reaction_energetics_enumeration_driver.py Command Help

Command: $SCHRODINGER/run reaction_energetics_enumeration_gui_dir/reaction_energetics_enumeration_driver.py

usage: $SCHRODINGER/run reaction_energetics_enumeration_gui_dir/reaction_energetics_enumeration_driver.py
       [-h]
       [-keywords KEYWORD=VALUE KEYWORD=VALUE ... [KEYWORD=VALUE KEYWORD=VALUE ... ...]]
       -enum ENUMERATION_BASE_NAME [-freeze WHAT] [-no_clean] [-TPP TPP]
       [-cpus REMOVED] [-HOST <hostname>]
       input_file output_file

Enumerate each step of a reaction and then run each step through Jaguar to
compute the energy of each step for each enumerated reaction. Copyright
Schrodinger, LLC. All rights reserved.

positional arguments:
  input_file            Input file of structures. Each file should be tagged
                        with the structure property
                        s_matsci_Reaction_Energetics_Moiety. The value of this
                        property must be one of reactant, tstate,
                        intermediate, or product. Each structure must also be
                        tagged with the structure property
                        i_matsci_Reaction_Energetics_Step_Index, with the
                        value being an integer indicating what order this this
                        structure appears in during the reaction path. Indexes
                        start at 1. The reactant should be index 1, and any
                        product should be index n, where n is the number of
                        structures in the path.
  output_file           Output file for processed reaction structures.

options:
  -h, -help             Show this help message and exit.
  -keywords KEYWORD=VALUE KEYWORD=VALUE ... [KEYWORD=VALUE KEYWORD=VALUE ... ...], -k KEYWORD=VALUE KEYWORD=VALUE ... [KEYWORD=VALUE KEYWORD=VALUE ... ...]
                        Jaguar keywords to include in calculations. If this is
                        the last flag before the input/output file names, use
                        -- to terminate the list of keywords. (default: None)
  -enum ENUMERATION_BASE_NAME, -e ENUMERATION_BASE_NAME
                        The base name of the enumeration files (default: None)
  -freeze WHAT, -f WHAT
                        What to freeze in all structures. "core" freezes all
                        atoms that are not part of an enumerated R-group.
                        "none" freezes no atoms. To freeze a custom set of
                        atoms, include the atom indexes to freeze as a comma-
                        separated list of numbers with no spaces - i.e.
                        1,2,4,5,6. For any option other than core, transition
                        state structures are first optimized with core frozen
                        to a minimum and then a transition state optimization
                        is performed with the specified constraints or lack
                        thereof. (default: core)
  -no_clean             The default is to do a force field minimization of
                        enumerated structures while holding the core frozen.
                        Use this flag to prevent this. (default: False)
  -TPP TPP              Specify the number of threads to use for parallelizing
                        each subjob that supports threading. (default: 1)
  -cpus REMOVED, -c REMOVED
                        The -cpus option was removed in Suite 2023-4. Use
                        -HOST:X to indicate that X subjobs should run
                        simultaneously and -TPP to indicate the number of
                        threads per subjob. (default: None)

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