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 FORCEFIELD] [-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 FORCEFIELD
                        Force field to use to convert the semi-crystal
                        structure to desmond ready system. (default: None)
  -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)