diff docs/scripts/txt/InfoPDBFiles.txt @ 0:4816e4a8ae95 draft default tip

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+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 <[e-mail]>
+
+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.
+