complex_enumeration_driver.py Command Help

Command: $SCHRODINGER/run complex_enumeration_gui_dir/complex_enumeration_driver.py

usage: $SCHRODINGER/run complex_enumeration_gui_dir/complex_enumeration_driver.py
       [-h] -metal ATOMIC_SYMBOL [-num NUMBER_OF_LIGANDS]
       [-geom VSEPR_GEOMETRY] [-homoleptic] [-min_unique NUMBER_OF_LIGANDS]
       [-max_unique NUMBER_OF_LIGANDS] [-sqp] [-flip]
       [-sqp_iso SQUARE_PLANAR_ISOMER] [-oct_iso OCTAHEDRAL_ISOMER]
       [-min [{ff,xtb}]] [-dedup] [-dedup_opt] [-dedup_tol ANGSTROMS]
       [-secondary LIGAND_FILE] [-num_secondary LIGANDS] [-HOST <hostname>]
       [-D] [-VIEWNAME <viewname>] [-JOBNAME JOBNAME]
       input_file

Utilities for complex enumeration and stability analysis. Copyright
Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file of ligand structures. Each structure should
                        be marked with a dummy atom at each dentation point.

options:
  -h, -help             Show this help message and exit.
  -metal ATOMIC_SYMBOL, -m ATOMIC_SYMBOL
                        Atomic symbol of the central atom of the complex.
                        (default: None)
  -num NUMBER_OF_LIGANDS
                        Number of ligands in each complex. Either -num or
                        -geom must be given, but not both. (default: None)
  -geom VSEPR_GEOMETRY  VSEPR geometry of the complex. Choices are octahedral,
                        trigonal_bipyramidal, square_planar, tetrahedral,
                        trigonal_planar, linear, pentagonal_bipyramidal,
                        square_antiprismatic, tricapped_trigonal_prismatic,
                        square_pyramidal. (default: None)
  -homoleptic           Create homoleptic complexes only. This is equivalent
                        to -min_unique 1 -max_unique 1 and overrides any
                        setting for those flags (default: False)
  -min_unique NUMBER_OF_LIGANDS
                        Complexes must have at least this many unique ligands
                        (default: None)
  -max_unique NUMBER_OF_LIGANDS
                        Complexes must not have more than this many unique
                        ligands (default: None)
  -sqp                  For 4-coordinate complexes, create square planar
                        complexes. The default is tetrahedral complexes.
                        (default: False)
  -flip                 For bidentate ligands, form both isomers by flipping
                        the two coordinating positions. (default: False)
  -sqp_iso SQUARE_PLANAR_ISOMER
                        For square planar complexes, prefer this isomer. The
                        option is only meaningful if bidentate ligands and
                        -sqp are used and -flip is not used. Bidentate ligands
                        should be defined consistently so that the R1 and R2
                        positions are meaningful for forming isomers. Choices
                        are cis or trans (default: cis)
  -oct_iso OCTAHEDRAL_ISOMER
                        For octahedral complexes, prefer this isomer. The
                        option is only meaningful if bidentate ligands are
                        used and -flip is not used. Bidentate ligands should
                        be defined consistently so that the R1 and R2
                        positions are meaningful for forming isomers. Choices
                        are facial or meridional (default: facial)
  -min [{ff,xtb}]       Do a minimization of each complex after building it.
                        This flag can take an optional value: ff specifies a
                        force field minimization, while xtb specifies an xTB
                        minimization. Including this flag but not specifying
                        any value is the same as specifying ff. (default:
                        False)
  -dedup                Remove duplicates via XYZ-coordinate matching.
                        (default: False)
  -dedup_opt            Count optical isomers as duplicates when removing
                        duplicates. (default: False)
  -dedup_tol ANGSTROMS  Threshold for the maximum difference in any atom
                        position when determining duplicate structures. If
                        -min is used, the geometry after minimization is used
                        for removing duplicates. (default: None)
  -secondary LIGAND_FILE
                        A second ligand file to draw ligands from. Each
                        complex will contain ligands from both the input file
                        and the secondary file. The number of ligands taken
                        from the secondary file is determined by the
                        -num_secondary flag. (default: None)
  -num_secondary LIGANDS
                        The number of ligands from the secondary ligand file
                        in each complex. See -secondary (default: 1)

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.
                        (default: localhost)
  -D, -DEBUG            Show details of Job Control operation. (default:
                        False)
  -VIEWNAME <viewname>  Specifies viewname used in job filtering in maestro.
                        (default: False)
  -JOBNAME JOBNAME      Provide an explicit name for the job. (default: None)