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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/scripts/html/ModifySDFilesDataFields.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,265 @@ +<html> +<head> +<title>MayaChemTools:Documentation:ModifySDFilesDataFields.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="./ModifyPDBFiles.html" title="ModifyPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Next</a></td><td width="34%" align="middle"><strong>ModifySDFilesDataFields.pl</strong></td><td width="33%" align="right"><a href="././code/ModifySDFilesDataFields.html" title="View source code">Code</a> | <a href="./../pdf/ModifySDFilesDataFields.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ModifySDFilesDataFields.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ModifySDFilesDataFields.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ModifySDFilesDataFields.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> +</table> +</div> +<p> +</p> +<h2>NAME</h2> +<p>ModifySDFilesDataFields.pl - Modify data fields in SDFile(s)</p> +<p> +</p> +<h2>SYNOPSIS</h2> +<p>ModifySDFilesDataFields.pl SDFile(s)...</p> +<p>ModifySDFilesDataFields.pl [<strong>-d, --detail</strong> infolevel] +[<strong>--datafieldscommon</strong> newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]] +[<strong>--datafieldsmap</strong> newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]] +[<strong>--datafieldsmapfile</strong> filename] [<strong>--datafieldURL</strong> URLDataFieldLabel, CGIScriptPath, CGIParamName, CmpdIDFieldLabel] +[<strong>-h, --help</strong>] [<strong>-k, --keepolddatafields</strong> all | unmappedonly | none] [<strong>-m, --mode</strong> molname | datafields | both] +[<strong>--molnamemode</strong> datafield | labelprefix] [<strong>--molname</strong> datafieldname or prefixstring] +[<strong>--molnamereplace</strong> always | empty] [<strong>-o, --overwrite</strong>] [<strong>-r, --root</strong> rootname] +[<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p> +<p> +</p> +<h2>DESCRIPTION</h2> +<p>Modify molname line and data fields in <em>SDFile(s)</em>. Molname line can be replaced by a +data field value or assigned a sequential ID prefixed with a specific string. For data +fields and modification of their values, these types of options are supported: replace +data field labels by another set of labels; combine values of multiple data fields and +assign a new label; add specific set of data field labels and values to all compound +records; and others.</p> +<p>The file names are separated by space.The valid file extensions are <em>.sdf</em> and <em>.sd</em>. +All other file names are ignored. All the SD files in a current directory can be specified +either by <em>*.sdf</em> or the current directory name.</p> +<p> +</p> +<h2>OPTIONS</h2> +<dl> +<dt><strong><strong>-d, --detail</strong> <em>infolevel</em></strong></dt> +<dd> +<p>Level of information to print about compound records being ignored. Default: <em>1</em>. Possible +values: <em>1, 2 or 3</em>.</p> +</dd> +<dt><strong><strong>--datafieldscommon</strong> <em>newfieldlabel, newfieldvalue, [newfieldlabel, newfieldvalue,...]</em></strong></dt> +<dd> +<p>Specify data field labels and values for addition to each compound record. It's a comma delimited +list of data field label and values pair. Default: <em>none</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + DepositionDate,YYYY-MM-DD +<br/> Source,www.domainname.org,ReleaseData,YYYY-MM-DD</div> +</dd> +<dt><strong><strong>--datafieldsmap</strong> <em>newfieldlabel, oldfieldlabel, [oldfieldlabel,...]; [newfieldlabel, oldfieldlabel, [oldfieldlabel,...]]</em></strong></dt> +<dd> +<p>Specify how various data field labels and values are combined to generate a new data field +labels and their values. All the comma delimited data fields, with in a semicolon delimited set, +are mapped to the first new data field label along with the data field values joined via new +line character. Default: <em>none</em>.</p> +<p>Examples:</p> +<div class="OptionsBox"> + Synonym,Name,SystematicName,Synonym;CmpdID,Extreg +<br/> HBondDonors,SumNHOH</div> +</dd> +<dt><strong><strong>--datafieldsmapfile</strong> <em>filename</em></strong></dt> +<dd> +<p>Filename containing mapping of data fields. Format of data fields line in this file corresponds +to <strong>--datafieldsmap</strong> option. Example:</p> +<div class="OptionsBox"> + Line 1: Synonym,Name,SystematicName,Synonym;CmpdID,Extreg +<br/> Line 2: HBondDonors,SumNHOH</div> +</dd> +<dt><strong><strong>--datafieldURL</strong> <em>URLDataFieldLabel, CGIScriptPath, CGIParamName, CmpdIDFieldLabel</em></strong></dt> +<dd> +<p>Specify how to generate a URL for retrieving compound data from a web server and add it +to each compound record. <em>URLDataFieldLabel</em> is used as the data field label for URL value +which is created by combining <em>CGIScriptPath,CGIParamName,CmpdIDFieldLabel</em> values: +CGIScriptPath?CGIParamName=CmpdIDFieldLabelValue. Default: <em>none</em>.</p> +<p>Example:</p> +<div class="OptionsBox"> + Source,<a href="http://www.yourdomain.org/GetCmpd.pl">http://www.yourdomain.org/GetCmpd.pl</a>,Reg_ID,Mol_ID</div> +</dd> +<dt><strong><strong>-h, --help</strong></strong></dt> +<dd> +<p>Print this help message.</p> +</dd> +<dt><strong><strong>-k, --keepolddatafields</strong> <em>all | unmappedonly | none</em></strong></dt> +<dd> +<p>Specify how to transfer old data fields from input SDFile(s) to new SDFile(s) during +<em>datafields | both</em> value of <strong>-m, --mode</strong> option: keep all old data fields; write out the ones +not mapped to new fields as specified by <strong>--datafieldsmap</strong> or <--datafieldsmapfile> options; +or ignore all old data field labels. For <em>molname</em> <strong>-m --mode</strong>, old datafields are always kept. +Possible values: <em>all | unmappedonly | none</em>. Default: <em>none</em>.</p> +</dd> +<dt><strong><strong>-m, --mode</strong> <em>molname | datafields | both</em></strong></dt> +<dd> +<p>Specify how to modify SDFile(s): <em>molname</em> - change molname line by another datafield or value; +<em>datafield</em> - modify data field labels and values by replacing one label by another, combining +multiple data field labels and values, adding specific set of data field labels and values to all compound, or +inserting an URL for compound retrieval to each record; <em>both</em> - change molname line and datafields +simultaneously. Possible values: <em>molname | datafields | both</em>. Default: <em>molname</em></p> +</dd> +<dt><strong><strong>--molnamemode</strong> <em>datafield | labelprefix</em></strong></dt> +<dd> +<p>Specify how to change molname line for <strong>-m --mode</strong> option values of <em>molname | both</em>: use +a datafield label value or assign a sequential ID prefixed with <em>labelprefix</em>. Possible values: +<em>datafield | labelprefix</em>. Default: <em>labelprefix</em>.</p> +</dd> +<dt><strong><strong>--molname</strong> <em>datafieldname or prefixstring</em></strong></dt> +<dd> +<p>Molname generation method. For <em>datafield</em> value of <strong>--molnamemode</strong> option, it corresponds +to datafield label name whose value is used for molname; otherwise, it's a prefix string used for +generating compound IDs like labelprefixstring<Number>. Default value, <em>Cmpd</em>, generates +compound IDs like Cmpd<Number> for molname.</p> +</dd> +<dt><strong><strong>--molnamereplace</strong> <em>always | empty</em></strong></dt> +<dd> +<p>Specify when to replace molname line for <strong>-m --mode</strong> option values of <em>molname | both</em>: +always replace the molname line using <strong>--molname</strong> option or only when it's empty. Possible +values: <em>always | empty</em>. Default: <em>empty</em>.</p> +</dd> +<dt><strong><strong>-o, --overwrite</strong></strong></dt> +<dd> +<p>Overwrite existing files.</p> +</dd> +<dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> +<dd> +<p>New SD file name is generated using the root: <Root>.<Ext>. Default new file +name: <InitialSDFileName>ModifiedDataFields.<Ext>. This option is ignored for multiple +input files.</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 replace empty molname lines by Cmpd<CmpdNumber> and generate a new SD file +NewSample1.sdf, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl -o -r NewSample1 Sample1.sdf</div> +<p>To replace all molname lines by Mol_ID data field generate a new SD file +NewSample1.sdf, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --molnamemode datafield + --molnamereplace always -r NewSample1 -o Sample1.sdf</div> +<p>To replace all molname lines by Mol_ID data field, map Name and CompoundName to +a new datafield Synonym, and generate a new SD file NewSample1.sdf, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --molnamemode datafield + --molnamereplace always --molname Mol_ID --mode both + --datafieldsmap "Synonym,Name,CompoundName" -r + NewSample1 -o Sample1.sdf</div> +<p>To replace all molname lines by Mol_ID data field, map Name and CompoundName to +a new datafield Synonym, add common fields ReleaseDate and Source, and +generate a new SD file NewSample1.sdf without keeping any old SD data fields, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --molnamemode datafield + --molnamereplace always --molname Mol_ID --mode both + --datafieldsmap "Synonym,Name,CompoundName" + --datafieldscommon "ReleaseDate,yyyy-mm-dd,Source, + www.mayachemtools.org" --keepolddatafields none -r + NewSample1 -o Sample1.sdf</div> +<p><strong>Preparing SD files PubChem deposition:</strong></p> +<p>Consider a SD file with these fields: Mol_ID, Name, Synonyms and Systematic_Name. +And Mol_ID data field uniquely identifies your compound.</p> +<p>To prepare a new SD file CmpdDataForPubChem.sdf containing only required +PUBCHEM_EXT_DATASOURCE_REGID field, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --m datafields + --datafieldsmap + "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID" + -r CmpdDataForPubChem -o Sample1.sdf</div> +<p>To prepare a new SD file CmpdDataForPubChem.sdf containing only required +PUBCHEM_EXT_DATASOURCE_REGID field and replace molname line with Mol_ID, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --molnamemode datafield + --molnamereplace always --molname Mol_ID --mode both + --datafieldsmap + "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID" + -r CmpdDataForPubChem -o Sample1.sdf</div> +<p>In addition to required PubChem data field, you can also add optional PubChem data +fields.</p> +<p>To map your Name, Synonyms and Systematic_Name data fields to optional +PUBCHEM_SUBSTANCE_SYNONYM data field along with required ID field, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --molnamemode datafield + --molnamereplace always --molname Mol_ID --mode both + --datafieldsmap + "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID; + PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName" + -r CmpdDataForPubChem -o Sample1.sdf</div> +<p>To add your <domain.org> as PUBCHEM_EXT_SUBSTANCE_URL and link substance +retrieval to your CGI script <http://www.yourdomain.org/GetCmpd.pl,Reg_ID,Mol_ID> +via PUBCHEM_EXT_DATASOURCE_REGID field along with optional and required +data fields, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --molnamemode datafield + --molnamereplace always --molname Mol_ID --mode both + --datafieldsmap + "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID; + PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName" + --datafieldscommon + "PUBCHEM_EXT_SUBSTANCE_URL,domain.org" + --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL, + <a href="http://www.yourdomain.org/GetCmpd.pl">http://www.yourdomain.org/GetCmpd.pl</a>,Reg_ID,Mol_ID" + -r CmpdDataForPubChem -o Sample1.sdf</div> +<p>And to add a publication date and request a release data using +PUBCHEM_PUBLICATION_DATE and PUBCHEM_DEPOSITOR_RECORD_DATE data fields +along with all the data fields in earlier examples, type: +optional fields, type:</p> +<div class="ExampleBox"> + % ModifySDFilesDataFields.pl --molnamemode datafield + --molnamereplace always --molname Mol_ID --mode both + --datafieldsmap + "PUBCHEM_EXT_DATASOURCE_REGID,Mol_ID; + PUBCHEM_SUBSTANCE_SYNONYM,Name,CompoundName" + --datafieldURL "PUBCHEM_EXT_DATASOURCE_URL, + <a href="http://www.yourdomain.org/GetCmpd.pl">http://www.yourdomain.org/GetCmpd.pl</a>,Reg_ID,Mol_ID" + --datafieldscommon + "PUBCHEM_EXT_SUBSTANCE_URL,domain.org, + PUBCHEM_PUBLICATION_DATE,YYY-MM-DD, + PUBCHEM_DEPOSITOR_RECORD_DATE,YYYY-MM-DD" + -r CmpdDataForPubChem -o Sample1.sdf</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="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./JoinSDFiles.html">JoinSDFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a>, <a href="./SplitSDFiles.html">SplitSDFiles.pl</a>, <a href="./SDFilesToHTML.html">SDFilesToHTML.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="./ModifyPDBFiles.html" title="ModifyPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ModifyTextFilesFormat.html" title="ModifyTextFilesFormat.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ModifySDFilesDataFields.pl</strong></td></tr> +</table> +</div> +<br /> +<center> +<img src="../../images/h2o2.png"> +</center> +</body> +</html>