stereoizer Command Help

Command: $SCHRODINGER/utilities/stereoizer

usage: stereoizer [-v] [-h] [-a] [-g] [-n <number>] [-pat {0,1,2,3}] [-retain]
                  [-pat_keep_orig_off] [-restrict_expansion] [-skip_bad]
                  [-dont_vary_double_bonds] [-vary_ring_anc <number>]
                  [-label_specified_chiralities] [-verb {0,1,2,3}]
                  input_file output_file

positional arguments:
  input_file            Input file name.
  output_file           Output file name.

options:
  -v, -version          Show the program's version and exit.
  -h, -help             Show this help message and exit.
  -a                    Disregard existing chirality properties and determine
                        the chiralities from geometry if possible. Assume that
                        all chiralities are variable for enumeration purposes.
  -g                    Ignore existing chirality properties and assign the
                        chiralities using geometry where possible. Do not
                        enumerate the newly determined chiralities.
  -n <number>           Generate up to this many stereoisomers.
  -pat {0,1,2,3}        Set the type of enforcement for combinations of chiral
                        atoms: 0 - no enforcement; 1 - enforce combinations
                        that should always be met (e.g. for bridging atoms in
                        norbornane); 2 - class 1 plus patterns which are
                        expected to be followed (e.g. conserved patterns of
                        chiralities in steriods); 3 - class 2 plus any
                        additional patterns in the database; The default is
                        class 2.
  -retain               Used with -a option. Ensure that the input chiral
                        properties are present in at least one output
                        structure.
  -pat_keep_orig_off    Turn off retention of original templates that fail to
                        specified patterns of chiral atoms.
  -restrict_expansion   Do not vary chiralities that are explicitly listed as
                        undefined in the input file.
  -skip_bad             During generation of specified number of
                        stereoisomers, skip all structures with bad chirality
                        combination.
  -dont_vary_double_bonds
                        During generation of the specified number of
                        stereoisomers, do not vary double-bonds whose parity
                        is labeled as variable.
  -vary_ring_anc <number>
                        Controls whether ring anc values are varied.
  -label_specified_chiralities
                        Set b_st_SpecifiedChirality atom property for chiral
                        atoms with specified (rather than sampled) chirality.
  -verb {0,1,2,3}       controls MMERR level of reporting. 0: MMERR_FATAL -
                        only report errors; 1: MMERR_WARNING - only report
                        errors and warnings; 2: MMERR_INFO - report errors,
                        warnings, and processing information; 3: MMERR_DEBUG -
                        report errors, warnings, processing information, and
                        debugging information.