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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 09:23:18 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/docs/scripts/man1/ExtractFromSDFiles.1 Wed Jan 20 09:23:18 2016 -0500 @@ -0,0 +1,466 @@ +.\" 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++. 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Always turn off hyphenation; it makes +.\" way too many mistakes in technical documents. +.if n .ad l +.nh +.SH "NAME" +ExtractFromSDFiles.pl \- Extract specific data from SDFile(s) +.SH "SYNOPSIS" +.IX Header "SYNOPSIS" +ExtractFromSDFiles.pl SDFile(s)... +.PP +ExtractFromSDFiles.pl [\fB\-h, \-\-help\fR] +[\fB\-d, \-\-datafields\fR \*(L"fieldlabel,...\*(R" | \*(L"fieldlabel,value,criteria...\*(R" | \*(L"fieldlabel,value,value...\*(R"] +[\fB\-\-datafieldsfile\fR filename] [\fB\-\-indelim\fR comma | tab | semicolon] [\fB\-m, \-\-mode\fR alldatafields | +commondatafields | | datafieldnotbylist | datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist | +datafielduniquebylist | molnames | randomcmpds | recordnum | recordnums | recordrange | 2dcmpdrecords | +3dcmpdrecords ] [\fB\-n, \-\-numofcmpds\fR number] [\fB\-\-outdelim\fR comma | tab | semicolon] +[\fB\-\-output\fR \s-1SD\s0 | text | both] [\fB\-o, \-\-overwrite\fR] [\fB\-q, \-\-quote\fR yes | no] +[\fB\-\-record\fR recnum | startrecnum,endrecnum] \fB\-\-RegexIgnoreCase\fR \fIyes or no\fR +[\fB\-r, \-\-root\fR rootname] [\fB\-s, \-\-seed\fR number] [\fB\-\-StrDataString\fR yes | no] +[\fB\-\-StrDataStringDelimiter\fR text] [\fB\-\-StrDataStringMode\fR StrOnly | StrAndDataFields] +[\fB\-\-ValueComparisonMode\fR \fINumeric | Alphanumeric\fR] +[\fB\-v, \-\-violations\-\fR number] [\fB\-w, \-\-workingdir\fR dirname] SDFile(s)... +.SH "DESCRIPTION" +.IX Header "DESCRIPTION" +Extract specific data from \fISDFile(s)\fR and generate appropriate \s-1SD\s0 or \s-1CSV/TSV\s0 text +file(s). The structure data from SDFile(s) is not transferred to \s-1CSV/TSV\s0 text file(s). +Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR +and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory +can be specified either by \fI*.sdf\fR or the current directory name. +.SH "OPTIONS" +.IX Header "OPTIONS" +.IP "\fB\-h, \-\-help\fR" 4 +.IX Item "-h, --help" +Print this help message. +.ie n .IP "\fB\-d, \-\-datafields\fR \fI""fieldlabel,..."" | ""fieldlabel,value,criteria..."" | ""fieldlabel,value,value,...""\fR" 4 +.el .IP "\fB\-d, \-\-datafields\fR \fI``fieldlabel,...'' | ``fieldlabel,value,criteria...'' | ``fieldlabel,value,value,...''\fR" 4 +.IX Item "-d, --datafields fieldlabel,... | fieldlabel,value,criteria... | fieldlabel,value,value,..." +This value is mode specific. In general, it's a list of comma separated data field labels +and associated mode specific values. +.Sp +For \fIdatafields\fR mode, input value format is: \fIfieldlabel,...\fR. Examples: +.Sp +.Vb 2 +\& Extreg +\& Extreg,CompoundName,ID +.Ve +.Sp +For \fIdatafieldsbyvalue\fR mode, input value format contains these triplets: +\&\fIfieldlabel,value, criteria...\fR. Possible values for criteria: \fIle, ge or eq\fR. +The values of \fB\-\-ValueComparisonMode\fR 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: +.Sp +.Vb 2 +\& MolWt,450,le +\& MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le +.Ve +.Sp +For \fIdatafieldsbyregex\fR mode, input value format contains these triplets: +\&\fIfieldlabel,regex, criteria...\fR. \fIregex\fR corresponds to any valid regular expression +and is used to match the values for specified \fIfieldlabel\fR. Possible values for criteria: + \fIeq or ne\fR. During \fIeq\fR and \fIne\fR values, data field label value is matched with +regular expression using =~ and !~ respectively. \fB\-\-RegexIgnoreCase\fR option +value is used to determine whether to ignore letter upper/lower case during +regular expression match. Examples: +.Sp +.Vb 2 +\& Name,ol,eq +\& Name,\*(Aq^pat\*(Aq,ne +.Ve +.Sp +For \fIdatafieldbylist\fR and \fIdatafielduniquebylist\fR mode, input value format is: +\&\fIfieldlabel,value1,value2...\fR. This is equivalent to \fIdatafieldsbyvalue\fR mode with +this input value format:\fIfieldlabel,value1,eq,fieldlabel,value2,eq,...\fR. For +\&\fIdatafielduniquebylist\fR mode, only unique compounds identified by first occurrence +of \fIvalue\fR associated with \fIfieldlabel\fR in \fISDFile(s)\fR are kept; any subsequent compounds +are simply ignored. +.Sp +For \fIdatafieldnotbylist\fR mode, input value format is: \fIfieldlabel,value1,value2...\fR. In this +mode, the script behaves exactly opposite of \fIdatafieldbylist\fR mode, and only those compounds +are extracted whose data field values don't match any specified data field value. +.IP "\fB\-\-datafieldsfile\fR \fIfilename\fR" 4 +.IX Item "--datafieldsfile filename" +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 \fB\-d \-\-datafields\fR. +.Sp +For \fIdatafields\fR mode, input file lines contain comma delimited field labels: +\&\fIfieldlabel,...\fR. Example: +.Sp +.Vb 2 +\& Line 1:MolId +\& Line 2:"Extreg",CompoundName,ID +.Ve +.Sp +For \fIdatafieldsbyvalue\fR mode, input file lines contains these comma separated triplets: +\&\fIfieldlabel,value, criteria\fR. Possible values for criteria: \fIle, ge or eq\fR. Examples: +.Sp +.Vb 1 +\& Line 1:MolWt,450,le +\& +\& Line 1:"MolWt",450,le,"LogP",5,le,"SumNumNO",10,le,"SumNHOH",5,le +\& +\& Line 1:MolWt,450,le +\& Line 2:"LogP",5,le +\& Line 3:"SumNumNO",10,le +\& Line 4: SumNHOH,5,le +.Ve +.Sp +For \fIdatafieldbylist\fR and \fIdatafielduniquebylist\fR mode, input file line format is: +.Sp +.Vb 2 +\& Line 1:fieldlabel; +\& Subsequent lines:value1,value2... +.Ve +.Sp +For \fIdatafieldbylist\fR, \fIdatafielduniquebylist\fR, and \fIdatafieldnotbylist\fR mode, input file +line format is: +.Sp +.Vb 2 +\& Line 1:fieldlabel; +\& Subsequent lines:value1,value2... +.Ve +.Sp +For \fIdatafielduniquebylist\fR mode, only unique compounds identified by first occurrence +of \fIvalue\fR associated with \fIfieldlabel\fR in \fISDFile(s)\fR are kept; any subsequent compounds +are simply ignored. Example: +.Sp +.Vb 5 +\& Line 1: MolID +\& Subsequent Lines: +\& 907508 +\& 832291,4642 +\& "1254","907303" +.Ve +.IP "\fB\-\-indelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--indelim comma | tab | semicolon" +Delimiter used to specify text values for \fB\-d \-\-datafields\fR and \fB\-\-datafieldsfile\fR options. +Possible values: \fIcomma, tab, or semicolon\fR. Default value: \fIcomma\fR. +.IP "\fB\-m, \-\-mode\fR \fIalldatafields | commondatafields | datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist | datafielduniquebylist | datafieldnotbylist | molnames | randomcmpds | recordnum | recordnums | recordrange | 2dcmpdrecords | 3dcmpdrecords\fR" 4 +.IX Item "-m, --mode alldatafields | commondatafields | datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist | datafielduniquebylist | datafieldnotbylist | molnames | randomcmpds | recordnum | recordnums | recordrange | 2dcmpdrecords | 3dcmpdrecords" +Specify what to extract from \fISDFile(s)\fR. Possible values: \fIalldatafields, commondatafields, +datafields, datafieldsbyvalue, datafieldsbyregex, datafieldbylist, datafielduniquebylist, datafieldnotbylist, +molnames, randomcmpds, recordnum, recordnums, recordrange, 2dcmpdrecords, 3dcmpdrecords\fR. +Default value: \fIalldatafields\fR. +.Sp +For \fIalldatafields\fR and \fImolnames\fR mode, only a \s-1CSV/TSV\s0 text file is generated; for all +other modes, however, a \s-1SD\s0 file is generated by default \- you can change the behavior to genereate +text file using \fI\-\-output\fR option. +.Sp +For \fI3DCmpdRecords\fR mode, only those compounds with at least one non-zero value for Z atomic coordinates +are retrieved; however, during retrieval of compounds in \fI2DCmpdRecords\fR mode, all Z atomic coordinates must +be zero. +.IP "\fB\-n, \-\-numofcmpds\fR \fInumber\fR" 4 +.IX Item "-n, --numofcmpds number" +Number of compouds to extract during \fIrandomcmpds\fR mode. +.IP "\fB\-\-outdelim\fR \fIcomma | tab | semicolon\fR" 4 +.IX Item "--outdelim comma | tab | semicolon" +Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR +Default value: \fIcomma\fR +.IP "\fB\-\-output\fR \fI\s-1SD\s0 | text | both\fR" 4 +.IX Item "--output SD | text | both" +Type of output files to generate. Possible values: \fI\s-1SD\s0, text, or both\fR. Default value: \fI\s-1SD\s0\fR. For +\&\fIalldatafields\fR and \fImolnames\fR mode, this option is ingored and only a \s-1CSV/TSV\s0 text file is generated. +.IP "\fB\-o, \-\-overwrite\fR" 4 +.IX Item "-o, --overwrite" +Overwrite existing files. +.IP "\fB\-q, \-\-quote\fR \fIyes | no\fR" 4 +.IX Item "-q, --quote yes | no" +Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values: +\&\fIyes or no\fR. Default value: \fIyes\fR. +.IP "\fB\-\-record\fR \fIrecnum | recnums | startrecnum,endrecnum\fR" 4 +.IX Item "--record recnum | recnums | startrecnum,endrecnum" +Record number, record numbers or range of records to extract during \fIrecordnum\fR, \fIrecordnums\fR +and \fIrecordrange\fR mode. Input value format is: <num>, <num1,num2,...> and <startnum, endnum> +for \fIrecordnum\fR, \fIrecordnums\fR and \fIrecordrange\fR modes recpectively. Default value: none. +.IP "\fB\-\-RegexIgnoreCase\fR \fIyes or no\fR" 4 +.IX Item "--RegexIgnoreCase yes or no" +Specify whether to ingnore case during \fIdatafieldsbyregex\fR value of \fB\-m, \-\-mode\fR option. +Possible values: \fIyes or no\fR. Default value: \fIyes\fR. +.IP "\fB\-r, \-\-root\fR \fIrootname\fR" 4 +.IX Item "-r, --root rootname" +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 \s-1SD\s0, comma/semicolon, and tab +delimited text files respectively.This option is ignored for multiple input files. +.IP "\fB\-s, \-\-seed\fR \fInumber\fR" 4 +.IX Item "-s, --seed number" +Random number seed used for \fIrandomcmpds\fR mode. Default:123456789. +.IP "\fB\-\-StrDataString\fR \fIyes | no\fR" 4 +.IX Item "--StrDataString yes | no" +Specify whether to write out structure data string to \s-1CSV/TSV\s0 text file(s). Possible values: +\&\fIyes or no\fR. Default value: \fIno\fR. +.Sp +The value of \fBStrDataStringDelimiter\fR option is used as a delimiter to join structure +data lines into a structure data string. +.Sp +This option is ignored during generation of \s-1SD\s0 file(s). +.IP "\fB\-\-StrDataStringDelimiter\fR \fItext\fR" 4 +.IX Item "--StrDataStringDelimiter text" +Delimiter for joining multiple stucture data lines into a string before writing to \s-1CSV/TSV\s0 text +file(s). Possible values: \fIany alphanumeric text\fR. Default value: \fI|\fR. +.Sp +This option is ignored during generation of \s-1SD\s0 file(s). +.IP "\fB\-\-StrDataStringMode\fR \fIStrOnly | StrAndDataFields\fR" 4 +.IX Item "--StrDataStringMode StrOnly | StrAndDataFields" +Specify whether to include \s-1SD\s0 data fields and values along with the structure data into structure +data string before writing it out to \s-1CSV/TSV\s0 text file(s). Possible values: \fIStrOnly or StrAndDataFields\fR. +Default value: \fIStrOnly\fR. +.Sp +The value of \fBStrDataStringDelimiter\fR option is used as a delimiter to join structure +data lines into a structure data string. +.Sp +This option is ignored during generation of \s-1SD\s0 file(s). +.IP "\fB\-\-ValueComparisonMode\fR \fINumeric | Alphanumeric\fR" 4 +.IX Item "--ValueComparisonMode Numeric | Alphanumeric" +Specify how to compare data field values during \fIdatafieldsbyvalue\fR mode: Compare +values using either numeric or string ((eq, le, ge) comparison operators. Possible values: +\&\fINumeric or Alphanumeric\fR. Defaule value: \fINumeric\fR. +.IP "\fB\-v, \-\-violations\fR \fInumber\fR" 4 +.IX Item "-v, --violations number" +Number of criterion violations allowed for values specified during \fIdatafieldsbyvalue\fR +and \fIdatafieldsbyregex\fR mode. Default value: \fI0\fR. +.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 retrieve all data fields from \s-1SD\s0 files and generate \s-1CSV\s0 text files, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-o Sample.sdf +\& % ExtractFromSDFiles.pl \-o *.sdf +.Ve +.PP +To retrieve all data fields from \s-1SD\s0 file and generate \s-1CSV\s0 text files containing +a column with structure data as a string with | as line delimiter, type: +.PP +.Vb 1 +\& % ExtractFromSDFiles.pl \-\-StrDataString Yes \-o Sample.sdf +.Ve +.PP +To retrieve \s-1MOL_ID\s0 data fileld from \s-1SD\s0 file and generate \s-1CSV\s0 text files containing +a column with structure data along with all data fields as a string with | as line +delimiter, type: +.PP +.Vb 3 +\& % ExtractFromSDFiles.pl \-m datafields \-d "Mol_ID" \-\-StrDataString Yes +\& \-\-StrDataStringMode StrAndDataFields \-\-StrDataStringDelimiter "|" +\& \-\-output text \-o Sample.sdf +.Ve +.PP +To retrieve common data fields which exists for all the compounds in +a \s-1SD\s0 file and generate a \s-1TSV\s0 text file NewSample.tsv, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m commondatafields \-\-outdelim tab \-r NewSample +\& \-\-output Text \-o Sample.sdf +.Ve +.PP +To retrieve MolId, ExtReg, and CompoundName data field from a \s-1SD\s0 file and generate a +\&\s-1CSV\s0 text file NewSample.csv, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m datafields \-d "Mol_ID,MolWeight, +\& CompoundName" \-r NewSample \-\-output Text \-o Sample.sdf +.Ve +.PP +To retrieve compounds from a \s-1SD\s0 which meet a specific set of criteria \- MolWt <= 450, +LogP <= 5 and SumNO < 10 \- from a \s-1SD\s0 file and generate a new \s-1SD\s0 file NewSample.sdf, +type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m datafieldsbyvalue \-d "MolWt,450,le,LogP +\& ,5,le,SumNO,10" \-r NewSample \-o Sample.sdf +.Ve +.PP +To retrive compounds from a \s-1SD\s0 file with a specific set of values for MolID and +generate a new \s-1SD\s0 file NewSample.sdf, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m datafieldbylist \-d "Mol_ID,159,4509,4619" +\& \-r NewSample \-o Sample.sdf +.Ve +.PP +To retrive compounds from a \s-1SD\s0 file with values for MolID not on a list of specified +values and generate a new \s-1SD\s0 file NewSample.sdf, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m datafieldnotbylist \-d "Mol_ID,159,4509,4619" +\& \-r NewSample \-o Sample.sdf +.Ve +.PP +To retrive 10 random compounds from a \s-1SD\s0 file and generate a new \s-1SD\s0 file RandomSample.sdf, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m randomcmpds \-n 10 \-r RandomSample +\& \-o Sample.sdf +.Ve +.PP +To retrive compound record number 10 from a \s-1SD\s0 file and generate a new \s-1SD\s0 file NewSample.sdf, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m recordnum \-\-record 10 \-r NewSample +\& \-o Sample.sdf +.Ve +.PP +To retrive compound record numbers 10, 20 and 30 from a \s-1SD\s0 file and generate a new \s-1SD\s0 file +NewSample.sdf, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m recordnums \-\-record 10,20,30 \-r NewSample +\& \-o Sample.sdf +.Ve +.PP +To retrive compound records between 10 to 20 from \s-1SD\s0 file and generate a new \s-1SD\s0 +file NewSample.sdf, type: +.PP +.Vb 2 +\& % ExtractFromSDFiles.pl \-m recordrange \-\-record 10,20 \-r NewSample +\& \-o Sample.sdf +.Ve +.SH "AUTHOR" +.IX Header "AUTHOR" +Manish Sud <msud@san.rr.com> +.SH "SEE ALSO" +.IX Header "SEE ALSO" +FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.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.