Mercurial > repos > deepakjadmin > mayatool3_test2
diff docs/scripts/man1/InfoPDBFiles.1 @ 0:4816e4a8ae95 draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:23:18 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/InfoPDBFiles.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,282 @@ +.\" Automatically generated by Pod::Man 2.25 (Pod::Simple 3.22) +.\" +.\" Standard preamble: +.\" ======================================================================== +.de Sp \" Vertical space (when we can't use .PP) +.if t .sp .5v +.if n .sp +.. +.de Vb \" Begin verbatim text +.ft CW +.nf +.ne \\$1 +.. +.de Ve \" End verbatim text +.ft R +.fi +.. +.\" Set up some character translations and predefined strings. \*(-- will +.\" give an unbreakable dash, \*(PI will give pi, \*(L" will give a left +.\" double quote, and \*(R" will give a right double quote. \*(C+ will +.\" give a nicer C++. Capital omega is used to do unbreakable dashes and +.\" therefore won't be available. \*(C` and \*(C' expand to `' in nroff, +.\" nothing in troff, for use with C<>. +.tr \(*W- +.ds C+ C\v'-.1v'\h'-1p'\s-2+\h'-1p'+\s0\v'.1v'\h'-1p' +.ie n \{\ +. ds -- \(*W- +. ds PI pi +. if (\n(.H=4u)&(1m=24u) .ds -- \(*W\h'-12u'\(*W\h'-12u'-\" diablo 10 pitch +. if (\n(.H=4u)&(1m=20u) .ds -- \(*W\h'-12u'\(*W\h'-8u'-\" diablo 12 pitch +. ds L" "" +. ds R" "" +. ds C` "" +. ds C' "" +'br\} +.el\{\ +. ds -- \|\(em\| +. ds PI \(*p +. ds L" `` +. ds R" '' +'br\} +.\" +.\" Escape single quotes in literal strings from groff's Unicode transform. +.ie \n(.g .ds Aq \(aq +.el .ds Aq ' +.\" +.\" If the F register is turned on, we'll generate index entries on stderr for +.\" titles (.TH), headers (.SH), subsections (.SS), items (.Ip), and index +.\" entries marked with X<> in POD. Of course, you'll have to process the +.\" output yourself in some meaningful fashion. +.ie \nF \{\ +. de IX +. tm Index:\\$1\t\\n%\t"\\$2" +.. +. nr % 0 +. rr F +.\} +.el \{\ +. de IX +.. +.\} +.\" +.\" Accent mark definitions (@(#)ms.acc 1.5 88/02/08 SMI; from UCB 4.2). +.\" Fear. Run. Save yourself. No user-serviceable parts. +. \" fudge factors for nroff and troff +.if n \{\ +. ds #H 0 +. ds #V .8m +. ds #F .3m +. ds #[ \f1 +. ds #] \fP +.\} +.if t \{\ +. ds #H ((1u-(\\\\n(.fu%2u))*.13m) +. ds #V .6m +. ds #F 0 +. ds #[ \& +. ds #] \& +.\} +. \" simple accents for nroff and troff +.if n \{\ +. ds ' \& +. ds ` \& +. ds ^ \& +. ds , \& +. ds ~ ~ +. ds / +.\} +.if t \{\ +. ds ' \\k:\h'-(\\n(.wu*8/10-\*(#H)'\'\h"|\\n:u" +. ds ` \\k:\h'-(\\n(.wu*8/10-\*(#H)'\`\h'|\\n:u' +. ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'^\h'|\\n:u' +. ds , \\k:\h'-(\\n(.wu*8/10)',\h'|\\n:u' +. ds ~ \\k:\h'-(\\n(.wu-\*(#H-.1m)'~\h'|\\n:u' +. ds / \\k:\h'-(\\n(.wu*8/10-\*(#H)'\z\(sl\h'|\\n:u' +.\} +. \" troff and (daisy-wheel) nroff accents +.ds : \\k:\h'-(\\n(.wu*8/10-\*(#H+.1m+\*(#F)'\v'-\*(#V'\z.\h'.2m+\*(#F'.\h'|\\n:u'\v'\*(#V' +.ds 8 \h'\*(#H'\(*b\h'-\*(#H' +.ds o \\k:\h'-(\\n(.wu+\w'\(de'u-\*(#H)/2u'\v'-.3n'\*(#[\z\(de\v'.3n'\h'|\\n:u'\*(#] +.ds d- \h'\*(#H'\(pd\h'-\w'~'u'\v'-.25m'\f2\(hy\fP\v'.25m'\h'-\*(#H' +.ds D- D\\k:\h'-\w'D'u'\v'-.11m'\z\(hy\v'.11m'\h'|\\n:u' +.ds th \*(#[\v'.3m'\s+1I\s-1\v'-.3m'\h'-(\w'I'u*2/3)'\s-1o\s+1\*(#] +.ds Th \*(#[\s+2I\s-2\h'-\w'I'u*3/5'\v'-.3m'o\v'.3m'\*(#] +.ds ae a\h'-(\w'a'u*4/10)'e +.ds Ae A\h'-(\w'A'u*4/10)'E +. \" corrections for vroff +.if v .ds ~ \\k:\h'-(\\n(.wu*9/10-\*(#H)'\s-2\u~\d\s+2\h'|\\n:u' +.if v .ds ^ \\k:\h'-(\\n(.wu*10/11-\*(#H)'\v'-.4m'^\v'.4m'\h'|\\n:u' +. \" for low resolution devices (crt and lpr) +.if \n(.H>23 .if \n(.V>19 \ +\{\ +. ds : e +. ds 8 ss +. ds o a +. ds d- d\h'-1'\(ga +. ds D- D\h'-1'\(hy +. ds th \o'bp' +. ds Th \o'LP' +. ds ae ae +. ds Ae AE +.\} +.rm #[ #] #H #V #F C +.\" ======================================================================== +.\" +.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 <msud@san.rr.com> +.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.