fep_groups.py Command Help

Command: $SCHRODINGER/run fep_groups.py

usage: 
    A Schrödinger script to set the pKa or relative populations of the compounds
    in FEP+ node groups.

    Using a population file
    $SCHRODINGER/run -FROM scisol fep_groups.py <in>.fmp -population-file <populations>.tsv -o <out>.fmp

    Note: If the populations were calculated at a known pH, use the
    "-ph <pH-value>" option to save it to the graph.

    Population files specify node grouping and populations using a three-column
    tab-separated value format:
    
	Title	Population	Group number
	Liga_neutral	0.9	0
	Liga_charge	0.1	0
	Ligb_neutral	0.8	1
	Ligb_charge	0.05	1
	Ligbt_neutral	0.05	1
	Ligbt_charge	0.10	1

    There are three things to note when specifying populations this way:
        1. the headers are mandatory
        2. the Group number column values have no meaning other than
           uniquely identifying the group to which each node belongs
        3. if a node has multiple conformers in the graph, only a single
           representative conformer should be chosen to represent all of them.
           Two nodes that are conformers of each other should not appear in the
           same population file.

    We also support reading population files that use an older format in which
    all of the data for a node group is put on the same row:
    
    # ligand ligand [...] percent percent [...]
    Liga_neutral Liga_charge 0.9 0.1
    Ligb_neutral Ligb_charge Ligbt_neutral Ligbt_charge 0.8 0.05 0.05 0.10

    Note that this format is deprecated and will not be supported beyond the
    2024-3 release.

    Using a pKa file
    $SCHRODINGER/run -FROM scisol fep_groups.py <in>.fmp -pka-file <pka-file>.txt -o <out>.fmp

    Example of pKa file
    
    pH  7.0

    # ligand     ligand      pka
    Liga_neutral Liga_charge 3.43
    Ligb_neutral Ligb_charge 3.25

    Using EpikX for predicting the solvent populations
    $SCHRODINGER/run -FROM scisol fep_groups.py <in>.fmp -epikx -ph <pH-value> -o <out>.fmp

    Note: EpikX population predictions will be normalized by default. To skip
    population normalization add the -skip-normalization option.
    

positional arguments:
  infmp                 Input fmp file path

options:
  -h, --help            show this help message and exit
  -epikx                Run EpikX at a target pH to predict solvent
                        populations of compounds in tautomer and protomer node
                        groups. Must also provide a -ph argument. (default:
                        False)
  -p POP_FILE_PATH, -population-file POP_FILE_PATH
                        File with populations of tautomer and pka related
                        molecules. (default: None)
  -pka-file PKA_FILE_PATH
                        File with pH and pKas of compounds. Cannot be used
                        with -ph option. (default: None)
  -pH PH, -ph PH        Set the pH of the system. When used with a
                        -population-file, this does not alter the given
                        populations. When used with -epikx, this specifies the
                        target pH of the system. Cannot be used with -pka-
                        file. (default: None)
  -s SEPARATOR, -separator SEPARATOR
                        Separator to split ligand names and population values
                        in pKa file or non-TSV population file. Ignored if no
                        such file is specified. By default, any run of
                        continuous whitespace characters are recognized as
                        separators. (default: None)
  -o OUT_FMP_PATH       Output fmp file path. (default:
                        group_corrected_out.fmp)
  -skip-normalization   Skip normalizing the populations that are set on the
                        graph. Note: This option is ignored unless the -epikx
                        option is also provided. (default: False)
  -out-population-file OUT_POP_FILE_PATH
                        Write the population data from the graph to the
                        specified .tsv file. The population data will be
                        written after any other options have been applied,
                        including population assignment via Epik or reading
                        parsing a pKa or population file. Note: if there are
                        multiple nodes in the same conformer group, only one
                        of them will appear in the resulting population file
                        because they all represent the same structure and
                        therefore have the same effective population.
                        (default: None)
  -debug                Print additional information to stdout. Run any epikx
                        calculations in the directory from which this script
                        was launched, rather than in a temporary directory.
                        (default: False)