extract_clusters_driver.py Command Help

Command: $SCHRODINGER/run extract_clusters_gui_dir/extract_clusters_driver.py

usage: $SCHRODINGER/run extract_clusters_gui_dir/extract_clusters_driver.py
       [-h] [-extract CLUSTER_TYPE] [-random QUANTITY] [-dist ANGSTROMS]
       [-measure MEASUREMENT]
       [-formula MOLECULAR_FORMULA | -index MOLECULAR_INDEX]
       [-specnum CRITERION] [-write_full_stuct] [-HOST <hostname>] [-D]
       [-VIEWNAME <viewname>] [-JOBNAME JOBNAME]
       input_file

Extracts clusters or dimers from a larger system Copyright Schrodinger, LLC.
All rights reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -extract CLUSTER_TYPE
                        What to extract. "molecules" are isolated molecules,
                        "dimers" are pairs of nearest neighbor molecules,
                        "clusters" have a single molecule at their center
                        surrounded by all nearest neighbors, and
                        "dimer_clusters" have a dimer at the center surrounded
                        by all nearest neighbors of either dimer molecule.
                        (default: dimers)
  -random QUANTITY      Extract this many clusters chosen randomly from all
                        possible clusters. The default is to extract all
                        possible clusters. (default: None)
  -dist ANGSTROMS       The threshold distance for two molecules to be nearest
                        neighbors.How the distance is measured is determined
                        by the -measure setting. (default: 4.0)
  -measure MEASUREMENT  What atoms determine whether two molecules meet the
                        -dist nearest neighbor criterion. "all" means all
                        atoms are considered, "heavy" means only heavy atoms
                        are considered, "com" means the center of mass of each
                        molecule is used. (default: all)
  -formula MOLECULAR_FORMULA
                        The molecular formula of a species that should or
                        should not be extracted. The formula must be in Hill
                        notation. See the -specnum flag for information on how
                        to indicate how this flag affects what is extracted.
                        If this flag is used then -specnum must also be used.
                        This flag may not be combined with -index. By default,
                        all species will be extracted. (default: None)
  -index MOLECULAR_INDEX
                        The molecule number of one example molecule in a
                        species that should or should not be extracted. See
                        the -specnum flag for information on how to indicate
                        how this flag affects what is extracted. If this flag
                        is used then -specnum must also be used. This flag may
                        not be combined with -formula. Note that molecule
                        numbers start with 1. (default: None)
  -specnum CRITERION    Limit extracted objects to ones that contain this
                        number of molecules that meet the -formula or -index
                        settings. This applies only to the central molecule(s)
                        of the cluster, not the nearest neighbors. For
                        instance, for a molecule cluster, this applies only to
                        the central molecule. For a dimer cluster, this
                        applies only to the two molecules in the dimer.
                        Choices are "none", "one", "some", or "two". some and
                        two only apply to dimers, and some means "at least
                        one". If this flag is used then -formula or -index
                        must also be used. (default: None)
  -write_full_stuct     Include the full structure with all molecules as the
                        first structure in the output file (default: False)

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)