same_graph.py Command Help

Command: $SCHRODINGER/run same_graph.py

usage: 
    $SCHRODINGER/run same_graph.py <pv_or_fmp> -t <template.fmp> -o <out>

    Generate <out>.fmp file using <pv_or_fmp> file as input, but only choose edges that is in
    existing fmp file. Graph optimization parameters will be taken from <template.fmp> if they
    are not specified.
    

Create fmp file with the same edges as a template fmp file.

positional arguments:
  pv_or_fmp             mae or fmp input file

options:
  -h, --help            show this help message and exit
  -t TEMPLATE, -template TEMPLATE
                        <template.fmp> input file
  -replace-receptor-only
                        Replace the receptor in template graph by the 1st
                        structure in the given pv file. Other options will be
                        ignored.
  -retain-atom-mapping  Retain atom mapping from template graph.
  -keep-experimental-dg
                        Keep the experimental dG values from the template.
  -o OUT, -output OUT   output basename. There will be two files <out>.fmp and
                        <out>.edge.
  -e ENVIRONMENT, -environment ENVIRONMENT
                        Number of environment structures (default 1) in .pv
                        file (if given).-1 means to use the environment
                        structures from the template.
  -m ATOM_MAPPING, -atom-mapping ATOM_MAPPING
                        atom-mapping for fep_mapper.py
  -mapping-scheme MAPPING_SCHEME
                        mapping-scheme for fep_mapper.py
  -rules RULES          rules