NAME
    PyMOLCalculateProperties.py - Calculate physicochemical properties

SYNOPSIS
    PyMOLCalculateProperties.py [--addHydrogens <yes or no>] [--chainIDs
    <First, All or ID1,ID2...>] [--list] [--keepInorganics <yes or no>]
    [--keepLigands <yes or no>] [--keepSolvents <yes or no>] [--mode <All or
    Name1,Name2,Name3,...>] [--overwrite] [--precision <number>] [--quiet
    <yes or no>] [-w <dir>] -i <infile1,infile2,infile3...> -o <outfile>

    PyMOLCalculateProperties.py -l | --list

    PyMOLCalculateProperties.py -h | --help | -e | --examples

DESCRIPTION
    Calculate physicochemical properties for macromolecules. The properties
    may be calculated for the complete complex or a specified list of chain
    IDs. Ligands, inorganics, and solvents may be optionally excluded during
    the calculation of properties.

    The supported input file format are: PDB (.pdb), mmCIF (.cif)

    The supported output file formats are: CSV (.csv), TSV (.tsv, .txt)

OPTIONS
    -a, --addHydrogens <yes or no> [default: yes]
        Add hydrogens before calculating physiochemical properties.

    -c, --chainIDs <First, All or ID1,ID2...> [default: All]
        List of chain IDs to use for calculating physicochemical properties.
        Possible values: First, All, or a comma delimited list of chain IDs.
        The default is to use all chain IDs in input file.

    -e, --examples
        Print examples.

    -h, --help
        Print this help message.

    -i, --infiles <infile1,infile2,infile3...>
        A comma delimited list of input files. The wildcards are also
        allowed in file names.

    --keepInorganics <yes or no> [default: yes]
        Keep inorganic molecules during calculation of physiochemical
        properties. The inorganic molecules are identified using inorganic
        selection operator available in PyMOL.

    --keepLigands <yes or no> [default: yes]
        Keep ligand molecules during calculation of physiochemical
        properties. The ligand molecules are identified using organic
        selection operator available in PyMOL.

    --keepSolvents <yes or no> [default: yes]
        Keep solvent molecules during calculation of physiochemical
        properties. The solvent molecules are identified using solvent
        selection operator available in PyMOL.

    -l, --list
        List available property names without performing any calculations.

    -m, --mode <All or Name1,Name2,Name3,...> [default: All]
        Comma delimited lists of physicochemical properties to calculate.
        Default: 'All'. The following properties may be calculated for
        macromolecules:

            CenterOfMass,MolecularWeight,MolecularSurfaceArea
            SumOfFormalCharges,SumOfPartialCharges,SolventAccessibleSurfaceArea

    -o, --outfile <outfile>
        Output file name for writing out calculated values. Supported text
        file extensions: csv, tsv or txt.

    --overwrite
        Overwrite existing files.

    -p, --precision <number> [default: 3]
        Floating point precision for writing the calculated property values.

    -q, --quiet <yes or no> [default: yes]
        Do not print information during the calculation of properties.

    -w, --workingdir <dir>
        Location of working directory which defaults to the current
        directory.

EXAMPLES
    To calculate all available properties for all chains in input file along
    with all ligands, inorganics and solvents after adding hydrogens and
    write out a CSV file containing calculated values and PDB IDs, type:

        % PyMOLCalculateProperties.py  -i Sample3.pdb -o Sample3Out.csv

    To calculate specified properties for all chains in input file along
    with all ligands, inorganics and solvents after adding hydrogens and
    write out a CSV file containing calculated values and PDB IDs, type:

        % PyMOLCalculateProperties.py  -m "MolecularWeight,CenterOfMass"
          -i Sample3.pdb -o Sample3Out.csv

    To calculate all available properties for chain E in input file without
    including ligands, inorganics and solvents, and addition of hydrogens,
    and write out a TSV file containing calculated values and PDB IDs, type:

        % PyMOLCalculateProperties.py  --addHydrogens no -c E --keepLigands
          no --keepInorganics  no --keepSolvents no -i Sample3.pdb -o
          Sample3Out.tsv

    To calculate all available properties for all chains in multiple files
    along with all ligands, inorganics and solvents after adding hydrogens
    and write out a CSV file containing calculated values and PDB IDs, type:

        % PyMOLCalculateProperties.py  -i "Sample3.pdb,Sample4.pdb,Sample5.pdb"
          -o SampleOut.csv

AUTHOR
    Manish Sud(msud@san.rr.com)

SEE ALSO
    PyMOLCalculateRMSD.py, PyMOLSplitChainsAndLigands.py,
    PyMOLVisualizeMacromolecules.py

COPYRIGHT
    Copyright (C) 2018 Manish Sud. All rights reserved.

    The functionality available in this script is implemented using PyMOL, a
    molecular visualization system on an open source foundation originally
    developed by Warren DeLano.

    This file is part of MayaChemTools.

    MayaChemTools is free software; you can redistribute it and/or modify it
    under the terms of the GNU Lesser General Public License as published by
    the Free Software Foundation; either version 3 of the License, or (at
    your option) any later version.

