NAME
    PyMOLAlignChains.py - Align chains

SYNOPSIS
    PyMOLAlignChains.py [--alignMethod <align, cealign, super>] [--alignMode
    <FirstChain or Complex>] [--alignRefFile <filename>] [--outSuffix
    <text>] [--overwrite] [-w <dir>] -i <infile1,infile2,infile3...>

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

DESCRIPTION
    Align chains in input files to a reference file and write out aligned
    files.

    The supported input and output file format are: PDB (.pdb), CIF(.cif)

    The names of the aligned output files are automatically generated from
    the names of input as shown below:

        <InfileRoot><OutSuffux>.pdb
        Default: <InfileRoot>_Aligned.pdb

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

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

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

    --alignRefFile <filename> [default: FirstInputFile]
        Reference input file name. The default is to use the first input
        file name specified using '-i, --infiles' option.

    -e, --examples
        Print examples.

    -h, --help
        Print this help message.

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

    --outSuffix <text> [default: _Aligned]
        Suffix to append to input file root for generating name of output
        file.

    --overwrite
        Overwrite existing files.

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

EXAMPLES
    To align first chain in all input files to the first chain in first
    input file and write out aligned output files, type:

        % PyMOLAlignChains.py -i "Sample3.pdb,Sample4.pdb,Sample5.pdb"

    To align first chain in all input files to the first chain in specific
    reference file and write out aligned output files, type:

        % PyMOLAlignChains.py --alignRefFile Sample5.pdb
          -i "Sample3.pdb,Sample4.pdb,Sample5.pdb"

    To align first chain in all input files to the first chain in first
    input file using a specific alignment method and write out aligned
    output files with specific suffix in names, type:

        % PyMOLAlignChains.py --alignMethod cealign --outSuffix "_aligned"
          -i "Sample3.pdb,Sample4.pdb,Sample5.pdb"

    To align all chains in each input files to all chains in first input
    file and write out aligned output files, type:

        % PyMOLAlignChains.py --alignMode Complex
          -i "Sample3.pdb,Sample4.pdb,Sample5.pdb"

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.

