NAME
    InfoPDBFiles.pl - List information about PDB files

SYNOPSIS
    InfoPDBFiles.pl PDBFile(s) PDB(s)...

    InfoPDBFiles.pl [-a, --all] [-b, --BoundingBox] [-c, --count
    "RecordType, [RecordType,...]" | All] [--chains] [-d, --detail
    infolevel] [-e, --experiment] [-f, --frequency] [-h, --help] [--header]
    [m, --MasterCheck] [--residues] [--ResiduesMode InChains | All | Both]
    [--ResidueNumbers] [-w, --WorkingDir dirname] PDBFile(s)...

DESCRIPTION
    List information about contents of *PDBFile(s)*: number of each record
    type, number of chains, count and percent distribution of residues in
    each chain, bounding box and so on. Multiple PDBFile names are separated
    by spaces. The valid file extension is *.pdb*. All other file name
    extensions are ignored during the wild card expansion. All the PDB files
    in a current directory can be specified either by **.pdb* or the current
    directory name.

    In PDB files containing data for multiple models, all ATOM/HETAM records
    for chains after the first model are ignored.

OPTIONS
    -a, --all
        List all the available information.

    -b, --BoundingBox
        List min/max XYZ coordiates of ATOM/HETATM records.

    -c, --count *RecordType,[RecordType,...]|All*
        Types of PDB records to count in *PDBFile(s)*. You can specify a
        list of any valid PDB record type or count all record types found in
        the files. Possible values: Comma delimited list of valid
        *RecordTypes* or *All*. Default: *ATOM,HETATM*. And this is also
        default behavior.

        The list of valid PDB record types includes: *HEADER, OBSLTE, TITLE,
        CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRN,
        REMARK, DBRE, SEQADV, SEQRES, MODRES, HET, HETNAM, HETSYN, FORMUL,
        HELIX, SHEET, TURN, SSBOND, LINK, HYDBND, SLTBRG, CISPEP, SITE,
        CRYST1, ORIGX1, ORIGX2, ORIGX3, SCALE1, SCALE2, SCALE3, MTRIX1
        MTRIX2 MTRIX3, TVECT, MODEL, ATOM, SIGATM, ANISOU, SIGUIJ, TER,
        HETATM, ENDMDL, CONECT, MASTER, END*.

    --chains
        Count number of chains.

    -d, --detail *infolevel*
        Level of information to print about PDB during various options.
        Default: *1*. Possible values: *1, 2 or 3*.

    -e, --experiment
        List experimental technique information along with any applicable
        resolution.

    -f, --frequency
        List distribution of residues: report count and percent of residues
        in individual chains and across all the chains, or for all the
        residues in the file. The value of option --residuesmode determines
        how residues are counted and what is listed. The list is sorted by
        frequency in descending order. By default, only residue count values
        are reported. To list percent distribution of residues, specify -d,
        --detail value of *2* or higher.

    -h, --help
        Print this help message.

    --header
        List header information.

    m, --MasterCheck
        Check master record by explicitly counting the number of REMARK,
        HET, HELIX, SHEET, TURN, SITE, ORIGX, SCALE, MTRIX, ATOM, HETATM,
        TER, CONECT and SEQRES records and comparing their values against
        contents of master record.

    --residues
        Count residues in *PDBFile(s)*. This is also default behavior.

        By default, only residue count values are reported. To list percent
        distribution of residues, specify -d, --detail value of *2* or
        higher.

    --ResiduesMode <InChains | All | Both>
        Specify how to count residues in *PDBFile(s)*: Count residue in each
        chain and across all the chains, list count iof all the residues in
        the file, or list both. Possible values: *InChains, All, or Both*.
        Default: *Both*.

    --ResidueNumbers
        List information about ATOM residue numbers in each chain before TER
        record: start and end residue number; gaps in residue numbers
        corresponding to non-sequential residue numbers; residue numbers not
        in ascending order.

    -w, --WorkingDir *dirname*
        Location of working directory. Default: current directory.

EXAMPLES
    To list total number of records and number of chain(s) residues in PDB
    files, type:

        % InfoPDBFiles.pl Sample1.pdb
        % InfoPDBFiles.pl Sample2.pdb

    To list all available information for PDB file Sample2.pdb, type:

        % InfoPDBFiles.pl -a Sample2.pdb

    To list all available information for PDB file Sample2.pdb with all
    available details, type:

        % InfoPDBFiles.pl -a -d Sample2.pdb

    To count ATOM and HETATM records in Sample2.pdb file, type:

        % InfoPDBFiles.pl -c "ATOM,HETATM" Sample2.pdb

    To list distribution of residues in chains across the whole PDB file
    Sample2.pdb along with percent distribution, type

        % InfoPDBFiles.pl --frequency -d 2 Sample2.pdb

    To list distribution of residues only across chains in PDB file
    Sample2.pdb along with percent distribution, type

        % InfoPDBFiles.pl --frequency -d 2 --ResiduesMode InChains Sample2.pdb

    To list min/max coordinates of the bounding box which encompasses the
    structure in Sample1.pdb file, type:

        % InfoPDBFiles.pl -b Sample1.pdb

AUTHOR
    Manish Sud <msud@san.rr.com>

SEE ALSO
    ExtractFromPDBFiles.pl, InfoAminoAcids.pl, InfoNucleicAcids.pl,
    InfoSequenceFiles.pl, ModifyPDBFiles.pl

COPYRIGHT
    Copyright (C) 2015 Manish Sud. All rights reserved.

    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.

