NAME
    PyMOLInfoMacromolecules.py - List information about macromolecules

SYNOPSIS
    PyMOLInfoMacromolecules.py [--all] [--boundingBox] [--chains]
    [--countResidues] [--header] [--inorganics] [--ligands]
    [--pocketLigands] [--pocketDistanceCutoff <number>] [--pocketSolvents]
    [--pocketInorganics] [--solvents] [-w <dir>] -i
    <infile1,infile2,infile3...>

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

DESCRIPTION
    List information regarding ID, classification, experimental technique,
    chains, solvents, inorganics, ligands, and ligand binding pockets in
    macromolecules present including proteins and nucleic acids.

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

OPTIONS
    -a, --all
        All available information.

    -b, --boundingBox
        Min and max coordinates for bounding box along with its size.

    -c, --chains
        Number of chains and their IDs. This is also default behavior.
        --countResidues Number of residues across chains. The chain residues
        are identified using polymer selection operator available in PyMOL.
        In addition, the non-standard amino acid residues are listed.

    -e, --examples
        Print examples.

    -h, --help
        Print this help message. --header Header information including
        experimental technique information along with any available
        resolution. This is also default behavior.

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

    --inorganics
        Inorganic residues across chains. The inorganic residues are
        identified using inorganic selection operator available in PyMOL.

    -l, --ligands
        Ligands across chains. This is also default behavior. The ligands
        residues are identified using organic selection operator available
        in PyMOL.

    -p, --pocketLigands
        Chain residues in ligand pockets.

    --pocketDistanceCutoff <number> [default: 5.0]
        Distance in Angstroms for identifying pocket residues around
        ligands.

    --pocketSolvents
        Solvent residues in ligand pockets. The solvent residues are
        identified using solvent selection operator available in PyMOL.

    --pocketInorganics
        Inorganic residues in ligand pockets. The inorganic residues are
        identified using Inorganic selection operator available in PyMOL.

    -s, --solvents
        Solvent residues across chains. The solvent residues are identified
        using solvent selection operator available in PyMOL.

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

EXAMPLES
    To list header, chains, and ligand information for macromolecules in
    input file, type:

        % PyMOLInfoMacromolecules.py  -i Sample3.pdb

    To list all available information for macromolecules in input files,
    type:

        % PyMOLInfoMacromolecules.py  -a  -i "Sample3.pdb,Sample4.pdb"

    To list pockets residues information along with other default
    information for marcomolecules in input file, type:

        % PyMOLInfoMacromolecules.py  -p --pocketDistanceCutoff 4.5 
        --pocketSolvents  --pocketInorganics -i Sample3.pdb

    To list chain residues information along with other default information
    for marcomolecules in input file, type:

        % PyMOLInfoMacromolecules.py  -c --countResidues --solvents
        --inorganics -i "Sample3.pdb,Sample4.pdb"

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

SEE ALSO
    DownloadPDBFiles.pl, 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.

