enumerate_reaction_workflow.py Command Help

Command: $SCHRODINGER/run enumerate_reaction_workflow.py

usage: $SCHRODINGER/run enumerate_reaction_workflow.py [-h] -rxnwf_file
                                                       RXNWF_FILE -rgroup_file
                                                       FILE_NAME INDEX
                                                       FILE_NAME INDEX -site
                                                       [KEEP_ATOM_INDEX REPLACE_ATOM_INDEX INDEX [STRUCTURE_INDEX]
                                                       ...]
                                                       [-force_hetero_substitution]
                                                       [-HOST <hostname>]

Driver for enumerating a reaction workflow. Copyright Schrodinger, LLC. All
rights reserved.

options:
  -h, -help             Show this help message and exit.
  -rxnwf_file RXNWF_FILE
                        Specify an input reaction workflow Maestro file whose
                        base name ends in "_rxnwf". (default: None)
  -rgroup_file FILE_NAME INDEX FILE_NAME INDEX
                        Specify each R-group file using this option. Define
                        each file using (1) the file name and (2) an
                        enumeration index which maps the file to sites (see
                        -site below). Files should be Maestro files containing
                        R-groups prepared with the R-Group Creator GUI. This
                        option may be specified multiple times. For example,
                        "-rgroup_file alkyl.mae 1 -rgroup_file aryl.mae 2
                        -rgroup_file alkyl.mae 3" means that for sites with
                        enumeration indices 1 and 3 the alkyl.mae file will be
                        used while for sites with enumeration index 2 the
                        aryl.mae file will be used. Note that when multiple
                        sites use the same file there is an additional option
                        -force_hetero_substitution which controls whether to
                        return only the hetero-substituted results or both
                        hetero- and homo-substituted results. (default: None)
  -site [KEEP_ATOM_INDEX REPLACE_ATOM_INDEX INDEX [STRUCTURE_INDEX] ...]
                        Specify each enumeration site using this option.
                        Define each site using at least three integers, (1) an
                        atom index which specifies the direction of the
                        substitution relative to (2), (2) an atom index which
                        specifies the substitution site, and (3) an
                        enumeration index which maps the site to an R-group
                        file (see -rgroup_file above). Atom indices for (1) (a
                        "from" atom) and (2) (a "to" atom) should be bonded
                        with a single acyclic bond and on substitution are
                        kept and replaced, respectively. This option may be
                        specified multiple times. For example, "-site 4 3 1
                        -site 23 17 2 -site 9 10 1" means that atoms 3 and 10
                        will be substituted with some R-group (indexed with
                        the 1 mapping to some file) such that atoms 4 and 9
                        respectively are kept, while atom 17 will be
                        substituted with a potentially different R-group
                        (indexed with the 2 potentially mapping to a different
                        file) such that atom 23 is kept. An optional fourth
                        integer could be specified that indexes in the given
                        input reaction workflow file the structure to which
                        this site applies to. If not provided then equivalent
                        indexing is assumed. (default: None)
  -force_hetero_substitution
                        By default when sites with different enumeration
                        indices use the same R-group file both hetero- and
                        homo-enumerated results are returned. Use this option
                        to return only hetero-enumerated results in such
                        cases. (default: False)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)