THERE IS NO ATOM NUMBERED 5
ERASING ...5
WHICH ATOM?:

>erase atom six                 Characters illegal
 erase atom six
 erase atom six
 erase atom six
SIX ISN'T AN EXPECTED RESPONSE HERE
ERASING ...SIX
WHICH ATOM?:

>erase atom -4                  Negative integers illegal
 erase atom -4
 erase atom -4
 erase atom -4
THERE IS NO ATOM NUMBERED -4
ERASING ...-4
WHICH ATOM?:

                ******************************


        IV.B.6.t    DONE
                    DONE
                    DONE
                    DONE

                **************************
                *                        *
                * Editstruc Command DONE *
                *                        *
                **************************


        The  DONE command  is  used to  terminate your  definition  of a
             DONE
             DONE
             DONE
substructure.    No  information   about  the   substructure   is  saved
permanently  by  CONGEN until  the  DONE command  is  issued.   Once the
                                    DONE
                                    DONE
                                    DONE
command is  issued, however,  the substructure  name and  definition are
saved away on file for  future use in your current session.   (Note that
the definition is not saved for use in subsequent CONGEN  sessions until
                  not                  subsequent
                  not                  subsequent
                  not                  subsequent
the CONGEN command SAVE (see Section IV.L) is issued.)
                   SAVE
                   SAVE
                   SAVE

                ******************************


        Assume that the substructure named XYZ, the steroid  skeleton of
                                           XYZ
                                           XYZ
                                           XYZ
androstane,  has been  defined by  the following  sequence  of commands,
issued all on one line:

>ring 10; join 5 10; branch 9 7; branch 10 1 13 1; join 8 14 13 17
 ring 10; join 5 10; branch 9 7; branch 10 1 13 1; join 8 14 13 17
 ring 10; join 5 10; branch 9 7; branch 10 1 13 1; join 8 14 13 17
 ring 10; join 5 10; branch 9 7; branch 10 1 13 1; join 8 14 13 17

>draw a                         Draw the result, atnamed
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:




                                  113
CONGEN manual                                              February 1981


               C
C-C     C-C   / \
|  \   /   \ /   C
C   C-C     C    |
 \ /   \    |    |
  C     C---C--C-C
 / \   /    |
C   C-C     C

>done                           Issue the DONE command
 done                                     DONE
 done                                     DONE
 done                                     DONE

XYZ DEFINED                     CONGEN replies that definition is
                                  complete

#                               Ready for next CONGEN command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        There are no error conditions other than trying to extend the
command, e.g.:

>done xyz                       XYZ not part of command
 done xyz                       XYZ
 done xyz                       XYZ
 done xyz                       XYZ
ERASING ...XYZ                  CONGEN erases and executes DONE command
                                                           DONE
                                                           DONE
                                                           DONE
XYZ DEFINED                     Definition complete
#                               Ready for next CONGEN command

        You can even define a substructure which has no atoms.

                ******************************


        IV.B.6.u    HALT
                    HALT
                    HALT
                    HALT

                **************************
                *                        *
                * Editstruc Command HALT *
                *                        *
                **************************


        The HALT command is used to exit from a  substructure definition
            HALT
            HALT
            HALT
without  saving  the  name  or definition!!  It  is  generally  used for
without  saving  the  name  or definition!!
without  saving  the  name  or definition!!
without  saving  the  name  or definition!!
abandoning a definition in which so many errors have occurred that it is
necessary to start over (alternatively, the Editstruc command ERASE ATOM
                                                              ERASE ATOM
                                                              ERASE ATOM
                                                              ERASE ATOM
ALL, see Section IV.B.6.s, achieves the same result without exiting from
ALL
ALL
ALL
Editstruc), or to exit Editstruc having decided that you did  not, after
all, want to define that substructure.

        The  message  from CONGEN  on  exiting Editstruc  with  the HALT
                                                                    HALT
                                                                    HALT
                                                                    HALT
command is that the exit is with no structure modifications.  This  is a




                                  114
CONGEN manual                                              February 1981


general  message  because  there is  another  path  into  Editstruc from
CONGEN, via  the CONGEN  command FIX  (see Section  IV.C).  In  the case
                                 FIX
                                 FIX
                                 FIX
of defining  a substructure,  the HALT exit  effectively erases  all you
                                  HALT
                                  HALT
                                  HALT
have done and  exits with no record  kept of that substructure.   In the
case of fixing a substructure, the HALT exit merely forgets the fixes to
                                   HALT
                                   HALT
                                   HALT
the substructure and exits retaining the original definition.

                *****************************

        ***** Use of the HALT command in Editstruc *****
              Use of the HALT command in Editstruc
              Use of the HALT command in Editstruc
              Use of the HALT command in Editstruc


        Assume that you are  trying to define a substructure  named XYZ,
                                                                    XYZ
                                                                    XYZ
                                                                    XYZ
and you have performed the following sequence of commands:

>ring 10                        That's OK
 ring 10
 ring 10
 ring 10
>branch 1 2 4 15                Oops - typo, didn't mean 15
 branch 1 2 4 15
 branch 1 2 4 15
 branch 1 2 4 15
>chain 33                       Oops - another typo, meant 3 3, not 33
 chain 33
 chain 33
 chain 33
>halt                           Give up, issue HALT command
 halt                                          HALT
 halt                                          HALT
 halt                                          HALT

(EXITING WITH NO STRUCTURE MODIFICATIONS)       CONGEN replies

#                               Ready for next CONGEN command

                *****************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        There are no error condition on the HALT command except
                                            HALT
                                            HALT
                                            HALT
attempting to extend the command with any text, e.g.,

>halt  freev                    FREEV not relevant
 halt  freev                    FREEV
 halt  freev                    FREEV
 halt  freev                    FREEV
ERASING ...FREEV                CONGEN erases and executes the HALT
                                                               HALT
                                                               HALT
                                                               HALT

(EXITING WITH NO STRUCTURE MODIFICATIONS)       Normal exit from HALT
                                                                 HALT
                                                                 HALT
                                                                 HALT
#                               Ready for next CONGEN command

                ******************************


















                                  115
CONGEN manual                                              February 1981


        IV.C    FIX and Subcommands
                FIX and Subcommands
                FIX and Subcommands
                FIX and Subcommands

                **********************
                *                    *
                * CONGEN command FIX *
                *                    *
                **********************


        The FIX command is the counterpart of the CONGEN command DEFINE,
            FIX                                                  DEFINE
            FIX                                                  DEFINE
            FIX                                                  DEFINE
Section  IV.B.  It  can, and  in  some cases  must, be  used  to correct
structural  information previously  specified with  the  DEFINE command.
                                                         DEFINE
                                                         DEFINE
                                                         DEFINE
The description of this command  will be brief, because the  items which
can be fixed and the input to CONGEN to fix them is essentially the same
as  for the  DEFINE  command.  To  review  the input  sequences  for the
             DEFINE
             DEFINE
             DEFINE
possible subcommands in FIX, see the following sections under the DEFINE
                        FIX                                       DEFINE
                        FIX                                       DEFINE
                        FIX                                       DEFINE
command, Section IV.B:

  FIX Subcommand
  FIX Subcommand
  FIX Subcommand
  FIX Subcommand

        TERMTYPE           Section IV.B.2
        TERMTYPE
        TERMTYPE
        TERMTYPE
        MOLFORM            Section IV.B.3
        MOLFORM
        MOLFORM
        MOLFORM
        ATOM               Section IV.B.4
        ATOM
        ATOM
        ATOM
        AROMATICS          Section IV.B.5
        AROMATICS
        AROMATICS
        AROMATICS
        SUBSTRUCTURE       Section IV.B.6
        SUBSTRUCTURE
        SUBSTRUCTURE
        SUBSTRUCTURE


        The TERMTYPE subcommand can be  used either by DEFINE or  FIX to
            TERMTYPE                                   DEFINE     FIX
            TERMTYPE                                   DEFINE     FIX
            TERMTYPE                                   DEFINE     FIX
change the terminal type, i.e., FIX TERMTYPE.
                                FIX TERMTYPE
                                FIX TERMTYPE
                                FIX TERMTYPE

        The  MOLFORM  subcommand  cannot  be  used  by  DEFINE  once the
             MOLFORM                                    DEFINE
             MOLFORM                                    DEFINE
             MOLFORM                                    DEFINE
molecular  formula has  been defined.   However, it  can be  changed, or
fixed, with the command FIX MOLFORM, even if the change  is inconsistent
                        FIX MOLFORM
                        FIX MOLFORM
                        FIX MOLFORM
with existing structures.

        An atom  already defined  by the DEFINE  ATOM command  cannot be
                                         DEFINE  ATOM
                                         DEFINE  ATOM
                                         DEFINE  ATOM
redefined.  However, it  can be fixed  (valence change), by  the command
FIX ATOM.
FIX ATOM
FIX ATOM
FIX ATOM

        Aromatic templates pertinent to  a problem can only  be changed,
once defined, by the FIX AROMATICS command.
                     FIX AROMATICS
                     FIX AROMATICS
                     FIX AROMATICS

        Errors in  substructures must  be corrected  by the  command FIX
                                                                     FIX
                                                                     FIX
                                                                     FIX
SUBSTRUCTURE followed by the name of the substructure.  CONGEN  will not
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE
allow  you to  edit  a previously  defined substructure  via  the DEFINE
                                                                  DEFINE
                                                                  DEFINE
                                                                  DEFINE
SUBSTRUCTURE command.
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE

        These points are illustrated with examples of CONGEN interaction
below.

                ******************************

        ***** Use of the FIX command in CONGEN *****
              Use of the FIX command in CONGEN
              Use of the FIX command in CONGEN
              Use of the FIX command in CONGEN



                                  116
CONGEN manual                                              February 1981


        For illustration, we  define, using the DEFINE  command, several
                                                DEFINE
                                                DEFINE
                                                DEFINE
pieces of structural information,  then show the responses of  CONGEN to
attempts to use DEFINE again to change that information.  The proper use
                DEFINE
                DEFINE
                DEFINE
of  the FIX  command  follows each  attempt.   See the  above  table for
        FIX
        FIX
        FIX
sections under the DEFINE command  which describe in detail use  of each
                   DEFINE
                   DEFINE
                   DEFINE
subcommand:

#define termtype 1              On one line, set the terminal type
 define termtype 1
 define termtype 1
 define termtype 1
OLD TERMINAL TYPE IS 1
THE TERMINAL TYPE HAS BEEN RESET TO 1   No change actually made
#                               Ready for next CONGEN command

#define molform                 Define a molecular formula
 define molform
 define molform
 define molform
MOLECULAR FORMULA:c 6 h 10
                  c 6 h 10
                  c 6 h 10
                  c 6 h 10
MOLECULAR FORMULA DEFINED
#                               Ready for next CONGEN command

#def atom s                     Define atom S and its valence
 def atom s
 def atom s
 def atom s
VALENCE:1
        1
        1
        1
S DEFINED
#                               Ready for next CONGEN command

#define aromatics               Define aromaticity
 define aromatics
 define aromatics
 define aromatics
TEMPLATES TO BE CONSIDERED AROMATIC:benzene     Select only benzene
                                    benzene
                                    benzene
                                    benzene
AROMATICS DEFINED
#                               Ready for next CONGEN command

#define substructure            Define a substructure XYZ
 define substructure                                  XYZ
 define substructure                                  XYZ
 define substructure                                  XYZ
NAME:xyz
     xyz
     xyz
     xyz
(NEW SUBSTRUCTURE)
>ring 10; join 5 10; branch 3 1; atname 11 o            On one line
 ring 10; join 5 10; branch 3 1; atname 11 o
 ring 10; join 5 10; branch 3 1; atname 11 o
 ring 10; join 5 10; branch 3 1; atname 11 o

>draw a                         Draw the result
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:

        C-C
       /  |
    C-C   C
   /  |  /
O-C   C-C
  |  /
  C-C

>done
XYZ DEFINED
#                               Ready for next CONGEN command


                *** FIX TERMTYPE Command ***
                    FIX TERMTYPE Command
                    FIX TERMTYPE Command
                    FIX TERMTYPE Command

#fix                            Issue the FIX command to
 fix                                      FIX
 fix                                      FIX
 fix                                      FIX
                                  fix termtype



                                  117
CONGEN manual                                              February 1981


DEFINITION TYPE:?               Ask for help
                ?
                ?
                ?

ATOM SUBSTRUCTURE AROMATICS MOLFORM TERMTYPE    CONGEN replies and

DEFINITION TYPE:termtype                          reprompts for type
                termtype
                termtype
                termtype

OLD TERMINAL TYPE IS 2          CONGEN replies and

NEW TERMINAL TYPE:1               prompts for new terminal type and
                  1
                  1
                  1

THE TERMINAL TYPE HAS BEEN RESET TO 1   notes the change

#                               Ready for next CONGEN command


                *** FIX MOLFORM Command ***
                    FIX MOLFORM Command
                    FIX MOLFORM Command
                    FIX MOLFORM Command

#define molform                 Try to redefine molform
 define molform
 define molform
 define molform

THE MOLECULAR FORMULA IS ALREADY DEFINED.  PLEASE USE THE
FIX COMMAND IF YOU WANT TO CHANGE IT.           Reply from CONGEN

#                               Ready for next CONGEN command

#fix molform                      But you can FIX MOLFORM
 fix molform                                  FIX MOLFORM
 fix molform                                  FIX MOLFORM
 fix molform                                  FIX MOLFORM

MOLECULAR FORMULA:c 6 h 10 o    New molecular formula
                  c 6 h 10 o
                  c 6 h 10 o
                  c 6 h 10 o

MOLECULAR FORMULA REDEFINED     CONGEN notes change

#                               Ready for next CONGEN command


                *** FIX ATOM Command ***
                    FIX ATOM Command
                    FIX ATOM Command
                    FIX ATOM Command

#define atom s                  Try to redefine atom S
 define atom s                                       S
 define atom s                                       S
 define atom s                                       S

S IS ALREADY DEFINED AS AN ATOM AND CAN'T BE USED HERE  Reply from
                                                          CONGEN
NAME:                           Reprompt for name

#fix atom                       But atom S can be fixed
 fix atom                                S
 fix atom                                S
 fix atom                                S

NAME:s                          Select atom name S
     s                                           S
     s                                           S
     s                                           S

VALENCE:2                       New valence, 2
        2
        2
        2

S REDEFINED                     Note from CONGEN

#                               Ready for next CONGEN command


                *** FIX AROMATICS Command ***
                    FIX AROMATICS Command
                    FIX AROMATICS Command
                    FIX AROMATICS Command



                                  118
CONGEN manual                                              February 1981


#define aromatics pyridine      Try to redefine aromatics
 define aromatics pyridine
 define aromatics pyridine
 define aromatics pyridine

AROMATICS ARE ALREADY DEFINED - PLEASE USE THE FIX COMMAND

TO CHANGE THEM.                 CONGEN replies and
ERASING ...PYRIDINE               erases

#                               Ready for next CONGEN command

#fix aromatics                   But you can fix them
 fix aromatics
 fix aromatics
 fix aromatics
                                Select pyridine

TEMPLATES TO BE CONSIDERED AROMATIC:pyridine
                                    pyridine
                                    pyridine
                                    pyridine

AROMATICS REDEFINED             CONGEN replies

#                               Ready for next CONGEN command


                *** FIX SUBSTRUCTURE Command ***
                    FIX SUBSTRUCTURE Command
                    FIX SUBSTRUCTURE Command
                    FIX SUBSTRUCTURE Command

#define substructure xyz          Try to redefine XYZ
 define substructure xyz                          XYZ
 define substructure xyz                          XYZ
 define substructure xyz                          XYZ

XYZ IS ALREADY DEFINED AS A SUBSTRUCTURE AND CAN'T BE USED HERE

                                CONGEN replies and reprompts
NAME:

#fix substructure xyz           But you can FIX XYZ
 fix substructure xyz                       FIX XYZ
 fix substructure xyz                       FIX XYZ
 fix substructure xyz                       FIX XYZ

(OLD SUBSTRUCTURE)              CONGEN notes a previously defined
                                  substructure, and restores definition
>draw n                      Draw the old definition - note that
 draw n
 draw n
 draw n
                                  the FIX SUBSTRUCTURE command places
                                      FIX SUBSTRUCTURE
                                      FIX SUBSTRUCTURE
                                      FIX SUBSTRUCTURE
SUBSTRUCTURE XYZ:                 you back into Editstruc
NON-C ATOMS: 11->O




















                                  119
CONGEN manual                                              February 1981


         6-7
        /  |
     4-5   8
    /  |  /
11-3  10-9
   |  /
   2-1

>atname 11 n                    Change it as required
 atname 11 n
 atname 11 n
 atname 11 n
>draw a                         Draw the result
 draw a
 draw a
 draw a

SUBSTRUCTURE XYZ:

        C-C
       /  |
    C-C   C
   /  |  /
N-C   C-C
  |  /
  C-C

>done                           Terminate the redefinition
 done
 done
 done
XYZ REDEFINED                   Note from CONGEN, XYZ redefined
                                                  XYZ
                                                  XYZ
                                                  XYZ
#                               Ready for next CONGEN command

                ******************************

        ***** Error conditions and CONGEN responses *****
              Error conditions and CONGEN responses
              Error conditions and CONGEN responses
              Error conditions and CONGEN responses

        1) Error on fixing termtype:

#fix termtype 4                Illegal terminal type
 fix termtype 4
 fix termtype 4
 fix termtype 4
OLD TERMINAL TYPE IS 1                  CONGEN replies
I DON'T UNDERSTAND - TYPE ? FOR HELP
NEW TERMINAL TYPE:?                     Ask for help
                  ?
                  ?
                  ?
SELECT THE NUMBER CORRESPONDING TO THE DRAWING BELOW WHICH LOOKS
MOST LIKE TETRAHEDRANE:
1     C
     /|\
    C--|-C
     \|/
      C

2     C
     /!\
    C---C      !
     \!/
      C

NEW TERMINAL TYPE:              Reprompt for legal terminal type

        2) Errors in fixing molecular formula:




                                  120
CONGEN manual                                              February 1981


#fix molform                    Assume molecular formula not defined
 fix molform
 fix molform
 fix molform
THE MOLECULAR FORMULA HASN'T BEEN DEFINED YET           CONGEN replies
#                               Ready for next CONGEN command

#fix molform                    Assume structures exist already
 fix molform
 fix molform
 fix molform
                                CONGEN replies

NOTE: CHANGING THE MOLECULAR FORMULA AT THIS POINT MAY LEAD TO
CONFUSION, SINCE YOUR STRUCTURES STILL REFLECT THE OLD FORMULA
SHALL I PROCEED ANYWAY?:n       Can answer no,
                        n
                        n
                        n
#                               Ready for next CONGEN command

                        or

SHALL I PROCEED ANYWAY?:y       Can answer yes and continue
                        y
                        y
                        y
MOLECULAR FORMULA:c 15 h 28 n 2         A new molecular formula
                  c 15 h 28 n 2
                  c 15 h 28 n 2
                  c 15 h 28 n 2
#                               Ready for next CONGEN command

        3) Errors on fixing atoms:

#fix atom br                    Assume BR not yet defined
 fix atom br                           BR
 fix atom br                           BR
 fix atom br                           BR
BR HASN'T BEEN DEFINED YET
ERASING ...BR
NAME:                           Reprompt for another name

        4) Errors on fixing aromatics:

#fix aromatics                Assume structures already exist
 fix aromatics
 fix aromatics
 fix aromatics
                                CONGEN notes that a change in
                                  definition will not affect existing
                                  structures

OK, BUT YOUR STRUCTURES WILL NOT REFLECT ANY CHANGES IN AROMATICS
UNTIL YOU AROMATIZE (OR IMBED) THEM.  ALSO, I MAY HAVE DISCARDED
'DUPLICATE' KEKULE STRUCTURES USING THE CURRENT AROMATICS LIST
SHALL I PROCEED ANYWAY?:        Can answer yes or no - see
                                  Section IV.H

        5) Errors in fixing substructures:

#fix substructure pdq           Assume PDQ not defined yet
 fix substructure pdq                  PDQ
 fix substructure pdq                  PDQ
 fix substructure pdq                  PDQ
PDQ HASN'T BEEN DEFINED YET     CONGEN replies and
ERASING ...PDQ                    erases and
NAME:                             reprompts for new name

#fix s cyc                      Assume structures already generated
 fix s cyc
 fix s cyc
 fix s cyc
                                  using CYC as a Superatom - CONGEN
                                        CYC
                                        CYC
                                        CYC
                                  replies with a warning

NOTE: CHANGING OR FORGETTING THE DEFINITION OF CYC AT THIS POINT MAY
LEAD TO CONFUSION BECAUSE YOUR STRUCTURES STILL REFLECT THE OLD
DEFINITION
SHALL I PROCEED ANYWAY?:y       You can choose to proceed to FIX,
                        y                                    FIX
                        y                                    FIX
                        y                                    FIX



                                  121
CONGEN manual                                              February 1981


(OLD SUBSTRUCTURE)                but be careful
>                               Editstruc prompt

                        or

SHALL I PROCEED ANYWAY?:n       Answer no
                        n
                        n
                        n
#                               Ready for next CONGEN command

                ******************************















































                                  122
CONGEN manual                                              February 1981


        IV.D    SEARCH and Subcommands
                SEARCH and Subcommands
                SEARCH and Subcommands
                SEARCH and Subcommands

                *************************
                *                       *
                * CONGEN command SEARCH *
                *                       *
                *************************


        The SEARCH command is used to retrieve  predefined substructures
            SEARCH
            SEARCH
            SEARCH
from existing libraries of  substructures associated with CONGEN.   If a
desired substructure is present in one of the libraries, then the SEARCH
command  represents  an  attractive alternative  to  the  CONGEN command
DEFINE for establishing the existence and definition of the substructure
DEFINE
DEFINE
DEFINE
for  your  current session.   Note  that CONGEN  does  not  search these
                                                       not
                                                       not
                                                       not
libraries automatically  whenever a substructure  is requested  by name;
you must explicitly  issue the SEARCH command  to retrieve the  name and
                               SEARCH
                               SEARCH
                               SEARCH
definition from the library.

        The use of the  SEARCH command is straightforward,  assuming you
                        SEARCH
                        SEARCH
                        SEARCH
have identified  by name  the substructure  you wish  to search  for and
retrieve  from  a specified  library  e.g., by  using  the  SHOW LIBRARY
                                                            SHOW LIBRARY
                                                            SHOW LIBRARY
                                                            SHOW LIBRARY
command,   Section   IV.J.6.    There  are   two   different   types  of
subcommands  which can  accompany  the SEARCH  command.  One  is  of the
                                       SEARCH
                                       SEARCH
                                       SEARCH
general form:

                SEARCH <library name>
                SEARCH
                SEARCH
                SEARCH

It  is  described  in  the  subsequent  section,  Section  IV.D.1.   The
second type of subcommand is the following:

                SEARCH MYLIB <file name>
                SEARCH MYLIB
                SEARCH MYLIB
                SEARCH MYLIB

It is described in Section IV.D.2.

                ******************************




















                                  123
CONGEN manual                                              February 1981


        IV.D.1    SEARCH <library name>
                  SEARCH <library name>
                  SEARCH <library name>
                  SEARCH <library name>

                ************************************
                *                                  *
                * SEARCH Subcommand <library name> *
                *                                  *
                ************************************


        The <library name> as the  subcommand for SEARCH can be  any one
                                                  SEARCH
                                                  SEARCH
                                                  SEARCH
of  a  number of  predefined  libraries.  A  list  of the  names  of the
substructures present in a library  can be obtained by using  the CONGEN
command  SHOW LIBRARY  <library name>,  Section IV.J.6}.   The following
         SHOW LIBRARY
         SHOW LIBRARY
         SHOW LIBRARY
libraries are  available and can  be accessed to  retrieve substructures
(whose drawings and connection tables  are shown in an addendum  to this
manual) by the command SEARCH <library name>:
                       SEARCH
                       SEARCH
                       SEARCH

Library
 Name                           Contents
-------                         --------

GENLIB        Contains generally useful substructures for many CONGEN
GENLIB
GENLIB
GENLIB
                problems, including small alkyl groups and various
                functional groups;

ISOLIB        Contains a selection of 2, 3 and 4 isoprene units
ISOLIB
ISOLIB
ISOLIB
                in head-to-tail or irregular linkages - for use in
                substructure constraints (see Section IV.E.2.b)
                expressing the isoprene test (see also Section V.B);

BMTERP        Contains the bicyclic monoterpane skeletons shown
BMTERP
BMTERP
BMTERP
                in T.K. Devon and A.I. Scott, "Handbook of Naturally
                Occurring Compounds," Vol. II, "Terpenes." Academic
                Press, New York, 1972;

BSTERP        Contains the bicyclic sesquiterpane skeletons shown
BSTERP
BSTERP
BSTERP
                in Devon and Scott (see BMTERP);
                                        BMTERP
                                        BMTERP
                                        BMTERP

TSTERP        Contains the tricyclic sequiterpane skeletons shown
TSTERP
TSTERP
TSTERP
                in Devon and Scott (see BMTERP);
                                        BMTERP
                                        BMTERP
                                        BMTERP

AMNACD        Contains amino acid skeletons;
AMNACD
AMNACD
AMNACD

SURVLIB       Contains a selection of substructures and functional
SURVLIB
SURVLIB
SURVLIB
                groups for use in the CONGEN command SURVEY (see
                                                     SURVEY
                                                     SURVEY
                                                     SURVEY
                Section IV.N); this is an expanded version of GENLIB;
                                                              GENLIB
                                                              GENLIB
                                                              GENLIB

MYLIB         Actually not a library, but a request by you to have
MYLIB
MYLIB
MYLIB
                CONGEN request a file name which represents a file
                saved by you (see CONGEN command SAVE, Section IV.L)
                                                 SAVE
                                                 SAVE
                                                 SAVE
                previously - see Section IV.D.2.

                ******************************



                                  124
CONGEN manual                                              February 1981


  ***** Use of the SEARCH <library name> command in CONGEN *****
        Use of the SEARCH <library name> command in CONGEN
        Use of the SEARCH <library name> command in CONGEN
        Use of the SEARCH <library name> command in CONGEN


        The use  of SEARCH will  be illustrated first  for GENLIB  - the
                    SEARCH                                 GENLIB
                    SEARCH                                 GENLIB
                    SEARCH                                 GENLIB
command works  precisely the  same for  ISOLIB, BMTERP,  BSTERP, TSTERP,
                                        ISOLIB  BMTERP   BSTERP  TSTERP
                                        ISOLIB  BMTERP   BSTERP  TSTERP
                                        ISOLIB  BMTERP   BSTERP  TSTERP
AMNACD  and  SURVLIB.  The  SEARCH  MYLIB command  is  described  in the
AMNACD       SURVLIB        SEARCH  MYLIB
AMNACD       SURVLIB        SEARCH  MYLIB
AMNACD       SURVLIB        SEARCH  MYLIB
subsequent  section,  Section  IV.D.2.   Remember  to  see   the  CONGEN
command  SHOW   LIBRARY  for  instructions   on  seeing  the   names  of
         SHOW   LIBRARY
         SHOW   LIBRARY
         SHOW   LIBRARY
substructures in each library (Section IV.J.6).

#search                         Issue the SEARCH command
 search                                   SEARCH
 search                                   SEARCH
 search                                   SEARCH

LIBRARY TO BE SEARCHED:?        Ask for help
                       ?
                       ?
                       ?

GENLIB ISOLIB BMTERP BSTERP TSTERP AMNACD SURVLIB MYLIB   CONGEN replies
                                                            with options
LIBRARY TO BE SEARCHED:genlib           Select GENLIB
                       genlib                  GENLIB
                       genlib                  GENLIB
                       genlib                  GENLIB

SUBSTRUCTURE TO BE RETRIEVED:?          CONGEN requests substructure
                             ?
                             ?
                             ?
                                          name (may be several names)
                                          to be retrieved - ask for help

A NAME (OTHER THAN X OR H) WHICH HAS    CONGEN replies and
NOT PREVIOUSLY BEEN DEFINED
SUBSTRUCTURE TO BE RETRIEVED:ket          reprompts for name(s), e.g.
                             ket
                             ket
                             ket
                                          KET
                                          KET
                                          KET
                                          KET
KET DEFINED                             CONGEN replies - KET defined
                                                         KET
                                                         KET
                                                         KET
#                                       Ready for next CONGEN command

#SEARCH GENLIB MET ET CH CH2 CH3        Ask to retrieve several
 SEARCH GENLIB MET ET CH CH2 CH3
 SEARCH GENLIB MET ET CH CH2 CH3
 SEARCH GENLIB MET ET CH CH2 CH3

CH, CH2, ET, CH3 AND MET DEFINED        CONGEN replies - all defined

#                                       Ready for next CONGEN command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies

        1) Attempt to retrieve a substructure with a name already
defined as an atom or substructure:

#search genlib                  Issue SEARCH command
 search genlib                        SEARCH
 search genlib                        SEARCH
 search genlib                        SEARCH
SUBSTRUCTURE TO BE RETRIEVED:ch3        Assume CH3 already defined as
                             ch3               CH3
                             ch3               CH3
                             ch3               CH3
                                          an atom
CH3 IS ALREADY DEFINED AS AN ATOM AND CAN'T BE USED HERE
SUBSTRUCTURE TO BE RETRIEVED:           CONGEN replies and reprompts

#search genlib me               Assume ME already defined as
 search genlib me                      ME
 search genlib me                      ME
 search genlib me                      ME
                                  substructure
ME IS ALREADY DEFINED AS A SUBSTRUCTURE AND CAN'T BE USED HERE
ERASING ...ME                   CONGEN replies and erases input and
SUBSTRUCTURE TO BE RETRIEVED:     reprompts for legal name



                                  125
CONGEN manual                                              February 1981


        2) Illegal input or non-existent substructure:

#search genlib 13               Integers illegal
 search genlib 13
 search genlib 13
 search genlib 13
I WAS EXPECTING A WORD          CONGEN replies and
ERASING ...13                     erases input and reprompts for name
SUBSTRUCTURE TO BE RETRIEVED:pdq        PDQ not in GENLIB
                             pdq        PDQ        GENLIB
                             pdq        PDQ        GENLIB
                             pdq        PDQ        GENLIB
THAT LIBRARY DOESN'T CONTAIN PDQ        CONGEN complains and exits
#                               Ready for next CONGEN command
















































                                  126
CONGEN manual                                              February 1981


        IV.D.2    SEARCH MYLIB <file name>
                  SEARCH MYLIB <file name>
                  SEARCH MYLIB <file name>
                  SEARCH MYLIB <file name>

                ***************************
                *                         *
                * SEARCH Subcommand MYLIB *
                *                         *
                ***************************


        The SEARCH command provides  an additional feature, and  that is
            SEARCH
            SEARCH
            SEARCH
the ability to search for  substructures in your own library.   Any file
                                            your own
                                            your own
                                            your own
saved  by you,  using  the CONGEN  command  SAVE, Section  IV.L,  can be
                                            SAVE
                                            SAVE
                                            SAVE
treated as  a library file.   The following procedure  may be  useful to
you.  Use  the CONGEN  command DEFINE  SUBSTRUCTURE, Section  IV.B.6, to
                               DEFINE  SUBSTRUCTURE
                               DEFINE  SUBSTRUCTURE
                               DEFINE  SUBSTRUCTURE
define  a  set  of  substructures of  particular  interest  to  your own
chemical problems.  When they are all defined, issue the  CONGEN command
SAVE to save them away, under a file name supplied by you.  From then on
SAVE
SAVE
SAVE
selected substructures can  be retrieved from  that file by  issuing the
SEARCH MYLIB command and providing the same file name to the  prompt for
SEARCH MYLIB
SEARCH MYLIB
SEARCH MYLIB
file name.  This use of SEARCH is illustrated in the example below.  You
                        SEARCH
                        SEARCH
                        SEARCH
can  use the  SHOW  LIBRARY MYLIB  command, Section  IV.J.6,  to refresh
              SHOW  LIBRARY MYLIB
              SHOW  LIBRARY MYLIB
              SHOW  LIBRARY MYLIB
your memory on the substructures in your own saved file.

                ******************************

   ***** Use of the MYLIB <file name> subcommand in SEARCH *****
         Use of the MYLIB <file name> subcommand in SEARCH
         Use of the MYLIB <file name> subcommand in SEARCH
         Use of the MYLIB <file name> subcommand in SEARCH

#search mylib                   Illustration of use of SEARCH MYLIB
 search mylib                                          SEARCH MYLIB
 search mylib                                          SEARCH MYLIB
 search mylib                                          SEARCH MYLIB
                                CONGEN replies with file name
                                                    file name
                                                    file name
                                                    file name
                                  request and reprompts

NAME OF A FILE YOU HAVE PREVIOUSLY SAVED:?      Ask for help
                                         ?
                                         ?
                                         ?

                                CONGEN replies with standard message
                                  about the format of file names

A WORD OF THE FORM XXXXXX.YYY WHERE XXXXXX IS A 'NAME' OF
FROM ONE TO SIX LETTERS AND/OR DIGITS AND WHERE YYY IS AN
OPTIONAL 'EXTENSION' OF FROM ONE TO THREE LETTERS AND/OR DIGITS.
THE '.' MAY BE OMITTED IF THE EXTENSION IS OMITTED
NAME OF A FILE YOU HAVE PREVIOUSLY SAVED:abcd.zxy       A previously
                                         abcd.zxy
                                         abcd.zxy
                                         abcd.zxy
                                                          saved file
SUBSTRUCTURE TO BE RETRIEVED:?          File OK, request for sub-
                             ?
                             ?
                             ?
                                          structure - ask for help
A NAME (OTHER THAN X OR H) WHICH HAS    CONGEN replies and
NOT PREVIOUSLY BEEN DEFINED
SUBSTRUCTURE TO BE RETRIEVED:             reprompts for name(s),
                                          supplied as in
                                          Section IV.D.1

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies



                                  127
CONGEN manual                                              February 1981


        1) Non-existent file name:

#search mylib
 search mylib
 search mylib
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                in  Structure Generation  in  CONGEN, Section  VI,  the generate
phase  of CONGEN  requires the  molecular formula,  a set  of predefined
Superatoms  (may  be none)  and  a  set of  constraints  on  desired and
undesired  structural  features  (may  be  none).   The  result  of  the
computation  is a  list of  intermediate structures.   If there  were no
                            intermediate structures
                            intermediate structures
                            intermediate structures
Superatoms,  then  the  intermediate  structures  are  in  fact complete
chemical  structures, or  final structures.   If there  were Superatoms,
then the representation for the intermediate structures  possesses names
of Superatoms as "atoms" in  the structure, with a valence given  by the
valence  available  for bonding  as  defined when  the  substructure was
created (see DEFINE SUBSTRUCTURE command, Section IV.B.6.
             DEFINE SUBSTRUCTURE
             DEFINE SUBSTRUCTURE
             DEFINE SUBSTRUCTURE

        The  concept  of  intermediate  structures  is  central  to  the
operation of CONGEN.  It keeps many structural problems to a finite size
to  allow  your examination  of  them and  your  application  of further
constraints  to  reduce  the  number;  there  are  generally  far  fewer
intermediate structures  than final,  complete structures.   Again, this
concept  is described  in  more detail  elsewhere in  the  document (see
Section  I.A and  Section VI).   You will  quickly become  familiar with
the concept and exploit  it for more efficient problem-solving  once you
have experimented with CONGEN a few times.

        Intermediate  structures may  possess Loops,  or intra-superatom
bonds.  Such bonds are allocated to Superatoms possessing more  than two
bonding sites during GENERATE, in all possible ways.  These loops appear
                     GENERATE
                     GENERATE
                     GENERATE
in structure drawings as the  letter "i", preceded by an integer  if two
or more  loops were  allocated, attached  to a  Superatom with  a single
bond.  However, loops will, on imbedding, each use two available bonding
sites.  Such  loops will  form internal bonds  in the  Superatoms during
imbedding.   Examples of  the representation  of loops  can be  found in
discussion  of  the  CONGEN  commands  DRAW,  Section  IV.I   and  SHOW,
                                       DRAW                        SHOW
                                       DRAW                        SHOW
                                       DRAW                        SHOW
Section  IV.J.   Further  information  including  references  to  other,
pertinent sections and an example  is given in discussion of  the CONGEN
command IMBED, Section IV.G.
        IMBED
        IMBED
        IMBED

        There is no real limit to the number of structures which  can be




                                  129
CONGEN manual                                              February 1981


generated because they  are saved on a  disk file as they  are produced.
Obviously,  such  resources  are  eventually  finite,  as  is  available
computer  time,  so  some  caution  is  required  to  prevent  excessive
structure  generation.   Several  helpful  hints  are  provided  in  the
detailed  discussion, Structure  Generation  in CONGEN,  Section  VI.  A
very  rough  estimate of  percent  completion is  presented  during long
very
very
very
computations.

        There are two phases to supplying information to the requests of
the  GENERATE  command,  Superatom  Input  and  constraint   input.   We
     GENERATE
     GENERATE
     GENERATE
differentiate  between them  because the  input sequences  are organized
that way and the treatment  of substructures supplied to both  phases is
different within  the program.   It should  be realized,  however, that,
conceptually,  substructures  used  as  Superatoms  and  constraints all
                                                                     all
                                                                     all
                                                                     all
represent constraints on how the molecular formula may be assembled into
complete structures.  The former  are required, may not overlap  and are
used as building blocks  for intermediate structures; the latter  may be
required or forbidden, may overlap to any extent and are  tested against
the  growing  structures  as  the  structure  generator   within  CONGEN
assembles structures.   These concepts are  discussed in more  detail in
Substructures in CONGEN, Section V.

        Superatoms must consist entirely of atoms.  They  cannot contain
atoms whose names are the names of other substructures, i.e., you cannot
use Superatoms within Superatoms.  Substructures used as constraints can
contain atoms whose  names are names  of other substructures,  a feature
which is useful to make structural statements of what Superatoms  may or
may not be  connected to other  Superatoms.  These points  are discussed
further in Substructures in CONGEN, Section V.

        A structural problem may be  specified to CONGEN in a  number of
different  ways.   However, there  is  one  factor to  keep  in  mind to
maximize the efficiency of CONGEN and minimize computer time spent  on a
problem.  It  is always  best to  include as  many of  the atoms  in the
molecular formula in Superatoms, and to make the Superatoms as  large as
possible  without overlapping,  i.e., so  that no  Superatoms  share any
          without overlapping
          without overlapping
          without overlapping
atoms in common.  Although required substructures can also  be specified
as  required constraints,  CONGEN  will be  much more  efficient  in the
former case.

        If  aromatic  templates   have  been  defined,   aromaticity  is
considered during GENERATE  for those atoms  which will be  "visible" to
                  GENERATE
                  GENERATE
                  GENERATE
CONGEN during GENERATE, i.e.,  those present in the  collapsed molecular
              GENERATE
              GENERATE
              GENERATE
formula.   The  aromatic nature  of  atoms within  Superatoms  cannot be
considered until  the Superatoms are  imbedded.  Aromatic types  are not
allowed  as  atom  properties in  substructures  used  as  Superatoms by
convention; CONGEN will ignore such properties and tell you so. Although
the aromatic nature of structures will be perceived,  possible resonance
duplicates will not be removed.  CONGEN warns you about this  fact.  See
Aromaticity in CONGEN, Section IX, for further details.

        Remember that all necessary  atoms and substructures for  use in




                                  130
CONGEN manual                                              February 1981


GENERATE  must  have been  defined  previously, via  the  CONGEN command
GENERATE
GENERATE
GENERATE
DEFINE (Section IV.B), or retrieved from library files using  the SEARCH
DEFINE                                                            SEARCH
DEFINE                                                            SEARCH
DEFINE                                                            SEARCH
command (Section IV.D).

                ******************************

        ***** Use of the GENERATE command in CONGEN *****
              Use of the GENERATE command in CONGEN
              Use of the GENERATE command in CONGEN
              Use of the GENERATE command in CONGEN


        The use  of the  GENERATE command  is simple.   The complexities
                         GENERATE
                         GENERATE
                         GENERATE
arise in supplying  input to the  Superatom and constraint  phases.  The
response  by  CONGEN is  eventually  for Superatom  input,  described in
detail   in   the   subsequent   section,   Section   IV.E.1.   Finally,
constraints are  requested and  the allowed  requests and  responses are
summarized in Constraint Input, Section IV.E.2.

        The command to generate structures is issued as follows:

        1) Molecular formula not defined previously:

#generate                       Issue the GENERATE command
 generate                                 GENERATE
 generate                                 GENERATE
 generate                                 GENERATE

MOLECULAR FORMULA:c 25 h 42 o 3         Request for formula
                  c 25 h 42 o 3
                  c 25 h 42 o 3
                  c 25 h 42 o 3

MOLECULAR FORMULA DEFINED       CONGEN notes definition

SUPERATOM:                      Prompt for Superatom input - see
                                  Section IV.E.1

                        or

        2) Molecular formula defined previously (see DEFINE MOLFORM,
                                                     DEFINE MOLFORM
                                                     DEFINE MOLFORM
                                                     DEFINE MOLFORM
Section IV.B.3):

#generate                       Issue GENERATE command
 generate                             GENERATE
 generate                             GENERATE
 generate                             GENERATE

SUPERATOM:                      Prompt for Superatom input - see
                                  Section IV.E.1
    .
    .
    .                           Input all Superatoms
    .
    .
SUPERATOM:                      Carriage return response terminates

'COLLAPSED' FORMULA IS ...      The molecular formula considering
                                  Superatoms as individual atoms, i.e.,
                                  the molecular formula of the resulting
                                  intermediate structures

PERINENT AROMATIC TEMPLATES: ...        Any aromatic templates (may be
                                  the word NONE) applicable to the
                                           NONE
                                           NONE
                                           NONE
                                  problem at this point, if any
                                                         if
                                                         if
                                                         if



                                  131
CONGEN manual                                              February 1981


                                  aromatics were defined, see
                                  Section IV.B.5.  Message omitted if
                                  no aromatics were defined.

CONSTRAINTS:                    Prompt for constraints input - see
                                  Section IV.E.2
    .
    .
    .
    .
    .
CONSTRAINTS:                    Carriage return response terminates

                                CONGEN prints one dot for each structure
                                  generated

........................................................................
........................................................................
........................................................................
.
                                A periodic report is provided for long
                                  structure generations
estimated completion = 50 - 58%
217 structures have been generated so far
........................................................................
........................................................................
........................................................................
.......................................

472 STRUCTURES WERE GENERATED   Final report on structure generation

I MIGHT HAVE PRODUCED MORE THAN ONE RESONANCE FORM FOR
SOME OF THE AROMATIC STRUCTURES.  THESE STRUCTURES SHOULD BE
'AROMATIZED' TO GUARANTEE FREEDOM FROM DUPLICATION.

                                The above message is obtained if there
                                  were any aromatic templates pertinent
                                  to the problem at the point of
                                  intermediate structures.
                                  Message omitted otherwise.

#                               Ready for next CONGEN command


                ******************************

        ***** Error Conditions and CONGEN Replies *****
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies


        There are many error conditions which can occur during  input of
Superatoms and  constraints to the  GENERATE command.  These  errors are
                                    GENERATE
                                    GENERATE
                                    GENERATE
described  in  the  following  sections,  Section  IV.E.1   and  Section




                                  132
CONGEN manual                                              February 1981


IV.E.2.  The  most important  error condition  relating to  the GENERATE
                                                                GENERATE
                                                                GENERATE
                                                                GENERATE
command itself is the message from CONGEN after structure generation:

        0 STRUCTURES WERE GENERATED

        Given that  no errors were  detected during input  of Superatoms
and  constraints,  the reason  why  no structures  are  possible  is, in
general,  a   subtle  problem  relating   to  incorrect   definition  of
substructures or  inadvertent selection  of combinations  of constraints
which  makes it  impossible  to generate  legal structures.   To  cite a
trivial example as an illustration, generation of alkanes of the general
molecular formula CnH2n+2 under the constraint of no methyl  groups will
yield 0 structures.  CONGEN  can only determine such  errors indirectly,
by generating all the structures and eventually rejecting them all based
on  the  constraints.   In such  circumstances,  you  should  review the
constraints   and  their   definitions  carefully.    For   review,  the
substructures used as constraints  can be drawn with the  CONGEN command
DRAW (Section IV.I),  or have their  connection tables presented  to you
DRAW
DRAW
DRAW
using  the  CONGEN command  SHOW  CTABLE (Section  IV.J.2).   The CONGEN
                            SHOW  CTABLE
                            SHOW  CTABLE
                            SHOW  CTABLE
command FIX SUBSTRUCTURE (Section IV.C) can be used to correct errors in
        FIX SUBSTRUCTURE
        FIX SUBSTRUCTURE
        FIX SUBSTRUCTURE
substructures.

***** Note (2/81): It is possible that if there are too many       *****
***** (approximatley 10 or 11) seperate pieces in the 'collapsed'  *****
***** formula prior to generation that the problem will be too     *****
***** large for generation to occur.  CONGEN crashes have resulted *****
***** from this type of input, and while it is admittedly messy,   *****
***** nothing is lost in a crash.  Attempts should be made to      *****
***** further define the problem before trying to generate.        *****



























                                  133
CONGEN manual                                              February 1981


        IV.E.1    Superatom Input
                  Superatom Input
                  Superatom Input
                  Superatom Input

                *******************************
                *                             *
                * Superatom Input to GENERATE *
                *                             *
                *******************************


        The first phase of input  to the CONGEN command GENERATE  is for
                                                        GENERATE
                                                        GENERATE
                                                        GENERATE
Superatoms.  Superatoms are the required,  non-overlapping substructural
features  of  your structural  problem.   The concept  of  Superatoms is
described  in  detail  in   Basic  CONGEN  concepts,  Section   I.A  and
Substructures in CONGEN, subsection Superatoms, Section V.A.

        GENERATE requests Superatoms by name and number.  The prompt for
        GENERATE
        GENERATE
        GENERATE
Superatom  is  answered  first  by  the  name  of  a  previously defined
substructure, as  illustrated below.   You are  allowed to  specify that
there may be more than one  of the named Superatoms.  Thus, if  you know
there are,  for example,  three methyl  groups, then  you need  name the
substructure only  once and specify  that there are  three (or  more) of
them.

        The prompt for the desired number is RANGE OF OCCURRENCES.  This
allows you to  input one of the  three following ranges to  indicate the
number of the Superatoms you desire:

 RANGE OF
OCCURRENCES             Implication
-----------             -----------
AT LEAST X      X of the Superatoms will be included in each
AT LEAST X
AT LEAST X
AT LEAST X
                intermediate structure, by name.  Additional
                "copies" of the Superatom are allowed and will be
                generated if possible as intact substructural units.

EXACTLY X       X of the Superatoms will be included in each
EXACTLY X
EXACTLY X
EXACTLY X
                intermediate structure, by name.  No additional
                                                  No
                                                  No
                                                  No
                copies of the Superatom will be constructed.
                Every structure will have exactly X of the Superatom,
                no more, no less  Repeat, no other substructures
                                          no
                                          no
                                          no
                corresponding to the Superatom will be constructed.
RANGE X TO Y    X of the Superatoms will be included in each
RANGE X TO Y
RANGE X TO Y
RANGE X TO Y
                intermediate structure, by name.  Additional copies
                of the Superatom, up to and including a total of Y
                will be generated if possible, as intact substructural
                units, but no more than Y.


        There  is  considerable  flexibility,  then,  in  specifying the
number of Superatom present in a structural problem.  This parallels the
sometimes uncertain structural information obtained from  spectral data.
Sometimes  it is  possible  to state  exactly  x of  a  substructures is
                                      exactly  x
                                      exactly  x
                                      exactly  x




                                  134
CONGEN manual                                              February 1981


present.   More  frequently,  you  know  that  some  definite  number is
present, but there may be more - you are allowed to say that with the at
                                                                      at
                                                                      at
                                                                      at
least and range options.
least     range
least     range
least     range

        We  wish  to  warn against  indiscriminate  use  of  the exactly
                                                                 exactly
                                                                 exactly
                                                                 exactly
option,  for  reasons that  are  described in  Superatoms,  Section V.A,
and Structure  Generation in  CONGEN, Section VI.   It means  just that,
exactly,  which  is  a powerful  constraint  if  correct;  if incorrect,
however, you will not generate  the correct structure.  If there  is any
doubt about the actual number of a substructure, use the option at least
                                                                at least
                                                                at least
                                                                at least
to specify the number of which you are sure.

***** Note (8/79) - the input sequence allows you to input the     *****
***** same Superatom name more than once, with the same or         *****
***** different ranges of occurrences. Don't do it!                *****
                                       Don't do it!
                                       Don't do it!
                                       Don't do it!
***** You can generate structures under such circumstances, but    *****
***** CONGEN's mechanism for using constraints implied by the      *****
***** range of occurrence may give you incorrect results.          *****
***** This will be fixed.                                          *****

        ***** Illustration of Superatom input to GENERATE *****
              Illustration of Superatom input to GENERATE
              Illustration of Superatom input to GENERATE
              Illustration of Superatom input to GENERATE


        Assume that all necessary substructures to be used as Superatoms
have  been defined  (see DEFINE  SUBSTRUCTURE command,  Section IV.B.6),
                         DEFINE  SUBSTRUCTURE
                         DEFINE  SUBSTRUCTURE
                         DEFINE  SUBSTRUCTURE
together with the molecular  formula.  The following is  an illustration
of the input sequence for  Superatoms; a real example is in  Section II,
Sample CONGEN Session.

#generate                       Issue the GENERATE command
 generate                                 GENERATE
 generate                                 GENERATE
 generate                                 GENERATE

SUPERATOM:?                     Ask for help
          ?
          ?
          ?

THE NAME OF A DEFINED           CONGEN replies and
SUBSTRUCTURE
SUPERATOM:abc                     reprompts for Superatom name
          abc
          abc
          abc

RANGE OF OCCURRENCES:?          CONGEN requests number of occurrences
                     ?
                     ?
                     ?
                                  Ask for help - CONGEN replies

PLEASE GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
AT LEAST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL

RANGE OF OCCURRENCES:at least 1           and reprompts
                     at least 1
                     at least 1
                     at least 1

SUPERATOM:def                   CONGEN requests another Superatom name
          def
          def
          def

RANGE OF OCCURRENCES:exactly 1       and range of occurrence
                     exactly 1
                     exactly 1
                     exactly 1

SUPERATOM:ghi range 1 to 2      Another Superatom, on one line
          ghi range 1 to 2
          ghi range 1 to 2
          ghi range 1 to 2




                                  135
CONGEN manual                                              February 1981


SUPERATOM:jkl a l 1             Another, on one line, short form
          jkl a l 1
          jkl a l 1
          jkl a l 1

SUPERATOM:                      When done with Superatoms, a carriage
                                  return terminates Superatom input
                                CONGEN replies with the reduced, or
                                  collapsed molecular formula which
                                  represents the actual structure
                                  generation problem and the formula of
                                  the resulting intermediate structures

'COLLAPSED' FORMULA IS O 3 ABC 1 DEF 1 GHI 1 JKL 1 H 28

PERTINENT AROMATIC TEMPLATES: ...       If any previously defined are
                                  pertinent.  See Section IV.E for
                                  additional information

CONSTRAINT:                     CONGEN next prompts for constraints -
                                  see Section IV.E.2

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies


        There  are many  possible  error conditions  in  Superatom input
because all error checking on the validity of the substructures  used as
Superatoms occurs as they are input.  Several of the errors  may require
redefinition of the Superatom  or the molecular formula.   The control-C
(see CONGEN  Input, Section  III) can be  used to  leave, or  abort, the
GENERATE phase and return to  CONGEN, namely, issue a control-C  and run
GENERATE
GENERATE
GENERATE
CONGEN again (see How to Start CONGEN, Section I.C).  Here is  a summary
of many of the error conditions:

        1) Non-existent substructure:

SUPERATOM:abd exactly 1         Assume ABD not defined
          abd exactly 1                ABD
          abd exactly 1                ABD
          abd exactly 1                ABD
ABD HASN'T BEEN DEFINED YET     CONGEN replies and
ERASING ...ABD EXACTLY 1          erases bad input
SUPERATOM:                        reprompts for another Superatom name

        2) Illegal input:

SUPERATOM:abc one               ONE not in possible responses to range
          abc one               ONE
          abc one               ONE
          abc one               ONE
ONE IS NOT AN EXPECTED KEYWORD HERE     of occurrences - CONGEN replies
ERASING ...ONE                          and erases bad input
RANGE OF OCCURRENCES:1          Integer not a legal range either
                     1
                     1
                     1
I WAS EXPECTING A WORD          CONGEN replies and
RANGE OF OCCURRENCES:exactly one        reprompts for range - ONE
                     exactly one                              ONE
                     exactly one                              ONE
                     exactly one                              ONE
I WAS EXPECTING A NUMBER                not legal - integer required
ERASING ...ONE                          CONGEN erases and
NUMBER:1                                reprompts for number - at last
       1
       1
       1
                                        a legal response
SUPERATOM:                      CONGEN prompts for next Superatom name



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        3) More atoms in Superatoms than in molecular formula:

***** Note (9/79) - this sequence illustrates an error in CONGEN   *****
***** which is only encountered after you attempt to generate.     *****
***** Fortunately, you cannot continue, as shown below.  You must  *****
***** re-enter the Superatom and constraints after fixing the      *****
***** substructures.                                               *****

SUPERATOM:abc ex 1              Legal input
          abc ex 1
          abc ex 1
          abc ex 1
SUPERATOM:def ex 1              But sum of atoms in ABC + DEF exceeds
          def ex 1                                  ABC   DEF
          def ex 1                                  ABC   DEF
          def ex 1                                  ABC   DEF
                                  molecular formula - CONGEN reports
                                  the atom type exceeded - Carbon

THERE ARE TOO FEW C'S IN THE UNUSED PORTION OF THE
MOLECULAR FORMULA TO ACCOUNT FOR DEF

SUPERATOM:                      DEF ignored - prompt for next name
                                DEF
                                DEF
                                DEF

'COLLAPSED' FORMULA IS C 4 ABC 1 H 6    Continue until all are input
CONSTRAINT:                     Specify no constraints
UNKNOWN ATOM TYPE DEF           CONGEN replies - this is the error
                                                 this is the error
                                                 this is the error
                                                 this is the error

#                               Ready for next CONGEN command -
                                  try again

        4) Atom name in Superatom which has not been defined:

SUPERATOM:abc ex 1              Assume ABC contains the undefined atom
          abc ex 1                     ABC
          abc ex 1                     ABC
          abc ex 1                     ABC
I CAN'T USE ABC AS A SUPERATOM BECAUSE:         S - CONGEN replies and
                                                S
                                                S
                                                S
1) ATOM 2 HAS A NAME THAT HASN'T BEEN DEFINED   reports the number of
                                                the offending atom

SUPERATOM:                      CONGEN prompts for next Superatom

        5) Substructure names as atom names in Superatoms:

SUPERATOM:xyz at least 1        Assume XYZ has atom 1 named with the
          xyz at least 1               XYZ
          xyz at least 1               XYZ
          xyz at least 1               XYZ
                                  the name of another substructure

I CAN'T USE XYZ AS A SUPERATOM BECAUSE:         CONGEN replies
1) ATOM 1 HAS A NAME THAT IS DEFINED, BUT NOT AS AN ATOM

SUPERATOM:                      Prompt for next name

        6) Valence violation:

SUPERATOM:abc ex 1              Assume ABC has too many bonds to atoms
          abc ex 1                     ABC
          abc ex 1                     ABC
          abc ex 1                     ABC
                                  3 and 4 - CONGEN replies

I CAN'T USE ABC AS A SUPERATOM BECAUSE:
1) EACH OF ATOMS 2 AND 3 HAS A VALENCE SMALLER THAN THE NUMBER OF
ATTACHED BONDS




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SUPERATOM:                      CONGEN prompts for next name

SUPERATOM:abc ex 1              Assume ABC has a nonsense hydrogen
          abc ex 1                     ABC
          abc ex 1                     ABC
          abc ex 1                     ABC
                                  range on atom 4 - CONGEN replies

I CAN'T USE ABC AS A SUPERATOM BECAUSE:
1) ATOM 4 HAS TOO LARGE A VALUE FOR THE MINIMUM NUMBER OF H'S

SUPERATOM:                      CONGEN prompts for next name

        7) Superatoms can't have link nodes

SUPERATOM:abc ex 1              Assume atom 3 has been declared a
          abc ex 1
          abc ex 1
          abc ex 1
                                  link node - CONGEN replies

I CAN'T USE ABC AS A SUPERATOM BECAUSE:
1) ATOM 3 HAS THE LNODE PROPERTY

SUPERATOM:                      CONGEN prompts for next name

        8) Attempt to designate aromatic atom type (either aromatic
or nonaromatic) in Superatoms:

SUPERATOM:abc ex 1              Assume an atom(s) have ARTYPE defined
          abc ex 1                                     ARTYPE
          abc ex 1                                     ARTYPE
          abc ex 1                                     ARTYPE

NOTE: ARTYPES ARE IGNORED IN SUPERATOMS.        CONGEN replies, but
                                  accepts ABC, ignoring artypes
                                          ABC
                                          ABC
                                          ABC
SUPERATOM:                      CONGEN prompts for next name

        9) Attempt to use X or POLYNAMEs as atom types:
                          X    POLYNAME
                          X    POLYNAME
                          X    POLYNAME

SUPERATOM:xyz ex 1              Assume XYZ has such names
          xyz ex 1                     XYZ
          xyz ex 1                     XYZ
          xyz ex 1                     XYZ
I CAN'T USE XYZ AS A SUPERATOM BECAUSE:
1) ATOM 2 HAS A POLYNAME
2) ATOM 1 HAS THE NAME X
SUPERATOM:                      Prompt for next Superatom

       10) Disjoint, or disconnected Superatoms:

SUPERATOM:xyz at least 1        Assume XYZ defined as two disconnected
          xyz at least 1               XYZ
          xyz at least 1               XYZ
          xyz at least 1               XYZ
                                  part structures

I CAN'T USE XYZ AS A SUPERATOM BECAUSE:         CONGEN replies
1) THE SUBSTRUCTURE IS COMPOSED OF TWO OR MORE DISCONNECTED PIECES

SUPERATOM:                      Prompt for new name

                ******************************








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        IV.E.2    Constraint Input
                  Constraint Input
                  Constraint Input
                  Constraint Input

                ********************************
                *                              *
                * Constraint Input to GENERATE *
                *                              *
                ********************************


        After specification of Superatoms and a report by CONGEN  of the
'collapsed' molecular formula (see Section IV.E.1), you are  prompted to
enter constraints on your structure generation.  The use  of constraints
in the  structure generator  within CONGEN is  described in  Section VI,
Structure Generation in CONGEN.  The use of Substructures as Constraints
is described in Section V.B.

        Constraints  represent  both undesired  structural  features for
your  structural   problem  (e.g.,  implausible   functionalities,  ring
systems,  ring  sizes) and  desired  features which  for  one  reason or
another were not expressed  as Superatoms (usually because there  was no
way  to  express  particular  features  within  the  stricture  of  non-
overlapping Superatoms).

        With each  constraint type  (with the  exception of  the Partial
constraint which  is used  to stop  CONGEN after  a specified  number of
structures  have been  built, see  Section IV.E.2.f)  you are  asked for
a range of occurrences as illustrated below.  The possible  responses to
this request and their structural implications are as follows:

 RANGE OF
OCCURRENCES             Structural Implication
-----------             ----------------------

NONE            No structures will possess the given constraint
NONE            No
NONE            No
NONE            No

AT LEAST X      All structures will possess X of the given
AT LEAST X      All                         X
AT LEAST X      All                         X
AT LEAST X      All                         X
                constraint, and more if the characteristics of the
                problem allow it.

AT MOST X       All structures will contain from 0-X of the given
AT MOST X       All                              0-X
AT MOST X       All                              0-X
AT MOST X       All                              0-X
                constraint, but no structure will possess more
                                no
                                no
                                no
                than X.
                     X
                     X
                     X

EXACTLY X       All structures will possess exactly X of the given
EXACTLY X       All                                 X
EXACTLY X       All                                 X
EXACTLY X       All                                 X
                constraint.

RANGE X TO Y    All structures will possess from X to Y, inclusive,
RANGE X TO Y    All                              X    Y
RANGE X TO Y    All                              X    Y
RANGE X TO Y    All                              X    Y
                of the given constraint, no more, no less.


        The warnings given for use of EXACTLY X in input  of superatoms,
                                      EXACTLY X
                                      EXACTLY X
                                      EXACTLY X
Section  IV.E.1, apply  here also.   If you  are certain  that  an exact




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number, or none,  of the constraint type  exist, then such  responses to
the range of occurrence  request are powerful constraints.   However, if
you are sure of a given  number but unsure of the occurrence  of others,
use AT LEAST X.
    AT LEAST X
    AT LEAST X
    AT LEAST X

        Aromaticity  is  considered  during  GENERATE  if   any  defined
                                             GENERATE
                                             GENERATE
                                             GENERATE
aromatic  templates  are  pertinent.   If  none  are  pertinent,  or  no
aromatics were defined, a specification of a substructure with  atoms of
type  aromatic will  result in  an error  message that  the substructure
cannot be used  because it has atom  types (i.e., aromatic  atoms) which
will not be present when the constraint is applied (see  error condition
2, in Substructure Constraints, below).

        The input sequence for Constraints is summarized below.  Details
on the input of each constraint type and associated error conditions are
included in  subsequent sections, following  the Glossary  of Constraint
Types, Section IV.E.2.a, as follows:

Constraint
  Type          Section
----------      -------

SUBSTRUCTURE    Section IV.E.2.b
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE
PROTON          Section IV.E.2.c
PROTON
PROTON
PROTON
RING            Section IV.E.2.d
RING
RING
RING
LOOP            Section IV.E.2.e
LOOP
LOOP
LOOP
PARTIAL         Section IV.E.2.f
PARTIAL
PARTIAL
PARTIAL

                ******************************

        ***** Responses to the Constraints Prompt in GENERATE *****
              Responses to the Constraints Prompt in GENERATE
              Responses to the Constraints Prompt in GENERATE
              Responses to the Constraints Prompt in GENERATE

        The following illustrates the  general form of responses  to the
request for constraints during GENERATE.  Details of the responses are a
                               GENERATE
                               GENERATE
                               GENERATE
function of  the individual  constraint types and  are described  in the
sections  summarized  above.   The illustration  begins  at  the  end of
Superatom Input, Section IV.E.1, when constraints are requested:

CONSTRAINT:?                    Constraints prompt - ask for help
           ?
           ?
           ?

FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL
                                        CONGEN replies and
CONSTRAINT:                               reprompts for type
    .
    .
    .                           Input constraints, any type in any
    .                             order
    .
    .
CONSTRAINT:                     Response of carriage return to last
                                  prompt automatically begins structure
                                  generation



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        IV.E.2.a    Glossary of Constraint Types
                    Glossary of Constraint Types
                    Glossary of Constraint Types
                    Glossary of Constraint Types

                ********************************
                *                              *
                * Glossary of Constraint Types *
                *                              *
                ********************************


        The  following is  a glossary  of the  available  constraints in
CONGEN, together with a brief description of their function.  Details of
the use of each constraint type are given in the subsequent  section, as
summarized in Constraint Input, Section IV.E.2.

Constraint
  Type                          Function
----------                      --------

SUBSTRUCTURE    For constraints which can be expressed as substructures.
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE
                Substructural constraints are expressed in terms of
                the structures which will be produced, i.e., some
                structural features may be invisible to CONGEN in
                intermediate structures (those with unimbedded Super-
                atoms), see Section V.

PROTON          A substructural constraint for counting the number of
PROTON
PROTON
PROTON
                hydrogen atoms in specified environments; the environ-
                ment is given by the substructure; a single tag (see
                Tagging in CONGEN, Section X represents the type
                of proton to be counted in proton constraints.

RING            For specifying ring size constraints.  Such
RING
RING
RING
                constraints, unlike substructural constraints, can
                be expressed in terms of final structures.  A ring
                size of two can be used to constrain multiple bonds
                (double, triple, ...).

LOOP            For specifying constraints on the allowed number of
LOOP
LOOP
LOOP
                internal bonds in specified Superatoms.  Otherwise,
                all possible internal bonds will be formed in every
                Superatom (see IMBED, Section IV.G, and Imbedding
                               IMBED
                               IMBED
                               IMBED
                in CONGEN, Section VIII).

PARTIAL         To stop CONGEN after a specified number of structures
PARTIAL
PARTIAL
PARTIAL
                have been produced.  You cannot continue; you must
                restart the task (GENERATE, PRUNE, IMBED) from the
                                  GENERATE  PRUNE  IMBED
                                  GENERATE  PRUNE  IMBED
                                  GENERATE  PRUNE  IMBED
                beginning.

                ******************************







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        IV.E.2.b    Substructure Constraints
                    Substructure Constraints
                    Substructure Constraints
                    Substructure Constraints

                ****************************
                *                          *
                * Substructure Constraints *
                *                          *
                ****************************


        Substructural  constraints  are  those  which  can  be expressed
through  substructures defined  by Editstruc  (see  DEFINE SUBSTRUCTURE,
                                                    DEFINE SUBSTRUCTURE
                                                    DEFINE SUBSTRUCTURE
                                                    DEFINE SUBSTRUCTURE
Section  IV.B.6), for  example, no  ethyl groups,  at most  two hydroxyl
groups, and so forth.  The  substructures used as constraints can  be of
arbitrary complexity.  Details  of the use  of this constraint  type are
given  in  Substructures  as  Constraints,  Section  V.B.    You  should
refer  to  this  section  to  determine  CONGEN's  method  for  counting
occurrences  of  substructures  to  ensure  that  you  make  the correct
responses to the RANGE OF OCCURRENCE prompt.

        Remember that substructural constraints refer to  the structures
which will be  produced by GENERATE (or  IMBED), or exist already  to be
                           GENERATE      IMBED
                           GENERATE      IMBED
                           GENERATE      IMBED
pruned.  The "collapsed"  molecular formula given after  Superatom input
to GENERATE  (or IMBED)  indicates the atoms  and Superatom  names which
   GENERATE      IMBED
   GENERATE      IMBED
   GENERATE      IMBED
will  result.  Substructural  constraints  refer to  structures  in this
representation  -  CONGEN  currently has  no  mechanism  for translating
substructural constraints  expressed in terms  of final  structures back
into the  representation for intermediate  structures.  As  discussed in
Substructures  as  Constraints,  Section  V.B,  this  drawback  also has
some advantages because you can constrain interconnections of Superatoms
in intermediate structures using simply  their names as atom names  in a
substructure  used as  a constraint  (see Substructures  as Constraints,
Section V.B).

        You must have defined  previously all substructures you  wish to
input for substructural constraints.

                ******************************

        ***** Use of Substructure Constraints *****
              Use of Substructure Constraints
              Use of Substructure Constraints
              Use of Substructure Constraints


        Assuming that you have defined some substructures, we illustrate
here the general  form of the  responses, beginning with  the CONSTRAINT
prompt:

CONSTRAINT:?                    Ask for help, CONGEN replies
           ?
           ?
           ?

FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL

CONSTRAINT:substructure           and reprompts for type
           substructure
           substructure
           substructure

SUBSTRUCTURE NAME:?             Ask for help on name
                  ?
                  ?
                  ?



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THE NAME OF A DEFINED           CONGEN replies and
SUBSTRUCTURE

SUBSTRUCTURE NAME:me              reprompts for name
                  me
                  me
                  me

RANGE OF OCCURRENCES:?          Ask for help, CONGEN replies and
                     ?
                     ?
                     ?

PLEASE GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
NONE     AT LEAST X     AT MOST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL

RANGE OF OCCURRENCES:at least           reprompts for range
                     at least
                     at least
                     at least

NUMBER:3                        Prompt for rest of range
       3
       3
       3

CONSTRAINT:s cyc                Partly on one line, short form
           s cyc
           s cyc
           s cyc

RANGE OF OCCURRENCES:exactly 1       Rest of response
                     exactly 1
                     exactly 1
                     exactly 1

CONSTRAINT:s oh at most 1       All on one line
           s oh at most 1
           s oh at most 1
           s oh at most 1

CONSTRAINT:s hyd r 1 2          All on one line, short form
           s hyd r 1 2
           s hyd r 1 2
           s hyd r 1 2

CONSTRAINT:                     Ready for next constraint type

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies


        There  are  several  error conditions  which  can  arise because
substructures are error-checked when input to constraints for integrity.
Most  of  the  important   error  conditions  were  summarized   in  the
corresponding  section  under  Superatom  Input,  Section  IV.E.1.   One
example,  a  substructure  with  valence  violations,  nonsense hydrogen
ranges and atom types  not present in the current,  perhaps "collapsed,"
molecular formula, is given here for illustration.

        1) Illegal response to constraint prompt:

CONSTRAINT:bad                  BAD not a constraint type
           bad                  BAD
           bad                  BAD
           bad                  BAD
BAD IS NOT AN EXPECTED KEYWORD HERE     CONGEN replies and
CONSTRAINT:3                              reprompts - number wrong
           3
           3
           3
I WAS EXPECTING A WORD          CONGEN replies and
CONSTRAINT:substructure           reprompts for type
           substructure
           substructure
           substructure

        2) Atoms in substructure not in molecular formula:

SUBSTRUCTURE NAME:bad           Assume BAD has a nitrogen, but no
                  bad                  BAD
                  bad                  BAD
                  bad                  BAD
                                  nitrogens in molecular formula
RANGE OF OCCURRENCES:at least 1         Range OK, but CONGEN replies
                     at least 1
                     at least 1
                     at least 1




                                  143
CONGEN manual                                              February 1981


TESTING FOR BAD DOESN'T MAKE SENSE HERE BECAUSE
ATOM 1 CAN'T MATCH ANY OF THE ATOMS WHICH
WILL BE PRESENT WHEN I APPLY THE TEST   General message for such atoms
                                        This message is also obtained
                                          for any atom bearing ARTYPE
                                                               ARTYPE
                                                               ARTYPE
                                                               ARTYPE
                                          aromatic if no aromaticity
                                          possible
        3) Too many atoms of one type:

CONSTRAINT:s ph ex 1            Too many carbons in PH
           s ph ex 1                                PH
           s ph ex 1                                PH
           s ph ex 1                                PH

TESTING FOR PH DOESN'T MAKE SENSE HERE BECAUSE
IT CONTAINS MORE ATOMS OF TYPE C                CONGEN replies and
THAN WILL BE PRESENT WHEN I APPLY THE TEST
CONSTRAINT:                                       reprompts

        4) Valence and hydrogen range problems:

CONSTRAINT:sub bad at least 1           On one line, CONGEN replies
           sub bad at least 1
           sub bad at least 1
           sub bad at least 1

I CAN'T USE BAD AS A CONSTRAINT BECAUSE:
1)EACH OF ATOMS 2 AND 3 HAS A VALENCE SMALLER THAN THE NUMBER OF
ATTACHED BONDS
2) ATOM 1 HAS TOO LARGE A VALUE FOR THE MINIMUM NUMBER OF H'S

CONSTRAINT:                     Reprompt for constraint type

                ******************************




























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        IV.E.2.c    Proton Constraints
                    Proton Constraints
                    Proton Constraints
                    Proton Constraints

                **********************
                *                    *
                * Proton Constraints *
                *                    *
                **********************


        Proton  constraints   are  a   special  type   of  substructural
constraint used  expressly to supply  CONGEN with  structural inferences
derived  from  1H NMR  data.   Although many  such  inferences  can, and
should,  be  incorporated  into  Superatoms  or   regular  substructural
constraints, there is no way certain constraints can be phrased by those
two alternatives.  These constraints involve primarily counts of various
                                                       counts
                                                       counts
                                                       counts
types of protons,  e.g., X vinyl protons,  in instances where  the exact
                         X
                         X
                         X
distribution  of  such  protons  on  specific  substructures  cannot  be
precisely stated.

        CONGEN works with a structural representation in  which hydrogen
atoms are suppressed.  Proton  constraints refer to hydrogen  atoms; the
tag  (given  to  an atom  during  substructure  definition,  see Section
IV.B.6.p), which  must be  associated with an  atom in  the substructure
used for this constraint type, can be viewed as representing the proton.
The  remainder of  the substructure  represents the  environment  of the
proton; the environment may be of arbitrary complexity.

        There are several details about  the use of tags for  proton (or
other  substructural)  constraints  with  which  you  should familiarize
yourself before indiscriminate use  of tags.  Tags influence the  way in
which occurrences of substructures  are counted in CONGEN in  order that
the  chemically correct  number of  protons, or  other tagged  atoms, is
determined. This is  discussed in detail  in Tagging in  CONGEN, Section
X.

        All  other  considerations   about  the  use   of  substructural
constraints (Section IV.E.2.b) apply here for proton constraints.

                ******************************

        ***** Use of Proton Constraints *****
              Use of Proton Constraints
              Use of Proton Constraints
              Use of Proton Constraints


        We illustrate here the general form of proton  constraint input,
and special  errors which  may be encountered;  otherwise the  input and
error conditions are the same as for substructural  constraints, Section
IV.E.2.b:

CONSTRAINT:?                    Ask for help, CONGEN replies
           ?
           ?
           ?

FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL




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CONSTRAINT:proton               Select proton constraints
           proton
           proton
           proton

SUBSTRUCTURE NAME:?             Ask for help
                  ?
                  ?
                  ?

THE NAME OF A DEFINED           CONGEN replies and
SUBSTRUCTURE

SUBSTRUCTURE NAME:pt1             reprompts
                  pt1
                  pt1
                  pt1

RANGE OF OCCURRENCES:?          Ask for help, CONGEN replies
                     ?
                     ?
                     ?

PLEASE GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
NONE     AT LEAST X     AT MOST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL

RANGE OF OCCURRENCES:exactly 2          Reprompt for range - remember
                     exactly 2
                     exactly 2
                     exactly 2
                                          this is the number of protons,
                                          not the number of occurrences
                                          of the substructure

CONSTRAINT:                     Prompt for next constraint

                ******************************

        ***** Error Conditions and CONGEN replies *****
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies

CONSTRAINT:proton pt0           Partly on one line, assume PT0 has
           proton pt0                                      PT0
           proton pt0                                      PT0
           proton pt0                                      PT0
                                  no tags
RANGE OF OCCURRENCES: a l 3     Short form
                      a l 3
                      a l 3
                      a l 3

PROTON-CONSTRAINT SUBSTRUCTURES SHOULD HAVE EXACTLY ONE TAG, BUT
PT0 DOESN'T HAVE ANY.           CONGEN replies and

CONSTRAINT:pr pt2 ex 3            reprompts - assume PT2 has two tags
           pr pt2 ex 3                               PT2
           pr pt2 ex 3                               PT2
           pr pt2 ex 3                               PT2

PROTON-CONSTRAINT SUBSTRUCTURES SHOULD HAVE EXACTLY ONE TAG, BUT
PT2 HAS MORE THAN ONE.          CONGEN replies and

CONSTRAINT:                       reprompts for constraint type

                ******************************














                                  146
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        IV.E.2.d    Ring Constraints
                    Ring Constraints
                    Ring Constraints
                    Ring Constraints

                ********************
                *                  *
                * Ring Constraints *
                *                  *
                ********************


        Ring constraints are designed to force CONGEN to  construct only
the specified  number of  designated ring  sizes.  Ring  constraints are
implemented in CONGEN  differently from substructural  constraints.  The
actual  sizes of  rings in  a structure  are counted  (or  inferred) and
compared  against  the  number  you  have  requested.   The  section  on
Constraints  in  CONGEN,  Section  VII,  describes  in  more  detail the
operation of the ring constraints.

        For the purposes of  this section, however, it is  sufficient to
know that  constraints on  ring sizes may  be stated  in terms  of final
structures  independent of  where you  are in  the  structure generation
sequence.  CONGEN will interpret these ring constraints  in intermediate
structures and will not reject a structure unless it is obvious that the
ring constraints will be violated.

        There are some warnings associated with use of ring constraints.
In particular:

        a) CONGEN does not attempt to scan the list of  ring constraints
to determine whether or  not the requested constraints are  in agreement
with the molecular formula.   Thus, it is possible to  perform structure
generations for simple cases such as molecular formula = C4H8, requiring
two rings of size 2, without any error message occurring.  Of  course, 0
structures result from such a generation.

        b) There are some cases where manual analysis might  reveal that
a particular intermediate structure  could be rejected because  no legal
imbedding of unimbedded Superatoms  could yield a legal  structure under
the given ring  size constraints.  One  such case is  illustrated below,
error condition 5.  Because CONGEN's analysis  of implied ring  sizes in
the presence of unimbedded Superatoms is not completely thorough, it may
be  possible  to  obtain  final  structures  which  do  not   obey  ring
constraints  supplied in  the original  GENERATE command;  it  is always
                                        GENERATE
                                        GENERATE
                                        GENERATE
advisable, if you are uncertain,  to state the constraints again  in the
final imbedding, or  prune the final structure  list to ensure  that all
ring constraints are obeyed.

        CONGEN views multiple bonds as small rings.  Thus, the number of
multiple bonds  allowed can  be constrained  using the  ring constraint.
However, double or triple bonds each  count as one ring of size  two! If
                                               one
                                               one
                                               one
more detailed statements on the  number of double and triple  bonds must
be  made,  substructural constraints  must  be used.   Double  bonds are
counted in  aromatic systems.   Thus, a  benzene ring  contributes three
double bonds to the count of "two-membered" rings.



                                  147
CONGEN manual                                              February 1981


                ******************************

        ***** Use of Ring Constraints *****
              Use of Ring Constraints
              Use of Ring Constraints
              Use of Ring Constraints


        Specification  of  ring  sizes involves  selection  of  the size
together with the desired  range of occurrences.  There  is considerable
error checking  involved, and  some caveats on  the checking,  which are
described below.  We begin with the CONSTRAINTS: prompt:

CONSTRAINT:?                    Ask for help, CONGEN replies
           ?
           ?
           ?

FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL

CONSTRAINT:ring                 Reprompt, specify ring
           ring
           ring
           ring

RING SIZE:?                     Ask for help
          ?
          ?
          ?

AN INTEGER GREATER THAN ZERO    CONGEN replies and

RING SIZE:2                       reprompts
          2
          2
          2

RANGE OF OCCURRENCES:?          Ask for help, CONGEN replies
                     ?
                     ?
                     ?

PLEASE GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
NONE     AT LEAST X     AT MOST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL

RANGE OF OCCURRENCES:exactly 1          Specify range
                     exactly 1
                     exactly 1
                     exactly 1

CONSTRAINT:ring 3               Prompt for next constraint, partly
           ring 3
           ring 3
           ring 3
                                  on one line
RANGE OF OCCURRENCES:none       Specify range
                     none
                     none
                     none

CONSTRAINT:ring 6 at least 1    All on one line
           ring 6 at least 1
           ring 6 at least 1
           ring 6 at least 1

CONSTRAINT:r 7 n                On one line, short form, no 7-membered
           r 7 n
           r 7 n
           r 7 n
                                  rings

                ******************************

        ***** Error Conditions and CONGEN replies *****
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies


        There are  several responses to  the ring constraints  which are
detected as errors.   However, certain responses which  appear incorrect
are not detected as errors by CONGEN until you issue the carriage return
to the final constraint and generation begins (see below).  Other errors
are not detected at all  (see above) and the outcome will  eventually be
zero structures,  either after  GENERATE or after  all IMBEDs  have been
                                GENERATE               IMBED
                                GENERATE               IMBED
                                GENERATE               IMBED




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accomplished under  the same constraint.   The reasons for  this involve
how rings  are detected by  CONGEN and are  explained in  Constraints in
CONGEN,  Section  VII.   As   a  general  rule,  errors  in   ring  size
constraints may not be detected if there are Superatoms bearing multiple
free  valences.   Also,  ring  counts in  bridged  ring  systems  may be
misleading.  For  example, the mythical  compound tetrahedrane  has only
three  rings by  the molecular  formula alone,  but  four three-membered
rings (each face  of the tetrahedron)  according to CONGEN  (see Section
VII).  Here are some examples of errors detected:

        1) Illegal input:

CONSTRAINT:6                            Integer not allowed
           6
           6
           6
I WAS EXPECTING A WORD                  CONGEN replies and
CONSTRAINT:ring 8                         reprompts
           ring 8
           ring 8
           ring 8
RANGE OF OCCURRENCES:at must 1          Mis-typing
                     at must 1
                     at must 1
                     at must 1
MUST IS NOT AN EXPECTED KEYWORD HERE    CONGEN replies and
ERASING ...MUST 1                         erases and
LEAST OR MOST?:                           reprompts - carriage return
I DON'T UNDERSTAND - TYPE ? FOR HELP    CONGEN doesn't understand, so
RANGE OF OCCURRENCES:aleast 1             reprompts for range
                     aleast 1
                     aleast 1
                     aleast 1
ALEAST IS NOT AN EXPECTED KEYWORD HERE  Illegal keyword
ERASING ...ALEAST 1                     Erases and
RANGE OF OCCURRENCES:                     reprompts - carriage return
EH?                                       response results in helpful
                                          error message and a
CONSTRAINT:                               reprompt for constraint

        2) Attempt to respecify the same ring size:

CONSTRAINT:ring 2 at least 3    Assume ring size two mentioned before
           ring 2 at least 3
           ring 2 at least 3
           ring 2 at least 3
                                  CONGEN replies
YOU HAVE ALREADY SPECIFIED A TEST FOR RINGS OF SIZE 2.
FURTHER TESTS INVOLVING THIS RING SIZE WILL BE IGNORED.

CONSTRAINT:                     Reprompt for constraint

        3) Nonsense ring sizes, assuming no Superatoms in current
"collapsed" molecular formula and only one double bond equivalent.
(Note that not all such illegal specifications are detected by CONGEN,
and 0 structures will result after GENERATE):
                                   GENERATE
                                   GENERATE
                                   GENERATE

CONSTRAINT:ring 3 at l 3        Request for too many three-mem. rings
           ring 3 at l 3
           ring 3 at l 3
           ring 3 at l 3
CONSTRAINT:ring 8 ex 20         Request for 20 eight-mem. rings
           ring 8 ex 20
           ring 8 ex 20
           ring 8 ex 20
                        Note that this error is not caught until
                          structure generation begins!
CONSTRAINT:             Last constraint input - carriage return here
                        CONGEN complains
YOUR RING-SIZE CONSTRAINTS REQUIRE MORE RINGS THAN CAN BE
PRESENT WHEN I APPLY THE TESTS

#                               Ready for next CONGEN command - no
                                  structure generation takes place



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                                You must begin GENERATE again
                                               GENERATE
                                               GENERATE
                                               GENERATE

        4) Ring constraints inconsistent with rings already present
in Superatoms:

CONSTRAINT:ring 3 none          Assume a Superatom already has a
           ring 3 none
           ring 3 none
           ring 3 none
                                  three-membered ring
CONSTRAINT:                     Last constraint prompt - carriage return

YOUR SUPERATOMS CONTAIN MORE RINGS OF SIZE 3    CONGEN complains and
THAN YOUR RING-SIZE CONSTRAINTS ALLOW             returns to # prompt

#                               Ready for next CONGEN command - no
                                  structure generation takes place
                                You must begin GENERATE again
                                               GENERATE
                                               GENERATE
                                               GENERATE

        5) Incomplete consideration of ring constraints by CONGEN
(assume the "collapsed" molecular formula does not allow
designated ring sizes; here, CYC is a three-membered ring bearing
                             CYC
                             CYC
                             CYC
four free valences and the molecular formula is C10H18O):

'COLLAPSED' FORMULA IS O 1 C 7 CYC 1 H 16
CONSTRAINT:ring 2 ex 2          Illegal ring count - too many two-
           ring 2 ex 2
           ring 2 ex 2
           ring 2 ex 2
                                  membered rings required - molform
                                  allows only one more but CONGEN does
                                  not check constraint completely

CONSTRAINT:                     End of constraints input
        .
        .
        .
472 STRUCTURES WERE GENERATED   Yet, structures generated anyways.  All
                                have part structure CYC=C which passes
                                                    CYC=C
                                                    CYC=C
                                                    CYC=C
                                ring constraint because of unimbedded
                                Superatom CYC, which bears multiple
                                          CYC
                                          CYC
                                          CYC
                                free valences

#draw atnamed 1                 Ask to draw one
 draw atnamed 1
 draw atnamed 1
 draw atnamed 1

#1

    C-C-C-O   C
   /       \ /                  Obviously, structure illegal - in
  C        CYC                    other situations it may not be
 /          =                     so obvious
C           C

#imbed
 imbed
 imbed
 imbed
        .
        .                       Imbed CYC under same RING 2 EX 2
                                      CYC            RING 2 EX 2
                                      CYC            RING 2 EX 2
                                      CYC            RING 2 EX 2
        .                         constraint
        .                       Now, constraint utilized correctly
NO STRUCTURES WERE OBTAINED



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THE ORIGINAL LIST HAS BEEN RESTORED

                ******************************





















































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        IV.E.2.e    Loop Constraints
                    Loop Constraints
                    Loop Constraints
                    Loop Constraints

                ********************
                *                  *
                * Loop Constraints *
                *                  *
                ********************


        Loops  in  CONGEN  are internal  bonds  allocated  to Superatoms
during the course  of structure generation.  Subsequently,  during IMBED
                                                                   IMBED
                                                                   IMBED
                                                                   IMBED
(Section  IV.G), all  such  loops will  be transformed  in  all possible
ways into intra-superatom bonds.  If the molecular formula and  the free
valence distribution of  a Superatom allow it,  additional unsaturations
in  the  form  of  rings  and double  bonds  can  be  allocated  to, and
eventually formed within, a Superatom by connection of  appropriate free
valences.   This may  or may  not be  desired.  The  important  point to
remember is  that, unless  limited by the  LOOP constraint,  CONGEN will
                                           LOOP
                                           LOOP
                                           LOOP
consider all possible  allocations of remaining degrees  of unsaturation
to every Superatom bearing more than two bonding sites (two are required
to support each  loop).  The loop  constraint type provides  a mechanism
for forcing  CONGEN to  consider only a  specified range  of occurrences
(may be none, of course) of internal bonds for specified Superatoms.

        Loops  appear  in  drawings of  intermediate  structures  as the
character "i" (for internal bond),  preceded by an integer if  more than
                   i
                   i
                   i
one  loop was  allocated to  a Superatom.   The "i"  is attached  to the
Superatom with a single bond  which acts merely as a pointer  - remember
that the loop  will eventually use two  bonding sites in  the Superatom.
Examples of how  loops may be visualized  are presented with  the CONGEN
commands DRAW (Section IV.I) and SHOW CTABLE (Section IV.J.2).
         DRAW                    SHOW CTABLE
         DRAW                    SHOW CTABLE
         DRAW                    SHOW CTABLE

        If  a  Superatom  has  free valences  on  adjacent  atoms  and a
                                                                   and
                                                                   and
                                                                   and
specified bond order between the atoms of ANY, then one way of  adding a
                                          ANY
                                          ANY
                                          ANY
loop(s) would be  to increase the bond  order, and CONGEN will  do that.
Otherwise,  addition of  loops results  only in  formation of  new rings
within the Superatom.
within
within
within

        The concept and representation of loops is discussed  in Section
I.A,  Basic CONGEN  Concepts, and  is illustrated  in the  Sample CONGEN
session, Section II.

                ******************************

        ***** Use of the Loop Constraints *****
              Use of the Loop Constraints
              Use of the Loop Constraints
              Use of the Loop Constraints


        We illustrate here examples of the form of the responses  to the
request  for loop  constraints, together  with common  error conditions,
beginning with the CONSTRAINT prompt:

CONSTRAINT:?                    Ask for help, CONGEN replies
           ?
           ?
           ?




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FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL

CONSTRAINT:loop                 Reprompt, ask for LOOP
           loop                                   LOOP
           loop                                   LOOP
           loop                                   LOOP

SUPERATOM:?                     Ask for help
          ?
          ?
          ?

THE NAME OF A DEFINED           CONGEN replies and
SUBSTRUCTURE

SUPERATOM:cyc                     reprompts
          cyc
          cyc
          cyc

RANGE OF OCCURRENCES:?          Ask for help, CONGEN replies
                     ?
                     ?
                     ?

PLEASE GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
NONE     AT LEAST X     AT MOST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL

RANGE OF OCCURRENCES:none       Reprompt, specify none
                     none
                     none
                     none

CONSTRAINT:                     Prompt for next constraint type, e.g.,
                                loop constraints on another Superatom

                ******************************

        ***** Error Conditions and CONGEN replies *****
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies

        1) Illegal input - same as for other constraints:

        2) Illegal number of loops:

CONSTRAINT:loop                 Ask for loop constraint
           loop
           loop
           loop

SUPERATOM:cyc at least 3        On one line, assume 3 loops
          cyc at least 3
          cyc at least 3
          cyc at least 3
                                  impossible, CONGEN replies

MY INFORMATION SHOWS CYC AS HAVING AT MOST 1 LOOP,
SO THERE CANNOT ALSO BE AT LEAST 3.

CONSTRAINT:                     Prompt for next constraint type

                ******************************













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        IV.E.2.f    Partial Constraint
                    Partial Constraint
                    Partial Constraint
                    Partial Constraint

                **********************
                *                    *
                * Partial Constraint *
                *                    *
                **********************


        The partial constraint is used to stop CONGEN after  a specified
number of structures have been obtained.  It can be used  in conjunction
with GENERATE, IMBED or PRUNE.  The constraint is particularly useful in
     GENERATE  IMBED    PRUNE
     GENERATE  IMBED    PRUNE
     GENERATE  IMBED    PRUNE
a  large  structural  problem  where  it  is  important  to  learn  what
structural  types  might  be  produced as  an  aid  to  incorporation of
additional  constraints  prior   to  running  the  problem   through  to
completion.  CONGEN  will stop after  producing the indicated  number of
structures with important messages about the fact that you have obtained
only a  partial structure  list.  You  can then  DRAW (Section  IV.I) or
                                                 DRAW
                                                 DRAW
                                                 DRAW
SHOW  (Section  IV.J)  them   to  see  if  additional   constraints  are
SHOW
SHOW
SHOW
required.

        If the total number of structures which can be obtained  is less
than  the  number  specified  for  the  partial   constraint,  structure
generation  proceeds  normally  to completion.   You  obtain  a complete
structure  list and  none of  the messages  from CONGEN  noted  below on
partial  structure  lists  are  output  to  you.   In  other  words, the
constraint has no effect whatsoever  and you can continue with  the rest
of the structural problem in the normal way.

        You cannot continue computation from the point where the partial
constraint  was fulfilled.   You must  begin the  GENERATE (or  PRUNE or
                                                  GENERATE      PRUNE
                                                  GENERATE      PRUNE
                                                  GENERATE      PRUNE
IMBED) again from the beginning  after a partial list has  been obtained
IMBED
IMBED
IMBED
if you wish to continue your problem to completion.

        The structures produced will not be a random sample  of possible
structural  types.   If  additional constraints  rule  out  some  of the
structures produced  to fulfill the  partial constraint,  then obtaining
the same number  of structures under  the same partial  constraint after
restarting will yield some new structures.  Two or more partial runs may
be useful in developing new constraints.

        ***** Use of the Partial Constraint *****
              Use of the Partial Constraint
              Use of the Partial Constraint
              Use of the Partial Constraint


        Here we provide an illustration of use of the partial constraint
and  the behavior  of  CONGEN after  obtaining the  specified  number of
structures, using the GENERATE  command.  We begin with  the CONSTRAINT:
                      GENERATE
                      GENERATE
                      GENERATE
prompt:

CONSTRAINT:?                    Ask for help, CONGEN replies
           ?
           ?
           ?

FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL



                                  154
CONGEN manual                                              February 1981


CONSTRAINT:partial              Reprompt - specify partial
           partial
           partial
           partial

MAXIMUM NUMBER OF STRUCTURES TO BE PRODUCED:?           Ask for help
                                            ?
                                            ?
                                            ?

AN INTEGER GREATER THAN ZERO                    CONGEN replies and

MAXIMUM NUMBER OF STRUCTURES TO BE PRODUCED:20    reprompts
                                            20
                                            20
                                            20

CONSTRAINT:                     Last constraint - begin generation

....................            Structures generated up to total of 20

20 STRUCTURES HAVE BEEN GENERATED SO FAR
                                Report by CONGEN and warning
20 STRUCTURES WERE GENERATED
!!!!! THIS IS ONLY A PARTIAL STRUCTURE LIST !!!!!

#save                           A SAVE of a partial list is OK
 save                             SAVE
 save                             SAVE
 save                             SAVE
FILE NAME:garb
SAVED ON GARB

#show status                    A SHOW STATUS reports partial list
 show status                      SHOW STATUS
 show status                      SHOW STATUS
 show status                      SHOW STATUS

!!!!! THIS IS ONLY A PARTIAL STRUCTURE LIST !!!!!
YOU CURRENTLY HAVE 20 STRUCTURES, WITH INDICES FROM #1 TO #20
        .
        .                       And so forth, with status report
        .

#restore                        A later RESTORE of SAVEd file is OK
 restore                                RESTORE    SAVE
 restore                                RESTORE    SAVE
 restore                                RESTORE    SAVE
INPUT FILE:garb
           garb
           garb
           garb
GARB RESTORED

#show status                    Status indicates partial list
 show status
 show status
 show status

!!!!! THIS IS ONLY A PARTIAL STRUCTURE LIST !!!!!
YOU CURRENTLY HAVE 20 STRUCTURES, WITH INDICES FROM #1 TO #20
        .
        .                       And so forth, with status report
        .

#imbed                          IMBED a partial list OK - warning
 imbed                          IMBED
 imbed                          IMBED
 imbed                          IMBED
SUPERATOM:cyc                     given at end, however
          cyc
          cyc
          cyc
NUMBER TO BE IMBEDDED:1
                      1
                      1
                      1
SUPERATOM:
THE 'EXPANDED' FORMULA IS O 1 C 10 H 18
CONSTRAINT:
#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
20 STRUCTURES WERE OBTAINED

!!!!! THIS IS ONLY A PARTIAL STRUCTURE LIST !!!!!

                ******************************



                                  155
CONGEN manual                                              February 1981


        IV.F    PRUNE
                PRUNE
                PRUNE
                PRUNE

                ************************
                *                      *
                * CONGEN Command PRUNE *
                *                      *
                ************************


        The  PRUNE  command  is  used to  examine  the  current  list of
             PRUNE
             PRUNE
             PRUNE
structures under a specified set  of constraints, and to throw  away all
structures which  do not  obey the  constraints.  The  structures thrown
away cannot be recovered (unless all are thrown away, in which  case the
                                 all
                                 all
                                 all
original  list,  i.e.,  the  list  prior  to  PRUNE,  of  structures  is
                                              PRUNE
                                              PRUNE
                                              PRUNE
restored).  For this reason, it is safest to use the CONGEN command SAVE
                                                                    SAVE
                                                                    SAVE
                                                                    SAVE
(Section IV.L) before  pruning a list  with constraints about  which you
are uncertain.

        If  all  constraints  could  be  applied  during  the  course of
structure  generation  or  imbedding, the  PRUNE  command  would  not be
                                           PRUNE
                                           PRUNE
                                           PRUNE
needed.  However, PRUNE is normally used frequently for two purposes:
                  PRUNE
                  PRUNE
                  PRUNE

        1)  after  examination  of a  list  of  structures  (using DRAW,
                                                                   DRAW
                                                                   DRAW
                                                                   DRAW
Section   IV.I,  or   SURVEY,   Section  IV.N),   to   remove  undesired
                      SURVEY
                      SURVEY
                      SURVEY
structures using constraints that were overlooked when the generation or
imbedding was performed; and

        2) after collection of additional data, yielding  new structural
inferences to be applied to a list of structures obtained at  an earlier
time.  These  additional constraints  would normally  be applied  to the
results  of  an  eralier  CONGEN  session  which  had  been   SAVEd  and
                                                              SAVE
                                                              SAVE
                                                              SAVE
subsequently RESTOREd (see Section IV.L and Section IV.M).
             RESTORE
             RESTORE
             RESTORE

        The  PRUNE command  works with  the same  set of  constraints as
             PRUNE
             PRUNE
             PRUNE
those  supplied for  GENERATE Section  IV.E and  IMBED Section  IV.G, as
                     GENERATE                    IMBED
                     GENERATE                    IMBED
                     GENERATE                    IMBED
illustrated below.  The user interaction is the same.

        For  each  structure tested  against  the  constraints supplied,
CONGEN shows the  result to you in  a shorthand form: 1)  each structure
which passes  is noted  by a  dot output  to your  terminal; or  2) each
structure which fails is noted  by an asterisk output to  your terminal.
Thus, there are  as many characters output  as there were  structures in
the list against which the constraints were tested.  Finally, the number
of structures resulting from the PRUNE is output, as shown below.
                                 PRUNE
                                 PRUNE
                                 PRUNE

                ******************************

        ***** Use of the PRUNE command in CONGEN *****
              Use of the PRUNE command in CONGEN
              Use of the PRUNE command in CONGEN
              Use of the PRUNE command in CONGEN

#prune                          Issue PRUNE command
 prune                                PRUNE
 prune                                PRUNE
 prune                                PRUNE

PERTINENT AROMATIC TEMPLATES: ...       If any aromatics defined, any
                                  pertinent are listed by name(s).  If



                                  156
CONGEN manual                                              February 1981


                                  none defined are pertinent, the word
                                  NONE is given.  If none defined, the
                                  NONE
                                  NONE
                                  NONE
                                  message is omitted

CONSTRAINT:?                    Ask for help, CONGEN replies with
           ?
           ?
           ?
                                  the standard response for constraints

FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL

CONSTRAINT:substructure         Illustrate for substructure constraint
           substructure
           substructure
           substructure

SUBSTRUCTURE NAME:?             Ask for help
                  ?
                  ?
                  ?

THE NAME OF A DEFINED           CONGEN replies
SUBSTRUCTURE

SUBSTRUCTURE NAME:et            Choose a substructure
                  et
                  et
                  et

RANGE OF OCCURRENCES:?          Standard request for range
                     ?
                     ?
                     ?
                                CONGEN replies

PLEASE GIVE ME A RANGE IN ONE OF THE FOLLOWING FORMS:
NONE     AT LEAST X     AT MOST X     EXACTLY X     RANGE X TO Y
WHERE X AND Y ARE POSITIVE INTEGERS (LESS THAN 100) WHICH YOU SUPPLY
THE WORDS 'AT' AND 'TO' ARE OPTIONAL

RANGE OF OCCURRENCES:at most 1          Specify the range
                     at most 1
                     at most 1
                     at most 1
CONSTRAINT:
        .
        .                       Continue with rest of constraints
        .
CONSTRAINT:                     When no more, respond with carriage
                                  return

.*.....*...*....*.*.*......*......*     CONGEN tests each structure
                                          and outputs a dot for each
                                          structure which passes, or an
                                          asterisk for each which fails,
                                          tests

27 STRUCTURES SURVIVED PRUNING          Final report on PRUNE results
                                                        PRUNE
                                                        PRUNE
                                                        PRUNE

#                               Ready for next CONGEN command

                ******************************

        ***** Error conditions and CONGEN replies *****
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies
              Error conditions and CONGEN replies


        The message PERTINENT AROMATIC TEMPLATES: may appear  after each
PRUNE  request, depending  on whether  any aromatics  are  defined.  The
PRUNE
PRUNE
PRUNE




                                  157
CONGEN manual                                              February 1981


message  is omitted  in all  examples of  error conditions,  below.  For
other  error  conditions,  see  Constraint  Input  to  Generate, Section
IV.E.2.


        1) Illegal input or error in substructure (one example):

#prune                          Issue PRUNE command
 prune                                PRUNE
 prune                                PRUNE
 prune                                PRUNE

CONSTRAINT:tr                   TR not a constraint type
           tr
           tr
           tr

TR IS NOT AN EXPECTED KEYWORD HERE      CONGEN replies

CONSTRAINT:sub                  Reprompt for constraint type
           sub
           sub
           sub

SUBSTRUCTURE NAME:uy            Assume UY undefined
                  uy                   UY
                  uy                   UY
                  uy                   UY

UY HASN'T BEEN DEFINED YET      CONGEN replies and

SUBSTRUCTURE NAME:ph            reprompts for substructure name
                  ph
                  ph
                  ph

RANGE OF OCCURRENCES:ed         ED not a legal range
                     ed         ED
                     ed         ED
                     ed         ED

ED IS NOT AN EXPECTED KEYWORD HERE      CONGEN replies and

RANGE OF OCCURRENCES:one                  reprompts for range
                     one
                     one
                     one

ONE IS NOT AN EXPECTED KEYWORD HERE

RANGE OF OCCURRENCES:at most one        Still a problem
                     at most one
                     at most one
                     at most one

I WAS EXPECTING A NUMBER                CONGEN replies and

ERASING ...ONE                            erases and

NUMBER:1                                  reprompts for number
       1
       1
       1

                                After all that, the substructure
                                  itself is in error - an example

TESTING FOR PH DOESN'T MAKE SENSE HERE BECAUSE
IT CONTAINS MORE ATOMS OF TYPES C AND H
THAN WILL BE PRESENT WHEN I APPLY THE TEST

CONSTRAINT:                     Prompt for next constraint

        2) Grievous error in constraints:

CONSTRAINT:ring 2 none          For this example, these ring
           ring 2 none
           ring 2 none
           ring 2 none
CONSTRAINT:ring 4 none            constraints can be assumed to
           ring 4 none
           ring 4 none
           ring 4 none
CONSTRAINT:ring 3 none            delete all structures - the
           ring 3 none
           ring 3 none
           ring 3 none
CONSTRAINT:ring 5 none            message is the same for all
           ring 5 none
           ring 5 none
           ring 5 none
CONSTRAINT:                       constraint types and combinations



                                  158
CONGEN manual                                              February 1981


                                  which delete all structures

***************************     Note that all structures deleted

NO STRUCTURES SURVIVED PRUNING          CONGEN notes the fact and
                                          assumes that you made an error

THE ORIGINAL LIST HAS BEEN RESTORED     CONGEN restores the original
                                          list of structures

#                               Ready for next CONGEN command - check
                                  the constraints carefully and PRUNE
                                                                PRUNE
                                                                PRUNE
                                                                PRUNE
                                  again when error found

        3) No structures in the structure list:

#prune                      Issue PRUNE command
 prune                            PRUNE
 prune                            PRUNE
 prune                            PRUNE

THERE ARE NO STRUCTURES TO PRUNE        CONGEN replies

#                               Ready for next CONGEN command

        4) No constraints given:

#prune                          Issue PRUNE command
 prune                                PRUNE
 prune                                PRUNE
 prune                                PRUNE

CONSTRAINT:                     Respond with carriage return

NO CONSTRAINTS WERE GIVEN       CONGEN replies

#                               Ready for next CONGEN command


                ******************************






















                                  159
CONGEN manual                                              February 1981


        IV.G    IMBED
                IMBED
                IMBED
                IMBED

                ************************
                *                      *
                * CONGEN Command IMBED *
                *                      *
                ************************


        The  IMBED command  is  used to  expand the  Superatom  names in
             IMBED
             IMBED
             IMBED
intermediate  structures  back   to  their  complete  identity   as  the
substructures represented by the names.  Eventually, when all Superatoms
have  been  imbedded,  final  structures  are  obtained.    During  this
procedure, additional parts of the structure become "visible"  to CONGEN
and additional substructural (and other) constraints may be applicable.

        Generally you  will have  more than one  Superatom with  a given
name,  or  several  Superatoms with  different  names,  present  in your
intermediate  structures.  Any  combination of  these Superatoms  can be
imbedded  at  one  time, up  to  and  including all  of  them.   In some
instances it  may, however, be  more efficient (i.e.,  use significantly
less  computer  time)  to  do  some  of  the  imbedding   stepwise.   In
particular,  if several  Superatoms can  be imbedded  without additional
constraints, or with constraints which apply to all of them,  then those
Superatoms  should all  be imbedded  at once.   If there  are individual
Superatoms whose imbedding requires  several constraints, it is  best to
imbed such  Superatoms individually  with their  respective constraints.
This approach  will keep the  total number of  structures passed  to the
next step as small as possible.

        If only some of many Superatoms are imbedded, CONGEN will report
a new "expanded"  molecular formula which is  the formula which  will be
possessed by structures resulting from the imbedding.  If all Superatoms
are  imbedded, the  "expanded" formula  will, in  fact, be  the original
molecular formula.   We have  referred to  such structures  elsewhere as
"final" structures.

        The imbedder  within CONGEN takes  full account  of aromaticity.
If any  aromatic templates  are defined  (see DEFINE  AROMATICS, Section
                                              DEFINE  AROMATICS
                                              DEFINE  AROMATICS
                                              DEFINE  AROMATICS
IV.B.5), IMBED checks them  against the 'expanded' formula  to determine
         IMBED
         IMBED
         IMBED
if  any are  pertinent to  the structures  which will  result  after the
requested  Superatoms are  imbedded.  A  message is  provided to  you on
which  are  pertinent  (may  be NONE).   If  no  aromatics  are defined,
                                NONE
                                NONE
                                NONE
aromaticity is not considered, and no message about  pertinent templates
            is not considered
            is not considered
            is not considered
is output.  More than one Kekule structure for an aromatic system may be
produced  if  aromaticity   is  not  considered,  leading   to  apparent
duplication in the  final structure list.  Consideration  of aromaticity
results in retention of only  one Kekule form.  Take particular  care in
defining  substructures   used  as   constraints  when   aromaticity  is
considered - substructures must have atom types of aromatic if  you wish
to test them against aromatic atoms in structures resulting  from IMBED.
                                                                  IMBED
                                                                  IMBED
                                                                  IMBED
Retention of only one Kekule form makes it dangerous to explicitly place




                                  160
CONGEN manual                                              February 1981


alternating double and single bonds in substructures used as constraints
to test  against aromatic  systems - the  substructure might  not match.
Assign bond orders of ANY to such systems.
                      ANY
                      ANY
                      ANY

        During imbedding, Loops,  or intra-superatom bonds,  are created
in any Superatom which has had loops allocated during GENERATE and which
                                                      GENERATE
                                                      GENERATE
                                                      GENERATE
is undergoing imbedding.  Further discussion of such internal  bonds can
be  found  in  Loop  Constraints,  Section  IV.E.2.e,  in  Basic  CONGEN
Concepts, Section I.A and in Imbedding in CONGEN, Section VIII.   At the
end  of  the  examples os  use  of  IMBED, below,  we  present  a simple
                                    IMBED
                                    IMBED
                                    IMBED
imbedding problem involving creation of internal bonds from loops.

        The results of imbedding are reported to you in a shorthand form
which indicates the results obtained for imbedding each structure.  As a
measure of progress as the imbedding is proceeding, a number sign (#) is
printed  for  each  of  the  original  structures  which  is  undergoing
imbedding.  Every new structure which  results is indicated to you  by a
dot  printed on  your terminal.   The number  of new,  unique structures
obtained  for  each original  structure  is simply  the  number  of dots
following th # sign.  If  no structures result due to  constraints, then
consecutive # signs will appear, for example, ###.....  . The  first two
structures yielded  no results,  while dots following  the third  # sign
indicate legal structures were obtained on imbedding.  There are ways in
which  duplicate  structures  can  be  produced  -  such  duplicates are
detected when encountered and the letter D is printed for each duplicate
(which  is  then thrown  away).   These points  are  illustrated  in the
example below.

                ******************************

        ***** Use of the IMBED command in CONGEN *****
              Use of the IMBED command in CONGEN
              Use of the IMBED command in CONGEN
              Use of the IMBED command in CONGEN


        The following is a brief summary of the sequence of commands and
responses  for  IMBED.    Detailed  descriptions  of  input   and  error
                IMBED
                IMBED
                IMBED
conditions  are  in   subsequent  sections,  Superatom   Input,  Section
IV.G.1, and Constraint Input Section IV.G.2.

#imbed                          Issue the IMBED command
 imbed                                    IMBED
 imbed                                    IMBED
 imbed                                    IMBED

SUPERATOM:?                     Ask for help (see
          ?
          ?
          ?
                                  Section IV.G.1)

THE NAME OF A DEFINED           CONGEN replies
SUBSTRUCTURE

SUPERATOM:db                    Reprompt for superatom name
          db
          db
          db

NUMBER TO BE IMBEDDED:?         Ask for help
                      ?
                      ?
                      ?

AN INTEGER GREATER THAN ZERO    CONGEN replies

NUMBER TO BE IMBEDDED:1         Reprompt for number
                      1
                      1
                      1



                                  161
CONGEN manual                                              February 1981


SUPERATOM:                      Prompt for next Superatom
        .
        .                       May be several more Superatoms
        .
SUPERATOM:                      Carriage return terminates input
                                CONGEN reports the "expanded" formula

THE 'EXPANDED' FORMULA IS C 4 PH 1 OH 1 ME 4    A report of the
                                  molecular formula of resulting
                                  structures

PERINENT AROMATIC TEMPLATES: ...        See above discussion
                                Begin constraint input
                                  (see Section IV.G.2)
CONSTRAINT:ring 7 none
           ring 7 none
           ring 7 none
           ring 7 none
        .
        .                       Input all constraints (may be none)
        .
CONSTRAINT:                     Answer prompt with carriage return
                                  when all constraints specified

                                IMBED begins
                                IMBED
                                IMBED
                                IMBED

#..#..#..#..#..#..#..#..#..#..#...#...#..#D.#D.#D.#D.#D.#D.#D.#D.#.#.#..
#.#..#DD#DD#DDD
                                One # for each structure, one dot for
                                  each resulting structure and D's for
                                  duplicates encountered and thrown
                                  away

43 STRUCTURES WERE OBTAINED     Final report of results

#                               Ready for next CONGEN command

                ******************************


        If  the  imbedding   is  simple  substitution   of  substructure
definitions for monovalent substituents, or in other cases where exactly
one structure is obtained for each imbedding, the output would appear as
follows:

#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
#.#.#.#.#.#.#.
43 STRUCTURES WERE OBTAINED     Final report of results

#                               Ready for next CONGEN command

                ******************************

        ***** Loops and their Treatment During Imbedding *****
              Loops and their Treatment During Imbedding
              Loops and their Treatment During Imbedding
              Loops and their Treatment During Imbedding





                                  162
CONGEN manual                                              February 1981


        We  illustrate the  treatment of  loops, or  internal  bonds, or
intra-superatom bonds  with a simple  example.  Keep in  mind that  in a
more  complex problem  there may  be several  Superatoms  bearing loops.
However,  the  representation  and  results  of  imbedding  parallel the
example no matter how many Superatoms are involved.

        For this example, assume the molecular formula is C6H6 and there
is  one Superatom,  defined  to be  a  six-membered ring  with  one free
valence on each  carbon atom.  The  complete definition is  included for
illustration, from the point immediately after starting CONGEN:

#def mol c 6 h 6                        Define molecular formula
 def mol c 6 h 6
 def mol c 6 h 6
 def mol c 6 h 6
MOLECULAR FORMULA DEFINED
#def s r6                               Define substructure R6
 def s r6                                                   R6
 def s r6                                                   R6
 def s r6                                                   R6
(NEW SUBSTRUCTURE)
>ring 6                                 Note that all bonds left
 ring 6
 ring 6
 ring 6
>freev 1 1 2 1 3 1 4 1 5 1 6 1            as single.  Therefore, the
 freev 1 1 2 1 3 1 4 1 5 1 6 1
 freev 1 1 2 1 3 1 4 1 5 1 6 1
 freev 1 1 2 1 3 1 4 1 5 1 6 1
>draw a                                   bond orders cannot be
 draw a
 draw a
 draw a
                                             increased during imbedding
SUBSTRUCTURE R6:


    |  /
    C-C
   /  |
 -C   C-
  |  /
  C-C
 /  |


>done
 done
 done
 done
R6 DEFINED
#generate                               Issue GENERATE command
 generate                                     GENERATE
 generate                                     GENERATE
 generate                                     GENERATE
SUPERATOM:r6 at least 1                 Only one Superatom, R6
          r6 at least 1                                     R6
          r6 at least 1                                     R6
          r6 at least 1                                     R6
SUPERATOM:
'COLLAPSED' FORMULA IS R6 1
CONSTRAINT:                             No constraints
.
1 STRUCTURE WAS GENERATED               Only one structure, R6 with
                                                            R6
                                                            R6
                                                            R6
#draw a 1                                 three internal bonds -
 draw a 1
 draw a 1
 draw a 1
                                          draw it
#1:

R6-3i                                   Note that "3i" represent the
                                                   3i
                                                   3i
                                                   3i
                                          three internal bonds, or loops
#imbed                                  Now, IMBED R6
 imbed                                       IMBED R6
 imbed                                       IMBED R6
 imbed                                       IMBED R6
SUPERATOM:r6 1
          r6 1
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                           ALL
                                                           ALL
                                                           ALL
                                          properly!
   ---C
C--    \|\
=      | \C
=       ||\
=        |\
=       ||\
=      | /C
C---   |//
    --C

#3:

C-C-C
= | =
C-C-C

#4:

C---C
|\  |\
| C--|-C
|/  |/
C---C

























                                  165
CONGEN manual                                              February 1981


#5:

  C-C
 /|/|
C--|/-C
|/|/
C-C

#                                       Ready for next CONGEN command















































                                  166
CONGEN manual                                              February 1981


        IV.G.1    Superatom Input
                  Superatom Input
                  Superatom Input
                  Superatom Input

                ****************************
                *                          *
                * Superatom Input to IMBED *
                *                          *
                ****************************


        The input  sequence for Superatoms  within the IMBED  command is
                                                       IMBED
                                                       IMBED
                                                       IMBED
straightforward.  IMBED requests the name and number of Superatoms to be
                  IMBED
                  IMBED
                  IMBED
imbedded.

        If  you answer  carriage return  to the  NUMBER TO  BE IMBEDDED:
prompt, all Superatoms with the specified name will be imbedded.

        Error checking involves only the existence of the given name and
                                only
                                only
                                only
number of  a Superatom in  intermediate structures.  If  Superatoms have
been redefined, or  if the redefinitions  have introduced errors  of the
types described under Superatom Input to GENERATE, Section  IV.E.1, then
                                         GENERATE
                                         GENERATE
                                         GENERATE
you are potentially in trouble and will get incorrect structures. Please
do  not,  for  your  own  safety,  attempt  to  redefine  a substructure
subsequent to generation.   CONGEN will allow you  to do so but  only if
you ignore an error message to the effect that redefinition is dangerous
(see the CONGEN command FIX, Section IV.C).
                        FIX
                        FIX
                        FIX

                ******************************

        ***** Example of Superatom Input to IMBED *****
              Example of Superatom Input to IMBED
              Example of Superatom Input to IMBED
              Example of Superatom Input to IMBED


        Assume that  the structure generation  yielded 29  structures as
indicated by the output from  GENERATE.  One such structure is  drawn so
                              GENERATE
                              GENERATE
                              GENERATE
that the  Superatom names are  obvious.  DB is  a double bond,  ME's are
                                         DB                     ME
                                         DB                     ME
                                         DB                     ME
methyl groups, OH  is an hydroxyl  group and PH  is a phenyl  group. The
               OH                            PH
               OH                            PH
               OH                            PH
status of the problem prior to imbedding is given below using the CONGEN
command SHOW, subcommand STATUS (see Section IV.J.3).
        SHOW             STATUS
        SHOW             STATUS
        SHOW             STATUS

.............................   Results from structure generation
29 STRUCTURES WERE GENERATED

#draw atnamed 1                 Draw the first structure
 draw atnamed 1
 draw atnamed 1
 draw atnamed 1

#1:

  PH    ME
   |  D |
OH-C--B=C
  /   |  \
ME   ME   ME

#show status                    SHOW STATUS, CONGEN replies with
 show status                    SHOW STATUS
 show status                    SHOW STATUS
 show status                    SHOW STATUS
                                  report (see Section IV.J.3)



                                  167
CONGEN manual                                              February 1981


YOU CURRENTLY HAVE 29 STRUCTURES, WITH INDICES FROM  1 TO  29

SUPERATOMS TO BE IMBEDDED: ME(4) OH(1) PH(1) DB(1)      Note report on
                                          Superatoms remaining

CURRENT DEFINITIONS:
ATOMS(VALENCES IN PARENTHESES): H(1) C(4) N(3) O(2)
SUBSTRUCTURES: ME ET OH PH C=C DB

AROMATIC TEMPLATES:BENZENE

MOLECULAR FORMULA IS C 14 H 18 O 1

#save                           Save the session before beginning
 save
 save
 save
                                  (see Section IV.L)
FILE NAME:garb.tst              Specify file name
          garb.tst
          garb.tst
          garb.tst

SAVED ON GARB.TST               CONGEN replies

#imbed                          Begin IMBED sequence
 imbed                                IMBED
 imbed                                IMBED
 imbed                                IMBED

SUPERATOM:?                     Ask for help
          ?
          ?
          ?

THE NAME OF A DEFINED           CONGEN replies
SUBSTRUCTURE

SUPERATOM:db                    Choose DB
          db                           DB
          db                           DB
          db                           DB

NUMBER TO BE IMBEDDED:?         Ask for help
                      ?
                      ?
                      ?

AN INTEGER GREATER THAN ZERO    CONGEN replies

NUMBER TO BE IMBEDDED:1         Reprompt for number
                      1
                      1
                      1

SUPERATOM:                      Carriage return - no more Superatoms
                                  specified

PERTINENT AROMATIC TEMPLATES:NONE       None pertinent yet - PH
                                                             PH
                                                             PH
                                                             PH
                                  remains unimbedded

THE 'EXPANDED' FORMULA IS C 4 PH 1 OH 1 ME 4    Report of expanded
                                                  formula

CONSTRAINT:                     No constraints specified

#..#..#..#..#..#..#..#..#..#..#...#...#..#D.#D.#D.#D.#D.#D.#D.#D.#.#.#..
#.#..#DD#DD#DDD            Output as IMBED is computing
                                     IMBED
                                     IMBED
                                     IMBED

43 STRUCTURES WERE OBTAINED     Final report of results

#                               Ready for next CONGEN command

#show status                    Show new status, CONGEN replies
 show status
 show status
 show status



                                  168
CONGEN manual                                              February 1981


YOU CURRENTLY HAVE 43 STRUCTURES, WITH INDICES FROM  1 TO  43

SUPERATOMS TO BE IMBEDDED: ME(4) OH(1) PH(1)

CURRENT DEFINITIONS:
ATOMS(VALENCES IN PARENTHESES): H(1) C(4) N(3) O(2)
SUBSTRUCTURES: ME ET OH PH C=C DB

AROMATIC TEMPLATES:BENZENE

MOLECULAR FORMULA IS C 14 H 18 O 1

#draw atnamed 22                Draw a specified structure as an
 draw atnamed 22
 draw atnamed 22
 draw atnamed 22
                                  example to illustrate remaining
#22:                              Superatoms

  ME   ME
    \ /
     C
    / \
PH-C   C-OH
  / \ =
ME   C
      \
       ME

#imbed                          Imbed two of the ME's
 imbed                                           ME
 imbed                                           ME
 imbed                                           ME

SUPERATOM:me 2
          me 2
          me 2
          me 2

SUPERATOM:                      Carriage return - no more Superatoms
                                  specified

THE 'EXPANDED' FORMULA IS C 6 PH 1 OH 1 ME 2 H 6        New formula

PERTINENT AROMATIC TEMPLATES:NONE

CONSTRAINT:                     No constraints specified

#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
#.#.#.#.#.#.#                   Report as IMBED computes
                                          IMBED
                                          IMBED
                                          IMBED

43 STRUCTURES WERE OBTAINED     Final report of results

#                               Ready for next CONGEN command

#imbed me                       Imbed all remaining Superatoms
 imbed me
 imbed me
 imbed me
                                   at one time
NUMBER TO BE IMBEDDED:          Answer carriage return, CONGEN replies
I'LL IMBED THE 2 REMAINING ME'S
SUPERATOM:ph 1
          ph 1
          ph 1
          ph 1
SUPERATOM:oh 1
          oh 1
          oh 1
          oh 1
SUPERATOM:



                                  169
CONGEN manual                                              February 1981


THE 'EXPANDED' FORMULA IS O 1 C 14 H 18         Back to original mol-
                                                  ecular formula

PERTINENT AROMATIC TEMPLATES:BENZENE    Now, benzene template is
                                          pertinent

CONSTRAINT:                     No constraints

#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.#.
#.#.#.#.#.#.#.                  Report while computing

43 STRUCTURES WERE OBTAINED     Final report of IMBED
                                                IMBED
                                                IMBED
                                                IMBED

#                               Ready for next CONGEN command

#draw atnamed 30                Draw one result - note that you
 draw atnamed 30
 draw atnamed 30
 draw atnamed 30
                                  now have final structures
#30:

      O  C    C-C
      |  |   =   =
C-C---C--C--C     C
   = /   |   \   /
    C    C    C=C
    |
    C

                ******************************

        ***** Error Conditions and CONGEN replies *****
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies

#imbed                          Issue IMBED command
 imbed                                IMBED
 imbed                                IMBED
 imbed                                IMBED

SUPERATOM:12                    Number illegal as name
          12
          12
          12

I WAS EXPECTING A WORD          CONGEN replies and

SUPERATOM:ert                     reprompts - assume ERT undefined
          ert                                        ERT
          ert                                        ERT
          ert                                        ERT

ERT HASN'T BEEN DEFINED YET     CONGEN replies and

SUPERATOM:c=c                     reprompts - assume C=C defined but
          c=c                                        C=C
          c=c                                        C=C
          c=c                                        C=C

THERE AREN'T ANY C=C'S LEFT       not Superatom in current structures

SUPERATOM:me                    Legal input but
          me
          me
          me

NUMBER TO BE IMBEDDED:5           too many specified
                      5
                      5
                      5

THERE ARE ONLY 4 ME'S LEFT      CONGEN replies and

NUMBER TO BE IMBEDDED:-2        reprompts - negative number illegal
                      -2
                      -2
                      -2




                                  170
CONGEN manual                                              February 1981


THIS QUANTITY SHOULD BE GREATER THAN ZERO

NUMBER TO BE IMBEDDED:2         Legal input, and can add more if
                      2
                      2
                      2
SUPERATOM:me                      still enough Superatoms of that
          me
          me
          me
NUMBER TO BE IMBEDDED:2           type in structures
                      2
                      2
                      2
SUPERATOM:me                    But eventually they are used up
          me
          me
          me
THERE AREN'T ANY ME'S LEFT      CONGEN replies and
SUPERATOM:                        reprompts for next Superatom

                ******************************














































                                  171
CONGEN manual                                              February 1981


        IV.G.2    Constraint Input
                  Constraint Input
                  Constraint Input
                  Constraint Input

                *****************************
                *                           *
                * Constraint Input to IMBED *
                *                           *
                *****************************


        The IMBED command has the facility for use of  constraints while
            IMBED
            IMBED
            IMBED
imbedding,  so  that  the  results  of  the  imbedding   obey  available
constraints.  The menu of  available constraints is exactly the  same as
that for Constraint Input to  GENERATE, Section IV.E.2, as is  the error
                              GENERATE
                              GENERATE
                              GENERATE
checking on such constraints.  For  this reason we only note  the prompt
for constraints and that the same menu is available.

                ******************************

        ***** Example of Constraint Input to IMBED *****
              Example of Constraint Input to IMBED
              Example of Constraint Input to IMBED
              Example of Constraint Input to IMBED

        Assume IMBED command was issued and all Superatom input has
               IMBED
               IMBED
               IMBED
been specified:

CONSTRAINT:?                    Constraint prompt - ask for help
           ?
           ?
           ?
                                  CONGEN replies with standard
                                  selection of constraints

FIRST, I NEED TO KNOW THE CONSTRAINT TYPE, ONE OF THE FOLLOWING:
SUBSTRUCTURE PROTON RING LOOP PARTIAL

CONSTRAINT:                     Reprompt for constraint type - if none,
                                  respond with carriage return.  When
                                  all constraints specified, answer
                                  the prompt with a carriage return to
                                  begin imbedding

                ******************************



















                                  172
CONGEN manual                                              February 1981


        IV.H    AROMATIZE
                AROMATIZE
                AROMATIZE
                AROMATIZE

                ****************************
                *                          *
                * CONGEN Command AROMATIZE *
                *                          *
                ****************************


        The AROMATIZE command  is used to  convert a list  of structures
            AROMATIZE
            AROMATIZE
            AROMATIZE
into a  new list  in which  the current  definition of  aromaticity (see
DEFINE  AROMATICS, Section  IV.B.5, and  Aromaticity in  CONGEN, Section
DEFINE  AROMATICS
DEFINE  AROMATICS
DEFINE  AROMATICS
IX) has  been taken  into account.   This command  is required  in order
to  remove  "resonance duplicates"  from  a list  of  structures  and to
associate with appropriate atoms the aromatic property.

        Resonance duplicates are  structures which are  duplicates which
arise in CONGEN when the resonating nature of alternate double  bonds in
aromatic systems has  not been taken  into account.  The  duplication is
manifested in generation of all of the possible Kekule structures for an
aromatic system (assuming constraints have not ruled out some  of them).
The same substitution pattern on two (or more) different Kekule forms of
a  structure will  be  regarded by  CONGEN as  two  different structures
unless  aromaticity  has  been  defined to  CONGEN  and  applied  to the
structures.  Structures #12 and  #20 in the example below  represent the
kind of duplication which can arise.

        The structure generator itself applies the current definition of
aromaticity to structures which are being generated, but does  not check
for resonance  duplicates.  Thus, it  is possible to  generate resonance
duplicates in some problems Another way of obtaining such  duplicates is
to  complete a  structural problem,  at least  through the  imbedding of
Superatoms  which   may  have   aromatic  character,   without  defining
aromaticity.  In either  case, the AROMATIZE  command can be  issued and
                                   AROMATIZE
                                   AROMATIZE
                                   AROMATIZE
such  duplicates removed  under the  current definition  of aromaticity.
CONGEN retains only one of the possible Kekule forms  when aromatization
takes place.

        It is possible to change the definition of aromaticity  part way
through a structural problem.  If the change is from no definition  to a
specified set of templates  (Section IV.B.5), CONGEN notes that  the new
definition will not be taken into account on the current  structure list
until you  ask to aromatize  it, or perform  another imbedding.   If the
change is from one definition  to another, or none, you are  warned that
the new definition may conflict with the old one, and  Kekule structures
which  were removed  as  duplicates under  the old  definition  might be
regarded  as unique  structures under  the new  definition.   You cannot
                                                              You cannot
                                                              You cannot
                                                              You cannot
recover  structures removed  in this  way without  repeating  the entire
recover  structures removed  in this  way without  repeating  the entire
recover  structures removed  in this  way without  repeating  the entire
recover  structures removed  in this  way without  repeating  the entire
structure generation.
structure generation
structure generation
structure generation

                ******************************

        ***** Use of the AROMATIZE Command in CONGEN *****
              Use of the AROMATIZE Command in CONGEN
              Use of the AROMATIZE Command in CONGEN
              Use of the AROMATIZE Command in CONGEN



                                  173
CONGEN manual                                              February 1981


        The use of  the AROMATIZE command  is illustrated with  a sample
                        AROMATIZE
                        AROMATIZE
                        AROMATIZE
problem.  Assume  that the  following list  of structures  was produced,
either  by GENERATE  (see  Section IV.E),  or by  a  GENERATE/IMBED (see
           GENERATE                                  GENERATE/IMBED
           GENERATE                                  GENERATE/IMBED
           GENERATE                                  GENERATE/IMBED
Section  IV.G) sequence,  with no  definition of  aromaticity.   In this
                               no
                               no
                               no
problem, this resulted in structures which are duplicates chemically due
to the aromatic nature of the benzene ring.  Application  of constraints
using  the  PRUNE (see  Section  IV.F) command  led  to  ten structures,
            PRUNE
            PRUNE
            PRUNE
reported as follows:

        .
        .
        .
10 STRUCTURES SURVIVED PRUNING

#draw a (1 10)                  Draw (see Section IV.I) all ten
 draw a (1 10)
 draw a (1 10)
 draw a (1 10)

#11:

OH
  \
   C--C   ME
   =   = /
   =    C
   C    |
    \   C
     \ =
      C
      |
     ME

#12:

ME
  \
   C=C
   |  \
ME-C   C-OH
    =  =
     C-C

















                                  174
CONGEN manual                                              February 1981


#14:

           OH
          /
      C==C
     /   |
    /    |
ME-C     C-ME
    =   =
     C-C

#15:

  ME
    \
     C=C
    /   \
OH-C     C-ME
    =   =
     C-C

#104:

     C
    / =
   C   C
   =   |
ME-C   C-OH
    \ =
     C
     |
    ME

#105:

     C
    / =
   C   C
   =   |
ME-C   C-ME
    \ =
     C
     |
    OH












                                  175
CONGEN manual                                              February 1981


#107:                           Note that this is a duplicate of
                                  structure #15
  ME
    \
     C-C
    =   =
OH-C     C-ME
    \   /
     C=C

#108:                           Note that this is a duplicate of
                                  structure #14
           OH
          /
      C--C
     =   =
    =    =
ME-C     C-ME
    \   /
     C=C

#118:                           Note that this is a duplicate of
                                  structure #104
     C
    = \
   C   C
   |   =
ME-C   C-OH
    = /
     C
     |
    ME

#120:                           Note that this is a duplicate of
                                  structure #12
ME
  \
   C-C
   =  =
ME-C   C-OH
    \  |
     C=C

#define aromatics               Issue the DEFINE AROMATICS command
 define aromatics                         DEFINE AROMATICS
 define aromatics                         DEFINE AROMATICS
 define aromatics                         DEFINE AROMATICS
                                CONGEN replies, warning that the
                                  new definition has not yet had
                                  any effect on the structures

OK, BUT YOUR STRUCTURES WILL NOT REFLECT ANY CHANGES IN AROMATICS
UNTIL YOU AROMATIZE (OR IMBED) THEM.

SHALL I PROCEED ANYWAY?:y       Answer yes
                        y
                        y
                        y




                                  176
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TEMPLATES TO BE CONSIDERED AROMATIC:benzene     Request just benzene
                                    benzene
                                    benzene
                                    benzene
AROMATICS DEFINED                                 template
#                               Ready for next CONGEN command

#aromatize                      Issue the AROMATIZE command
 aromatize                                AROMATIZE
 aromatize                                AROMATIZE
 aromatize                                AROMATIZE

PERTINENT AROMATIC TEMPLATES:BENZENE    CONGEN reminds you after
                             BENZENE
                             BENZENE
                             BENZENE
                                          checking that template is
                                          applicable
......DDDD                      Report from CONGEN - note the last
6 STRUCTURES WERE OBTAINED        four structures were duplicates and
                                  were eliminated

                ******************************

        ***** Error Conditions and CONGEN replies *****
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies
              Error Conditions and CONGEN replies


        The following error conditions  are in the context of  the above
example:

        1) No definition of aromatics:

#aromatize                      Issue aromatize command
 aromatize
 aromatize
 aromatize
YOU HAVE NO AROMATIC TEMPLATES DEFINED.         CONGEN replies
#                               Ready for next CONGEN command

        2) Aromatics defined, but no templates currently pertinent
(assume, for example, the aromatics list contained pyridine, not
benzene):

#aromatize                      Issue aromatize command
 aromatize
 aromatize
 aromatize
PERTINENT AROMATIC TEMPLATES:NONE               CONGEN replies
(AROMATIIZE COMMAND IGNORED)
#                               Ready for next CONGEN command

        3) Attempt to change the definition of aromaticity in the
middle of a problem:

#fix aromatics                  Issue the FIX AROMATICS command
 fix aromatics                            FIX AROMATICS
 fix aromatics                            FIX AROMATICS
 fix aromatics                            FIX AROMATICS
                                CONGEN replies with warning

OK, BUT YOUR STRUCTURES WILL NOT REFLECT ANY CHANGES IN AROMATICS
UNTIL YOU AROMATIZE (OR IMBED) THEM.  ALSO, I MAY HAVE DISCARDED
'DUPLICATE' KEKULE STRUCTURES USING THE CURRENT AROMATICS LIST

SHALL I PROCEED ANYWAY?:y       Request by CONGEN for continuing
                        y
                        y
                        y

TEMPLATES TO BE CONSIDERED AROMATIC:pyridine    Select new template
                                    pyridine
                                    pyridine
                                    pyridine

AROMATICS REDEFINED             CONGEN replies
#                               Ready for next CONGEN command




                                  177
CONGEN manual                                              February 1981


        4) No structures to aromatize

#forget (1 6)                   Forget the six
 forget (1 6)
 forget (1 6)
 forget (1 6)

FORGETTING #1 #2 #3 #4 #5 #6            CONGEN replies
SHALL I REALLY FORGET?:y        and asks for confirmation
                       y
                       y
                       y

#aromatize                      Ask to aromatize
 aromatize
 aromatize
 aromatize

THERE ARE NO STRUCTURES TO AROMATIZE    No structures

#                               Ready for next CONGEN command

                ******************************










































                                  178
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        IV.I    DRAW
                DRAW
                DRAW
                DRAW

                ***********************
                *                     *
                * CONGEN Command DRAW *
                *                     *
                ***********************


        The DRAW command is used to print drawings of your structures or
            DRAW
            DRAW
            DRAW
substructures on  your computer terminal.   The CONGEN command  uses the
same structure drawing program as described under the description of the
Editstruc command  DRAW (see  Section IV.B.6.d).   Both commands  can be
                   DRAW
                   DRAW
                   DRAW
used  to  produce  drawings   with  atom  names  (ATNAMED)   or  numbers
                                                  ATNAMED
                                                  ATNAMED
                                                  ATNAMED
(NUMBERED).   However, the  CONGEN command  DRAW is  much  more flexible
 NUMBERED                                   DRAW
 NUMBERED                                   DRAW
 NUMBERED                                   DRAW
because it can be used to draw any previously defined  substructures and
any  selection of  structures in  the current  list of  structures.  The
available methods for selecting drawings are described below.

        Occasionally,  structures  may  be  drawn  in  an  unitelligible
format.  This is an inherent limitation in the teletype drawing program.
To aid in interpretation of such structures, use the CONGEN command SHOW
                                                                    SHOW
                                                                    SHOW
                                                                    SHOW
CTABLE, Section IV.J.2.
CTABLE
CTABLE
CTABLE

        There are two ways to specify structures to be drawn from a list
of structures.  The first is simply by number; using the numbers n,m,...
                                                                 n m
                                                                 n m
                                                                 n m
gives you drawings of the  nth, mth,... structure in the list.   After a
                           nth  mth
                           nth  mth
                           nth  mth
structure  generation  or  imbedding, these  numbers  correspond  to the
actual  numbers associated  with the  structures (see  the  headings for
structure  drawings, below).   However, after  pruning a  structure list
some structures will have been removed.  Thus, the nth structure  in the
                                                   nth
                                                   nth
                                                   nth
resulting list  after pruning may  no longer be  structure #n,  but some
                                                            n
                                                            n
                                                            n
number  greater than  n.   You can  follow  the fate  of  any particular
                      n
                      n
                      n
structure  number during  pruning by  asking to  DRAW it  by  its actual
                                                 DRAW
                                                 DRAW
                                                 DRAW
number,  which  will  remain associated  with  the  structure.   This is
illustrated below.

        Structures produced by  GENERATE may have Loops  associated with
                                GENERATE
                                GENERATE
                                GENERATE
them.  These loops are internal bonds which will subsequently  be placed
during  IMBED. (For  further discussion,  see Loop  Constraints, Section
        IMBED
        IMBED
        IMBED
IV.E.2.e, IMBED, Section IV.G,  and Imbedding in CONGEN,  Section VIII).
          IMBED
          IMBED
          IMBED
The appearance of loops in structure drawings is illustrated at  the end
of the following section on use of the DRAW command.
                                       DRAW
                                       DRAW
                                       DRAW

                ******************************

        ***** Use of the DRAW Command in CONGEN *****
              Use of the DRAW Command in CONGEN
              Use of the DRAW Command in CONGEN
              Use of the DRAW Command in CONGEN

#draw                           Issue the DRAW command
 draw                                     DRAW
 draw                                     DRAW
 draw                                     DRAW

TYPE OF DRAWING:?               Ask for help
                ?
                ?
                ?

NUMBERED ATNAMED                CONGEN replies and



                                  179
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TYPE OF DRAWING:atnamed           reprompts for type
                atnamed
                atnamed
                atnamed

ITEMS TO BE DRAWN:?             Ask for help, CONGEN replies
                  ?
                  ?
                  ?

PLEASE TYPE ONE OR MORE ENTRIES IN ANY OF THE FOLLOWING FORMS:

    THE NAME OF A DEFINED SUBSTRUCTURE

OR: AN INTEGER N, INDICATING THE NTH STRUCTURE IN YOUR CURRENT LIST

OR: A PAIR OF INTEGERS IN PARENTHESES, E.G. (1 10); (M N) INDICATES A
    RANGE OF THE MTH THROUGH THE NTH STRUCTURES IN YOUR CURRENT LIST

OR: A # FOLLOWED BY AN INTEGER (E.G. #3) INDICATING THE STRUCTURE WHICH
    IS 'ATTACHED' TO THE INDEX N (THIS INDEX IS PRINTED IN DRAWINGS)

OR: A PAIR (#M #N) INDICATING A THE RANGE OF STRUCTURES ASSOCIATED WITH
    INDICES M THROUGH N

ITEMS TO BE DRAWN:db            Reprompt for items - specify a
                  db
                  db
                  db
                                  substructure, DB
                                                DB
                                                DB
                                                DB

SUBSTRUCTURE DB:                CONGEN draws it

C=C

#                               Ready for next CONGEN command

#draw atnamed ph db             Two substructures, on one line
 draw atnamed ph db
 draw atnamed ph db
 draw atnamed ph db
                                CONGEN draws both
SUBSTRUCTURE PH:

    C-C
   =   =
 -C     C
   \   /
    C=C

SUBSTRUCTURE DB:

C=C

#draw atnamed 1 10 29           A selection of structures
 draw atnamed 1 10 29
 draw atnamed 1 10 29
 draw atnamed 1 10 29

#1:

  PH    ME
   |  D |
OH-C--B=C
  /   |  \
ME   ME   ME

#10:



                                  180
CONGEN manual                                              February 1981


       OH          PH
        \         /
         \       /
          \     /
           \   /
            \ /
             C
            /|
           / |
          /  |
         /   |
        /    |
ME-----C----DB-----ME
      /      |
     /       |
    /        |
   /         |
  /          |
 ME          ME


#29:

ME  ME    PH
  \  |  D/
   C=C--B-ME
   |    |
  ME   OH

#draw a (1 3)                   A range of structures
 draw a (1 3)
 draw a (1 3)
 draw a (1 3)
                                  including numbers one through three
#1:                              in the structure list

  PH    ME
   |  D |
OH-C--B=C
  /   |  \
ME   ME   ME

#2:

  PH    OH
   |  D |
ME-C--B=C
  /   |  \
ME   ME   ME

#3:

  PH    ME
   |  D |
ME-C--B=C
  /   |  \



                                  181
CONGEN manual                                              February 1981


ME   OH   ME

                                Assume that PRUNE was used to remove
                                            PRUNE
                                            PRUNE
                                            PRUNE
..*..*....*.*..*.*..*..*.*..*   certain undesired structures from the
                                list of 29, above
19 STRUCTURES SURVIVED PRUNING  Final report from PRUNE
                                                  PRUNE
                                                  PRUNE
                                                  PRUNE

#draw numbered 2 3              Now the 2nd and 3rd structures
 draw numbered 2 3
 draw numbered 2 3
 draw numbered 2 3
                                are structure #'s 2 and 4
#2:
NON-C ATOMS: 3->DB, 4->PH, 5->OH, 6->ME, 7->ME, 8->ME, 9->ME

  4    5
  |    |
6-1--3=2
 /   |  \
7    9   8

#4:
NON-C ATOMS: 3->DB, 4->PH, 5->OH, 6->ME, 7->ME, 8->ME, 9->ME

  5    4
  |    |
6-1--3=2
 /   |  \
7    9   8

#draw a (1 3)                   Draw a range - note differences
 draw a (1 3)
 draw a (1 3)
 draw a (1 3)
                                between range and actual structure #'s
#1:

  PH    ME
   |  D |
OH-C--B=C
  /   |  \
ME   ME   ME

#2:

  PH    OH
   |  D |
ME-C--B=C
  /   |  \
ME   ME   ME

#4:

  OH    PH
   |  D |
ME-C--B=C
  /   |  \
ME   ME   ME




                                  182
CONGEN manual                                              February 1981


#draw a #1 (#2 #4)              Draw by structure #
 draw a #1 (#2 #4)
 draw a #1 (#2 #4)
 draw a #1 (#2 #4)

#1:

  PH    ME
   |  D |
OH-C--B=C
  /   |  \
ME   ME   ME

#2:

  PH    OH
   |  D |
ME-C--B=C
  /   |  \
ME   ME   ME

#4:                             Note that #3 not drawn although it is
                                  in designated range - it was pruned
  OH    PH                        away - see above
   |  D |
ME-C--B=C
  /   |  \
ME   ME   ME

#draw a ph 13 (4 5) #5 (#7 #9)          Draw many different
 draw a ph 13 (4 5) #5 (#7 #9)
 draw a ph 13 (4 5) #5 (#7 #9)
 draw a ph 13 (4 5) #5 (#7 #9)
                                          things, all on one line
#5:

  ME    PH
   |  D |
ME-C--B=C
  /   |  \
ME   ME   OH

#7:

  OH    ME
   |  D |
ME-C--B=C
  /   |  \
ME   PH   ME

#8:

  ME    OH
   |  D |
ME-C--B=C
  /   |  \
ME   PH   ME

#9:



                                  183
CONGEN manual                                              February 1981


       ME          PH
        \         /
         \       /
          \     /
           \   /
            \ /
             C
            /|
           / |
          /  |
         /   |
        /    |
OH-----C----DB-----ME
      /      |
     /       |
    /        |
   /         |
  /          |
 ME          ME


#19:

  OH   PH
   |    |
ME-C--C=DB
  /   |  \
ME   ME   ME

SUBSTRUCTURE PH:

    C-C
   =   =
 -C     C
   \   /
    C=C
        ***** Representation of Loops in Drawings *****
              Representation of Loops in Drawings
              Representation of Loops in Drawings
              Representation of Loops in Drawings

        Assume the following simple problem was defined to CONGEN.  This
problem reults in intermediate structures with from zero to three loops.
A drawing of two of each type is included for illustration:

#def m c 8 h 10                         Define molecular formula
 def m c 8 h 10
 def m c 8 h 10
 def m c 8 h 10
MOLECULAR FORMULA DEFINED
#def s r6                               Define substructure R6
 def s r6                                                   R6
 def s r6                                                   R6
 def s r6                                                   R6
(NEW SUBSTRUCTURE)
>ring 6
 ring 6
 ring 6
 ring 6
>done
 done
 done
 done
R6 DEFINED
#generate                               Generate structures
 generate
 generate
 generate
SUPERATOM:r6 at least 1
          r6 at least 1
          r6 at least 1
          r6 at least 1
SUPERATOM:
'COLLAPSED' FORMULA IS C 2 R6 1 H 10



                                  184
CONGEN manual                                              February 1981


CONSTRAINT:
...................
19 STRUCTURES WERE GENERATED
#draw a 1 2 4 5 8 13 17 19              Draw selected results
 draw a 1 2 4 5 8 13 17 19
 draw a 1 2 4 5 8 13 17 19
 draw a 1 2 4 5 8 13 17 19

#1:                                     Zero loops

C-R6
 #|
  C

#2:                                     One loop

C#C-R-i
    6

#4:                                     One loop

    C
   /=
i-R-C
  6

#5:                                     Zero loops

C=R6
 \=
  C

#8:                                     Two loops

C=C-R-2i
    6

#13:                                    Two loops

     C
    /|
2i-R-C
   6

#17:                                    Three loops

C-C-R-3i
    6

#19:                                    Three loops

     C
    /
3i-R6
   |
   C



                                  185
CONGEN manual                                              February 1981


#                                       Ready for next CONGEN command

                ******************************

        ***** Error Conditions and CONGEN Replies *****
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies

        1) Illegal type (not atnamed or numbered):

#draw s                         S not a legal selection
 draw s                         S
 draw s                         S
 draw s                         S

S IS NOT AN EXPECTED KEYWORD HERE       CONGEN replies and
ERASING ...S                              erases and
TYPE OF DRAWING:                          reprompts for type

        2) Non-existent substructure or structure:

#draw a gh                      Assume GH not defined
 draw a gh                             GH
 draw a gh                             GH
 draw a gh                             GH
GH ISN'T DEFINED                CONGEN replies and
ERASING ...GH                     erases and
ITEMS TO BE DRAWN:34 35           reprompts for items - 34,35
                  34 35
                  34 35
                  34 35
                                  larger than length of structure list

I'LL USE 19 INSTEAD OF 34       CONGEN chooses last structure in list
I'LL USE 19 INSTEAD OF 35         for both, but draws only one copy

#28:                            Note that the 19th structure in the
                                  list is structure #28
ME  OH    PH
  \  |  D/
   C=C--B-ME
   |    |
  ME   ME

#draw a #3                      Structure #3 pruned away earlier
 draw a #3
 draw a #3
 draw a #3
EMPTY STRUCTURE RANGE           CONGEN replies and
#                                 returns to CONGEN prompt

#draw atnamed #31               Structure #31 beyond end of list
 draw atnamed #31
 draw atnamed #31
 draw atnamed #31
I'LL USE #28 INSTEAD OF #31     CONGEN chooses last structure

#28:

ME  OH    PH
  \  |  D/
   C=C--B-ME
   |    |
  ME   ME

        3) Invalid range:

#draw a (3 1)                   Range inverted
 draw a (3 1)
 draw a (3 1)
 draw a (3 1)

INCORRECT OR INCOMPLETE RANGE - TYPE ? FOR HELP



                                  186
CONGEN manual                                              February 1981


ERASING ...1)                   CONGEN replies and erases and
ITEMS TO BE DRAWN:                reprompts - note erasure misleading
                                  because all line erased

#draw a (1 #4)                  Range of mixed structure numbers
 draw a (1 #4)
 draw a (1 #4)
 draw a (1 #4)

INCORRECT OR INCOMPLETE RANGE - TYPE ? FOR HELP
ERASING ...#4)                  CONGEN replies as above, erases, and
ITEMS TO BE DRAWN:                reprompts - all line erased, however

        4) No structures to be drawn:

#draw a 1                       Assume no structures exist
 draw a 1
 draw a 1
 draw a 1
THERE ARE NO STRUCTURES; ONLY SUBSTRUCTURE NAMES
MAKE ANY SENSE AT THIS POINT            CONGEN complains and
ITEMS TO BE DRAWN:                        reprompts for items

                ******************************






































                                  187
CONGEN manual                                              February 1981


        IV.J    SHOW and Subcommands
                SHOW and Subcommands
                SHOW and Subcommands
                SHOW and Subcommands

                ***********************
                *                     *
                * CONGEN Command SHOW *
                *                     *
                ***********************


        The SHOW  command can be  used to show  several aspects  of your
            SHOW
            SHOW
            SHOW
structural problem, using various subcommands to choose what needs to be
shown.   The SHOW  CTABLE command  facilitates reviewing  the connection
             SHOW  CTABLE
             SHOW  CTABLE
             SHOW  CTABLE
tables of specified  substructures or structures (particularly  when the
latter are drawn in an unintelligible format).  The SHOW  STATUS command
                                                    SHOW  STATUS
                                                    SHOW  STATUS
                                                    SHOW  STATUS
is very useful  for a "snapshot" summary  of the current status  of your
CONGEN session.   The contents of  available libraries  of substructures
can also be visualized with  SHOW LIBRARY.  The SHOW AROMATICS  and SHOW
                             SHOW LIBRARY       SHOW AROMATICS      SHOW
                             SHOW LIBRARY       SHOW AROMATICS      SHOW
                             SHOW LIBRARY       SHOW AROMATICS      SHOW
HISTORY commands are not implemented as of 9/79.
HISTORY
HISTORY
HISTORY

        The  selections which  are available  as  subcommands, including
references to subsequent sections  where descriptions can be  found, are
summarized in the Glossary of SHOW commands, Section IV.J.1.
                              SHOW
                              SHOW
                              SHOW

                ******************************

        ***** Use of the SHOW command in CONGEN *****
              Use of the SHOW command in CONGEN
              Use of the SHOW command in CONGEN
              Use of the SHOW command in CONGEN

#show                           Issue the SHOW command
 show                                     SHOW
 show                                     SHOW
 show                                     SHOW

WHAT TO SHOW?:?                 Ask for help
              ?
              ?
              ?

CTABLE STATUS HISTORY AROMATICS LIBRARY         CONGEN replies and

WHAT TO SHOW?:                                    reprompts

(see subsequent sections for individual commands)

                ******************************


















                                  188
CONGEN manual                                              February 1981


        IV.J.1    Glossary of SHOW Subcommands
                  Glossary of SHOW Subcommands
                  Glossary of SHOW Subcommands
                  Glossary of SHOW Subcommands

                ********************************
                *                              *
                * Glossary of SHOW Subcommands *
                *                              *
                ********************************

  SHOW
  SHOW
  SHOW
  SHOW
Subcommand      Section                 Function
----------      -------                 --------

CTABLE          Section IV.J.2  To SHOW the connection table of any
CTABLE                             SHOW
CTABLE                             SHOW
CTABLE                             SHOW
                                 structure(s) or substructure(s)

STATUS          Section IV.J.3  To SHOW the status of your CONGEN
STATUS                             SHOW
STATUS                             SHOW
STATUS                             SHOW
                                 session, summarizing all information

HISTORY         Section IV.J.4  Not yet implemented 9/79
HISTORY
HISTORY
HISTORY

AROMATICS       Section IV.J.5  Not yet implemented 9/79
AROMATICS
AROMATICS
AROMATICS

LIBRARY         Section IV.J.6  To SHOW the contents of any sub-
LIBRARY                            SHOW
LIBRARY                            SHOW
LIBRARY                            SHOW
                                 structure library

                ******************************






























                                  189
CONGEN manual                                              February 1981


        IV.J.2    SHOW CTABLE
                  SHOW CTABLE
                  SHOW CTABLE
                  SHOW CTABLE

                **************************
                *                        *
                * SHOW Subcommand CTABLE *
                *                        *
                **************************


        The SHOW CTABLE  command can be used  to print on  your terminal
            SHOW CTABLE
            SHOW CTABLE
            SHOW CTABLE
the connection table of any defined substructure (in the same  format as
the corresponding SHOW command in Editstruc, Section IV.B.6.c).   It can
                  SHOW
                  SHOW
                  SHOW
also be used to show the  connection table of any structure or  range of
structures in the current list of structures, by position in the list or
by actual structure #'s.  SHOW  CTABLE is thus an adjunct to  the CONGEN
                          SHOW  CTABLE
                          SHOW  CTABLE
                          SHOW  CTABLE
command DRAW, in particular for substructures where  certain information
        DRAW
        DRAW
        DRAW
like  hydrogen  ranges  cannot  be drawn.  Use  SHOW  CTABLE  to  aid in
                                                SHOW  CTABLE
                                                SHOW  CTABLE
                                                SHOW  CTABLE
comprehension of unintelligible structure drawings.

        The  connection  tables  presnted  to  you  will  summarize  all
relevant  atom and  bond  properties, including,  for  example, aromatic
types, hydrogen ranges, free valences, bond orders and loops.

        The  SHOW CTABLE  command  is a  useful way  of  refreshing your
             SHOW CTABLE
             SHOW CTABLE
             SHOW CTABLE
memory on  the identity  of various  substructures, particularly  if the
same substructures are drawn at the same time.

                ******************************

        ***** Use of the CTABLE subcommand in SHOW *****
              Use of the CTABLE subcommand in SHOW
              Use of the CTABLE subcommand in SHOW
              Use of the CTABLE subcommand in SHOW


        The items for which connection tables can be shown are  the same
as for those which can be drawn.  Refer to Section IV.I for more details
on input and error conditions.

#show                           Issue the SHOW command
 show                                     SHOW
 show                                     SHOW
 show                                     SHOW

WHAT TO SHOW:?                  Ask for help
             ?
             ?
             ?

CTABLE STATUS HISTORY AROMATICS LIBRARY         CONGEN replies

WHAT TO SHOW:ctable             Reprompt for item to be shown
             ctable
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                o the LOOP column
                                                     LOOP
                                                     LOOP
                                                     LOOP



                                  191
CONGEN manual                                              February 1981


  3     R6   2             1    One loop on R6
                                            R6
                                            R6
                                            R6

                ******************************





















































                                  192
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        IV.J.3    SHOW STATUS
                  SHOW STATUS
                  SHOW STATUS
                  SHOW STATUS

                **************************
                *                        *
                * SHOW Subcommand STATUS *
                *                        *
                **************************


        The SHOW STATUS command can be used to print a  complete summary
            SHOW STATUS
            SHOW STATUS
            SHOW STATUS
of the  current status  of your  CONGEN session  at your  terminal.  The
summary   includes  the   number  of   structures,  defined   atoms  and
substructures,  the molecular  formula,  Superatoms which  remain  to be
imbedded and so  forth.  The command can  be issued any time  to refresh
your memory on where you are in a particular problem.

                ******************************

        ***** Use of the STATUS Subcommand of SHOW *****
              Use of the STATUS Subcommand of SHOW
              Use of the STATUS Subcommand of SHOW
              Use of the STATUS Subcommand of SHOW


        Assume that we wish to SHOW the STATUS of a  structural problem,
                               SHOW     STATUS
                               SHOW     STATUS
                               SHOW     STATUS
in fact, the one used as one of the illustrations for the CONGEN command
DRAW, Section IV.I.  Here is an example of the summary you see output to
DRAW
DRAW
DRAW
your terminal.  The output is self-explanatory.

#show status                    Issue the SHOW STATUS command
 show status                              SHOW STATUS
 show status                              SHOW STATUS
 show status                              SHOW STATUS

YOU CURRENTLY HAVE 19 STRUCTURES, WITH INDICES FROM #1 TO #28

SUPERATOMS TO BE IMBEDDED: ME(4) OH(1) PH(1) DB(1)

CURRENT DEFINITIONS:
ATOMS(VALENCES IN PARENTHESES): H(1) C(4) N(3) O(2)
SUBSTRUCTURES: ME ET OH PH C=C DB XXX

AROMATIC TEMPLATES:BENZENE

MOLECULAR FORMULA IS C 14 H 18 O 1

#                               Ready for next CONGEN command

                ******************************













                                  193
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        IV.J.4    SHOW HISTORY
                  SHOW HISTORY
                  SHOW HISTORY
                  SHOW HISTORY

                ***************************
                *                         *
                * SHOW Subcommand HISTORY *
                *                         *
                ***************************


        The SHOW HISTORY command is  not yet implemented as of  9/79, so
            SHOW HISTORY
            SHOW HISTORY
            SHOW HISTORY
the only response you get is as follows:

#show history                   Issue SHOW HISTORY command
 show history                         SHOW HISTORY
 show history                         SHOW HISTORY
 show history                         SHOW HISTORY
NOT YET IMPLEMENTED             CONGEN replies
#                               Ready for next CONGEN command









































                                  194
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        IV.J.5    SHOW AROMATICS
                  SHOW AROMATICS
                  SHOW AROMATICS
                  SHOW AROMATICS

                *****************************
                *                           *
                * SHOW Subcommand AROMATICS *
                *                           *
                *****************************


        The SHOW AROMATICS command is not implemented as of 9/79, so the
            SHOW AROMATICS
            SHOW AROMATICS
            SHOW AROMATICS
only response you get on issuing the command is as follows:

#show aromatics                 Issue SHOW AROMATICS command
 show aromatics                       SHOW AROMATICS
 show aromatics                       SHOW AROMATICS
 show aromatics                       SHOW AROMATICS
NOT YET IMPLEMENTED             CONGEN replies
#                               Ready for next CONGEN command









































                                  195
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        IV.J.6    SHOW LIBRARY
                  SHOW LIBRARY
                  SHOW LIBRARY
                  SHOW LIBRARY

                ***************************
                *                         *
                * SHOW Subcommand LIBRARY *
                *                         *
                ***************************


        The SHOW LIBRARY command is  used to determine the names  of all
            SHOW LIBRARY
            SHOW LIBRARY
            SHOW LIBRARY
substructures  present  in  a specified  LIBRARY.   This  command  is an
                                         LIBRARY
                                         LIBRARY
                                         LIBRARY
adjunct to  the CONGEN command  SEARCH (Section IV.D)  which is  used to
                                SEARCH
                                SEARCH
                                SEARCH
retrieve substructures by name from a specified library.

        You  have the  option of  showing the  contents of  a  number of
libraries available to CONGEN.   In addition, you can show  the contents
of your  own library.  The  mechanism for creating  your own  library of
substructures for  subsequent retrieval was  discussed in  Section IV.D,
namely, using the MYLIB subcommand to SEARCH, or SHOW,  substructures in
                  MYLIB               SEARCH     SHOW
                  MYLIB               SEARCH     SHOW
                  MYLIB               SEARCH     SHOW
a CONGEN file  saved by you using  the CONGEN SAVE command  (see Section
                                              SAVE
                                              SAVE
                                              SAVE
IV.L).   The following  libraries are  available and  can be  shown (see
Section IV.D for reference to source of terpane skeletons):

Library                         Contents
-------                         --------

GENLIB          A general library of substructures containing common
GENLIB
GENLIB
GENLIB
                  alkyl and alkenyl groups and simple heteroatomic
                  functionalities

ISOLIB          A library of 2,3 and 4 isoprene units linked in
ISOLIB
ISOLIB
ISOLIB
                  specified ways, for testing structures against the
                  isoprene rule.

BMTERP          Bicyclic monoterpane skeletons.
BMTERP
BMTERP
BMTERP

BSTERP          Bicyclic sesquiterpane skeletons.
BSTERP
BSTERP
BSTERP

TSTERP          Tricyclic sesquiterpane skeletons.
TSTERP
TSTERP
TSTERP

AMNACD          Amino acid skeletons.
AMNACD
AMNACD
AMNACD

SURVLIB         Library of functionalities for use in the CONGEN
SURVLIB
SURVLIB
SURVLIB
                  command SURVEY (Section IV.N).
                          SURVEY
                          SURVEY
                          SURVEY

MYLIB           Actually not a library, but a request to CONGEN to ask
MYLIB
MYLIB
MYLIB
                  you for a file name which contains your own library.

                ******************************

        ***** Use of the SHOW Subcommand LIBRARY *****
              Use of the SHOW Subcommand LIBRARY
              Use of the SHOW Subcommand LIBRARY
              Use of the SHOW Subcommand LIBRARY





                                  196
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#show library                   Issue SHOW LIBRARY command
 show library                         SHOW LIBRARY
 show library                         SHOW LIBRARY
 show library                         SHOW LIBRARY
                                  to show library genlib
LIBRARY TO BE SHOWN:?           Ask for help, CONGEN replies
                    ?
                    ?
                    ?

GENLIB ISOLIB BMTERP BSTERP TSTERP AMNACD SURVLIB MYLIB

LIBRARY TO BE SHOWN:genlib      Select GENLIB - here are contents
                    genlib             GENLIB
                    genlib             GENLIB
                    genlib             GENLIB

THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

1)METHYL 2)ME 3)MET 4)CH3 5)ETHYL 6)ET 7)C2H5 8)PROPYL 9)PRO 10)PR
11)ISOPROPYL 12)I-PROPYL 13)IPR 14)C1 15)C2 16)CH2 17)C3 18)CH 19)C4
20)PRIMARYC 21)SECONDARYC 22)TERTIARYC 23)QUATERNARYC 24)HO 25)OH
26)HYDROXY 27)HYDROXYL 28)SH 29)THIO 30)THIOL 31)NH2 32)N1 33)PRIMARYN
34)NH 35)N2 36)SECONDARYN 37)N3 38)TERTIARYN 39)PRIMARYOH 40)SECONDARYOH
41)TERTIARYOH 42)KET 43)KETO 44)CO 45)ALD 46)PHENYL 47)BENZYL 48)PH
49)PRIMARYCH3 50)SECONDARYCH3 51)TERTIARYCH3 52)METHYLENE 53)METHINE
54)C=C 55)DB 56)H2C=C 57)CH2=C 58)CH2=CH 59)CH=CH

#                               Ready for next CONGEN command

#show library isolib          Show contents of ISOLIB
 show library isolib                           ISOLIB
 show library isolib                           ISOLIB
 show library isolib                           ISOLIB

THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

1)2-HT 2)2-IRR 3)3-HT-HT 4)3-IRR 5)4-HT-HT-HT 6)4-IRR

#                               Ready for next CONGEN command

#show library bmterp          Show contents of BMTERP
 show library bmterp                           BMTERP
 show library bmterp                           BMTERP
 show library bmterp                           BMTERP

THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

1)AFENCHANE 2)BFENCHANE 3)ISOCAMPHANE 4)CARANE 5)CAMPHANE 6)PINANE
7)FENCHANE 8)THUJANE 9)FILIFOLANE 10)B020 11)B001

#                               Ready for next CONGEN command

#show library bsterp          Show contents of BSTERP
 show library bsterp                           BSTERP
 show library bsterp                           BSTERP
 show library bsterp                           BSTERP

THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

1)CHAMIGRANE 2)VALERANE 3)TUTIN 4)DRIMANE 5)CARYOPHYLLANE 6)CUPARANE
7)ACORANE 8)CAROTANE 9)PSEUDO-GUAIANE 10)EREMOPHILANE 11)VETISPIRANE
12)EUDESMANE 13)SANTALANE 14)LAURANE 15)CADINANE 16)GUAIANE
17)HIMANCHLANE 18)TRICHOTHECANE 19)S023 20)S027 21)S016 22)S076 23)S011
24)S010 25)S057 26)S049 27)S021 28)S025 29)S047 30)S002 31)S013 32)S064
33)S005 34)S020 35)S065 36)S059 37)S073 38)S051 39)S036 40)S077 41)S030
42)S056 43)S034 44)S072 45)S028 46)S001 47)S044 48)S074 49)S018 50)S014
51)S068 52)S007 53)S071 54)S017 55)S045

#                               Ready for next CONGEN command




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#show library tsterp          Show contents of TSTERP
 show library tsterp                           TSTERP
 show library tsterp                           TSTERP
 show library tsterp                           TSTERP

THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

1)AROMADENDRANE 2)KHUSANE 3)ARISTOLANE 4)MAALIANE 5)PATCHOULANE
6)CEDRANE 7)WIDDRANE 8)T034 9)T049 10)T051 11)T047 12)T048 13)T005
14)T046 15)T011 16)T041 17)T007 18)T018 19)T010 20)T006 21)T029 22)T022
23)T012 24)T019 25)T045 26)T009 27)T030 28)T040 29)T001 30)T031 31)T036
32)T033 33)T044 34)T039

#                               Ready for next CONGEN command

#show library survlib         Show contents of SURVLIB
 show library survlib                          SURVLIB
 show library survlib                          SURVLIB
 show library survlib                          SURVLIB

THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

1)C=C 2)MONOSUBSC=C 3)SYMDISUBSC=C 4)UNSYMDISUBSC=C 5)TRISUBSC=C
6)TETRASUBSC=C 7)CONJDIENE 8)ALKYNE 9)ALLENE 10)ALCOHOL 11)ALLYLICOH
12)PRIMARYOH 13)SECONDARYOH 14)TERTIARYOH 15)GEMDIOL 16)GLYCOL
17)PINACOL 18)ETHER 19)VINYLETHER 20)PEROXIDE 21)ACID 22)PERACID
23)PEROL 24)ANHYDRIDE 25)ESTER 26)PERESTER 27)ORTHOESTER 28)ALDEHYDE
29)ABUNSATALDEHYDE 30)KETONE 31)KETENE 32)ABUNSATKETONE 33)ENOL
34)HEMIACETAL 35)ACETAL 36)KETAL 37)ALDOL 38)C=N 39)IMIDOESTER
40)IMIDOACID 41)ALDIMINE 42)KETIMINE 43)N-O 44)N-OR 45)N=O
46)HYDROXYLAMINE 47)ALDOXIME 48)KETOXIME 49)HYDRAZONE 50)SEMICARBAZONE
51)AMINE 52)PRIMARYAMINE 53)SECONDARYAMINE 54)TERTIARYAMINE 55)NITRILE
56)AMIDE 57)HYDRAZINE 58)AZO 59)CNITROSO 60)NNITROSO 61)DIAZOHYDROXIDE
62)ISOCYANATE 63)AMIDINE 64)N-N 65)THIOL 66)SULFIDE 67)DISULFIDE
68)O=C-S 69)S=C-O 70)S=C-S 71)THIOALDEHYDE 72)THIOKETONE 73)THIOCYANATE
74)ISOTHIOCYANATE 75)S=C-N 76)S-C=N 77)S-O 78)HYDROXYSULFIDE 79)S-N
80)S=N 81)EPOXIDES 82)CYCLOPROPANONES 83)CYCLOPROPENES 84)CYCLOBUTENES
85)SMALLFUSEDRINGS

#                               Ready for next CONGEN command

#show library mylib           Show contents of your own library
 show library mylib
 show library mylib
 show library mylib

NAME OF A FILE YOU HAVE PREVIOUSLY SAVED:?      Ask for help
                                         ?
                                         ?
                                         ?

                                CONGEN replies

A WORD OF THE FORM XXXXXX.YYY WHERE XXXXXX IS A 'NAME' OF
FROM ONE TO SIX LETTERS AND/OR DIGITS AND WHERE YYY IS AN
OPTIONAL 'EXTENSION' OF FROM ONE TO THREE LETTERS AND/OR DIGITS.
THE '.' MAY BE OMITTED IF THE EXTENSION IS OMITTED

NAME OF A FILE YOU HAVE PREVIOUSLY SAVED:       Reprompt for file name

                                Supply file name, get substructure list

#                               Ready for next CONGEN command

                ******************************



                                  198
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        ***** Error Conditions and CONGEN Replies *****
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies


        The  primary error  conditions are  those given  for  the CONGEN
command SEARCH, Section IV.D,  namely, illegal input, bad  library names
        SEARCH
        SEARCH
        SEARCH
or requests for non-existent files.  See SEARCH for details.
                                         SEARCH
                                         SEARCH
                                         SEARCH

        In large CONGEN problems with many substructures, it is remotely
possible that you will  encounter the following messages on  showing the
contents of several libraries:

#show library tsterp            After showing others
 show library tsterp
 show library tsterp
 show library tsterp

THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:

1)AROMADENDRANE 2)KHUSANE 3)ARISTOLANE 4)MAALIANE 5)PATCHOULANE
6)CEDRANE 7)WIDDRANE 8)T034 9)T049 10)T051 11)T047 12)T048 13)T005
14)T046 15)T011 16)T041 17)T007 18)T018 19)T010 20)T006 21)T029 22)T022

NOTE:  I'M ALMOST OUT OF STRING-CATALOG SPACE.  Warning from CONGEN
                                                Warning from CONGEN
                                                Warning from CONGEN
                                                Warning from CONGEN

23)T012 24)T019 25)T045 26)T009 27)T030 28)T040 29)T001 30)T031 31)T036
32)T033

SORRY, I'LL HAVE TO STOP; I'VE RUN OUT OF STRING-CATALOG SPACE.

#                               Ready for next CONGEN command

                                Continuation may run into same problem
                                It is best to SAVE and EXIT, restart
                                              SAVE     EXIT
                                              SAVE     EXIT
                                              SAVE     EXIT
                                CONGEN and RESTORE to continue
                                           RESTORE
                                           RESTORE
                                           RESTORE

                ******************************























                                  199
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        IV.K    FORGET
                FORGET
                FORGET
                FORGET

                *************************
                *                       *
                * CONGEN Command FORGET *
                *                       *
                *************************


        The  FORGET   command  can  be   used  to  forget,   or  discard
             FORGET
             FORGET
             FORGET
(permanently) any defined substructure(s) or structure(s) in the current
 permanently
 permanently
 permanently
list of structures.   The selection of items  which can be  forgotten is
the  same as  that which  can  be drawn  with the  CONGEN  command DRAW,
                                                                   DRAW
                                                                   DRAW
                                                                   DRAW
Section  IV.I, or  shown with  the CONGEN  command SHOW  CTABLE, Section
                                                   SHOW  CTABLE
                                                   SHOW  CTABLE
                                                   SHOW  CTABLE
IV.J.

        The  FORGET command  is useful  when, for  example, you  wish to
             FORGET
             FORGET
             FORGET
define a  substructure with  the same  name as  one you  have previously
defined but no longer want.  (Alternatively, you could FIX it, erase all
                                                       FIX
                                                       FIX
                                                       FIX
the atoms and  redefine it with  Editstruc).  More frequently,  you will
note  a  few  structures  in  your  structure  list  which  are  clearly
implausible.   Rather than  trying to  define a  specific  constraint to
eliminate  those few  structures  with the  PRUNE command,  it  is often
                                            PRUNE
                                            PRUNE
                                            PRUNE
easier to FORGET just those few structures.
          FORGET
          FORGET
          FORGET

                ******************************

        ***** Use of the FORGET command in CONGEN *****
              Use of the FORGET command in CONGEN
              Use of the FORGET command in CONGEN
              Use of the FORGET command in CONGEN


        The items which can be forgotten are the same as those which can
be drawn using  the CONGEN command DRAW,  Section IV.I, or  shown, using
                                   DRAW
                                   DRAW
                                   DRAW
the CONGEN command SHOW Section IV.J.  Therefore, the description of the
                   SHOW
                   SHOW
                   SHOW
prompting sequence and legal and illegal responses for FORGET  is brief;
                                                       FORGET
                                                       FORGET
                                                       FORGET
refer to the other sections for more details and descriptions of errors.

        The  example used  is the  set of  19 structures  last described
under the SHOW STATUS command, Section IV.J.3.
          SHOW STATUS
          SHOW STATUS
          SHOW STATUS

#forget                         Issue the FORGET command
 forget                                   FORGET
 forget                                   FORGET
 forget                                   FORGET

ITEMS TO BE FORGOTTEN:?         Ask for help
                      ?
                      ?
                      ?
                                CONGEN replies with the usual list
                                  of items

PLEASE TYPE ONE OR MORE ENTRIES IN ANY OF THE FOLLOWING FORMS:

    THE NAME OF A DEFINED ATOM OR SUBSTRUCTURE

OR: AN INTEGER N, INDICATING THE NTH STRUCTURE IN YOUR CURRENT LIST

OR: A PAIR OF INTEGERS IN PARENTHESES, E.G. (1 10); (M N) INDICATES A
    RANGE OF THE MTH THROUGH THE NTH STRUCTURES IN YOUR CURRENT LIST



                                  200
CONGEN manual                                              February 1981


OR: A # FOLLOWED BY AN INTEGER (E.G. #3) INDICATING THE STRUCTURE WHICH
    IS 'ATTACHED' TO THE INDEX N (THIS INDEX IS PRINTED IN DRAWINGS)

OR: A PAIR (#M #N) INDICATING A THE RANGE OF STRUCTURES ASSOCIATED WITH
    INDICES M THROUGH N

ITEMS TO BE FORGOTTEN:c=c       Reprompt, reply with an existing
                      c=c
                      c=c
                      c=c
                                  substructure, C=C
                                                C=C
                                                C=C
                                                C=C
FORGETTING C=C                  CONGEN replies and, to be sure,
SHALL I REALLY FORGET?:y        requests confirmation
                       y
                       y
                       y

#forget 1                       Forget the first structure - it is
 forget 1
 forget 1
 forget 1
                                  also structure #1
FORGETTING #1

SHALL I REALLY FORGET?:y        Confirm
                       y
                       y
                       y

#forget #4 #28                  Forget a list of items
 forget #4 #28
 forget #4 #28
 forget #4 #28

FORGETTING #4 #28               CONGEN replies

SHALL I REALLY FORGET?:y        Confirm
                       y
                       y
                       y

#forget (#5 #9)                 Forget a range of structure #'s
 forget (#5 #9)
 forget (#5 #9)
 forget (#5 #9)

FORGETTING #5 #7 #8 #9          CONGEN replies

SHALL I REALLY FORGET?:y        Confirm
                       y
                       y
                       y

#show status                    Show new status
 show status
 show status
 show status

YOU CURRENTLY HAVE 12 STRUCTURES, WITH INDICES FROM #2 TO #27

SUPERATOMS TO BE IMBEDDED: ME(4) OH(1) PH(1) DB(1)

CURRENT DEFINITIONS:
ATOMS(VALENCES IN PARENTHESES): H(1) C(4) N(3) O(2)
SUBSTRUCTURES: ME ET OH PH DB XXX

AROMATIC TEMPLATES: BENZENE

MOLECULAR FORMULA IS C 14 H 18 O 1

#                               Ready for next CONGEN command

                ******************************

        ***** Error Conditions and CONGEN Replies *****
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies

        1) Attempt to FORGET a substructure (XYZ) present as a Superatom
                      FORGET                 XYZ
                      FORGET                 XYZ
                      FORGET                 XYZ
name in the current list of structures:

#forget xyz                     XYZ present in intermediate structures
 forget xyz                     XYZ
 forget xyz                     XYZ
 forget xyz                     XYZ



                                  201
CONGEN manual                                              February 1981


                                CONGEN replies
NOTE: CHANGING OR FORGETTING THE DEFINITION OF XYZ
AT THIS POINT MAY LEAD TO CONFUSION BECAUSE YOUR
STRUCTURES STILL REFLECT THE OLD DEFINITION
FORGETTING XYZ
SHALL I REALLY FORGET?:         Forgetting XYZ would
                                           XYZ
                                           XYZ
                                           XYZ
                                  seem to be incorrect - answer no

        2) Substructure not defined, structure number too large:

#forget xyz                     XYZ not defined
 forget xyz                     XYZ
 forget xyz                     XYZ
 forget xyz                     XYZ
XYZ ISN'T DEFINED               CONGEN replies and
ERASING ...XYZ                    erases and prompts for new item
ITEMS TO BE FORGOTTEN:34        There are fewer than 34 structures
                      34
                      34
                      34
I'LL USE 12 INSTEAD OF 34       CONGEN assumes you mean the last one
FORGETTING #27                    which is numbered #27
SHALL I REALLY FORGET?:n        That's not what you meant, so
                       n
                       n
                       n
                                  do not confirm
(NOTHING FORGOTTEN)             CONGEN replies
#                               Ready for next CONGEN command

        3) Attempt to FORGET all structures - it's OK if that is
                      FORGET
                      FORGET
                      FORGET
what you really want to do:

#forget (1 12)                  You can forget all the structures
 forget (1 12)
 forget (1 12)
 forget (1 12)
                                CONGEN replies

FORGETTING #2 #10 #12 #14 #15 #17 #19 #20 #22 #23 #25 #27

SHALL I REALLY FORGET?:y        If you confirm,
                       y
                       y
                       y
#show status                      they are
 show status
 show status
 show status
YOU CURRENTLY HAVE NO STRUCTURES    all gone, sorry

        ...rest of status

#                               Ready for next CONGEN command

                ******************************


















                                  202
CONGEN manual                                              February 1981


        IV.L    SAVE
                SAVE
                SAVE
                SAVE

                ***********************
                *                     *
                * CONGEN Command SAVE *
                *                     *
                ***********************


        The SAVE  command is meant  to save, on  a named disk  file, the
            SAVE
            SAVE
            SAVE
current CONGEN session,  including all defined atoms  and substructures,
aromatics,  molecular  formula  and  current  set  of  structures.  SAVE
                                                                    SAVE
                                                                    SAVE
                                                                    SAVE
provides  a convenient  mechanism for  both protecting  yourself against
your own  mistakes and failures  of the computer  system.  It  should be
used after each major computation to ensure that the results will not be
lost on  system failure, but  can be recovered  (see the  CONGEN command
RESTORE, Section  IV.M) at  a later  time.  Also,  many problems  can be
RESTORE
RESTORE
RESTORE
taken to an intermediate stage, but no further until additional data are
gathered to constrain the problem further.  By using SAVE you  can store
                                                     SAVE
                                                     SAVE
                                                     SAVE
away all  your earlier work  and continue the  next day, or  week, right
where you left off.

                ******************************

        ***** Use of the SAVE Command in CONGEN *****
              Use of the SAVE Command in CONGEN
              Use of the SAVE Command in CONGEN
              Use of the SAVE Command in CONGEN


        The SAVE command  requests a file name.   Note that if  the same
            SAVE
            SAVE
            SAVE
name is given for  DEC-10 systems operating under the  TOPS-10 operating
system, the old file is overwritten, and you are warned about  that.  If
                        overwritten
                        overwritten
                        overwritten
you  wish to  SAVE more  than one  time and  keep the  results separate,
              SAVE
              SAVE
              SAVE
simply use different file names.  Eventually, you will have to  erase or
archive unneeded files, of course.  On SUMEX, use of the same  file name
results in a new version being created; the old version is  deleted.  (A
deleted file can be undeleted  before you log off SUMEX,  thereby saving
it for  future use.  Note,  however, that you  cannot specify  a version
number to CONGEN.  If you  want to RESTORE an earlier version,  the file
                                   RESTORE
                                   RESTORE
                                   RESTORE
must be renamed to a legal  file name (see below for what  constitutes a
legal file name).  Note that if you logoff, all deleted files are erased
(expunged) from SUMEX.) On SUMEX,  up to five versions are  saved before
the sixth causes the first  to disappear from the file system  (only the
five most recent will be saved at SUMEX; the four earlier  versions will
be in deleted status).  Here is the simple command sequence:

#save                           Issue the SAVE command
 save                                     SAVE
 save                                     SAVE
 save                                     SAVE

FILE NAME:?                     Ask for help
          ?
          ?
          ?

A WORD OF THE FORM XXXXXX.YYY WHERE XXXXXX IS A 'NAME' OF
FROM ONE TO SIX LETTERS AND/OR DIGITS AND WHERE YYY IS AN
OPTIONAL 'EXTENSION' OF FROM ONE TO THREE LETTERS AND/OR DIGITS.
THE '.' MAY BE OMITTED IF THE EXTENSION IS OMITTED




                                  203
CONGEN manual                                              February 1981


FILE NAME:trial                 Supply a legal file name
          trial
          trial
          trial

SAVED ON TRIAL                  CONGEN replies to confirm

#                               Ready for next CONGEN command

#save trial.tst                 The use of an extension is sometimes
 save trial.tst
 save trial.tst
 save trial.tst
                                  helpful to keep other parts of the
                                  session together under the same name
SAVED ON TRIAL.TST              CONGEN confirms

#                               Ready for next CONGEN command

                ******************************

        ***** Error Conditions and CONGEN Replies *****
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies

        1) Bad file names:

#save abcdefg                   Name too long, CONGEN replies and
 save abcdefg
 save abcdefg
 save abcdefg


INCORRECT FORMAT FOR FILE NAME - TYPE ? FOR HELP
ERASING ...ABCDEFG                erases bad name and

FILE NAME:abc.defg                reprompts for name - extension
          abc.defg
          abc.defg
          abc.defg
                                  too long - CONGEN replies

INCORRECT FORMAT FOR FILE NAME - TYPE ? FOR HELP

FILE NAME:                      Reprompt for name

        2) File name used before (may be what you want to do!):
                                                  want
                                                  want
                                                  want

#save trial                     TRIAL used before
 save trial                     TRIAL
 save trial                     TRIAL
 save trial                     TRIAL

YOU ALREADY HAVE A FILE BY THAT NAME.   CONGEN replies and asks
SHALL I OVERWRITE IT?:n                   if overwrite OK - if no,
                      n
                      n
                      n
FILE NAME:trial.tst                       prompt for new name
          trial.tst
          trial.tst
          trial.tst
YOU ALREADY HAVE A FILE BY THAT NAME.   CONGEN replies and asks
SHALL I OVERWRITE IT?:y                   if overwrite OK - if yes,
                      y
                      y
                      y
SAVED ON TRIAL.TST                           CONGEN saves file

#                               Ready for next CONGEN command

                ******************************










                                  204
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        IV.M    RESTORE
                RESTORE
                RESTORE
                RESTORE

                **************************
                *                        *
                * CONGEN Command RESTORE *
                *                        *
                **************************


        The RESTORE command is used to retrieve a previously saved file,
            RESTORE
            RESTORE
            RESTORE
stored away using the  CONGEN command SAVE, Section IV.L.   This command
                                      SAVE
                                      SAVE
                                      SAVE
restores all saved information  about a previous session,  including all
definitions and  structures.  Thus,  you can pick  up a  problem exactly
where you left it,  and continue without having to  re-do time-consuming
computations.

        The  RESTORE  command  is  destructive  of  your  current CONGEN
             RESTORE               destructive
             RESTORE               destructive
             RESTORE               destructive
session.  It operates by replacing all of the structural  information in
                         replacing
                         replacing
                         replacing
your current session with the structural information stored in  the file
whose name you supply (see below).  If you wish to  selectively retrieve
substructures from a file and add them to your current session,  use the
                              add
                              add
                              add
CONGEN command SEARCH, Section IV.D.
               SEARCH
               SEARCH
               SEARCH

                ******************************

        ***** Use of the RESTORE Command in CONGEN *****
              Use of the RESTORE Command in CONGEN
              Use of the RESTORE Command in CONGEN
              Use of the RESTORE Command in CONGEN


        The file  name must be  given exactly, character  for character,
                                      exactly
                                      exactly
                                      exactly
the same name as that under which as it was saved.

#restore                        Issue the RESTORE command
 restore                                  RESTORE
 restore                                  RESTORE
 restore                                  RESTORE
INPUT FILE:?                    Ask for help
           ?
           ?
           ?
                                CONGEN replies

A WORD OF THE FORM XXXXXX.YYY WHERE XXXXXX IS A 'NAME' OF
FROM ONE TO SIX LETTERS AND/OR DIGITS AND WHERE YYY IS AN
OPTIONAL 'EXTENSION' OF FROM ONE TO THREE LETTERS AND/OR DIGITS.
THE '.' MAY BE OMITTED IF THE EXTENSION IS OMITTED

INPUT FILE:trial                Reprompt for file name
           trial
           trial
           trial

TRIAL RESTORED                  A legal name - CONGEN restores and
                                  confirms
#show status                    Check the status
 show status
 show status
 show status

YOU CURRENTLY HAVE NO STRUCTURES

CURRENT DEFINITIONS:
ATOMS(VALENCES IN PARENTHESES): H(1) C(4) N(3) O(2)
SUBSTRUCTURES: ME ET OH PH DB XXX

AROMATIC TEMPLATES: BENZENE



                                  205
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MOLECULAR FORMULA IS C 14 H 18 O 1

#                               Ready for next CONGEN command

                ******************************

        ***** Error Conditions and CONGEN Replies *****
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies
              Error Conditions and CONGEN Replies

#restore 14                     Integer name illegal
 restore 14
 restore 14
 restore 14

I CAN'T SEEM TO FIND THAT FILE          CONGEN replies and reprompts

INPUT FILE:trew                 Name OK, but file non-existent
           trew
           trew
           trew

I CAN'T SEEM TO FIND THAT FILE          CONGEN replies and reprompts

INPUT FILE:dhs.dic              Name OK, file exists, but it's not
           dhs.dic
           dhs.dic
           dhs.dic
                                  a CONGEN SAVE file

THAT FILE DOESN'T SEEM TO BE A SAVE FILE I MADE         CONGEN replies

INPUT FILE:                     Reprompt for file name - carriage return
                                  would terminate attempt to restore

#                               Ready for next CONGEN command

                ******************************





























                                  206
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        IV.N    SURVEY
                SURVEY
                SURVEY
                SURVEY

                *************************
                *                       *
                * CONGEN Command SURVEY *
                *                       *
                *************************


        The primary  purpose of the  SURVEY command is  to allow  you to
                                     SURVEY
                                     SURVEY
                                     SURVEY
scan through large  sets of generated  structures in order  to determine
the  frequency  of  occurrence  of  selected  substructures.  A  typical
application might be to  determine how many candidate structures  for an
unknown urinary metabolite,  isolated from human urine,  incorporate any
one of the twenty normal amino acid skeletons.

        Usually,  the  SURVEY  command is  used  in  association  with a
                       SURVEY
                       SURVEY
                       SURVEY
library of substructures.   The standard libraries provided  with CONGEN
have  been  discussed earlier  in  association with  the  SEARCH command
                                                          SEARCH
                                                          SEARCH
                                                          SEARCH
Section IV.D and the SHOW LIBRARY command Section IV.J.6. Of course, any
library that you  have created yourself (see  Section IV.D) may  also be
employed in this context. The contents of a library may  be supplemented
for use  in SURVEY by  any of the  substructures that your  have defined
            SURVEY
            SURVEY
            SURVEY
earlier in your current CONGEN session. It is possible to use either ALL
                                                                     ALL
                                                                     ALL
                                                                     ALL
substructures  in  a  given  library  (strictly,  all  those   that  are
compatible with your molecular  formula), or to select entries  from the
library  if  you  are  interested  only  in  the  occurrence  of certain
specified  substructures.    There  is   a  limit   on  the   number  of
substructures that may  be employed; this  limit was imposed  to prevent
the SURVEY  functions from  taking up  too much  space in  the computer.
    SURVEY
    SURVEY
    SURVEY
While this limit may vary  in different versions of CONGEN  on different
machines, usually you cannot have more than a total of about six hundred
atoms  in  all  the  substructures  that  you  are  employing.  In  most
applications  this  limit  is not  onerous;  however,  certain libraries
containing large numbers of large substructures (e.g. the BSTERP library
                                                          BSTERP
                                                          BSTERP
                                                          BSTERP
containing 55  different 15 atom  substructures) cannot be  processed in
their entirety during use  of SURVEY (approaches to handling  such large
                              SURVEY
                              SURVEY
                              SURVEY
libraries  are  illustrated  in  the  sample  SURVEY   session,  Section
                                              SURVEY
                                              SURVEY
                                              SURVEY
IV.N.1).

        SURVEY  examines  your candidate  structures  for  the requested
        SURVEY
        SURVEY
        SURVEY
substructures and generates a  report on their frequency  of occurrence.
In this report, those substructures that did not occur in  any candidate
are listed first, then substructures present in all candidates are noted
and, finally, a list is given of those substructural features that occur
only in certain candidates and which consequently serve  to discriminate
among  different  candidates.  The  frequency  of  occurrence   of  such
discriminating substructures is listed in this report. Once  this report
has been generated, it is possible either to return directly to CONGEN's
# command prompt, or to  enter a subcommand mode of SURVEY.  In SURVEY's
                                                    SURVEY      SURVEY
                                                    SURVEY      SURVEY
                                                    SURVEY      SURVEY
subcommand mode  you can determine  which structures  possess particular
logical  (Boolean) combinations  of  substructural features  and,  if so




                                  207
CONGEN manual                                              February 1981


desired,  prune out  candidates that  exhibit undesired  combinations of
features. The  subcommand mode,  Section IV.N.2,  will be  considered in
more detail  after the  first example on  the sample  session on  use of
SURVEY, Section IV.N.1.
SURVEY
SURVEY
SURVEY

        Note that the  PRUNE command in  CONGEN, Section IV.F,  does not
                       PRUNE
                       PRUNE
                       PRUNE
allow  complete flexibility  in testing  structures for  combinations of
constraints.  In particular, PRUNE does not allow you to constrain a set
                             PRUNE
                             PRUNE
                             PRUNE
of structures with one structural feature or another structural feature.
                                          or
                                          or
                                          or
SURVEY  thus allows  you  effecttively to  PRUNE,  by using  one  of the
SURVEY                                     PRUNE
SURVEY                                     PRUNE
SURVEY                                     PRUNE
subcommands REMOVE or REPLACE (see Glossary of SURVEY  commands, Section
            REMOVE    REPLACE                  SURVEY
            REMOVE    REPLACE                  SURVEY
            REMOVE    REPLACE                  SURVEY
IV.N.2.a).












































                                  208
CONGEN manual                                              February 1981


        IV.N.1    SURVEY First Sample Session
                  SURVEY First Sample Session
                  SURVEY First Sample Session
                  SURVEY First Sample Session

                *******************************
                *                             *
                * SURVEY First Sample Session *
                *                             *
                *******************************

        The  basic use  of SURVEY,  just to  determine the  frequency of
                           SURVEY
                           SURVEY
                           SURVEY
occurrence  of  standard  substructural  features,  will  be illustrated
through  an  example  application  involving  an  analysis  of  some 570
different  structures for  C15  alcohols to  determine  which structures
contain known bicyclic sesquiterpene skeletons from the  BSTERP library.
                                                         BSTERP
                                                         BSTERP
                                                         BSTERP
(This is an example of the  case where an entire library cannot  in fact
be processed in one step because of the size limitations we  have chosen
to impose on the SURVEY functions).
                 SURVEY
                 SURVEY
                 SURVEY


#survey
 survey
 survey
 survey

DO YOU WANT TO USE A LIBRARY OF SUBSTRUCTURES?y         It is possible
                                              y
                                              y
                                              y
                                         to forgo the use of a library
                                         and work solely with
                                         substructures defined earlier
                                         in your current CONGEN session
                                         by answering no.

WHICH LIBRARY FILE? ?                        Usual request for help,
                    ?
                    ?
                    ?
                                         CONGEN replies

GENLIB ISOLIB BMTERP BSTERP TSTERP AMNACD SURVLIB MYLIB

WHICH LIBRARY FILE? bsterp
                    bsterp
                    bsterp
                    bsterp

WHICH SUBSTRUCTURES :all                     Other options for selecting
                     all
                     all
                     all
                                         substructures are illustrated
                                         later.

READING ENTRIES FROM LIBRARY FILE.              CONGEN prints a dot for
                                         each entry in the library
                                         compatible with your molecular
                                         formula.

.........................................

LIMIT ON NUMBER OF ATOMS HAS BEEN REACHED.     Warning from CONGEN, the
                                         entire library would be too
                                         large to process, the program
                                         will proceed with those
                                         substructures read so far.

LAST LIBRARY ENTRY USED IS 41 S030              CONGEN identifies the
                                         last substructure read from



                                  209
CONGEN manual                                              February 1981


                                         the library so that you may
                                         continue and process the
                                         remaining entries in a
                                         subsequent call to SURVEY.
                                                            SURVEY
                                                            SURVEY
                                                            SURVEY



SCANNING THROUGH STRUCTURES.                 SURVEY checks each of your
                                             SURVEY
                                             SURVEY
                                             SURVEY
                                         structures for the presence
                                         of each substructure taken
                                         from the library. A dot is
                                         printed after each structure
                                         has been processed simply
                                         in order to indicate how the
                                         calculations are progressing.
........................................................................
........................................................................
........................................................................
etc
........................................................................
......................................................................

THE FOLLOWING LIBRARY FEATURES WERE NOT FOUND IN ANY STRUCTURE.
CHAMIGRANE                                      This is SURVEY's report.
                                                        SURVEY
                                                        SURVEY
                                                        SURVEY
VALERANE
TUTIN
DRIMANE
CARYOPHYLLANE
CUPARANE
ACORANE
CAROTANE
PSEUDO-GUAIANE
EREMOPHILANE
VETISPIRANE
EUDESMANE
SANTALANE
LAURANE
CADINANE
HIMANCHLANE
TRICHOTHECANE
S016
S076
S011
S010
S057
S049
S021
S025
S047
S064
S020
S065
S059



                                  210
CONGEN manual                                              February 1981


S073
S051
S077
S030

#STRUCTURES WITH DISCRIMINATING FEATURES:
         6    GUAIANE               SURVEY lists the substructure names,
                                    SURVEY
                                    SURVEY
                                    SURVEY
         6    S023               and gives the number of structures
        24    S027               containing each substructural
        42    S002               feature that might be used to
         6    S013               discriminate amongst the structures.
       144    S005
         6    S036


DO YOU WANT TO SELECT STRUCTURES WITH COMBINATIONS OF FEATURES?n
                                                               n
                                                               n
                                                               n
                                            A "NO" reply at this point
                                               NO
                                               NO
                                               NO
                                    takes you back to CONGEN's # prompt.

                *************************




































                                  211
CONGEN manual                                              February 1981


        IV.N.2    SURVEY Subcommand Mode
                  SURVEY Subcommand Mode
                  SURVEY Subcommand Mode
                  SURVEY Subcommand Mode


                ***************************
                *                         *
                * SURVEY Subcommand Mode  *
                *                         *
                ***************************


        Although it is sometimes  sufficient to know just  the frequency
of occurrence  of standard  substructures, more often  you will  want to
identify which candidate structures contain particular substructures and
what  combinations  of  different substructures  occur  in  your  set of
candidates.  This  kind  of  analysis  requires  the  use   of  SURVEY's
                                                                SURVEY
                                                                SURVEY
                                                                SURVEY
subcommand mode.

        The  basic  concept used  in  SURVEY's subcommand  mode  is "the
                                      SURVEY
                                      SURVEY
                                      SURVEY
currently   selected  set   of  structures."   Using   SURVEY's  various
                                                       SURVEY
                                                       SURVEY
                                                       SURVEY
subcommands, Section IV.N.2.a, you may:

            1)  define  and apply  some selection  criterion for
        picking out candidate structures,

            2)  get a list of the index number of the structures
        satisfying your current selection criterion,

            3)  determine the frequency of occurrence, among the
        currently   selected   structures,   of   your   various
        substructural features


            and


            4)  you may apply  pruning operations that  can, for
        example,  permanently  remove  the  structures   in  the
        current  subset   from  your   full  set   of  candidate
        structures.

        SURVEY's subcommand mode is  identified by the "->"  prompt. The
        SURVEY
        SURVEY
        SURVEY
commands  that  you  may  enter  in  response  to  the  "->"  prompt are
summarized  in  the  next  section  Section  IV.N.2.a.    Upon  entering
SURVEY's subcommand  mode, your "currently  selected set  of structures"
SURVEY
SURVEY
SURVEY
includes all  your candidate  structures and  no selection  criterion is
defined.  The  SELECT  command allows  you  to  enter  logical (Boolean)
               SELECT
               SELECT
               SELECT
expressions defining selection  criteria. These expressions  define that
                                          These expressions  define that
                                          These expressions  define that
                                          These expressions  define that
combination  of  substructural  features  that  must  be  present  in  a
combination  of  substructural  features  that  must  be  present  in  a
combination  of  substructural  features  that  must  be  present  in  a
combination  of  substructural  features  that  must  be  present  in  a
candidate  structure  for that  candidate  to remain  in  "the currently
candidate  structure  for that  candidate  to remain  in  "the currently
candidate  structure  for that  candidate  to remain  in  "the currently
candidate  structure  for that  candidate  to remain  in  "the currently
selected  set".  For example,  if  you checked  your  set  of candidates
selected  set"
selected  set"
selected  set"
against SURVLIB and found 18 structures characterized as  containing one
        SURVLIB
        SURVLIB
        SURVLIB
or more  "CYCLOPROPENES" and  24 containing  one or  more "CYCLOBUTENES"
          CYCLOPROPENES                                    CYCLOBUTENES
          CYCLOPROPENES                                    CYCLOBUTENES
          CYCLOPROPENES                                    CYCLOBUTENES




                                  212
CONGEN manual                                              February 1981


then  the  request  "CYCLOPROPENES AND  CYCLOBUTENES"  would  select any
                     CYCLOPROPENES AND  CYCLOBUTENES
                     CYCLOPROPENES AND  CYCLOBUTENES
                     CYCLOPROPENES AND  CYCLOBUTENES
candidates containing both  at least one  CYCLOPROPENE and at  least one
                      both                CYCLOPROPENE
                      both                CYCLOPROPENE
                      both                CYCLOPROPENE
CYCLOBUTENE substructure.
CYCLOBUTENE
CYCLOBUTENE
CYCLOBUTENE

        Selection  requests can  be  built up  as  conventional, logical
combinations of substructure- (feature-) names and the  standard logical
operators AND, OR  and NOT. Parentheses should  be used to  indicate how
you intend to group terms in complex logical expressions.  Once you have
defined some selection criterion  through one application of  the SELECT
                                                                  SELECT
                                                                  SELECT
                                                                  SELECT
command then, unless you undo that selection request through a  RESET or
                                                                RESET
                                                                RESET
                                                                RESET
RESTART command,  subsequent selection  requests are  ANDed on.  Thus, a
RESTART
RESTART
RESTART
request for  "KETENE" followed  by a  request for  "ACID" will  give you
              KETENE                                ACID
              KETENE                                ACID
              KETENE                                ACID
those structures containing both a KETENE and an ACID  substructure i.e.
                                   KETENE        ACID
                                   KETENE        ACID
                                   KETENE        ACID
the combined requests are equivalent to a single request for "KETENE AND
                                                              KETENE AND
                                                              KETENE AND
                                                              KETENE AND
ACID".  (SURVEY  will not  allow  you  to combine  more  than  five such
ACID     SURVEY
ACID     SURVEY
ACID     SURVEY
separate requests).

                **********************************






































                                  213
CONGEN manual                                              February 1981


        IV.N.2.a    Glossary of SURVEY Subcommands
                    Glossary of SURVEY Subcommands
                    Glossary of SURVEY Subcommands
                    Glossary of SURVEY Subcommands
                ***********************************
                *                                 *
                * Glossary of SURVEY Subcommands  *
                *                                 *
                ***********************************

SURVEY   Short
SURVEY
SURVEY
SURVEY
command  form                   Purpose
-------  ----                   -------
SELECT   SE       To define a new, or an additional, logical
SELECT
SELECT
SELECT
                  expression identifying a combination of substructural
                  features that characterizes the desired candidate
                  structures. This new selection criterion is "ANDed"
                  with any selection criterion currently in force.

STATUS   ST       To get a summary of the number of structures
STATUS
STATUS
STATUS
                  in the currently selected set and the selection
                  criterion that they satisfy.

LIST     LI       To get a list of the index number of those
LIST
LIST
LIST
                  structures in the currently selected set.

TERMS    TE       To get a list showing the frequency of occurrence
TERMS
TERMS
TERMS
                  of your defined substructural features among the
                  structures in your currently selected set.

RESET    RESET    To undo, or erase, the last SELECT command.
RESET                                         SELECT
RESET                                         SELECT
RESET                                         SELECT

RESTART  RESTART  To remove all selection criteria, restoring all
RESTART
RESTART
RESTART
                  remaining candidate structures to "the currently
                  selected set". However, it cannot undo a REMOVE
                                                           REMOVE
                                                           REMOVE
                                                           REMOVE
                  or a REPLACE command.
                       REPLACE
                       REPLACE
                       REPLACE

DONE     DO       To exit the SURVEY functions and return to
DONE                          SURVEY
DONE                          SURVEY
DONE                          SURVEY
                  CONGEN.

REMOVE   REMOVE   To delete all structures identified as being
REMOVE
REMOVE
REMOVE
                  in the currently selected set from your
                  structure file. This is a permanent pruning
                  operation that may NOT be reversed.
                                     NOT
                                     NOT
                                     NOT

REPLACE  REPLACE  To retain, by deleting all other structures,
REPLACE
REPLACE
REPLACE
                  those structures identified as being in the
                  currently selected set will remain. This is a
                  permanent pruning operation that may NOT be
                                                       NOT
                                                       NOT
                                                       NOT
                  reversed.

                *****************************







                                  214
CONGEN manual                                              February 1981


        IV.N.2.b    SELECT Command Format 
                    SELECT Command Format 
                    SELECT Command Format 
                    SELECT Command Format 

                **************************
                *                        *
                * SELECT Command Format  *
                *                        *
                **************************


        After giving the SELECT command you will get the prompt "DESIRED
                         SELECT
                         SELECT
                         SELECT
FEATURES>". The correct response  to this prompt is a  logical (Boolean)
expression   constructed  using   the  names   of   your  substructures,
parentheses and the operators AND, OR and NOT.

        Some examples of reasonable responses are:

DESIRED FEATURES>primaryoh or secondaryoh
                 primaryoh or secondaryoh
                 primaryoh or secondaryoh
                 primaryoh or secondaryoh

DESIRED FEATURES>(alcohol or amine) and not (alcohol and amine)
                 (alcohol or amine) and not (alcohol and amine)
                 (alcohol or amine) and not (alcohol and amine)
                 (alcohol or amine) and not (alcohol and amine)

DESIRED FRATURES>not epoxides
                 not epoxides
                 not epoxides
                 not epoxides


        There are a variety of  errors that you could make on  trying to
enter a selection request. Several different error messages  may appear;
these  different messages  are intended  to give  you some  idea  of the
nature of your  error. After printing one  of the error  messages SURVEY
                                                                  SURVEY
                                                                  SURVEY
                                                                  SURVEY
will print  "ABANDONED", clear out  any partially  interpreted selection
request  and return  you to  the "DESIRED  FEATURES>" prompt.   The more
common error messages are:

        Message                                 Normal cause.
        -------                                 -------------

1) XYZYZY IS NOT ONE OF YOUR SELECTION FEATURES.
                                You mistyped the name of a substructure.

2) NO CLOSING PARENTHESIS.
                                You left out a ")" somewhere.

3) SELECTION REQUEST IMPROPERLY TERMINATED.
                                You have too many ")"s.

4) EXPECTED A STRING.
                                You have something like (A AND ),
                                                        (A AND )
                                                        (A AND )
                                                        (A AND )
                                the program was expecting the name of
                                a substructure.

                *******************************







                                  215
CONGEN manual                                              February 1981


        IV.N.3    SURVEY Second Sample Session
                  SURVEY Second Sample Session
                  SURVEY Second Sample Session
                  SURVEY Second Sample Session

                ********************************
                *                              *
                * SURVEY Second Sample Session *
                *                              *
                ********************************

        This  second example  of the  use of  SURVEY continues  from the
                                              SURVEY
                                              SURVEY
                                              SURVEY
earlier  example  (Section  IV.N.1).  Firstly,  CONGEN's   SHOW  LIBRARY
                                                           SHOW  LIBRARY
                                                           SHOW  LIBRARY
                                                           SHOW  LIBRARY
command, see  Section IV.J.6, was  used to find  how much of  the BSTERP
                                                                  BSTERP
                                                                  BSTERP
                                                                  BSTERP
library had not been processed in the previous application of SURVEY.
                                                              SURVEY
                                                              SURVEY
                                                              SURVEY

#show library
 show library
 show library
 show library
LIBRARY TO BE SHOWN:bsterp
                    bsterp
                    bsterp
                    bsterp
THAT LIBRARY CONTAINS THE FOLLOWING SUBSTRUCTURES:
1)CHAMIGRANE 2)VALERANE 3)TUTIN 4)DRIMANE 5)CARYOPHYLLANE 6)CUPARANE
7)ACORANE 8)CAROTANE 9)PSEUDO-GUAIANE 10)EREMOPHILANE 11)VETISPIRANE
12)EUDESMANE 13)SANTALANE 14)LAURANE 15)CADINANE 16)GUAIANE
17)HIMANCHLANE 18)TRICHOTHECANE 19)S023 20)S027 21)S016 22)S076 23)S011
24)S010 25)S057 26)S049 27)S021 28)S025 29)S047 30)S002 31)S013 32)S064
33)S005 34)S020 35)S065 36)S059 37)S073 38)S051 39)S036 40)S077 41)S030
42)S056 43)S034 44)S072 45)S028 46)S001 47)S044 48)S074 49)S018 50)S014
51)S068 52)S007 53)S071 54)S017 55)S045

In this second call on SURVEY, particular entries will be  selected from
                       SURVEY
                       SURVEY
                       SURVEY
the  BSTERP  library  including  GUAIANE  (16)  and  those  entries  not
     BSTERP                      GUAIANE
     BSTERP                      GUAIANE
     BSTERP                      GUAIANE
previously processed (41 S030 to 55 S045). In addition, checks are to be
made for a substructure "GEMDIMETHYLCYCLOPROPYL", defined earlier in the
                         GEMDIMETHYLCYCLOPROPYL
                         GEMDIMETHYLCYCLOPROPYL
                         GEMDIMETHYLCYCLOPROPYL
CONGEN session,

#survey
 survey
 survey
 survey

DO YOU WANT TO USE A LIBRARY OF SUBSTRUCTURES?y
                                              y
                                              y
                                              y

WHICH LIBRARY FILE? bsterp
                    bsterp
                    bsterp
                    bsterp

WHICH SUBSTRUCTURES :?                       Request for help
                     ?
                     ?
                     ?

ALL OR A LIST OF INDEX NUMBERS AND INDEX RANGES, E.G. 1 3 (6 10)
                                        CONGEN replies with an
                                explanation of the forms allowed
                                for selecting entries from a library.

WHICH SUBSTRUCTURES :16 (41 55)      Entries with index numbers
                     16 (41 55)
                     16 (41 55)
                     16 (41 55)
                                16 and in the range 41-55 inclusive
                                are requested.


READING ENTRIES FROM LIBRARY FILE.
................

Do you want to use additional substructures?y
                                            y
                                            y
                                            y



                                  216
CONGEN manual                                              February 1981


                                        Because there is still space
                                for more substructures, CONGEN asks
                                you if any of those defined in
                                current session are to be included.

SUBSTRUCTURE NAME : gemdimethylcyclopropyl
                    gemdimethylcyclopropyl
                    gemdimethylcyclopropyl
                    gemdimethylcyclopropyl
                                        In this case, just the one
                                additional substructure GEMDIMETH...
                                                        GEMDIMETH
                                                        GEMDIMETH
                                                        GEMDIMETH
                                was desired. Prompts for additional
                                substructures will occur until
                                a null reply (just a carriage return)
                                is given or the limit on the number
                                of substructures has been reached.

SUBSTRUCTURE NAME :

SCANNING THROUGH STRUCTURES.
........................................................................
........................................................................
........................................................................
etc
......................................................................

THE FOLLOWING LIBRARY FEATURES WERE NOT FOUND IN ANY STRUCTURE.
S030                                    Again, we get SURVEY's
                                                      SURVEY
                                                      SURVEY
                                                      SURVEY
S056                                      report.
S074
S018
S014
S068
S071
S017
S045

#STRUCTURES WITH DISCRIMINATING FEATURES:
         6    GUAIANE
         6    S034
         6    S072
         6    S028
         6    S001
         6    S044
       144    S007
        39    GEMDIMETHYLCYCLOPROPYL

Do you want to select structures with combinations of features?y
                                                               y
                                                               y
                                                               y
                                        This time, instead
                                of returning directly to CONGEN,
                                SURVEY's subcommand mode is entered
                                SURVEY
                                SURVEY
                                SURVEY
                                in order to select structures with
                                particular combinations of features.


->?                                  Request for help at
  ?
  ?
  ?



                                  217
CONGEN manual                                              February 1981


                                SURVEY's "->" prompt.
                                SURVEY
                                SURVEY
                                SURVEY

DONE INDEX REMOVE REPLACE RESET RESTART SELECT STATUS TERMS
                                        SURVEY replies with
                                        SURVEY
                                        SURVEY
                                        SURVEY
                                a list of its subcommands,
                                (see Section IV.N.2.a for details).

->terms
  terms
  terms
  terms
                                        A request that the
                                substructural features and their
                                frequencies be listed again.

DISCRIMINATING FEATURES ARE:
FREQUENCY  FEATURE
       6   GUAIANE
       6   S034
       6   S072
       6   S028
       6   S001
       6   S044
     144   S007
      39   GEMDIMETHYLCYCLOPROPYL

->select
  select
  select
  select
                                        To define a new structure
                                selection criterion in terms of
                                combinations of substructures.

DESIRED FEATURES>gemdimethylcyclopropyl
                 gemdimethylcyclopropyl
                 gemdimethylcyclopropyl
                 gemdimethylcyclopropyl
                                        The selection criterion
                                here was simply for any structure
                                containing one, or more, instances of
                                a GEMDIMETHYLCYCLOPROPYL substructure.
                                  GEMDIMETHYLCYCLOPROPYL
                                  GEMDIMETHYLCYCLOPROPYL
                                  GEMDIMETHYLCYCLOPROPYL

39 STRUCTURES.
                                        SURVEY replies that the
                                        SURVEY
                                        SURVEY
                                        SURVEY
                                currently selected set contains 39
                                structures.

->index
  index
  index
  index
                                        Issue command to get a list
                                of the index numbers of structures
                                in the current set.

39 structures currently selected.
Index numbers are:
  548  554  559  560  615  620  625  626  627  681  687  692
  693 1090 1091 1092 1093 1161 1166 1171 1175 1176 1231 1235
 1240 1241 1289 1290 1291 1292 1361 1367 1373 1374 1421 1422
 1423 1424 1425

->terms
  terms
  terms
  terms
                                        Show the frequency of



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CONGEN manual                                              February 1981


                                occurrence of the various substructures
DISCRIMINATING FEATURES ARE:
FREQUENCY  FEATURE
       6   GUAIANE
       6   S034
       6   S072
       6   S028
       6   S001
       6   S044
      18   S007
      39   GEMDIMETHYLCYCLOPROPYL

->select
  select
  select
  select
                                        Define a new selection
                                criterion that will further refine
                                the requirements imposed on "the
                                currently selected set of structures".

DESIRED FEATURES>guaiane or s034
                 guaiane or s034
                 guaiane or s034
                 guaiane or s034

12 STRUCTURES.

->status
  status
  status
  status
                                        Request a status report
                                to get a summary of size of the
                                currently selected set of structures
                                and of the constraints that they
                                satisfy.

12 STRUCTURES.

CURRENT SELECTION CRITERION IS :

(GEMDIMETHYLCYCLOPROPYL) AND
(GUAIANE OR S034)

->index
  index
  index
  index

12 STRUCTURES CURRENTLY SELECTED.
INDEX NUMBERS ARE:
  548  559  681  692 1090 1091 1240 1241 1289 1290 1361 1367

->?
  ?
  ?
  ?

DONE INDEX REMOVE REPLACE RESET RESTART SELECT STATUS TERMS

->reset
  reset
  reset
  reset
                                        Undo that last selection
                                request.

39 structures.

->status
  status
  status
  status



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CONGEN manual                                              February 1981


39 STRUCTURES.

CURRENT SELECTION CRITERION IS :

(GEMDIMETHYLCYCLOPROPYL)


->reset
  reset
  reset
  reset

574 STRUCTURES.


->terms
  terms
  terms
  terms

DISCRIMINATING FEATURES ARE:
FREQUENCY  FEATURE
       6   GUAIANE
       6   S034
       6   S072
       6   S028
       6   S001
       6   S044
     144   S007
      39   GEMDIMETHYLCYCLOPROPYL

->select
  select
  select
  select

DESIRED FEATURES>?
                 ?
                 ?
                 ?
                                        Request for help from
                                SELECT's "Desired features>" prompt,
                                SELECT
                                SELECT
                                SELECT
                                SURVEY replies with a simple
                                SURVEY
                                SURVEY
                                SURVEY
                                example of a selection request:

SOME LOGICAL COMBINATION OF FEATURENAMES E.G. A AND (B OR C)

DESIRED FEATURES>s007 and not gemdimethylcyclopropyl
                 s007 and not gemdimethylcyclopropyl
                 s007 and not gemdimethylcyclopropyl
                 s007 and not gemdimethylcyclopropyl

126 STRUCTURES.

->status
  status
  status
  status
126 STRUCTURES.

CURRENT SELECTION CRITERION IS :

(S007 AND NOT GEMDIMETHYLCYCLOPROPYL)

->done
  done
  done
  done

                        ***********************







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        IV.O    STEREO and Subcommands
                STEREO and Subcommands
                STEREO and Subcommands
                STEREO and Subcommands

                *************************
                *                       *
                * CONGEN Command STEREO *
                *                       *
                *************************


        The   STEREO  command   is   used  to   explore   the  potential
              STEREO
              STEREO
              STEREO
configurational stereochemical  isomerism of any  CONGEN substructure(s)
or  structure(s)  in  the  current  structure  list.   The  treatment of
stereoisomers  covers  tetrahedral  centers  including  carbon  and non-
inverting  nitrogen,  together  with  cis/trans  isomerism  about double
bonds.

        A  structure  generation  sequence  in  CONGEN  (i.e.,  GENERATE
                                                                GENERATE
                                                                GENERATE
                                                                GENERATE
followed by perhaps several IMBEDs) eventually leads to final structures
                            IMBED
                            IMBED
                            IMBED
which are topological isomers, or better, constitutional isomers for the
given molecular formula.  These structures possess only  atom properties
and  connectivity  information  as expressed  in  the  representation of
structure as a  connection table.  Nothing  about the potential  two- or
three-dimensional  nature  of   such  structures  is  conveyed   by  our
representation.   Yet  molecules  are  inherently  three-dimensional  in
nature  and   can  possess   both  configurational   and  conformational
variability.   Treatment  of  stereochemistry  in  CONGEN  is  currently
limited   to    generation   and   visualization    of   configurational
stereoisomers, i.e., isomers of  a given constitution which can  only be
interconverted by  rupture of chemical  bonds.  Cis/trans  isomerism and
the two possible configurations of four substituents about a tetrahedral
center  are  the  most common  examples  which  lead  to configurational
isomerism.

        Although we are currently developing methods for  generation and
visualization   of   conformational  stereoisomers,   no   treatment  of
conformation is included in the present version of CONGEN.  In addition,
the  current   version  of  the   STEREO  module  in   CONGEN  generates
                                  STEREO
                                  STEREO
                                  STEREO
stereoisomers without constraints.   Thus, many implausible  isomers are
constructed, including for example,  isomers with trans double  bonds in
small rings, bridged  ring systems with  an inverted bridgehead,  and so
forth.   Future  versions  of  the STEREO  module  will  have  a  set of
                                   STEREO
                                   STEREO
                                   STEREO
constraints on the stereo  structure generator, just as CONGEN  allows a
set of constraints on constitutional isomers.

        We first summarize the available subcommands under STEREO in the
                                                           STEREO
                                                           STEREO
                                                           STEREO
Glossary, Section  IV.O.1.  Then  we present a  sample session  in which
the commands are illustrated with an example, Section IV.O.2.

                ******************************







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CONGEN manual                                              February 1981


        IV.O.1    Glossary of STEREO Subcommands
                  Glossary of STEREO Subcommands
                  Glossary of STEREO Subcommands
                  Glossary of STEREO Subcommands

                **********************************
                *                                *
                * Glossary of STEREO Subcommands *
                *                                *
                **********************************


STEREO     Short
STEREO
STEREO
STEREO
command    form                Purpose
-------    -----               -------

PROJECT    PR       To give a Fischer projection for one stereocenter of
PROJECT
PROJECT
PROJECT
                    one stereoisomer

NEWMAN     NE       To give a Newman projection for two adjacent
NEWMAN
NEWMAN
NEWMAN
                    tetravalent stereocenters for one stereoisomer

CONFIGS    CO       To give the configurations for all the stereocenters
CONFIGS
CONFIGS
CONFIGS
                    for one stereoisomer.  This command also gives the
                    numbers of the stereocenters.

SYMGROUP   SY       To give the symmetry group of one stereoisomer.  The
SYMGROUP
SYMGROUP
SYMGROUP
                    group elements are represented as permutations of
                    the stereocenters.

EQUIVATOMS EQ       To give the equivalent atoms by symmetry for one
EQUIVATOMS
EQUIVATOMS
EQUIVATOMS
                    stereoisomer.

LIST       LI       To give a list of the generated stereoisomers and
LIST
LIST
LIST
                    chirality designations.

SEGMENT    SE       To define a connected segment of the structure in
SEGMENT
SEGMENT
SEGMENT
                    order to draw several stereocenters.  This can be
                    done for as many stereocenters as desired.

DONE       DO       To leave the STEREO program and return to CONGEN.
DONE                             STEREO
DONE                             STEREO
DONE                             STEREO

                ******************************
















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        IV.O.2    STEREO Sample Session
                  STEREO Sample Session
                  STEREO Sample Session
                  STEREO Sample Session

                *************************
                *                       *
                * STEREO Sample Session *
                *                       *
                *************************



        The STEREO module is begun by responding STEREO to the  CONGEN #
            STEREO                               STEREO
            STEREO                               STEREO
            STEREO                               STEREO
prompt.   The commands  which can  be given  after the  ST>  prompt from
STEREO are  summarized in the  preceding Glossary, Section  IV.O.1.  The
STEREO
STEREO
STEREO
STEREO command should be  given only for completed structures  which are
STEREO
STEREO
STEREO
either generated by CONGEN or constructed as substructures by  using the
DEFINE  SUBSTRUCTURE command,  Section IV.B.6.   The STEREO  program can
DEFINE  SUBSTRUCTURE                                 STEREO
DEFINE  SUBSTRUCTURE                                 STEREO
DEFINE  SUBSTRUCTURE                                 STEREO
handle atoms up to valence  four but considers trivalents to  be capable
of existing in  stable configurations.  Thus a  tri-substituted nitrogen
atom will  be considered as  a stereocenter.  If  the STEREO  command is
                                                      STEREO
                                                      STEREO
                                                      STEREO
given  for a  list of  structures, the  result will  be a  count  of the
stereoisomers for  each structure,  the total  count, and  the generated
stereoisomers for the last structure on the list.  Further details about
the  use  of   the  program,  the  effect   of  the  commands   and  the
interpretation of the output are given with the sample session, below.

        First, you must  define the substructure or  generate structures
for  which  stereoisomers  are  to be  generated.   The  sample  case is
3,4,7,8-tetramethyl-5-decene named, arbitrarily, DEC.  This substructure
                                                 DEC
                                                 DEC
                                                 DEC
is  built  using  the  DEFINE SUBSTRUCTURE  command  in  CONGEN.   It is
                       DEFINE SUBSTRUCTURE
                       DEFINE SUBSTRUCTURE
                       DEFINE SUBSTRUCTURE
important  to  request  a numbered  drawing  before  issuing  the STEREO
                                                                  STEREO
                                                                  STEREO
                                                                  STEREO
command to facilitate the interpretation of the output.

#DEFINE                         Issue the DEFINE command to define
 DEFINE                                   DEFINE
 DEFINE                                   DEFINE
 DEFINE                                   DEFINE
DEFINITION TYPE:SUBSTRUCTURE      the required substructure
                SUBSTRUCTURE
                SUBSTRUCTURE
                SUBSTRUCTURE
NAME:DEC
     DEC
     DEC
     DEC
(NEW SUBSTRUCTURE)
>CHAIN 10
 CHAIN 10
 CHAIN 10
 CHAIN 10
>BRANCH 3 1 4 1 7 1 8 1
 BRANCH 3 1 4 1 7 1 8 1
 BRANCH 3 1 4 1 7 1 8 1
 BRANCH 3 1 4 1 7 1 8 1
>JOIN 5 6
 JOIN 5 6
 JOIN 5 6
 JOIN 5 6
>DRAW A
 DRAW A
 DRAW A
 DRAW A

SUBSTRUCTURE DEC:

      C     C
      |     |
      C-C=C-C
     /       \
C-C-C         C-C-C
    |         |
    C         C

>DRAW N
 DRAW N
 DRAW N
 DRAW N




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CONGEN manual                                              February 1981


SUBSTRUCTURE DEC:

     12    13
      |     |
      4-5=6-7
     /       \
1-2-3         8-9-10
    |         |
   11        14

>DONE                           Definition complete
 DONE
 DONE
 DONE
DEC DEFINED


        To initiate the  STEREO program, the  user types STEREO  and the
                         STEREO                          STEREO
                         STEREO                          STEREO
                         STEREO                          STEREO
name  of  the  substructure  or  number  of  the  structure   for  which
stereoisomers are desired. The possible formats for  specifying entities
to process in STEREO are the same as for the DRAW command, Section IV.I.
              STEREO                         DRAW
              STEREO                         DRAW
              STEREO                         DRAW

#STEREO DEC                     Explore stereoisomers of DEC
 STEREO DEC                                              DEC
 STEREO DEC                                              DEC
 STEREO DEC                                              DEC
STEREOCOUNT=20                  Report of number of stereoisomers
ST>?                            Ask for help
   ?
   ?
   ?
PROJECT NEWMAN CONFIGS SYMGROUP         CONGEN replies with options
EQUIVATOMS LIST SEGMENT DONE


        The  program returns  the number  of stereoisomers  (20  in this
case) and the symbols  ST> indicating its readiness to  accept commands.
The user has typed a ? to get a list of the possible commands.

        The user  then types LIST  to get a  list of  the stereoisomers.
                             LIST
                             LIST
                             LIST
Each stereoisomer is given a number and a letter.  The number identifies
the stereoisomer and the letters are "A" for achiral and "C" for chiral.
Thus the first stereoisomer is 0A  which means that its number is  0 and
it is  achiral.  Enantiomeric pairs  of chiral stereoisomers  are listed
together.  Thus, stereoisomer 1 is  the enantiomer of 8.  It  is helpful
to issue  the command  LIST first  in order  to get  the numbers  of the
                       LIST
                       LIST
                       LIST
stereoisomers, as this will simplify the use of the  remaining commands.
Note that the numbers associated with the stereoisomers do  not increase
monotonically and that there are gaps in the numbering.

ST>LIST                       Ask to list the stereoisomers
   LIST
   LIST
   LIST

0A 1C 8C 2C 4C 3C 12C 5C 10C 6A 16A 17C 24C 18C 20C
19C 28C 21C 26C 22A


        The   command   CONFIGS   gives   the   configurations   of  the
                        CONFIGS
                        CONFIGS
                        CONFIGS
stereocenters  for  one of  the  stereoisomers.  The  user  requests the
configurations of  the stereocenters  of stereoisomer  number 1.   It is
helpful to issue the CONFIGS command second (after the LIST)  command in
                     CONFIGS                           LIST
                     CONFIGS                           LIST
                     CONFIGS                           LIST
order to get the atom numbers and configurations of each stereocenter.




                                  224
CONGEN manual                                              February 1981


ST>CONFIGS 1                  Ask for configurations
   CONFIGS 1
   CONFIGS 1
   CONFIGS 1

3:1  4:0  7:0  8:0  5:TRANS 4,7


        The output means that stereocenter 3 is in the  1 configuration,
stereocenter 4 is in the 0 configuration,...,stereocenter 5  (the double
bond) has substituents  4 and 7 trans.   This information is  not easily
interpreted so the user  requests some drawings to help  visualize these
configurations.

        The command PROJECT will give a Fischer projection for  a single
                    PROJECT
                    PROJECT
                    PROJECT
stereocenter for a single stereoisomer.  The user requests  a projection
for  stereocenter  3 of  stereoisomer  0.  The  projection  formulas are
interpreted  in  the usual  way  with the  top  and  bottom substituents
considered to be behind the plane of the page.

ST>PROJECT                    Ask for projections
   PROJECT
   PROJECT
   PROJECT
STEREOISOMER NUMBER: 0
                     0
                     0
                     0
STEREOCENTER NUMBER: 3
                     3
                     3
                     3

     11
     :
     :
 4>>>3<<<2
     :
     :
     H


        The  user  then  requests a  projection  for  stereocenter  5 of
stereoisomer  0 using  the  shortened form  of the  command.   Note that
either end of the double bond (5 or 6) could be given here.

ST>PR 0 5
   PR 0 5
   PR 0 5
   PR 0 5

 H       7
  \     /
   5===6
  /     \
 4       H


        It  is  possible  to  get  a  Newman  projection   for  adjacent
tetravalent  (i.e.   not  double bonds)  stereocenters  with  the NEWMAN
                                                                  NEWMAN
                                                                  NEWMAN
                                                                  NEWMAN
command.  The user requests a Newman projection for stereocenters  3 and
4 of stereoisomer 0.  The  user chooses 3 to be the  front stereocenter.
Three  projections are  returned with  no regard  for  their feasibility
based on energetics.

ST>NEWMAN                     Ask for Newman projections
   NEWMAN
   NEWMAN
   NEWMAN
STEREOISOMER NUMBER: 0
                     0
                     0
                     0
FRONT STEREOCENTER: 3
                    3
                    3
                    3



                                  225
CONGEN manual                                              February 1981


REAR STEREOCENTER: 4
                   4
                   4
                   4
     12                5                H
 H    !    2      H    !    2      H    !    2
  \      /         \      /         \      /
    \  /             \  /             \  /
      3                3                3
      !                !                !
  /   !  \         /   !  \         /   !  \
 5    !    H      H    !   12     12    !    5
     11               11               11

The  user   then  (incorrectly)  asks   for  a  Newman   projection  for
stereocenters 3 and 5 of  steroisomer 0 using the shortened form  of the
command.   The  program notes  this  mistake and  points  out  that only
stereocenter 4 is adjacent to stereocenter 3.  The user then types 4 and
gets the same output as before.

ST>NE 0 3 5
   NE 0 3 5
   NE 0 3 5
   NE 0 3 5

5 IS NOT A TETRAHEDRAL STEREOCENTER ADJACENT TO 3.  CHOOSE ONE OF:
 4

REAR STEREOCENTER: 4
                   4
                   4
                   4
     12                5                H
 H    !    2      H    !    2      H    !    2
  \      /         \      /         \      /
    \  /             \  /             \  /
      3                3                3
      !                !                !
  /   !  \         /   !  \         /   !  \
 5    !    H      H    !   12     12    !    5
     11               11               11

The  command  SYMGROUP will  give  the  symmetry group  for  one  of the
              SYMGROUP
              SYMGROUP
              SYMGROUP
stereoisomers.  The user requests the symmetry group of stereoisomer 0.

ST>SYMGROUP                   Issue the SYMGROUP subcommand
   SYMGROUP                             SYMGROUP
   SYMGROUP                             SYMGROUP
   SYMGROUP                             SYMGROUP
STEREOISOMER NUMBER: 0
                     0
                     0
                     0

1= 3  2= 4  3= 7  4= 8  5= 5  6= 6
1 2 3 4 5 6 +1
4 3 2 1 6 5 -1


        This output is somewhat more difficult to interpret.   The first
line gives a renumbering of the stereocenters.  Thus stereocenter atom 3
in substructure DEC has been given the number 1, stereocenter atom  4 in
                DEC
                DEC
                DEC
DEC  has  been given  2,  etc.   The symmetry  group  is  represented as
DEC
DEC
DEC
permutations  of these  new numbers.   In this  case the  symmetry group
contains two elements, one of which is the identity, given as 1 2 3  4 5
6 +1.  This means that none of the stereocenters are permuted and the +1
means  that  the  configurations of  the  sterocenters  aren't inverted.




                                  226
CONGEN manual                                              February 1981


(This  is the  distinction between  a rotation  and a  reflection).  The
other symmetry element exchanges stereocenters  1 and 4, 2 and 3,  and 5
and 6.   In addition  this symmetry element  is a  reflection operation.
The command EQUIVATOMS gives the equivalent sets of atoms for one of the
            EQUIVATOMS
            EQUIVATOMS
            EQUIVATOMS
stereoisomers.  The  user requests this  information for  stereoisomer 0
and finds there are 7 sets of equivalent atoms, each with two members.

ST>EQUIVATOMS 0               Equivalent atoms subcommand
   EQUIVATOMS 0
   EQUIVATOMS 0
   EQUIVATOMS 0

EQUIVALENT SETS OF ATOMS:
 (1 10 )  (2 9 )  (3 8 )  (4 7 )  (5 6 )
 (11 14 )  (12 13 )

The  command  SEGMENT  allows  the user  to  specify  a  segment  of the
              SEGMENT
              SEGMENT
              SEGMENT
structure  for   which  he  wants   a  drawing  with   the  stereocenter
configurations represented.  Since the structure chosen as an example is
itself a single chain, the drawing in this example can be of  the entire
structure.  The user requests a segment of length 10 and gives  the atom
numbers  1 through  10.  These  must be  connected atoms,  otherwise the
output  will  be meaningless.   The  user then  requests  a  drawing for
stereoisomer 0 and then for  stereoisomer 22.  A carriage return  to the
prompt  STEREOISOMER  NUMBER:   will  return  the  prompt   ST>.   These
projection formulas are considered to have the vertical bonds projecting
out of the page (the opposite of the Fischer projection convention given
above). The  plane of  symmetry present in  stereoisomer 22  is apparent
from the drawing.

ST>SEGMENT
   SEGMENT
   SEGMENT
   SEGMENT
HOW LONG?10
         10
         10
         10
LIST ATOM NUMBERS: 1 2 3 4 5 6 7 8 9 10
                   1 2 3 4 5 6 7 8 9 10
                   1 2 3 4 5 6 7 8 9 10
                   1 2 3 4 5 6 7 8 9 10

STEREOISOMER NUMBER: 0
                     0
                     0
                     0

    H  H  H  H     H  H  H
    !  !  !  !     !  !  !
 1--2--3--4--5==6--7--8--9-10
    !  !  !     !  !  !  !
    H 11 12     H 13 14  H

STEREOISOMER NUMBER: 22
                     22
                     22
                     22

    H  H 12       13  H  H
    !  !  !        !  !  !
 1--2--3--4--5==6--7--8--9-10
    !  !  !  !  !  !  !  !
    H 11  H  H  H  H 14  H

STEREOISOMER NUMBER:


        To leave  the STEREO  program, the  user types  DONE to  the ST>
                      STEREO                            DONE
                      STEREO                            DONE
                      STEREO                            DONE
prompt  and  the  statement  NO  FURTHER  INFORMATION  REQUESTED appears
followed by the usual CONGEN prompt #.



                                  227
CONGEN manual                                              February 1981


ST>DONE
   DONE
   DONE
   DONE
NO FURTHER INFORMATION REQUESTED

#                               Ready for next CONGEN command

                ******************************


        Further notes
        Further notes
        Further notes
        Further notes

        If the  input structure  has only  one stereoisomer,  the STEREO
                                                                  STEREO
                                                                  STEREO
                                                                  STEREO
program will usually only indicate that fact and will then return to the
CONGEN prompt #.  If the  user tries to input incorrect numbers  for the
stereoisomers or stereocenters an error message will result with  a list
of the possible correct choices.  In effect, this is an  alternative way
to obtain  this information.  Configurations  of cumulated  double bonds
are best visualized by using the PROJECT command which considers whether
                                 PROJECT
                                 PROJECT
                                 PROJECT
there are an odd or even number of double bonds in the cumulene.

                ******************************




































                                  228
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        IV.P    EXIT
                EXIT
                EXIT
                EXIT

                ***********************
                *                     *
                * CONGEN Command EXIT *
                *                     *
                ***********************


        The EXIT command  is the proper way  to leave CONGEN.   Not only
            EXIT
            EXIT
            EXIT
does  it terminate  your session  properly, but  it also  cleans  up and
deletes a number of temporary files used during your session.  Before it
exits, however, you are given one last chance to SAVE your session, just
                                                 SAVE
                                                 SAVE
                                                 SAVE
in case  you forgot.   On TOPS-10 systems  you can  designate a  file in
which  to  save  the  recording  (on  SUMEX  the  recording   is  placed
automatically in a repository from which it can be  retrieved, examined,
listed, etc.).

                ******************************

        ***** Use of the EXIT Command in CONGEN *****
              Use of the EXIT Command in CONGEN
              Use of the EXIT Command in CONGEN
              Use of the EXIT Command in CONGEN

#exit                           Issue the EXIT command
 exit                                     EXIT
 exit                                     EXIT
 exit                                     EXIT

DO YOU WANT TO SAVE YOUR SESSION ON FILE?:?     Ask for help
                                          ?
                                          ?
                                          ?

PLEASE ANSWER YES OR NO         CONGEN replies and reprompts

DO YOU WANT TO SAVE YOUR SESSION ON FILE?:yes           Yes response
                                          yes
                                          yes
                                          yes

FILE NAME:?                     Prompt for file name, CONGEN replies
          ?
          ?
          ?
                                  to request for help

A WORD OF THE FORM XXXXXX.YYY WHERE XXXXXX IS A 'NAME' OF
FROM ONE TO SIX LETTERS AND/OR DIGITS AND WHERE YYY IS AN
OPTIONAL 'EXTENSION' OF FROM ONE TO THREE LETTERS AND/OR DIGITS.
THE '.' MAY BE OMITTED IF THE EXTENSION IS OMITTED

FILE NAME:foo.1                 Opportunity to supply file name
          foo.1
          foo.1
          foo.1
SAVED ON FOO.1                  CONGEN replies
                        (The following is only for TOPS-10 versions)
DO YOU WANT TO SAVE THE RECORDING OF YOUR SESSION ON FILE?:y
                                                           y
                                                           y
                                                           y
                                If you answer no, recording lost
FILE NAME:foo.2                 Request for file name, format as above
          foo.2
          foo.2
          foo.2
RECORDING SAVED ON FOO.2        CONGEN replies

EXIT.
^C                             CONGEN exits back to operating system
@







                                  229
CONGEN manual                                              February 1981


        V    Substructures in CONGEN
             Substructures in CONGEN
             Substructures in CONGEN
             Substructures in CONGEN

                ***************************
                *                         *
                * Substructures in CONGEN *
                *                         *
                ***************************


        Earlier in the document we have described several aspects of the
definition and  use of  substructures in CONGEN.   The section  on Basic
CONGEN Concepts,  Section I.A,  introduces the  concept of  required and
forbidden  substructures  in a  structural  problem and  the  concept of
Superatoms as  a special  kind of  required substructure,  namely, those
required  substructures  which  do  not  overlap  one  another  in final
structural  candidates.   The section  on  DEFINE  SUBSTRUCTURE, Section
                                           DEFINE  SUBSTRUCTURE
                                           DEFINE  SUBSTRUCTURE
                                           DEFINE  SUBSTRUCTURE
IV.B.6 discusses how  substructures are defined  to CONGEN, and  in that
section and in the description of the GENERATE command (Section IV.E) we
                                      GENERATE
                                      GENERATE
                                      GENERATE
mention  some of  the requirements  and potential  error  conditions for
substructures used as Superatoms or constraints.

        In this section we want to reiterate some of the  earlier points
and  give  some  helpful  hints on  effective  use  of  substructures as
Superatoms and constraints.  We first discuss some general  points, then
in  subsequent  sections  (Superatoms,  Section  V.A,  and Substructures
as  Constraints,  Section V.B)  mention  some points  that  are peculiar
to use of substructures for respective purposes, for example,  what atom
and bond properties are allowed and not allowed for Superatoms.

        The first general point is that all substructures are defined in
the  same  way, using  Editstruc,  Section IV.B.6.a,  within  the DEFINE
                                                                  DEFINE
                                                                  DEFINE
                                                                  DEFINE
SUBSTRUCTURE  command  Section  IV.B.6.  Presumably  you  know  when you
SUBSTRUCTURE
SUBSTRUCTURE
SUBSTRUCTURE
define  them  whether  they  will  be  used  as  building  blocks,  i.e.
Superatoms, or as  constraints.  However, within certain  limits, namely
atom properties, a given substructure can be used either as  a Superatom
                                                  either
                                                  either
                                                  either
or as a constraint, or both.  For example, you can define a substructure
named, arbitrarily, ME, corresponding to a methyl group, and use several
                    ME
                    ME
                    ME
such substructures as Superatoms in structure generation.  If later data
place  additional  restrictions  on  the  number  of  methyls,  the same
substructure can be used to constrain the existing structures to conform
to the new data.

        The next general point  is intimately connected with  the first.
Because  CONGEN  represents  Superatoms  as  single  atoms  in structure
generation  (see  Section  I.A and  Section  V.A  to  yield intermediate
structures,  it  is  possible  to do  special  tests  which  may  not be
intuitive until you  gain some experience  with the program.   If, using
the above example of substructure ME, the new restrictions on the number
                                  ME
                                  ME
                                  ME
of methyls could be applied to intermediate structures in which ME's are
                                                                ME
                                                                ME
                                                                ME
not imbedded, then using ME as a substructure constraint must  take into
                         ME
                         ME
                         ME
account those  ME's which  exist as Superatom  names, whose  identity is
               ME
               ME
               ME
hidden  from the  constraint-testing  mechanism.  For  example,  say you




                                  230
CONGEN manual                                              February 1981


specified  at least  three ME's  as Superatoms  (see Superatom  Input to
                           ME
                           ME
                           ME
GENERATE, Section IV.E.1.  The intermediate structures will  all contain
GENERATE
GENERATE
GENERATE
three atoms named ME  and, potentially, several other carbons  as methyl
                  ME
                  ME
                  ME
groups.  If you determine that there are in fact exactly four,  then the
way to  apply the test  is to constrain  the intermediate  structures to
only one  additional substructure  whose definition  is a  methyl group,
     one
     one
     one
i.e., 4 total minus 3  "hidden".  If, however, all the methyls  had been
imbedded, the constraint can be applied as exactly four methyls, because
now all the original three are "visible" to the constraints testing.

        In  fact,  this mechanism  is  used by  CONGEN  automatically to
ensure that only  the number of  Superatoms requested is  produced.  For
example, again  using ME,  if data available  at the  beginning required
                      ME
                      ME
                      ME
exactly four methyls, and you specified exactly four as Superatoms, then
CONGEN automatically  will apply a  constraint, using the  definition of
substructure ME, that no additional methyls be produced.  This is why we
             ME          additional
             ME          additional
             ME          additional
warned earlier  Section IV.E.1  about using the  range of  occurrence of
Superatoms  as  EXACTLY  X.   If this  statement  is  made,  CONGEN will
                EXACTLY  X
                EXACTLY  X
                EXACTLY  X
automatically ensure that only X are produced, without the necessity for
                          only X
                          only X
                          only X
you to apply the constraint again.

        The  potential  aromaticity of  substructures  is  not perceived
                                                           not
                                                           not
                                                           not
automatically by  CONGEN when  the substructures  are defined  and used.
Aromatic atom types should not  be assigned to substructures to  be used
as  Superatoms.  Perception  of aromaticity  only occurs  for Superatoms
when  the  Superatom  is incorporated  into  a  structure  and undergoes
"aromatization" either explicity,  using the AROMATIZE  command, Section
                                             AROMATIZE
                                             AROMATIZE
                                             AROMATIZE
IV.H, or during  imbedding of the  Superatom (see IMBED,  Section IV.G).
                                                  IMBED
                                                  IMBED
                                                  IMBED
The  aromatic  nature  of  substructures  used  as  constraints  must be
assigned explicitly  by you during  definition of the  susbtructure.  In
such  definitions, remember  also to  specify aromatic  bonds  with bond
order "any,"  because CONGEN  will retain only  one of  possibly several
Kekule structures on aromatization and you must ensure you do not choose
the wrong  one by  explicit placement of  alternating single  and double
bonds.

        The  final general  point  concerns available  bonding  sites on
substructures.  We discuss under the HRANGE (Section IV.B.6.n) and FREEV
                                     HRANGE                        FREEV
                                     HRANGE                        FREEV
                                     HRANGE                        FREEV
(Section  IV.B.6.o)  commands   in  Editstruc  two  different   ways  of
specifying available bonding sites.  It is important to keep in mind the
interpretation of  hydrogen ranges  or free valences  by CONGEN.   If no
hydrogen ranges or free  valences are assigned, then all  valences which
                                                     all
                                                     all
                                                     all
are available (i.e., all  bonds which are not connected  to non-hydrogen
neighbors) can potentially be used to connect the substructure  to other
atoms in a structure.  (We  stress potentially because they need  not be
                                   potentially
                                   potentially
                                   potentially
connected to other, non-hydrogen atoms; the valences may also  be filled
with hydrogen  atoms).  If  you use  only the  HRANGE command,  then the
                                               HRANGE
                                               HRANGE
                                               HRANGE
assignment  of bonding  sites is  explicit, though  potentially tedious.
Atoms which are assigned hydrogen ranges (may be a range which forces an
exact number) will conform to those ranges in final structures.  If only
some atoms  are given hydrogen  ranges, the others  will again  have all
valences potentially available for bonding to non-hydrogen atoms.




                                  231
CONGEN manual                                              February 1981


        If free valences are assigned explicitly with the FREEV command,
                                                          FREEV
                                                          FREEV
                                                          FREEV
then the  interpretation by CONGEN  is quite different.   These explicit
free  valences are  forced  to connect  to non-hydrogen  atoms  in final
                    forced  to connect  to non-hydrogen  atoms
                    forced  to connect  to non-hydrogen  atoms
                    forced  to connect  to non-hydrogen  atoms
structures.  More importantly, all atoms which do not bear free valences
are assumed to have the indicated number of hydrogens attached, i.e., to
be  saturated with  hydrogens,  and hydrogen  ranges on  such  atoms are
ignored (CONGEN  tells you  so).  Because  of the  prevalence of  1H NMR
data,  hydrogen   distributions  in   substructures  are   usually  well
characterized and the FREEV command represents a simpler way  of stating
                      FREEV
                      FREEV
                      FREEV
hydrogen ranges.

        Please note that the  same interpretation of hydrogen  ranges or
free valences holds for substructures used as Superatoms or constraints.
The meaning  of free valences  in Superatoms is  obvious - they  are the
sites which will be used to connect the Superatom within the other atoms
and  Superatoms  in  the problem.   The  same  interpretation  holds for
constraints.  If a substructure used as a constraint bears explicit free
valences, then the substructure  will "fit" (see Constraints  in CONGEN,
Section  VII) in  a structure  only at  places where  such  valences are
connected   to  non-hydrogen   atoms  outside   the  periphery   of  the
substructure constraint.

                ******************************

































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        V.A    Superatoms
               Superatoms
               Superatoms
               Superatoms

                        **************
                        *            *
                        * Superatoms *
                        *            *
                        **************


        Superatoms  are  required  substructures  for   your  structural
problem which cannot overlap  one another.  This is a  restriction which
              cannot overlap  one another
              cannot overlap  one another
              cannot overlap  one another
is  inherent  to the  mechanism  for structure  generation  and  must be
adhered  to  in order  that  you  always are  certain  that  the correct
structure is present in the  list of structures produced by  CONGEN.  We
now have (9/79) an  experimental program which removes  this restriction
and thus is in many ways easier to use, but as long as you are using the
program named CONGEN, the restriction holds.

        This restriction forces you  to perform a significant  amount of
manual analysis of a structural problem to ensure that atoms included in
one Superatom cannot be the same as atoms included in another Superatom.
              cannot
              cannot
              cannot
At the same time,  if more atoms can  be included in Superatoms,  and if
the Superatoms can be made larger, the structure generation will be much
more  efficient.   Thus  you  must  strike  a  balance   between  making
Superatoms  larger  while  still  being  certain  that  they   are  non-
overlapping.  If your Superatoms do accidentally share atoms CONGEN will
not produce the correct  structure (assuming that such sharing  does not
result in inconsistent input deteced as an error condition by CONGEN, or
in obtaining 0 structures).

        Always  keep  in  mind  the  fact  that  the  representation  of
intermediate structures  in CONGEN  after structure  generation includes
Superatoms by  name only.   This is  discussed in  more detail  in Basic
CONGEN  Concepts,  Section I.A,  and  illustrated in  the  Sample CONGEN
Session, Section  II.  This introduces  considerable efficiency  to many
problems because the number of such intermediate structures is generally
far  less  than  the   number  of  final  structures   after  imbedding.
Eliminating  some  intermediate   structures  early  in  a   problem  by
recognizing  implausible connections  among Superatoms  and  other atoms
helps keep the problem manageable in terms of number of  structures.  It
is a somewhat artificial concept, however, so be sure to keep it in mind
when   designing  constraints,   because  the   mechanism   for  testing
constraints  Section  VII  cannot  examine  the  internal  structure  of
Superatoms which appear as atom names in intermediate structures.

        There are several restrictions on atom properties which apply to
substructures used  as Superatoms.   Because a  Superatom is  a specific
combination of atoms and bonds, variable atom names such as  a polyname,
or X for any name, make  no sense to CONGEN.  For the same  reason, link
   X
   X
   X
nodes which  represent variable  length chains of  atoms make  no sense.
Also, aromaticity  is detected  automatically by  CONGEN, setting  up an
artificial  situation in  which  CONGEN will  complain  about Superatoms




                                  233
CONGEN manual                                              February 1981


bearing any designation  for aromatic atom  type other than  the default
"either." CONGEN will detect the  aromatic nature of atoms and  bonds in
aromatic systems during its computations.

        Superatoms  can  have  the  variable  bond  order  ANY, however.
                                                           ANY
                                                           ANY
                                                           ANY
Normally, with  explicit bond  orders, CONGEN  will not  form additional
                                                    not
                                                    not
                                                    not
bonds between adjacent atoms in Superatoms, thereby increasing  the bond
order.  Usually you know  the multiple bond distribution well  enough to
be able  to make explicit  assignments of bond  orders between  atoms in
Superatoms.   However,  in  some instances  the  structural  problem may
involve  determining the  various ways  in which,  for  example, several
double bonds may be allocated  to a large superatom in  conjunction with
placement of other rings or  substituents.  In order to allow  CONGEN to
increase a bond  order (will occur  during imbedding), you  must specify
                                                            must
                                                            must
                                                            must
all bond orders where the increase might be possible as possessing order
ANY.
ANY
ANY
ANY

                ******************************






































                                  234
CONGEN manual                                              February 1981


        V.B    Substructures as Constraints
               Substructures as Constraints
               Substructures as Constraints
               Substructures as Constraints

                ********************************
                *                              *
                * Substructures as Constraints *
                *                              *
                ********************************


        Any substructure can be used as a constraint.  Other than actual
errors in  defining a  substructure, there are  no restrictions  on what
properties the atoms or bonds in a substructure can possess.  Using link
nodes, atom and bond type "any," and no specification of restrictions on
hydrogen  ranges, very  general substructures  can be  defined.   At the
other extreme, a substructure can be made as large as a  final structure
and explicit enough to test (e.g., PRUNE or SURVEY) for the  presence of
                                   PRUNE    SURVEY
                                   PRUNE    SURVEY
                                   PRUNE    SURVEY
a single structure in a list of structures.

        Substructure constraints can be used to require the  presence of
certain structural  features, in addition  to forbidding them.   For the
sake  of  efficiency,  all  required  substructures  should  be  used as
Superatoms  if  (and only  if)  you  can meet  the  requirement  of non-
            if
            if
            if
overlapping  substructures   for  Superatoms   (Section  V.A).    It  is
incredibly more  efficient to  use Superatoms than  to generate  tens of
thousands of structures,  only to throw most  of them away  because they
fail to contain certain required features.

        In many  cases, however,  substructures inferred  from available
data may overlap, to an unknown extent.  In such instances,  using these
substructures as required constraints  may be the only way  to implement
the  constraint.   Overlapping  substructures  can  be  used  freely  as
constraints because CONGEN checks for their presence independent  of one
another.

        When defining substructures  which will be used  as constraints,
and  while specifying  the  number of  occurrences to  be  considered in
GENERATE, PRUNE or IMBED,  there are two important  considerations.  The
GENERATE  PRUNE    IMBED
GENERATE  PRUNE    IMBED
GENERATE  PRUNE    IMBED
first concerns the representation of structures.  If your structure list
contains intermediate structures (those with unimbedded Superatoms), all
substructural constraints have  to be phrased in  terms of the  atom and
Superatom  names  present  at  that point.   This  is  discussed  in the
previous section  (Section V.A)  and in  Basic CONGEN  concepts (Section
I.A).   You  can use  a  substructural constraint  which  refers  to the
internal atom and bond distribution of Superatoms only  during imbedding
of that Superatom, or, using PRUNE, subsequent to the imbedding  of that
                             PRUNE
                             PRUNE
                             PRUNE
Superatom.

        The  other  consideration  is  how  to  specify  the  number  of
occurrences of a particular substructure.  You can do this without error
only  if  you  know  CONGEN's  convention  for  counting  the  number of
occurrences of substructures  in larger structures.  For  many problems,
the number you expect is the number detected by CONGEN.  For some cases,




                                  235
CONGEN manual                                              February 1981


however,  the  number  counted  may  be  unexpected.   Please  refer  to
Constraints  in CONGEN,  Section VII,  for a  precise definition  of the
convention and some simple examples.

                ******************************



















































                                  236
CONGEN manual                                              February 1981


        VI    Structure Generation in CONGEN
              Structure Generation in CONGEN
              Structure Generation in CONGEN
              Structure Generation in CONGEN

                **********************************
                *                                *
                * Structure Generation in CONGEN *
                *                                *
                **********************************


        Many  of the  important points  concerning  structure generation
have been made in previous sections, primarily in Basic CONGEN Concepts,
Section  I.A and  in  the description  of the  CONGEN  command GENERATE.
                                                               GENERATE
                                                               GENERATE
                                                               GENERATE
Briefly, these points  are as follows.   Structures are produced  by the
structure  generator with  any  Superatoms represented  as  single atoms
which possess the name of the Superatom and the valence specified by the
available bonding sites in the definition of the Superatom  (see Section
V.A).   These structures  are  called intermediate  structures  and must
undergo  imbedding before  final structures,  with all  atoms  and bonds
specified, are obtained.

        If no Superatoms are specified, the molecular formula  itself is
used to generate structures, and the results of this generation would be
final structures.   However, the  number of  structural isomers  of even
simple molecular formulas (e.g.,  C10H16O) is so astronomical  that such
an  approach  can only  be  used practically  for  very  small molecular
formulas.

        The  structure  generator  is  constrained  by  the  constraints
specified by you during input to the GENERATE command  (Section IV.E.2).
                                     GENERATE
                                     GENERATE
                                     GENERATE
Although a  description of the  algorithm for structure  generation with
constraints is beyond the scope of this text, CONGEN tests structures as
they  are  being  assembled against  constraints  relevant  to  the part
structures  being  produced,  in  an  attempt  to  throw  out  undesired
structures  as early  in the  generation process  as possible.   You can
generate structures without constraints  if you wish, hoping to  use the
PRUNE command (Section IV.F) later to reject those which  are undesired.
PRUNE
PRUNE
PRUNE
This is very inefficient  and might consume excessive computer  time and
file space to  store all the  structures produced from  an unconstrained
structure generation.

        There are many  structural problems which admit  the possibility
of additional bonds internal to  one or more Superatoms (bonds  may form
new  rings   or  multiple  bonds).    CONGEN  will  consider   all  such
                                                               all
                                                               all
                                                               all
possibilities in a single generation step.  In many cases it is possible
to place constraints on the number of such internal bonds, which we term
"loops," and  this can  be done  with the  CONGEN constraint  type LOOP.
                                                                   LOOP
                                                                   LOOP
                                                                   LOOP
These loops are represented  in intermediate structures by the  letter i
                                                                       i
                                                                       i
                                                                       i
connected to the appropriate Superatom  (may be ni for n>1  loops); such
                                                ni     n>1
                                                ni     n>1
                                                ni     n>1
loops can be constrained by the constraint type LOOP - see  Basic CONGEN
                                                LOOP
                                                LOOP
                                                LOOP
Concepts,  Section  I.A,  the  Sample  Session,  Section  II,  and  loop
constraints,  Section  IV.E.2.e  for  examples  of   representation  and
constraints.




                                  237
CONGEN manual                                              February 1981


        The  structure  generator  has  a  mathematical  proof   of  its
completeness   (it   generates  all   structures   possible   under  the
constraints) and irredundancy (duplicate structures are not  produced in
the  final output).   We  are currently  (9/79) unaware  of  any program
errors which might subvert  the claim of completeness  and irredundancy.
A large number  of tests against lists  of structures produced  by other
computational methods,  including programs  of others,  have led  in all
cases to agreement with the  results of the current CONGEN  program.  Of
course, CONGEN must have correct Superatoms and constraints if  there is
to be  a guarantee that  the correct  structure is in  the final  set of
structures.  This is why you  play such a crucial role in  the effective
use of the program.












































                                  238
CONGEN manual                                              February 1981


        VII    Constraints in CONGEN
               Constraints in CONGEN
               Constraints in CONGEN
               Constraints in CONGEN

                *************************
                *                       *
                * Constraints in CONGEN *
                *                       *
                *************************


        There are a few important things to understand about  how CONGEN
applies constraints to a structure or partial structure being  tested to
determine  if  constraints are  obeyed.   In this  section  we  focus on
application of substructural  constraints, which include  the constraint
types SUBSTRUCTURE, Section IV.E.2.b, and PROTON, Section  IV.E.2.c, and
      SUBSTRUCTURE                        PROTON
      SUBSTRUCTURE                        PROTON
      SUBSTRUCTURE                        PROTON
on RING, Section IV.E.2.d, constraints.  Application of the LOOP Section
   RING                                                     LOOP
   RING                                                     LOOP
   RING                                                     LOOP
IV.E.2.e, and PARTIAL  Section IV.E.2.f, constraints  is straightforward
              PARTIAL
              PARTIAL
              PARTIAL
and will be discussed only briefly below.

        The basic  task of  application of constraints  is to  search in
turn  each structure  for  the presence  and,  if found,  the  number of
occurrences of a particular constraint type.  Depending on  the required
range of occurrences (see Section IV.E.2) the structure passes  or fails
the test.  If it fails  it is discarded from further  consideration.  If
it passes it is tested against  the next constraint and so on  until all
tests have been passed or the structure has been discarded.

        The required  range of occurrences  is the  critical controlling
parameter  of  the  computation.  Although  there  are  several possible
responses  to  the  range  of  occurrence  request  (Section  IV.E.2, it
simplifies the following  discussion to refer  simply to a  range, where
the  range may  be zero  (no occurrences  required) or  a  number (e.g.,
exactly 3), in addition to a range.  If the range is not met by counting
the occurrences of a particular constraint, be it substructure  or ring,
in a structure, the structure is rejected.  There are  some efficiencies
in the  procedure to avoid  unnecessary counting, which  can be  a time-
consuming  process.  For  example, if  the request  is for  "none"  of a
particular constraint, then the structure can be rejected as soon as the
first  instance is  encountered.   If there  is a  range  requested, all
occurrences must be checked to ensure that both the min and max (min may
equal max) criteria are met.

        Substructure  Constraints.   The  number  of  occurrences  of  a
        Substructure  Constraints
        Substructure  Constraints
        Substructure  Constraints
substructure in a larger  structure is determined by a  procedure called
"graph  matching."  Graph  matching  determines  the  ways  in  which  a
substructure can  fit into  a structure.  The  legal fittings  take into
account all  atoms and bonds  and their respective  properties specified
for the substructure (see DEFINE SUBSTRUCTURE command,  Section IV.B.6);
                          DEFINE SUBSTRUCTURE
                          DEFINE SUBSTRUCTURE
                          DEFINE SUBSTRUCTURE
the fit must be exact.   This number of occurrences is  compared against
the  requested  range  of  occurrences  given  when  the  constraint was
specified (see Section IV.E.2).

        For most problems, the counting of the number of  occurrences is




                                  239
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obvious and  corresponds to chemical  intuition.  However, in  order for
CONGEN to perform graph matching and count occurrences  of substructures
there must  be precise  criteria defined for  what constitutes  a match.
The criteria used for a matching are simply that a match occurs when all
properties of the substructure  match the corresponding properties  of a
part  of  the  structure,  including  all  atoms  and  their  respective
connectivities  and  associated  properties.  In  order  to  exploit the
criterion for matching you need  only be sure that your  substructure is
defined  to  be  exactly  what you  mean.   For  example,  the following
substructure definition

#define substructure xyz
 define substructure xyz
 define substructure xyz
 define substructure xyz
>chain 3
 chain 3
 chain 3
 chain 3
>done
 done
 done
 done

defines a three carbon atom substructure which will match any place in a
structure  where three  carbon  atoms are  connected,  including several
places  in a  six-membered ring,  an isopropyl  group, a  three membered
ring,  and so  forth;  nothing was  stated about  hydrogen  ranges, free
valences  or  interconnections  among atoms  in  the  substructure.  If,
however, the following definition was made

#define substructure xyz
 define substructure xyz
 define substructure xyz
 define substructure xyz
>chain 3
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                tes the  brutal consistency of CONGEN  in counting
matches, and  also illustrates  why a range  of occurrence  is sometimes
better stated as  "at least" rather  than as "exact."  Consider mythical
tetrahedrane:

  1
 /|\
2 | 3-
 \|/
  4

and ask how many four-membered ring substructures:

1-2
| |
3-4

are present in tetrahedrane.   Intuitively, you might consider  none, or
perhaps  one, but  there are  three  as indicated  by the  edge  sets in
tetrahedrane matched by the four-membered ring:

Substructure
Matches Atoms              Edge Set
-------------              --------

  1,2,3,4               1-2,2-3,3-4,1-4
  1,2,3,4               1-2,2-4,3-4,1-3
  1,2,3,4               1-4,2-4,2-3,1-3

Note that the sets of atoms matched are the same for all  matchings, but
the node sets differ.  We can illustrate that CONGEN does, indeed, count
substructures this way through the following example:

#define molform c 4 h 4         Molecular formula of tetrahedrane
 define molform c 4 h 4
 define molform c 4 h 4
 define molform c 4 h 4
MOLECULAR FORMULA DEFINED
#generate                       GENERATE with no superatoms
 generate                       GENERATE
 generate                       GENERATE
 generate                       GENERATE
SUPERATOM:
'COLLAPSED' FORMULA IS C 4 H 4
CONSTRAINT:ring 2 none          Prohibit multiple bonds
           ring 2 none
           ring 2 none
           ring 2 none
CONSTRAINT:



                                  241
CONGEN manual                                              February 1981


.
1 STRUCTURE WAS GENERATED
#draw a 1                       Only one structure,
 draw a 1
 draw a 1
 draw a 1

#1:                               tetrahedrane

  C
 /|\
C--|-C
 \|/
  C

#def s r4                       Short form, define a four-membered
 def s r4
 def s r4
 def s r4
(NEW SUBSTRUCTURE)                ring
>ring 4
 ring 4
 ring 4
 ring 4
>done
 done
 done
 done
R4 DEFINED
#                               Ready for next CONGEN command

#def s r3                       Short form, define a three-membered
 def s r3
 def s r3
 def s r3
(NEW SUBSTRUCTURE)                ring
>ring 3
 ring 3
 ring 3
 ring 3
>done
 done
 done
 done
R3 DEFINED
#                               Ready for next CONGEN command

#prune substructure r3 ex 4     Test for exactly four three-mem.
 prune substructure r3 ex 4
 prune substructure r3 ex 4
 prune substructure r3 ex 4
CONSTRAINT:                       rings
.
1 STRUCTURE SURVIVED PRUNING    Passes test
#                               Ready for next CONGEN command

#prune substructure r3 ex 3     Test for only three R3's
 prune substructure r3 ex 3                         R3
 prune substructure r3 ex 3                         R3
 prune substructure r3 ex 3                         R3
CONSTRAINT:
*                               Fails test
NO STRUCTURES SURVIVED PRUNING          CONGEN restores original list
THE ORIGINAL LIST HAS BEEN RESTORED
#                               Ready for next CONGEN command

#prune substructure r4 none     Test for no four-membered rings
 prune substructure r4 none
 prune substructure r4 none
 prune substructure r4 none
CONSTRAINT:
*                               Fails test
NO STRUCTURES SURVIVED PRUNING
THE ORIGINAL LIST HAS BEEN RESTORED
#                               Ready for next CONGEN command

#prune substructure r4 ex 3     Test for three, as indicated in text,
 prune substructure r4 ex 3
 prune substructure r4 ex 3
 prune substructure r4 ex 3
                                  above
CONSTRAINT:
.                               Yes, passes test - tetrahedrane
                                  contains three four-membered rings
1 STRUCTURE SURVIVED PRUNING      by CONGEN's definition
#                               Ready for next CONGEN command



                                  242
CONGEN manual                                              February 1981


        Seldom  will you  encounter an  example like  the one  given for
tetrahedrane, but the previous example with isobutane is more  likely to
be encountered.  Often it  is possible to define your  substructure with
sufficient specificity that any matchings will be exactly what  you mean
and make common sense chemically.  But you have to think  very logically
and  systematically  in  some of  the  harder  cases.   Knowing CONGEN's
criteria for matching should be of some assistance.

        Ring Constraints. CONGEN  applies ring constraints  by examining
        Ring Constraints.
        Ring Constraints.
        Ring Constraints.
each structure for rings of  various sizes and comparing the  ring sizes
and numbers found  with the requested range  of occurrence of  each ring
size input as a constraint.  Ring constraints can be expressed  in terms
of  final structures,  i.e.,  you can  require  the number  of  rings of
specified  size  that you  want  in  final structures  at  any  point in
speifying ring constraints, including the initial  structure generation.
CONGEN perceives  the ring distribution  in Superatoms in  applying ring
constraints (in this respect  the behavior of CONGEN is  quite different
from application of  substructure constraints discussed in  the previous
section, where CONGEN cannot currently utilize the internal structure of
unimbedded  Superatoms  in  applying  substructural   constraints).   In
addition, CONGEN can  make some conclusions  about new ring  sizes which
will  result  when Superatoms  are  imbedded.  As  discussed  under Ring
Constraints in GENERATE, Section IV.E.2.d, CONGEN does not  perform such
               GENERATE
               GENERATE
               GENERATE
analysis completely rigorously.  Thus, some intermediate structures will
be  kept  which  will  eventually  be  discarded  using  the  same  ring
constraints during imbedding.  CONGEN, if there is any doubt  about ring
sizes obtained in future imbeddings, will be extremely  conservative and
will  keep  intermediate structures  if  it perceives  that  it  is even
remotely  possible  to  obtain  one  legal  structure   from  subsequent
imbeddings under the given ring constraint.

        Remember that  multiple bonds  are detected  by CONGEN  as small
rings, of size two.   Use of ring size two  as a constraint is  a simple
way of limiting multiple  bonds present in structures.  However,  both a
                                                        However,  both a
                                                        However,  both a
                                                        However,  both a
double  and a  triple  bond each  count as  one  ring of  size  two.  If
double  and a  triple  bond each  count as  one  ring of  size  two
double  and a  triple  bond each  count as  one  ring of  size  two
double  and a  triple  bond each  count as  one  ring of  size  two
different constraints must  be applied to  double and triple  bonds, the
constraints  must   be  stated  at   least  in  part   as  substructural
constraints.

        In  order for  you  to apply  ring constraints  properly,  it is
important to  understand how  CONGEN detects  and counts  rings.  CONGEN
detects all  rings in  a structure,  whether or  not a  ring encompasses
        all
        all
        all
other  rings  (the  10-membered ring  of  decalin  encompasses  two six-
membered rings), or is composed  of atoms which are totally  included in
other rings (the two six-membered  rings of decalin are included  in the
10-membered  ring).  This  concept may  be somewhat  artificial  in that
chemists are  often interested only  in small rings  and tend  to ignore
large rings if the large ring  is made up of small rings (e.g.,  the 10-
membered ring in decalin).  But CONGEN applies this  concept rigorously,
and as  long as you  understand it you  can apply ring  size constraints
properly.





                                  243
CONGEN manual                                              February 1981


        CONGEN counts rings  ("cycle finding") using an  algorithm which
is related in  some respects to the  algorithm used for  graph matching.
In particular, the method used to count rings in the cycle  finder bases
the  count  on different  edge  sets that  make  up a  ring,  not merely
different nodes (the concept of  edge sets is discussed in  the previous
section).  The practical implication of this is that  unexpected numbers
of rings may  be found in highly  fused ring systems.  In  such systems,
what constitutes  a ring  might be arguable,  but CONGEN's  criterion is
consistent  and  conforms  to  the  criterion  discussed   for  counting
substructures  in  the previous  section.   Again using  the  example of
tetrahedrane, let  us examine  the behavior  of CONGEN  as it  tests the
structure  for  rings of  various  sizes.  From  the  above  tests using
substructures,  we know  that there  are four  three-membered  rings and
three four-membered rings:
#prune                          Again, we are pruning the single
 prune
 prune
 prune
                                  structure in the list, tetrahedrane.
CONSTRAINT:ring 3 ex 4
           ring 3 ex 4
           ring 3 ex 4
           ring 3 ex 4
CONSTRAINT:ring 4 none          This test should reject the structure
           ring 4 none
           ring 4 none
           ring 4 none
CONSTRAINT:
*                               It does
NO STRUCTURES SURVIVED PRUNING
THE ORIGINAL LIST HAS BEEN RESTORED
#prune                         Try again, with expected number of
 prune
 prune
 prune
                                  four-membered rings
CONSTRAINT:ring 3 ex 4
           ring 3 ex 4
           ring 3 ex 4
           ring 3 ex 4
CONSTRAINT:ring 4 ex 3
           ring 4 ex 3
           ring 4 ex 3
           ring 4 ex 3
CONSTRAINT:
.                               OK, test works, structure survives
1 STRUCTURE SURVIVED PRUNING
#                               Ready for next CONGEN command


        Loop Constraints.  Loop constraints are  designed to  allow only
        Loop Constraints.
        Loop Constraints.
        Loop Constraints.
certain numbers, or a range, of internal bonds  (called "intra-superatom
bonds")  to be  formed  in designated  Superatoms.  The  number  may, of
course, be zero,  in which case no  extra internal bonds, or  Loops, are
allowed.  The application  of the constraint is  straightforward because
it  is   applied  to  the   Superatom  representation   in  intermediate
structures,  where  only Superatom  names  are present.  The  process of
structure  generation  allocates  loops  in  all  possible  ways  to all
Superatoms.  The bonds are not actually created; rather, they are simply
noted as part of the internal structural representation in CONGEN  to be
utilized during imbedding  to actually form the  bonds.  As long  as the
Superatom remains unimbedded, the number of loops can be  checked easily
in the internal representation and the constraint applied.

        A  given  range  of  occurrences  of  loops  can  be  applied to
Superatoms with a specified name.  This may be a limitation if there are
several Superatoms  with the  same name.  You  cannot apply  a different
range  of occurrences  to different  Superatoms with  the same  name.  A
structural problem  which would require  such specification  is probably
quite rare.




                                  244
CONGEN manual                                              February 1981


        Partial  Constraint.  The  mechanism  for  applying  the partial
        Partial  Constraint.
        Partial  Constraint.
        Partial  Constraint.
constraint  is  trivial.  The  number  input as  the  maximum  number of
structures to be generated is simply compared against the length  of the
growing structure list.  CONGEN stops when they are equal.

        Remember that  if the  limit is reached  before completion  of a
problem, CONGEN will keep track of  and remind you of the fact  that the
structure list is only  partial, i.e., incomplete.  You  cannot continue
the computation from  that point.  You must  always start over,  we hope
with more constraints.

        If the  total number  of structures generated  is less  than the
limit supplied  under the  partial constraint, CONGEN  will stop  with a
complete structure list. No warnings will be issued about the list being
partial, because it is not.

                ******************************







































                                  245
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        VIII    Imbedding in CONGEN
                Imbedding in CONGEN
                Imbedding in CONGEN
                Imbedding in CONGEN

                ***********************
                *                     *
                * Imbedding in CONGEN *
                *                     *
                ***********************


        The IMBED command in  CONGEN performs the function  of expanding
            IMBED
            IMBED
            IMBED
Superatoms, which  are only names  in the intermediate  structures, into
their complete structures.  The  concept of imbedding is  introduced and
discussed in some detail in  Basic CONGEN Concepts, Section I.A,  and in
IMBED (Section IV.G).  In this section we reiterate briefly some  of the
IMBED
IMBED
IMBED
important points to keep in mind while imbedding Superatoms.

        During  imbedding, all  connections between  a  given Superatom,
which is being imbedded, and  the remaining atoms and Superatoms  in the
structure are specified.  Superatoms which were connected to other atoms
or Superatoms  by "multiple" bonds  (see Basic CONGEN  Concepts, Section
I.A) will have  after imbedding the  details of that  bonding specified.
Such  bonds may  result  in formation  of  new multiple  bonds  to other
chemical atoms, but only if there is a single atom in the Superatom with
sufficient  free valence  to  form such  a bond.   More  generally, such
"multiple" bonds will result in formation of new ring systems.

        Each imbedding may yield several, possibly hundreds,  of results
for each intermediate structure depending on the complexity of  both the
Superatoms  and  the  intermediate  structure.  We   recommend  whenever
possible  that  you  exercise your  option  of  using  constraints while
imbedding so  that undesired structural  features which  were heretofore
hidden within Superatoms can be detected and structures  containing them
thrown away.  If there are several Superatoms which can be imbedded with
no additional constraints, then it  is more efficient to imbed  them all
at once.  However, if there are different constraints which apply to the
imbedding of different Superatoms, we encourage you to do  the imbedding
stepwise so that constraints appropriate to each step can be applied.

        The reason  for this suggestion  is that constraints  are tested
against structures after all Superatoms you requested to imbed have been
                   after
                   after
                   after
imbedded.  There is  no reason to  imbed several Superatoms  and produce
many thousands of structures  most of which are  discarded.  Frequently,
imbedding  a  single  Superatom to  which  several  new  constraints are
applicable  will  discard many  resulting  structures,  thereby avoiding
further expansion and later rejection of all those structures  which are
undesired.

        Loops, or internal bonds, are formed during the imbedding of any
Superatom which bears one or  more loops.  These new bonds will  be used
to form new rings within the Superatom.  The internal bonds can  be used
to increase  the bond order  between adjacent atoms  if and only  if the
                                                     if and only  if
                                                     if and only  if
                                                     if and only  if
bond  order  between  those  atoms in  the  original  definition  of the
Superatoms was specified as "any."



                                  246
CONGEN manual                                              February 1981


        Remember, CONGEN has no knowledge of the internal structure of a
Superatom name in an intermediate structure until imbedding takes place.

                ******************************




















































                                  247
CONGEN manual                                              February 1981


        IX    Aromaticity in CONGEN
              Aromaticity in CONGEN
              Aromaticity in CONGEN
              Aromaticity in CONGEN

                *************************
                *                       *
                * Aromaticity in CONGEN *
                *                       *
                *************************


        Many of the important  points about treatment of  aromaticity in
CONGEN have  been introduced  and discussed  under the  DEFINE AROMATICS
                                                        DEFINE AROMATICS
                                                        DEFINE AROMATICS
                                                        DEFINE AROMATICS
command, Section IV.B.5, and the AROMATIZE command, Section IV.H.
                                 AROMATIZE
                                 AROMATIZE
                                 AROMATIZE

        The definition of  aromaticity used by  CONGEN is based  on your
selection  of  templates  from  a  selection  representing  most  of the
important  nuclei capable  of  possessing aromatic  character  either in
isolation or in combination with other aromatic nuclei.  These templates
include  BENZENE,  PYRIDINE,  PYRIMIDINE,  FURAN,   PYRROLE,  THIOPHENE,
         BENZENE   PYRIDINE   PYRIMIDINE   FURAN    PYRROLE   THIOPHENE
         BENZENE   PYRIDINE   PYRIMIDINE   FURAN    PYRROLE   THIOPHENE
         BENZENE   PYRIDINE   PYRIMIDINE   FURAN    PYRROLE   THIOPHENE
IMIDAZOLE  and AZULENE.   You  must specify  the templates  you  wish to
IMIDAZOLE      AZULENE
IMIDAZOLE      AZULENE
IMIDAZOLE      AZULENE
consider aromatic.

        CONGEN starts with no templates defined, i.e., no  definition of
aromaticity.  You  must decide  whether or  not your  structural problem
merits a definition  of aromaticity and  choose the templates  which you
consider aromatic.   Each template  is a  substructure which  defines an
aromatic  nucleus  which  may  occur  by  itself  or  within  a  larger,
polycyclic system.  Thus, if BENZENE is included on the  AROMATICS list,
                             BENZENE                     AROMATICS
                             BENZENE                     AROMATICS
                             BENZENE                     AROMATICS
then not only benzene derivatives, but also derivatives  of naphthalene,
anthracene, etc., will be recognized as aromatic.  Internally,  there is
associated with each template a valence-bond representation of  the ring
in  the  parent  compound  (e.g.,  a  6-membered  carbocyclic  ring with
alternating double  and single  bonds for  BENZENE).  For  a ring  to be
                                           BENZENE
                                           BENZENE
                                           BENZENE
recognized as aromatic  in a given structure,  it must match one  of the
templates  on  the  AROMATICS  list, both  in  atom  names  and  in bond
                    AROMATICS
                    AROMATICS
                    AROMATICS
multiplicity, except that  double bonds in  the template are  allowed to
match single bonds which are members of neighboring, aromatic rings.

        Thus,  if BENZENE  and  PYRROLE are  on  the list,  then  in the
                  BENZENE       PYRROLE
                  BENZENE       PYRROLE
                  BENZENE       PYRROLE
structure:

                  C==C
                 /    \
                C      C
                 =    =
                  C--C
                  |   \
                  |    N
                  |   /
                  C==C


        (one  of the  resonance  forms of  indole) the  pyrrole  ring is




                                  248
CONGEN manual                                              February 1981


detected as aromatic even though it does not directly match the template
for pyrrole:

                C==C
                |   \
                |    N
                |   /
                C==C


        With BENZENE and PYRIDINE,  the program also takes  into account
             BENZENE     PYRIDINE
             BENZENE     PYRIDINE
             BENZENE     PYRIDINE
the  true  symmetry  of   the  aromatic  rings,  and  thus   avoids  the
construction of resonance duplicates.

        The  AROMATIZE command  Section  IV.H provides  a  mechanism for
             AROMATIZE
             AROMATIZE
             AROMATIZE
detection  and removal  of  structures which  are  resonance duplicates,
either  after  an  initial  GENERATE  which  might  have   created  such
                            GENERATE
                            GENERATE
                            GENERATE
structures,  or  in  intermediate stages  of  analysis  if  the previous
definition of aromaticity (may have been none) was incorrect.   Only one
of the possible Kekule forms of the duplicate (or  replicate) structures
is retained on aromatization.

        To reiterate points made  in previous sections, CONGEN  does not
automatically  perceive the  aromatic nature  of  defined substructures.
The  aromaticity  of  substructures  used  as  Superatoms  need  not  be
specified  - it  will be  perceived at  later points  in  the structural
analysis in the  context of complete  structures.  The aromatic  type of
atoms used in substructural  constraints must be assigned  explicitly by
you (either is the default,  non- or aromatic may be assigned)  in order
to be applied to  structures.  CONGEN will perceive the  aromatic nature
of structures,  if appropriate templates  have been defined  (see DEFINE
                                                                  DEFINE
                                                                  DEFINE
                                                                  DEFINE
AROMATICS command, Section IV.B.5), during use of the  GENERATE (Section
AROMATICS                                              GENERATE
AROMATICS                                              GENERATE
AROMATICS                                              GENERATE
IV.E), AROMATIZE (Section IV.H) and IMBED (Section IV.G) commands.
       AROMATIZE                    IMBED
       AROMATIZE                    IMBED
       AROMATIZE                    IMBED

        The AROMATICS list for a problem is saved when the  SAVE command
            AROMATICS                                       SAVE
            AROMATICS                                       SAVE
            AROMATICS                                       SAVE
is issued, and is restored during RESTORE.
                                  RESTORE
                                  RESTORE
                                  RESTORE

                ******************************


















                                  249
CONGEN manual                                              February 1981


        X    Tagging in CONGEN
             Tagging in CONGEN
             Tagging in CONGEN
             Tagging in CONGEN

                *********************
                *                   *
                * Tagging in CONGEN *
                *                   *
                *********************


        The concept of a tag  associated with an atom in  a substructure
was introduced in the  discussion of the Editstruc command  TAG, Section
                                                            TAG
                                                            TAG
                                                            TAG
IV.B.6.p. Tags represent a convenient mechanism for having  CONGEN count
the number of certain atoms in substructures.  Spectral  data, primarily
1H and 13C NMR, often provide information on the number of various types
                                                 number
                                                 number
                                                 number
of protons or  carbons, respectively.  Frequently, this  information can
be translated by  you directly into  specific substructures and  used as
Superatoms  or  constraints.   However,  sometimes  there  is  no simple
translation.   For example,  1H  NMR may  indicate the  number  of vinyl
protons in a structure possessing several double bonds, or the number of
aromatic protons in a structure possessing several aromatic nuclei.  13C
NMR  may provide  a count  of  the number  of sp2  carbons  in molecules
bearing  double bonds,  involving  carbon, of  several  different types.
Assignment  of   specific  substructures  to   account  for   all  these
observations is often difficult if not impossible.

        In  order to  exploit the  observed structural  information, the
concept of a tag has been included in CONGEN.  The special substructural
constraint  PROTON,  Section  IV.E.2.c,  utilizes  a  single  tag  in  a
            PROTON
            PROTON
            PROTON
substructure  effectively to  represent the  hydrogen atom  for  which a
count is desired to fulfill  your specified range of occurrence  for the
proton constraints.   The remainder of  the substructure  represents the
environment of the hydrogen atom.  This environment may be  of arbitrary
complexity, but is chosen to pinpoint the precise structural environment
of the proton constraint.

        The existence of a tag in a substructure for  proton constraints
results  in  special  treatment within  CONGEN  when  the  constraint is
actually  applied  to  a   structure.   The  use  of   substructures  as
constraints  has  been  discussed previously  in  Section  V.B.   In the
presence  of  a  tag,  the graph  matching  procedure  used  is modified
somewhat from that described earlier (Section V.B).  Without  going into
details of the procedure,  the graph matcher locates the  environment in
the structure specified by  the substructure and for each  occurrence of
the environment accumulates  a count of the  number of hydrogens  on the
tagged atom.  Because the  tag effectively differentiates the  atom from
other  atoms,  the  correct   count  is  obtained  in   instances  where
substructures  would normally  be considered  to match  only  once.  For
example, a substructure representing a double bond will match  only once
to a  double bond  in a structure  - the  alternative matching,  made by
flipping the double  bond around, possesses  the same edge  set (Section
V.B)  and  is  not  counted.   If  the  substructure  used  as  a proton
constraint was




                                  250
CONGEN manual                                              February 1981


*-C=C

however, both carbons of the double  bonds are used in the count  of the
         both
         both
         both
number of vinyl protons, in this example.

        The concept  might be clarified  with some examples.   The above
substructure  represents  vinyl  protons,  or  protons  on carbon-carbon
double  bonds.   A  proton constraint  using  this  substructure  with a
specified range  of occurrences  would perform the  desired test  for an
observed number of vinyl  protons.  As another example, assume  that you
possessed a count of the number of cyclopropyl hydrogens,  or cyclohexyl
hydrogens.  The following  two substructures would,  respectively, count
such protons if used in the PROTON constraint:
                            PROTON
                            PROTON
                            PROTON

  C
 / \
C---C-*

  C
 / \
C   C-*
|   |
C   C
 \ /
  C

Application of proton constraints  is performed taking into  account all
atom and bond properties of  the substructure bearing the tag.   If, for
example,  you  wanted to  count  only  those vinyl  protons  on  CH2 sp2
                                                                 CH2
                                                                 CH2
                                                                 CH2
carbons, then the above  C=C substructure would be modified,  giving the
                         C=C
                         C=C
                         C=C
carbon bearing the tag a  hydrogen range of exactly two.  With  a little
imagination you can probably concoct appropriate proton  constraints for
counting  protons in  very special  and specific  environments,  such as
those on carbons alpha to  aromatic rings (*-C-C, where the  rightmost C
has the property "aromatic").

        A  feature  of  CONGEN  which  has  until  this  point  not been
                                                                not
                                                                not
                                                                not
discussed because of  the difficulty new users  of CONGEN have  had with
the concept, is the  general applicability of tags.  CONGEN  will accept
and  utilize  any  tagged   substructure,  not  just  those   in  proton
constraints.  For purposes such as counting carbon types  discerned from
13C  NMR,  the  tag  can  be  used  in  a  substructure  used  in normal
substructure constraints, Section  IV.E.2.b.  The interpretation  of the
tag by  CONGEN is  slightly different  in these  instances than  for the
proton  constraints.   In  substructure  constraints  CONGEN  counts the
number of occurrences of the tagged atom in the environment given by the
                             tagged atom
                             tagged atom
                             tagged atom
substructure.   If the  interpretation  of the  proton  constraint seems
clear to you, then the  following examples should make sense,  using the
tagged substructures as normal substructural constraints.

        To count the number of  sp2 carbons, *-C=X.  Remember, X  is the
                                             *-C=X             X
                                             *-C=X             X
                                             *-C=X             X
CONGEN convention for atom type "any" (see ATNAME command  of Editstruc,
                                           ATNAME
                                           ATNAME
                                           ATNAME




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Section  IV.B.6.m).   Note  that  X could  also  match  the  name  of an
                                  X
                                  X
                                  X
unimbedded Superatom, where C=X  might not represent a real  double bond
                            C=X        not
                            C=X        not
                            C=X        not
in  final structures,  in  which case  the constraint  would  be applied
incorrectly!
incorrectly
incorrectly
incorrectly

        To  count  the  number  of carbons  in  any  four  membered ring
(remember  that the  ring may  be larger  than four  atoms if  there are
unimbedded Superatoms, whose names will match X):
                                              X
                                              X
                                              X

X--C-*
|  |
X--X


        To count the  number of aromatic carbons,  *-C, where the  C has
                                                   *-C             C
                                                   *-C             C
                                                   *-C             C
been given the aromatic type "aromatic."

        In all such cases using tags in normal substructures,  the range
of  occurrence  specified  is  not  the  range  of  occurrence   of  the
substructure, but  the actual count  of the number  of tagged  atoms you
wish to have in your structure.

        It is possible to use more than one tag in normal substructures,
but  we recommend  against it  because of  the increasing  complexity of
interpretation of what you mean by such a statement and also  how CONGEN
will interpret it.

                ******************************




























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        XI    Link Nodes in CONGEN
              Link Nodes in CONGEN
              Link Nodes in CONGEN
              Link Nodes in CONGEN

                ************************
                *                      *
                * Link Nodes in CONGEN *
                *                      *
                ************************


        The concept of link  nodes was introduced in the  description of
the Editstruc command LNODE, Section IV.B.6.q.  A link node is simply an
                      LNODE
                      LNODE
                      LNODE
atom in a substructure that represents a variable length chain of atoms,
whose length is specified by the  range of lengths input as part  of the
LNODE command.  If the  atom designated to be a  link node is in  a ring
LNODE
LNODE
LNODE
system,  the link  node  then helps  represent ring  systems  of various
sizes.  If  the link node  is in  an acyclic chain,  then the  link node
helps represent chains of various lengths.  As a simple example,  if you
required a count of three- to six-membered, saturated, carbocyclic rings
in a structure, you would define:

  C-@                           LNODE length min = 1, max = 4
                                LNODE
                                LNODE
                                LNODE
 / \
C---C


        The atom  properties associated  with the  node designated  as a
link node  will be  associated with  every atom  making up  the variable
                                     every
                                     every
                                     every
length chain.   In the above  example, the link  node has the  atom name
carbon.   That  substructure  will  match  only  three-  to six-membered
                                           only
                                           only
                                           only
carbocyclic  rings,  and  not  any  rings  bearing  heteroatoms.   Other
carbocyclic
carbocyclic
carbocyclic
relevant  properties which  a  link node  may possess  besides  name are
aromatic type and hydrogen range.

        If the bond  orders from a linknode  to its neighbors  are other
than ANY, the linknode will match a chain only if the bond orders at the
     ANY
     ANY
     ANY
two termini of the chain agree with the corresponding bond orders of the
attachments of the linknode  to other atoms in the  substructure.  There
is a possible  ambiguity when a linknode  is attached to only  one other
                                                         only  one
                                                         only  one
                                                         only  one
atom with  a bond  of multiplicity greater  than 3.   For example,  if a
quadruple bond is indicated by the symbol $ and a triple bond by #, then
the subgraph  C$L (where  L is a  linknode) is  considered to  be within
both:

                C=C       C#C
                =/    or  |/
                C         C

because the sum of the bond orders to L is four in both structures.

        Limitations: There  are several  limitation to  the use  of link
        Limitations:
        Limitations:
        Limitations:
nodes which must be noted:

        A LNODE may only be bonded to non-linknodes.
          LNODE
          LNODE
          LNODE



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        A LNODE can have no more than two neighboring atoms.
          LNODE
          LNODE
          LNODE

        If a LNODE has only one neighbor, the order of the bond  to that
             LNODE
             LNODE
             LNODE
neighbor cannot be 1.  (ie, no monovalent LNODES).
                                          LNODES
                                          LNODES
                                          LNODES

        A LNODE cannot bear a TAG (ie, LNODE cannot be used to count the
          LNODE               TAG      LNODE
          LNODE               TAG      LNODE
          LNODE               TAG      LNODE
number of protons in chains of atoms).

        Every connected component of a Substructure (ie,  every "piece")
must contain at least one atom  which is not an LNODE.  Thus,  one could
                                                LNODE
                                                LNODE
                                                LNODE
not refer to a ring using L1=L2 (L1, L2 linknodes) as a substructure.

        In counting the number of times a substructure fits into a given
structure, the graph matching  routine does not count multiple  fits for
multiple matchings  of a given  linknode.  Thus, the  substructure O-L-O
                                                                   O-L-O
                                                                   O-L-O
                                                                   O-L-O
where L is a linknode  of type C with length  from 1 to 2 will  fit only
      L                        C
      L                        C
      L                        C
once in the structure:


                              C
                             / \
                            O   O
                            |   |
                            C---C


        Further,  the  atoms  matched  by  a  given  linknode   are  not
considered to  be "used"  when two fittings  are tested  for equivalence
(recall  that  two  fittings  of a  substructure  are  considered  to be
equivalent  if they  utilize  the same  edge  set (Section  V.B)  in the
structure  being  tested).  Thus,  the  substructure O=L  where  L  is a
                                                     O=L         L
                                                     O=L         L
                                                     O=L         L
linknode of type X,  length 4, will be  counted as fitting twice  in the
                 X
                 X
                 X
above structure.  Contrast this with the substructure:

                       O
                      / \
                     X   X
                     |   |
                     X---X

which fits the above only once.

        It is currently your responsibility to see that  the limitations
are observed  - there  is no  error checking  as yet.   Note that  it is
possible to say perfectly legal things with LNODES which other  parts of
                                            LNODES
                                            LNODES
                                            LNODES
the program consider to be  non-fatal errors.  For example, to  say that
there are two C#C's (recall # is the triple bond symbol) separated  by 2
or 3 carbons, one might define the subgraph C#C#C where the  middle node
is an LNODE  with min=4, max=5.   The current error  checking mechanisms
      LNODE
      LNODE
      LNODE
will complain that the valence of the central carbon is violated.






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CONGEN manual                                              February 1981


                                 Index
                                 Index
                                 Index
                                 Index




'COLLAPSED' FORMULA  18, 29, 136      CONGEN Input  31
'EXPANDED' FORMULA  22, 23, 29,       constitutional isomers  221
   160, 162                           Constraint Input to GENERATE  139
                                      Constraint Input to IMBED  172
                                      Constraints  2, 18, 21, 25, 129,
abort  33                                139, 230, 235
AMNACD  124, 196                      Constraints in CONGEN  239
Aromatic type  55                     control-C  33
aromaticity  130, 231                 CTABLE  189, 190
Aromaticity in CONGEN  173, 248       cycle finding  244
AROMATICS  39, 40, 48, 116, 173,
   189, 195
AROMATIZE  9, 36, 37, 173, 248        DEFINE  8, 12, 35, 37, 38
ARTYPE  55, 58, 59, 104               DEFINE AROMATICS  48, 248
ATNAME  15, 55, 58, 59, 86            DEFINE ATOM  46
ATNAMED  14, 179                      DEFINE MOLFORM  12, 43
ATOM  39, 40, 46, 116                 DEFINE Subcommand AROMATICS  48
Atom names  55                        DEFINE Subcommand ATOM  46
Atom properties  55                   DEFINE Subcommand MOLFORM  43
                                      DEFINE Subcommand SUBSTRUCTURE  51
                                      DEFINE Subcommand TERMTYPE  41
Basic CONGEN Concepts  2              DEFINE SUBSTRUCTURE  13, 51, 239
BMTERP  124, 196                      DONE  15, 58, 59, 113, 214, 222,
Bond orders  55, 164                     228
Bond properties  55                   DRAW  8, 13, 19, 36, 37, 57, 59,
BORD  55, 58, 59, 80                     61, 179
BRANCH  13, 57, 59, 72
BSTERP  124, 196
                                      Editstruc  3, 13, 51, 54, 230
                                      Editstruc Command ARTYPE  104
CHAIN  15, 57, 59, 67                 Editstruc Command ATNAME  86
CONFIGS  222, 225                     Editstruc Command BORD  80
configurational stereoisomers  221    Editstruc Command BRANCH  72
conformational stereoisomers  221     Editstruc Command CHAIN  67
CONGEN Command AROMATIZE  173         Editstruc Command DONE  113
CONGEN Command DEFINE  38             Editstruc Command DRAW  61
CONGEN Command DRAW  179              Editstruc Command ERASE  107
CONGEN Command EXIT  229              Editstruc Command FREEV  94
CONGEN command FIX  116               Editstruc Command GET  64
CONGEN Command FORGET  200            Editstruc Command HALT  114
CONGEN Command GENERATE  129          Editstruc Command HRANGE  91
CONGEN Command IMBED  160             Editstruc Command JOIN  78
CONGEN Command PRUNE  156             Editstruc Command LINK  74
CONGEN Command RESTORE  205           Editstruc Command LNODE  101
CONGEN Command SAVE  203              Editstruc Command RING  69
CONGEN command SEARCH  123            Editstruc Command SHOW  60
CONGEN Command SHOW  188              Editstruc Command TAG  98
CONGEN Command STEREO  221            Editstruc Command UNJOIN  83
CONGEN Command SURVEY  207            EQUIVATOMS  222, 227
CONGEN Commands  34                   ERASE  17, 58, 59, 107

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CONGEN manual                                              February 1981







ERASE ARTYPE  111                     Imbedding in CONGEN  246
ERASE ATNAME  108                     input  31
ERASE ATOM  111                       intermediate structures  4, 19,
ERASE FREEV  110                         129, 147, 152, 184, 230, 233,
ERASE HRANGE  109                        237, 244, 246
ERASE LNODE  111                      internal bonds  6, 19, 129, 152,
ERASE TAG  110                           161, 163, 237, 244, 246
EXIT  9, 25, 33, 36, 37, 229          interrupt  33
Exit from CONGEN  33                  Interruption of CONGEN  33
                                      intra-superatom bonds  6, 129,
                                         152, 161, 163, 244
final structures  4, 24, 129, 147,    INTRODUCTION  2
   160, 170, 221, 233, 237            Introduction to Editstruc  54
Fischer projection  222, 225          ISOLIB  124, 196
FIX  8, 35, 37, 116
FIX AROMATICS  116, 118, 121, 177
FIX ATOM  116, 118                    JOIN  55, 58, 59, 78
FIX MOLFORM  116, 118
FIX SUBSTRUCTURE  116, 119
FIX TERMTYPE  116, 117                LIBRARY  16, 189, 196
FORGET  8, 36, 37, 200                LINK  57, 59, 74
Free valences  55, 91                 Link nodes  55
FREEV  15, 24, 52, 55, 58, 59, 91,    Link Nodes in CONGEN  253
   94, 231                            LIST  214, 222, 224
                                      LNODE  55, 58, 59, 101, 253
                                      LOOP  19, 141, 152, 237, 239
GENERATE  8, 17, 35, 37, 129, 237     Loop Constraints  152, 244
GENLIB  16, 124, 196                  loops  6, 19, 129, 152, 161, 162,
GET  57, 59, 64                          179, 184, 244, 246
Glossary of CONGEN Commands  35
Glossary of Constraint Types  141
Glossary of DEFINE Subcommands  40    molecular formula  2, 8, 12, 43
Glossary of Editstruc Commands  57    MOLFORM  12, 39, 40, 43, 116
Glossary of SHOW Subcommands  189     MYLIB  124, 196
Glossary of STEREO Subcommands
   222
Glossary of SURVEY Subcommands        NEWMAN  222, 225
   214                                Newman projection  222, 225
Graph matching  239                   Normal Sequence of Commands  8
                                      NUMBERED  13, 179

HALT  58, 59, 114
HISTORY  189, 194                     PARTIAL  141, 239
HRANGE  14, 52, 55, 58, 59, 91,       Partial Constraint  154, 245
   95, 231                            PROJECT  222, 225
Hydrogen ranges  55, 91               PROTON  141, 239, 250
                                      Proton Constraints  145, 250
                                      PRUNE  8, 25, 35, 37, 156, 208
IMBED  9, 22, 36, 37, 160, 246
imbedding  4

                                  256
CONGEN manual                                              February 1981







REMOVE  208, 214                      Substructure Numbering Conventions
REPLACE  208, 214                        55
RESET  214                            Substructures as Constraints  235,
RESTART  214                             250
RESTORE  9, 26, 36, 37, 205           Substructures in CONGEN  230
RING  13, 18, 57, 59, 69, 141, 239    Superatom Input to GENERATE  134
Ring Constraints  147, 243            Superatom Input to IMBED  167
                                      Superatoms  3, 17, 21, 129, 134,
                                         230, 233, 237
Sample CONGEN Session  12             SURVEY  9, 36, 37, 207, 209
SAVE  8, 25, 36, 37, 203              SURVEY First Sample Session  209
SEARCH  8, 16, 35, 37, 123            SURVEY Second Sample Session  216
SEARCH MYLIB <file name>  123         SURVEY Subcommand Mode  212
SEARCH Subcommand <library name>      SURVLIB  124, 196
   124                                SYMGROUP  222, 226
SEARCH Subcommand MYLIB  127
SEARCH <library name>  123
SEGMENT  222, 227                     TAG  55, 58, 59, 98, 250
SELECT  214                           Tagging in CONGEN  250
SELECT Command Format  215            TERMS  214
SHOW  9, 14, 36, 37, 57, 59, 60,      TERMTYPE  39, 40, 41, 116
   188                                topological isomers  221
SHOW AROMATICS  195                   TSTERP  124, 196
SHOW CTABLE  190
SHOW HISTORY  194
SHOW LIBRARY  16, 196                 UNJOIN  55, 58, 59, 84
show library bmterp  197
show library bsterp  197
show library genlib  197
show library isolib  197
show library mylib  198
show library survlib  198
show library tsterp  198
SHOW STATUS  193
SHOW Subcommand AROMATICS  195
SHOW Subcommand CTABLE  190
SHOW Subcommand HISTORY  194
SHOW Subcommand LIBRARY  196
SHOW Subcommand STATUS  193
STATUS  189, 193, 214
STEREO  9, 36, 37, 221, 223
STEREO Sample Session  223
Structure Generation in CONGEN
   237
structure generator  2, 129, 237
SUBSTRUCTURE  13, 39, 40, 51, 116,
   141, 239
Substructure Constraints  142,
   235, 239, 251


                                  257
