order_parameter_driver.py Command Help

Command: $SCHRODINGER/run order_parameter_gui_dir/order_parameter_driver.py

usage: $SCHRODINGER/run order_parameter_gui_dir/order_parameter_driver.py
       [-h] -director_abc_coeffs float float float -descriptors_file filename
       [-HOST <hostname>]
       cms_file

Driver for order parameter analysis.

Copyright Schrodinger, LLC. All rights reserved.

positional arguments:
  cms_file              Specify the Desmond output *cms file on which to run
                        the order parameter analysis.

options:
  -h, -help             Show this help message and exit.
  -director_abc_coeffs float float float
                        Specify the static reference director vector used to
                        determine the order parameters. Provide three
                        coefficients taken in the basis of lattice vectors.
                        For example, 0. 0. 1. means along the c-lattice vector
                        which for a cubic cell is typically the Cartesian
                        z-axis.
  -descriptors_file filename
                        Specify a *json file containing descriptors. A
                        separate order parameter analysis is performed for
                        each of the given descriptors. Descriptors provide the
                        system vectors used to determine the order parameters.
                        Fields include a top-level "name" property, which is
                        just a string to reference the descriptor, "group",
                        which is a string allowing the order parameters for
                        related descriptors to be grouped into a single output
                        *csv file and plotted in the Order Parameter Analysis
                        Viewer GUI as avg. order parameter vs ASL rather than
                        as order parameter vs frame, "asl", which is an ASL
                        specifying over which part of the system to compute
                        descriptors, "atype", which specifies the type of
                        descriptor, and "smarts", which is the SMARTS pattern
                        for the descriptor when using SMARTS-based
                        descriptors. The meanings of the types of descriptors
                        are dipole is an electric dipole moment,
                        moment_of_inertia is the largest principle moment of
                        inertia axis, SMARTS_nonunique_bonds includes
                        contributions from all matched bonds,
                        SMARTS_unique_pair includes contributions from unique
                        matching pairs, and SMARTS_unique_triple_normal
                        includes contributions from plane normals of the
                        unique matching triples. See the file format below.

Job Control Options:
  -HOST <hostname>      Run job remotely on the indicated host entry.

The descriptors file has the following format:

{
    "some_name_1":{
        "group":"some_group",
        "asl":"some_ASL",
        "atype":"some_type",
        "smarts":"some_SMARTS"
    },
    "some_name_2": ...
}