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NAME

ExtractFromSDFiles.pl - Extract specific data from SDFile(s)

SYNOPSIS

ExtractFromSDFiles.pl SDFile(s)...

ExtractFromSDFiles.pl [-h, --help] [-d, --datafields ''fieldlabel,...'' | ''fieldlabel,value,criteria...'' | ''fieldlabel,value,value...''] [--datafieldsfile filename] [--indelim comma | tab | semicolon] [-m, --mode alldatafields | commondatafields | datafields | datafieldsbyvalue | datafieldbylist | datafielduniquebylist | molnames | randomcmpds | recordnum | recordsrange] [-n, --numofcmpds number] [--outdelim comma | tab | semicolon] [--output SD | text | both] [-o, --overwrite] [-q, --quote yes | no] [--record recnum | startrecnum,endrecnum] [-r, --root rootname] [-s, --seed number] [-v, --violations- number] [-w, --workingdir dirname] SDFile(s)...

DESCRIPTION

Extract specific data from SDFile(s) 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 .sdf and .sd. All other file names are ignored. All the SD files in a current directory can be specified either by *.sdf or the current directory name.

OPTIONS

-h, --help

Print this help message

-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.

For datafields mode, input value format is: fieldlabel,.... Examples:

Extreg
Extreg,CompoundName,ID

For datafieldsbyvalue mode, input value format contains these triplets: fieldlabel,value, criteria.... Possible values for criteria: le, ge or eq. Examples:

MolWt,450,le
MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le

For datafieldbylist and datafielduniquebylist mode, input value format is: fieldlabel,value1,value2.... This is equivalent to datafieldsbyvalue mode with this input value format:fieldlabel,value1,eq,fieldlabel,value2,eq,.... For datafielduniquebylist mode, only unique compounds identified by first occurrence of value associated with fieldlabel in SDFile(s) are kept; any subsequent compounds are simply ignored

--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 -d --datafields.

For datafields mode, input file lines contain comma delimited field labels: fieldlabel,.... Example:

Line 1:MolId
Line 2:"Extreg",CompoundName,ID

For datafieldsbyvalue mode, input file lines contains these comma separated triplets: fieldlabel,value, criteria. Possible values for criteria: le, ge or eq. Examples:

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

For datafieldbylist and datafielduniquebylist mode, input file line format is:

Line 1:fieldlabel;
Subsequent lines:value1,value2...

For datafielduniquebylist mode, only unique compounds identified by first occurrence of value associated with fieldlabel in SDFile(s) are kept; any subsequent compounds are simply ignored. Example:

Line 1: MolID
Subsequent Lines:
907508
832291,4642
"1254","907303"

--indelim comma | tab | semicolon

Delimiter used to specify text values for -d --datafields and --datafieldsfile options. Possible values: comma, tab, or semicolon. Default value: comma

-m, --mode alldatafields | commondatafields | datafields | datafieldsbyvalue | datafieldbylist | datafielduniquebylist | molnames | randomcmpds | recordnum | recordsrange

Specify what to extract from SDFile(s). Possible values: alldatafields, commondatafields, datafields, datafieldsbyvalue, datafieldbylist, datafielduniquebylist, molnames, randomcmpds, recordnum, recordsrange. Default value: alldatafields.

For alldatafields and molnames 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 --output option.

-n, --numofcmpds number

Number of compouds to extract during randomcmpds mode

--outdelim comma | tab | semicolon

Delimiter for output CSV/TSV text file(s). Possible values: comma, tab, or semicolon Default value: comma

--output SD | text | both

Type of output files to generate. Possible values: SD, text, or both. Default value: SD. For alldatafields and molnames mode, this option is ingored and only a CSV/TSV text file is generated.

-o, --overwrite

Overwrite existing files

-q, --quote yes | no

Put quote around column values in output CSV/TSV text file(s). Possible values: yes or no. Default value: yes

--record recnum | startrecnum,endrecnum

Record number or range of records to extract during recordnum and recordrange mode. input value format is: <num> and <startnum, endnum> for recordnum and recordrange modes recpectively. Default value: none.

-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 SD, comma/semicolon, and tab delimited text files respectively.This option is ignored for multiple input files.

-s, --seed number

Random number seed used for randomcmpds mode. Default:999999999

-v, --violations number

Number of criterion violations allowed for values specified during datafieldsbyvalue mode. Default value: 0

-w, --workingdir dirname

Location of working directory. Default: current directory

EXAMPLES

To retrieve all data fields from SD files and generate CSV text files, type:

To retrieve common data fields which exists for all the compounds in a SD file and generate a TSV text file NewSample.tsv, type:

To retrieve MolId, ExtReg, and CompoundName data field from a SD file and generate a CSV text file NewSample.csv, type:

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:

To retrive compounds from a SD file with a specific set of values for MolID and generate a new SD file NewSample.sdf, type:

To retrive 10 random compounds from a SD file and generate a new SD file RandomSample.sdf, type:

To retrive compound record number 10 from a SD file and generate a new SD file NewSample.sdf, type:

To retrive compound records between 10 to 20 from SD file and generate a new SD file NewSample.sdf, type:

AUTHOR

Manish Sud

SEE ALSO

FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl

COPYRIGHT

Copyright (C) 2004-2008 Manish Sud. All rights reserved.

This file is part of MayaChemTools.

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.