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<html> <head> <title>MayaChemTools:Documentation:ExtractFromSDFiles.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="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Next</a></td><td width="34%" align="middle"><strong>ExtractFromSDFiles.pl</strong></td><td width="33%" align="right"><a href="././code/ExtractFromSDFiles.html" title="View source code">Code</a> | <a href="./../pdf/ExtractFromSDFiles.pdf" title="PDF US Letter Size">PDF</a> | <a href="./../pdfgreen/ExtractFromSDFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a> | <a href="./../pdfa4/ExtractFromSDFiles.pdf" title="PDF A4 Size">PDFA4</a> | <a href="./../pdfa4green/ExtractFromSDFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr> </table> </div> <p> </p> <h2>NAME</h2> <p>ExtractFromSDFiles.pl - Extract specific data from SDFile(s)</p> <p> </p> <h2>SYNOPSIS</h2> <p>ExtractFromSDFiles.pl SDFile(s)...</p> <p>ExtractFromSDFiles.pl [<strong>-h, --help</strong>] [<strong>-d, --datafields</strong> "fieldlabel,..." | "fieldlabel,value,criteria..." | "fieldlabel,value,value..."] [<strong>--datafieldsfile</strong> filename] [<strong>--indelim</strong> comma | tab | semicolon] [<strong>-m, --mode</strong> alldatafields | commondatafields | | datafieldnotbylist | datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist | datafielduniquebylist | molnames | randomcmpds | recordnum | recordnums | recordrange | 2dcmpdrecords | 3dcmpdrecords ] [<strong>-n, --numofcmpds</strong> number] [<strong>--outdelim</strong> comma | tab | semicolon] [<strong>--output</strong> SD | text | both] [<strong>-o, --overwrite</strong>] [<strong>-q, --quote</strong> yes | no] [<strong>--record</strong> recnum | startrecnum,endrecnum] <strong>--RegexIgnoreCase</strong> <em>yes or no</em> [<strong>-r, --root</strong> rootname] [<strong>-s, --seed</strong> number] [<strong>--StrDataString</strong> yes | no] [<strong>--StrDataStringDelimiter</strong> text] [<strong>--StrDataStringMode</strong> StrOnly | StrAndDataFields] [<strong>--ValueComparisonMode</strong> <em>Numeric | Alphanumeric</em>] [<strong>-v, --violations-</strong> number] [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p> <p> </p> <h2>DESCRIPTION</h2> <p>Extract specific data from <em>SDFile(s)</em> and generate appropriate SD or CSV/TSV text file(s). The structure data from SDFile(s) is not transferred to CSV/TSV text file(s). Multiple SDFile names are separated by spaces. 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>-h, --help</strong></strong></dt> <dd> <p>Print this help message.</p> </dd> <dt><strong><strong>-d, --datafields</strong> <em>"fieldlabel,..." | "fieldlabel,value,criteria..." | "fieldlabel,value,value,..."</em></strong></dt> <dd> <p>This value is mode specific. In general, it's a list of comma separated data field labels and associated mode specific values.</p> <p>For <em>datafields</em> mode, input value format is: <em>fieldlabel,...</em>. Examples:</p> <div class="OptionsBox"> Extreg <br/> Extreg,CompoundName,ID</div> <p>For <em>datafieldsbyvalue</em> mode, input value format contains these triplets: <em>fieldlabel,value, criteria...</em>. Possible values for criteria: <em>le, ge or eq</em>. The values of <strong>--ValueComparisonMode</strong> indicates whether values are compared numerical or string comarison operators. Default is to consider data field values as numerical values and use numerical comparison operators. Examples:</p> <div class="OptionsBox"> MolWt,450,le <br/> MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le</div> <p>For <em>datafieldsbyregex</em> mode, input value format contains these triplets: <em>fieldlabel,regex, criteria...</em>. <em>regex</em> corresponds to any valid regular expression and is used to match the values for specified <em>fieldlabel</em>. Possible values for criteria: <em>eq or ne</em>. During <em>eq</em> and <em>ne</em> values, data field label value is matched with regular expression using =~ and !~ respectively. <strong>--RegexIgnoreCase</strong> option value is used to determine whether to ignore letter upper/lower case during regular expression match. Examples:</p> <div class="OptionsBox"> Name,ol,eq <br/> Name,'^pat',ne</div> <p>For <em>datafieldbylist</em> and <em>datafielduniquebylist</em> mode, input value format is: <em>fieldlabel,value1,value2...</em>. This is equivalent to <em>datafieldsbyvalue</em> mode with this input value format:<em>fieldlabel,value1,eq,fieldlabel,value2,eq,...</em>. For <em>datafielduniquebylist</em> mode, only unique compounds identified by first occurrence of <em>value</em> associated with <em>fieldlabel</em> in <em>SDFile(s)</em> are kept; any subsequent compounds are simply ignored.</p> <p>For <em>datafieldnotbylist</em> mode, input value format is: <em>fieldlabel,value1,value2...</em>. In this mode, the script behaves exactly opposite of <em>datafieldbylist</em> mode, and only those compounds are extracted whose data field values don't match any specified data field value.</p> </dd> <dt><strong><strong>--datafieldsfile</strong> <em>filename</em></strong></dt> <dd> <p>Filename which contains various mode specific values. This option provides a way to specify mode specific values in a file instead of entering them on the command line using <strong>-d --datafields</strong>.</p> <p>For <em>datafields</em> mode, input file lines contain comma delimited field labels: <em>fieldlabel,...</em>. Example:</p> <div class="OptionsBox"> Line 1:MolId <br/> Line 2:"Extreg",CompoundName,ID</div> <p>For <em>datafieldsbyvalue</em> mode, input file lines contains these comma separated triplets: <em>fieldlabel,value, criteria</em>. Possible values for criteria: <em>le, ge or eq</em>. Examples:</p> <div class="OptionsBox"> Line 1:MolWt,450,le</div> <div class="OptionsBox"> Line 1:"MolWt",450,le,"LogP",5,le,"SumNumNO",10,le,"SumNHOH",5,le</div> <div class="OptionsBox"> Line 1:MolWt,450,le <br/> Line 2:"LogP",5,le <br/> Line 3:"SumNumNO",10,le <br/> Line 4: SumNHOH,5,le</div> <p>For <em>datafieldbylist</em> and <em>datafielduniquebylist</em> mode, input file line format is:</p> <div class="OptionsBox"> Line 1:fieldlabel; <br/> Subsequent lines:value1,value2...</div> <p>For <em>datafieldbylist</em>, <em>datafielduniquebylist</em>, and <em>datafieldnotbylist</em> mode, input file line format is:</p> <div class="OptionsBox"> Line 1:fieldlabel; <br/> Subsequent lines:value1,value2...</div> <p>For <em>datafielduniquebylist</em> mode, only unique compounds identified by first occurrence of <em>value</em> associated with <em>fieldlabel</em> in <em>SDFile(s)</em> are kept; any subsequent compounds are simply ignored. Example:</p> <div class="OptionsBox"> Line 1: MolID <br/> Subsequent Lines: <br/> 907508 <br/> 832291,4642 <br/> "1254","907303"</div> </dd> <dt><strong><strong>--indelim</strong> <em>comma | tab | semicolon</em></strong></dt> <dd> <p>Delimiter used to specify text values for <strong>-d --datafields</strong> and <strong>--datafieldsfile</strong> options. Possible values: <em>comma, tab, or semicolon</em>. Default value: <em>comma</em>.</p> </dd> <dt><strong><strong>-m, --mode</strong> <em>alldatafields | commondatafields | datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist | datafielduniquebylist | datafieldnotbylist | molnames | randomcmpds | recordnum | recordnums | recordrange | 2dcmpdrecords | 3dcmpdrecords</em></strong></dt> <dd> <p>Specify what to extract from <em>SDFile(s)</em>. Possible values: <em>alldatafields, commondatafields, datafields, datafieldsbyvalue, datafieldsbyregex, datafieldbylist, datafielduniquebylist, datafieldnotbylist, molnames, randomcmpds, recordnum, recordnums, recordrange, 2dcmpdrecords, 3dcmpdrecords</em>. Default value: <em>alldatafields</em>.</p> <p>For <em>alldatafields</em> and <em>molnames</em> mode, only a CSV/TSV text file is generated; for all other modes, however, a SD file is generated by default - you can change the behavior to genereate text file using <em>--output</em> option.</p> <p>For <em>3DCmpdRecords</em> mode, only those compounds with at least one non-zero value for Z atomic coordinates are retrieved; however, during retrieval of compounds in <em>2DCmpdRecords</em> mode, all Z atomic coordinates must be zero.</p> </dd> <dt><strong><strong>-n, --numofcmpds</strong> <em>number</em></strong></dt> <dd> <p>Number of compouds to extract during <em>randomcmpds</em> mode.</p> </dd> <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt> <dd> <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em> Default value: <em>comma</em></p> </dd> <dt><strong><strong>--output</strong> <em>SD | text | both</em></strong></dt> <dd> <p>Type of output files to generate. Possible values: <em>SD, text, or both</em>. Default value: <em>SD</em>. For <em>alldatafields</em> and <em>molnames</em> mode, this option is ingored and only a CSV/TSV text file is generated.</p> </dd> <dt><strong><strong>-o, --overwrite</strong></strong></dt> <dd> <p>Overwrite existing files.</p> </dd> <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt> <dd> <p>Put quote around column values in output CSV/TSV text file(s). Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p> </dd> <dt><strong><strong>--record</strong> <em>recnum | recnums | startrecnum,endrecnum</em></strong></dt> <dd> <p>Record number, record numbers or range of records to extract during <em>recordnum</em>, <em>recordnums</em> and <em>recordrange</em> mode. Input value format is: <num>, <num1,num2,...> and <startnum, endnum> for <em>recordnum</em>, <em>recordnums</em> and <em>recordrange</em> modes recpectively. Default value: none.</p> </dd> <dt><strong><strong>--RegexIgnoreCase</strong> <em>yes or no</em></strong></dt> <dd> <p>Specify whether to ingnore case during <em>datafieldsbyregex</em> value of <strong>-m, --mode</strong> option. Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p> </dd> <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt> <dd> <p>New file name is generated using the root: <Root>.<Ext>. Default for new file names: <SDFileName><mode>.<Ext>. The file type determines <Ext> value. The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab delimited text files respectively.This option is ignored for multiple input files.</p> </dd> <dt><strong><strong>-s, --seed</strong> <em>number</em></strong></dt> <dd> <p>Random number seed used for <em>randomcmpds</em> mode. Default:123456789.</p> </dd> <dt><strong><strong>--StrDataString</strong> <em>yes | no</em></strong></dt> <dd> <p>Specify whether to write out structure data string to CSV/TSV text file(s). Possible values: <em>yes or no</em>. Default value: <em>no</em>.</p> <p>The value of <strong>StrDataStringDelimiter</strong> option is used as a delimiter to join structure data lines into a structure data string.</p> <p>This option is ignored during generation of SD file(s).</p> </dd> <dt><strong><strong>--StrDataStringDelimiter</strong> <em>text</em></strong></dt> <dd> <p>Delimiter for joining multiple stucture data lines into a string before writing to CSV/TSV text file(s). Possible values: <em>any alphanumeric text</em>. Default value: <em>|</em>.</p> <p>This option is ignored during generation of SD file(s).</p> </dd> <dt><strong><strong>--StrDataStringMode</strong> <em>StrOnly | StrAndDataFields</em></strong></dt> <dd> <p>Specify whether to include SD data fields and values along with the structure data into structure data string before writing it out to CSV/TSV text file(s). Possible values: <em>StrOnly or StrAndDataFields</em>. Default value: <em>StrOnly</em>.</p> <p>The value of <strong>StrDataStringDelimiter</strong> option is used as a delimiter to join structure data lines into a structure data string.</p> <p>This option is ignored during generation of SD file(s).</p> </dd> <dt><strong><strong>--ValueComparisonMode</strong> <em>Numeric | Alphanumeric</em></strong></dt> <dd> <p>Specify how to compare data field values during <em>datafieldsbyvalue</em> mode: Compare values using either numeric or string ((eq, le, ge) comparison operators. Possible values: <em>Numeric or Alphanumeric</em>. Defaule value: <em>Numeric</em>.</p> </dd> <dt><strong><strong>-v, --violations</strong> <em>number</em></strong></dt> <dd> <p>Number of criterion violations allowed for values specified during <em>datafieldsbyvalue</em> and <em>datafieldsbyregex</em> mode. Default value: <em>0</em>.</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 retrieve all data fields from SD files and generate CSV text files, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -o Sample.sdf <br/>% ExtractFromSDFiles.pl -o *.sdf</div> <p>To retrieve all data fields from SD file and generate CSV text files containing a column with structure data as a string with | as line delimiter, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl --StrDataString Yes -o Sample.sdf</div> <p>To retrieve MOL_ID data fileld from SD file and generate CSV text files containing a column with structure data along with all data fields as a string with | as line delimiter, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m datafields -d "Mol_ID" --StrDataString Yes --StrDataStringMode StrAndDataFields --StrDataStringDelimiter "|" --output text -o Sample.sdf</div> <p>To retrieve common data fields which exists for all the compounds in a SD file and generate a TSV text file NewSample.tsv, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m commondatafields --outdelim tab -r NewSample --output Text -o Sample.sdf</div> <p>To retrieve MolId, ExtReg, and CompoundName data field from a SD file and generate a CSV text file NewSample.csv, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m datafields -d "Mol_ID,MolWeight, CompoundName" -r NewSample --output Text -o Sample.sdf</div> <p>To retrieve compounds from a SD which meet a specific set of criteria - MolWt <= 450, LogP <= 5 and SumNO < 10 - from a SD file and generate a new SD file NewSample.sdf, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m datafieldsbyvalue -d "MolWt,450,le,LogP ,5,le,SumNO,10" -r NewSample -o Sample.sdf</div> <p>To retrive compounds from a SD file with a specific set of values for MolID and generate a new SD file NewSample.sdf, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m datafieldbylist -d "Mol_ID,159,4509,4619" -r NewSample -o Sample.sdf</div> <p>To retrive compounds from a SD file with values for MolID not on a list of specified values and generate a new SD file NewSample.sdf, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m datafieldnotbylist -d "Mol_ID,159,4509,4619" -r NewSample -o Sample.sdf</div> <p>To retrive 10 random compounds from a SD file and generate a new SD file RandomSample.sdf, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m randomcmpds -n 10 -r RandomSample -o Sample.sdf</div> <p>To retrive compound record number 10 from a SD file and generate a new SD file NewSample.sdf, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m recordnum --record 10 -r NewSample -o Sample.sdf</div> <p>To retrive compound record numbers 10, 20 and 30 from a SD file and generate a new SD file NewSample.sdf, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m recordnums --record 10,20,30 -r NewSample -o Sample.sdf</div> <p>To retrive compound records between 10 to 20 from SD file and generate a new SD file NewSample.sdf, type:</p> <div class="ExampleBox"> % ExtractFromSDFiles.pl -m recordrange --record 10,20 -r NewSample -o Sample.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="./FilterSDFiles.html">FilterSDFiles.pl</a>, <a href="./InfoSDFiles.html">InfoSDFiles.pl</a>, <a href="./SplitSDFiles.html">SplitSDFiles.pl</a>, <a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.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="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Previous</a> <a href="./index.html" title="Table of Contents">TOC</a> <a href="./ExtractFromSequenceFiles.html" title="ExtractFromSequenceFiles.html">Next</a></td><td width="34%" align="middle"><strong>March 29, 2015</strong></td><td width="33%" align="right"><strong>ExtractFromSDFiles.pl</strong></td></tr> </table> </div> <br /> <center> <img src="../../images/h2o2.png"> </center> </body> </html>