Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/scripts/html/InfoPDBFiles.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/InfoPDBFiles.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,179 @@ +<html> +<head> +<title>MayaChemTools:Documentation:InfoPDBFiles.pl</title> +<meta http-equiv="content-type" content="text/html;charset=utf-8"> +<link rel="stylesheet" type="text/css" href="../../css/MayaChemTools.css"> +</head> +<body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> +<br/> +<center> +<a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> +</center> +<br/> +<div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Next</a></td><td width="34%" align="middle"><strong>InfoPDBFiles.pl</strong></td><td width="33%" align="right"><a href="././code/InfoPDBFiles.html" title="View source code">Code</a> | <a href="./../pdf/InfoPDBFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/InfoPDBFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/InfoPDBFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/InfoPDBFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>InfoPDBFiles.pl - List information about PDB files</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>InfoPDBFiles.pl PDBFile(s) PDB(s)...</p> +<p>InfoPDBFiles.pl [<strong>-a, --all</strong>] [<strong>-b, --BoundingBox</strong>] +[<strong>-c, --count</strong> "RecordType, [RecordType,...]" | All] [<strong>--chains</strong>] +[<strong>-d, --detail</strong> infolevel] [<strong>-e, --experiment</strong>] [<strong>-f, --frequency</strong>] +[<strong>-h, --help</strong>] [<strong>--header</strong>] [<strong>m, --MasterCheck</strong>] [<strong>--residues</strong>] +[<strong>--ResiduesMode</strong> InChains | All | Both] [<strong>--ResidueNumbers</strong>] +[<strong>-w, --WorkingDir</strong> dirname] PDBFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>List information about contents of <em>PDBFile(s)</em>: 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 <em>.pdb</em>. +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 <em>*.pdb</em> or the current directory name.</p> +<p>In PDB files containing data for multiple models, all ATOM/HETAM records for chains after the first model +are ignored.</p> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-a, --all</strong></strong></dt> +<dd> +<p>List all the available information.</p> +</dd> +<dt><strong><strong>-b, --BoundingBox</strong></strong></dt> +<dd> +<p>List min/max XYZ coordiates of ATOM/HETATM records.</p> +</dd> +<dt><strong><strong>-c, --count</strong> <em>RecordType,[RecordType,...]|All</em></strong></dt> +<dd> +<p>Types of PDB records to count in <em>PDBFile(s)</em>. 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 <em>RecordTypes</em> or <em>All</em>. Default: <em>ATOM,HETATM</em>. And this is also <strong>default behavior</strong>.</p> +<p>The list of valid PDB record types includes: <em>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</em>.</p> +</dd> +<dt><strong><strong>--chains</strong></strong></dt> +<dd> +<p>Count number of chains.</p> +</dd> +<dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> +<dd> +<p>Level of information to print about PDB during various options. Default: <em>1</em>. +Possible values: <em>1, 2 or 3</em>.</p> +</dd> +<dt><strong><strong>-e, --experiment</strong></strong></dt> +<dd> +<p>List experimental technique information along with any applicable resolution.</p> +</dd> +<dt><strong><strong>-f, --frequency</strong></strong></dt> +<dd> +<p>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 <strong>--residuesmode</strong> +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 <strong>-d, --detail</strong> value of <em>2</em> or higher.</p> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>--header</strong></strong></dt> +<dd> +<p>List header information.</p> +</dd> +<dt><strong><strong>m, --MasterCheck</strong></strong></dt> +<dd> +<p>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.</p> +</dd> +<dt><strong><strong>--residues</strong></strong></dt> +<dd> +<p>Count residues in <em>PDBFile(s)</em>. This is also <strong>default behavior</strong>.</p> +<p>By default, only residue count values are reported. To list percent distribution of residues, +specify <strong>-d, --detail</strong> value of <em>2</em> or higher.</p> +</dd> +<dt><strong><strong>--ResiduesMode</strong> <InChains | All | Both></strong></dt> +<dd> +<p>Specify how to count residues in <em>PDBFile(s)</em>: Count residue in each chain and across all the chains, +list count iof all the residues in the file, or list both. Possible values: <em>InChains, All, or Both</em>. +Default: <em>Both</em>.</p> +</dd> +<dt><strong><strong>--ResidueNumbers</strong></strong></dt> +<dd> +<p>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.</p> +</dd> +<dt><strong><strong>-w, --WorkingDir</strong> <em>dirname</em></strong></dt> +<dd> +<p>Location of working directory. Default: current directory.</p> +</dd> +</dl> +<p> +</p> +<h2>EXAMPLES</h2> +<p>To list total number of records and number of chain(s) residues in PDB files, type:</p> +<div class="ExampleBox"> + % InfoPDBFiles.pl Sample1.pdb + <br/>% InfoPDBFiles.pl Sample2.pdb</div> +<p>To list all available information for PDB file Sample2.pdb, type:</p> +<div class="ExampleBox"> + % InfoPDBFiles.pl -a Sample2.pdb</div> +<p>To list all available information for PDB file Sample2.pdb with all available details, type:</p> +<div class="ExampleBox"> + % InfoPDBFiles.pl -a -d Sample2.pdb</div> +<p>To count ATOM and HETATM records in Sample2.pdb file, type:</p> +<div class="ExampleBox"> + % InfoPDBFiles.pl -c "ATOM,HETATM" Sample2.pdb</div> +<p>To list distribution of residues in chains across the whole PDB file Sample2.pdb along with +percent distribution, type</p> +<div class="ExampleBox"> + % InfoPDBFiles.pl --frequency -d 2 Sample2.pdb</div> +<p>To list distribution of residues only across chains in PDB file Sample2.pdb along with +percent distribution, type</p> +<div class="ExampleBox"> + % InfoPDBFiles.pl --frequency -d 2 --ResiduesMode InChains Sample2.pdb</div> +<p>To list min/max coordinates of the bounding box which encompasses the structure in Sample1.pdb +file, type:</p> +<div class="ExampleBox"> + % InfoPDBFiles.pl -b Sample1.pdb</div> +<p> +</p> +<h2>AUTHOR</h2> +<p><a href="mailto:msud@san.rr.com">Manish Sud</a></p> +<p> +</p> +<h2>SEE ALSO</h2> +<p><a href="./ExtractFromPDBFiles.html">ExtractFromPDBFiles.pl</a>, <a href="./InfoAminoAcids.html">InfoAminoAcids.pl</a>, <a href="./InfoNucleicAcids.html">InfoNucleicAcids.pl</a>, <a href="./InfoSequenceFiles.html">InfoSequenceFiles.pl</a>, <a href="./ModifyPDBFiles.html">ModifyPDBFiles.pl</a> +</p> +<p> +</p> +<h2>COPYRIGHT</h2> +<p>Copyright (C) 2015 Manish Sud. All rights reserved.</p> +<p>This file is part of MayaChemTools.</p> +<p>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.</p> +<p> </p><p> </p><div class="DocNav"> +<table width="100%" border=0 cellpadding=0 cellspacing=2> +<tr align="left" valign="top"><td width="33%" align="left"><a href="./InfoNucleicAcids.html" title="InfoNucleicAcids.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./InfoPeriodicTableElements.html" title="InfoPeriodicTableElements.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>InfoPDBFiles.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>