NAME
    PyMOLCalculateRMSD.py - Calculate RMSD between macromolecules

SYNOPSIS
    PyMOLCalculateRMSD.py [--alignMethod <align, cealign, super>]
    [--alignMode <FirstChain or Complex>] [--mode <OneToOne, AllToAll,
    FirstToAll>] [--outMatrix <yes or no>] [--overwrite] [-w <dir>] -p
    <probefile1,probefile2,probefile3...> -r <reffile1,reffile2,reffile3...>
    -o <outfile>

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

DESCRIPTION
    Calculate Root Mean Square Distance (RMSD) between a set of similar
    macromolecules in reference and probe input files. The probe and
    reference files are spatially aligned before the the calculation of RMSD
    values.

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

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

OPTIONS
    -a, --alignMethod <align, cealign, super> [default: super]
        Alignment methodology to use for aligning probe input files to
        reference files.

    --alignMode <FirstChain or Complex> [default: FirstChain]
        Portion of probe and reference files to use for spatial alignment of
        probe files against reference files. Possible values: FirstChain or
        Complex.

        The FirstChain mode allows alignment of the first chain in probe
        files to the first chain in reference files along with moving the
        rest of the complex to coordinate space of the reference files. The
        complete complex in probe files is aligned to the complete complex
        in reference files for the Complex mode.

    -e, --examples
        Print examples.

    -h, --help
        Print this help message.

    -m, --mode <OneToOne, AllToAll, FirstToAll> [default: OneToOne]
        Specify how reference and probe input files are handled during the
        calculation of RMSD between reference and probe files. Possible
        values: OneToOne, AllToAll and AllToFirst. For OneToOne mode, the
        number of reference input files must be equal to the number of probe
        input files. The RMSD is calculated for each pair of reference and
        probe file and written to the output file. For AllToAll mode, the
        RMSD is calculated for each reference input file against all probe
        input files. For FirstToAll mode, however, the RMSD is only
        calculated for the first reference input file against all probe
        files.

    -p, --probefiles <probefile1,probefile2,probelfile3...>
        A comma delimited list of probe input files. The wildcards are also
        allowed in file names.

    -r, --reffiles <reffile1,reffile2,reffile3...>
        A comma delimited list of reference input files. The wildcards are
        also allowed in file names.

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

    --outMatrix <yes or no> [default: yes]
        Output file in a matrix format during 'AllToAll' value for '-m,
        --mode' option.

    --overwrite
        Overwrite existing files.

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

EXAMPLES
    To calculate RMSD between pair of macromolecules in reference and probe
    files using only first chain in each file and write out a CSV file
    containing calculated RMSD values along with IDs, type:

        % PyMOLCalculateRMSD.py  -r "Sample3.pdb,Sample4.pdb,Sample5.pdb"
          -p "Sample3.pdb,Sample4.pdb,Sample5.pdb" -o SampleOut.csv

    To calculate RMSD between all macromolecules in reference and probe
    files using complete complex and write out a CSV matrix file, type:

        % PyMOLCalculateRMSD.py  -m AllToAll --alignMode Complex
           --outMatrix Yes -r "Sample3.pdb,Sample4.pdb,Sample5.pdb"
          -p "Sample3.pdb,Sample4.pdb" -o SampleOut.csv

    To calculate RMSD between macromolecule in first reference against all
    probe files using only first chain in each file and write out a TSV file
    containing calculated RMSD values along with IDs, type:

        % PyMOLCalculateRMSD.py  -m FirstToAll
          -r "Sample3.pdb,Sample4.pdb,Sample5.pdb"
          -p "Sample3.pdb,Sample4.pdb,Sample5.pdb" -o SampleOut.tsv

    To calculate RMSD between pair of macromolecules in reference and probe
    files using only first chain in each file along with a specific
    alignment method and write out a CSV file containing calculated RMSD
    values, type:

        % PyMOLCalculateRMSD.py  --alignMethod align
          -r "Sample3.pdb,Sample4.pdb,Sample5.pdb"
          -p "Sample3.pdb,Sample4.pdb,Sample5.pdb" -o SampleOut.csv

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

SEE ALSO
    PyMOLAlignChains.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.

