distribute_voids_driver.py Command Help

Command: $SCHRODINGER/run distribute_voids_gui_dir/distribute_voids_driver.py

usage: $SCHRODINGER/run distribute_voids_gui_dir/distribute_voids_driver.py
       [-h] [-num STRUCTURES] [-void_pct PERCENT] [-force] [-dist ANGSTROMS]
       [-retries NUMBER_OF_TRIES] [-atoms NUMBER_OF_ATOMS] [-bound OPERATOR]
       [-seed SEED]
       input_file

Delete molecules in a system to create voids that are distributed semi-
randomly throughout the system. An attempt is made to not place voids next to
each other. Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file

options:
  -h, -help             Show this help message and exit.
  -num STRUCTURES       Number of structures to create with different void
                        configurations (default: 1)
  -void_pct PERCENT     Remove this percent of molecules to create voids. The
                        actual number of molecules removed will be rounded to
                        the nearest integer. (default: 5.0)
  -force                Remove the requested number of molecules even if
                        neighbors must be removed to meet the -void_pct
                        criterium. (default: False)
  -dist ANGSTROMS       Distance threshold for which a molecule is considered
                        a neighbor. (default: 4.0)
  -retries NUMBER_OF_TRIES
                        The number of tries to find a set of void locations
                        that are non-adjacent. After this many tries, the most
                        voids found will be used unless -force is given.
                        (default: 1000)
  -atoms NUMBER_OF_ATOMS
                        Threshold for number of atoms in molecules that may be
                        removed to create voids. See -bound. (default: None)
  -bound OPERATOR       Whether the threshold given by -atoms is a lower bound
                        (lower), upper bound (upper), or the exact number
                        (exact) for the number of atoms in molecules that can
                        be removed to make a void. (default: lower)
  -seed SEED            Seed for random number generator. (default: 1234)