semi_crystal_builder_driver.py Command Help

Command: $SCHRODINGER/run semi_crystal_builder_gui_dir/semi_crystal_builder_driver.py

usage: $SCHRODINGER/run semi_crystal_builder_gui_dir/semi_crystal_builder_driver.py
       [-h] -input_file INPUT_FILE [-extend_cell EXTEND_CELL]
       [-num_repeats NUM_REPEATS] [-chains CHAINS] [-density DENSITY]
       [-crystallinity CRYSTALLINITY] [-search_radius SEARCH_RADIUS]
       [-forcefield FORCE_FIELD] [-enable_metal_force_field]
       [-vdw_scale VDW_SCALE] [-tries_per_mol TRIES_PER_MOL]
       [-tries_per_dc TRIES_PER_DC] [-nucleation_factor NUCLEATION_FACTOR]
       [-rep_style {wire,tube,thick_tube,ball_and_stick}]
       [-color_by {element,molecule_number,crystallinity}] [-ncells NCELLS]
       [-ortho] [-search_nf] [-pre_exisiting] [-debug_log] [-seed SEED]
       [-HOST <hostname>] [-D] [-VIEWNAME <viewname>] [-JOBNAME JOBNAME]

This script will launch semi-crystalline builder using the given crystal
structure. Copyright Schrodinger, LLC. All rights reserved.

options:
  -h, -help             Show this help message and exit.
  -input_file INPUT_FILE
                        Input file (default: None)
  -extend_cell EXTEND_CELL
                        Replicate the unit cell by in a,b,c directions.
                        (default: 5,5,5)
  -num_repeats NUM_REPEATS
                        Number of monomers in a chain. (default: 50)
  -chains CHAINS        Number of chains in the system. (default: 5)
  -density DENSITY      Target density of the semi-crystal structure.
                        (default: None)
  -crystallinity CRYSTALLINITY
                        Target percentage ratio of amorphous to crystal
                        backbone atoms. (default: 70)
  -search_radius SEARCH_RADIUS
                        Search distance for bonding the tail atom to active
                        crystal atom. (default: 5)
  -forcefield FORCE_FIELD
                        Force field to use to convert the semi-crystal
                        structure to desmond ready system. (default: None)
  -enable_metal_force_field
                        Use the metal force field for metal atoms. This is
                        only relevant if using OPLS5, and if not specified
                        then the standard OPLS5 force field will be used for
                        all atoms including metals. (default: False)
  -vdw_scale VDW_SCALE  Initial clash vdW scale factor (default: 0.25)
  -tries_per_mol TRIES_PER_MOL
                        Placement attempts per chain. (default: 10)
  -tries_per_dc TRIES_PER_DC
                        Attempts per clash distance. (default: 5)
  -nucleation_factor NUCLEATION_FACTOR
                        Nucleation factor for the crystal. Setting it to 1
                        bias towards having only one nuclei and 0 will lead to
                        multiple of them. (default: None)
  -rep_style {wire,tube,thick_tube,ball_and_stick}
                        How to represent output structure. "wire", "tube",
                        thick_tube, and ball_and_stick are default Maestro
                        representation,Wire, Tube, Thick tube, and Ball and
                        stick (default: wire)
  -color_by {element,molecule_number,crystallinity}
                        How to color atoms in the final structure.
                        "crystallinity" colors crystal atoms with element
                        style andamorphous atoms magenta. "element" and
                        "molecule_number" are the default Maestro element and
                        molecule number coloring scheme respectively. The
                        default is crystallinity. (default: crystallinity)
  -ncells NCELLS        The number of cells to produce. Each cell will be
                        generated with a different random seed so that the
                        cells have different amorphous phase distribution.
                        (default: 1)
  -ortho                Enforce the final cell to be orthorhombic. (default:
                        False)
  -search_nf            Search for the nucleation factor for given input
                        parameters. (default: False)
  -pre_exisiting        Input structure comprises of pre-existing crystal and
                        monomer. (default: False)
  -debug_log            Write debug log file. (default: False)
  -seed SEED            Seed for random number generator. (default: 1234)

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)