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.\" ========================================================================
.\"
.IX Title "INFOPDBFILES 1"
.TH INFOPDBFILES 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
InfoPDBFiles.pl \- List information about PDB files
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
InfoPDBFiles.pl PDBFile(s) \s-1PDB\s0(s)...
.PP
InfoPDBFiles.pl [\fB\-a, \-\-all\fR] [\fB\-b, \-\-BoundingBox\fR]
[\fB\-c, \-\-count\fR \*(L"RecordType, [RecordType,...]\*(R" | All] [\fB\-\-chains\fR]
[\fB\-d, \-\-detail\fR infolevel] [\fB\-e, \-\-experiment\fR] [\fB\-f, \-\-frequency\fR]
[\fB\-h, \-\-help\fR] [\fB\-\-header\fR] [\fBm, \-\-MasterCheck\fR] [\fB\-\-residues\fR]
[\fB\-\-ResiduesMode\fR InChains | All | Both] [\fB\-\-ResidueNumbers\fR]
[\fB\-w, \-\-WorkingDir\fR dirname] PDBFile(s)...
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
List information about contents of \fIPDBFile(s)\fR: 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 \fI.pdb\fR.
All other file name extensions are ignored during the wild card expansion. All the \s-1PDB\s0 files
in a current directory can be specified either by \fI*.pdb\fR or the current directory name.
.PP
In \s-1PDB\s0 files containing data for multiple models, all \s-1ATOM/HETAM\s0 records for chains after the first model
are ignored.
.SH "OPTIONS"
.IX Header "OPTIONS"
.IP "\fB\-a, \-\-all\fR" 4
.IX Item "-a, --all"
List all the available information.
.IP "\fB\-b, \-\-BoundingBox\fR" 4
.IX Item "-b, --BoundingBox"
List min/max \s-1XYZ\s0 coordiates of \s-1ATOM/HETATM\s0 records.
.IP "\fB\-c, \-\-count\fR \fIRecordType,[RecordType,...]|All\fR" 4
.IX Item "-c, --count RecordType,[RecordType,...]|All"
Types of \s-1PDB\s0 records to count in \fIPDBFile(s)\fR. You can specify a list of any valid \s-1PDB\s0
record type or count all record types found in the files. Possible values: Comma delimited list
of valid \fIRecordTypes\fR or \fIAll\fR. Default: \fI\s-1ATOM\s0,HETATM\fR. And this is also \fBdefault behavior\fR.
.Sp
The list of valid \s-1PDB\s0 record types includes: \fI\s-1HEADER\s0, \s-1OBSLTE\s0, \s-1TITLE\s0, \s-1CAVEAT\s0, \s-1COMPND\s0, \s-1SOURCE\s0, \s-1KEYWDS\s0,
\&\s-1EXPDTA\s0, \s-1AUTHOR\s0, \s-1REVDAT\s0, \s-1SPRSDE\s0, \s-1JRN\s0, \s-1REMARK\s0, \s-1DBRE\s0, \s-1SEQADV\s0, \s-1SEQRES\s0, \s-1MODRES\s0, \s-1HET\s0, \s-1HETNAM\s0, \s-1HETSYN\s0,
\&\s-1FORMUL\s0, \s-1HELIX\s0, \s-1SHEET\s0, \s-1TURN\s0, \s-1SSBOND\s0, \s-1LINK\s0, \s-1HYDBND\s0, \s-1SLTBRG\s0, \s-1CISPEP\s0, \s-1SITE\s0, \s-1CRYST1\s0, \s-1ORIGX1\s0, \s-1ORIGX2\s0, \s-1ORIGX3\s0,
\&\s-1SCALE1\s0, \s-1SCALE2\s0, \s-1SCALE3\s0, \s-1MTRIX1\s0 \s-1MTRIX2\s0 \s-1MTRIX3\s0, \s-1TVECT\s0, \s-1MODEL\s0, \s-1ATOM\s0, \s-1SIGATM\s0, \s-1ANISOU\s0, \s-1SIGUIJ\s0, \s-1TER\s0,
\&\s-1HETATM\s0, \s-1ENDMDL\s0, \s-1CONECT\s0, \s-1MASTER\s0, \s-1END\s0\fR.
.IP "\fB\-\-chains\fR" 4
.IX Item "--chains"
Count number of chains.
.IP "\fB\-d, \-\-detail\fR \fIinfolevel\fR" 4
.IX Item "-d, --detail infolevel"
Level of information to print about \s-1PDB\s0 during various options. Default: \fI1\fR.
Possible values: \fI1, 2 or 3\fR.
.IP "\fB\-e, \-\-experiment\fR" 4
.IX Item "-e, --experiment"
List experimental technique information along with any applicable resolution.
.IP "\fB\-f, \-\-frequency\fR" 4
.IX Item "-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 \fB\-\-residuesmode\fR
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 \fB\-d, \-\-detail\fR value of \fI2\fR or higher.
.IP "\fB\-h, \-\-help\fR" 4
.IX Item "-h, --help"
Print this help message.
.IP "\fB\-\-header\fR" 4
.IX Item "--header"
List header information.
.IP "\fBm, \-\-MasterCheck\fR" 4
.IX Item "m, --MasterCheck"
Check master record by explicitly counting the number of \s-1REMARK\s0, \s-1HET\s0, \s-1HELIX\s0, \s-1SHEET\s0, \s-1TURN\s0, \s-1SITE\s0,
\&\s-1ORIGX\s0, \s-1SCALE\s0, \s-1MTRIX\s0, \s-1ATOM\s0, \s-1HETATM\s0, \s-1TER\s0, \s-1CONECT\s0 and \s-1SEQRES\s0 records and comparing their
values against contents of master record.
.IP "\fB\-\-residues\fR" 4
.IX Item "--residues"
Count residues in \fIPDBFile(s)\fR. This is also \fBdefault behavior\fR.
.Sp
By default, only residue count values are reported. To list percent distribution of residues,
specify \fB\-d, \-\-detail\fR value of \fI2\fR or higher.
.IP "\fB\-\-ResiduesMode\fR <InChains | All | Both>" 4
.IX Item "--ResiduesMode <InChains | All | Both>"
Specify how to count residues in \fIPDBFile(s)\fR: Count residue in each chain and across all the chains,
list count iof all the residues in the file, or list both. Possible values: \fIInChains, All, or Both\fR.
Default: \fIBoth\fR.
.IP "\fB\-\-ResidueNumbers\fR" 4
.IX Item "--ResidueNumbers"
List information about \s-1ATOM\s0 residue numbers in each chain before \s-1TER\s0 record: start and end residue
number; gaps in residue numbers corresponding to non-sequential residue numbers; residue
numbers not in ascending order.
.IP "\fB\-w, \-\-WorkingDir\fR \fIdirname\fR" 4
.IX Item "-w, --WorkingDir dirname"
Location of working directory. Default: current directory.
.SH "EXAMPLES"
.IX Header "EXAMPLES"
To list total number of records and number of chain(s) residues in \s-1PDB\s0 files, type:
.PP
.Vb 2
\&    % InfoPDBFiles.pl Sample1.pdb
\&    % InfoPDBFiles.pl Sample2.pdb
.Ve
.PP
To list all available information for \s-1PDB\s0 file Sample2.pdb, type:
.PP
.Vb 1
\&    % InfoPDBFiles.pl \-a Sample2.pdb
.Ve
.PP
To list all available information for \s-1PDB\s0 file Sample2.pdb with all available details, type:
.PP
.Vb 1
\&    % InfoPDBFiles.pl \-a \-d Sample2.pdb
.Ve
.PP
To count \s-1ATOM\s0 and \s-1HETATM\s0 records in Sample2.pdb file, type:
.PP
.Vb 1
\&    % InfoPDBFiles.pl \-c "ATOM,HETATM" Sample2.pdb
.Ve
.PP
To list distribution of residues in chains across the whole \s-1PDB\s0 file Sample2.pdb along with
percent distribution, type
.PP
.Vb 1
\&    % InfoPDBFiles.pl \-\-frequency \-d 2 Sample2.pdb
.Ve
.PP
To list distribution of residues only across chains in \s-1PDB\s0 file Sample2.pdb along with
percent distribution, type
.PP
.Vb 1
\&    % InfoPDBFiles.pl \-\-frequency \-d 2 \-\-ResiduesMode InChains Sample2.pdb
.Ve
.PP
To list min/max coordinates of the bounding box which encompasses the structure in Sample1.pdb
file, type:
.PP
.Vb 1
\&    % InfoPDBFiles.pl \-b Sample1.pdb
.Ve
.SH "AUTHOR"
.IX Header "AUTHOR"
Manish Sud <[e-mail]>
.SH "SEE ALSO"
.IX Header "SEE ALSO"
ExtractFromPDBFiles.pl, InfoAminoAcids.pl, InfoNucleicAcids.pl, InfoSequenceFiles.pl, ModifyPDBFiles.pl
.SH "COPYRIGHT"
.IX Header "COPYRIGHT"
Copyright (C) 2015 Manish Sud. All rights reserved.
.PP
This file is part of MayaChemTools.
.PP
MayaChemTools is free software; you can redistribute it and/or modify it under
the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
Software Foundation; either version 3 of the License, or (at your option)
any later version.