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ExtractFromSDFiles.pl - Extract specific data from SDFile(s)
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 | | datafieldnotbylist | datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist | datafielduniquebylist | molnames | randomcmpds | recordnum | recordnums | recordrange | 2dcmpdrecords | 3dcmpdrecords ] [-n, --numofcmpds number] [--outdelim comma | tab | semicolon] [--output SD | text | both] [-o, --overwrite] [-q, --quote yes | no] [--record recnum | startrecnum,endrecnum] --RegexIgnoreCase yes or no [-r, --root rootname] [-s, --seed number] [--StrDataString yes | no] [--StrDataStringDelimiter text] [--StrDataStringMode StrOnly | StrAndDataFields] [--ValueComparisonMode Numeric | Alphanumeric] [-v, --violations- number] [-w, --workingdir dirname] SDFile(s)...
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.
Print this help message.
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:
For datafieldsbyvalue mode, input value format contains these triplets: fieldlabel,value, criteria.... Possible values for criteria: le, ge or eq. The values of --ValueComparisonMode 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:
For datafieldsbyregex mode, input value format contains these triplets: fieldlabel,regex, criteria.... regex corresponds to any valid regular expression and is used to match the values for specified fieldlabel. Possible values for criteria: eq or ne. During eq and ne values, data field label value is matched with regular expression using =~ and !~ respectively. --RegexIgnoreCase option value is used to determine whether to ignore letter upper/lower case during regular expression match. Examples:
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.
For datafieldnotbylist mode, input value format is: fieldlabel,value1,value2.... In this mode, the script behaves exactly opposite of datafieldbylist mode, and only those compounds are extracted whose data field values don't match any specified data field value.
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:
For datafieldsbyvalue mode, input file lines contains these comma separated triplets: fieldlabel,value, criteria. Possible values for criteria: le, ge or eq. Examples:
For datafieldbylist and datafielduniquebylist mode, input file line format is:
For datafieldbylist, datafielduniquebylist, and datafieldnotbylist mode, input file line format is:
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:
Delimiter used to specify text values for -d --datafields and --datafieldsfile options. Possible values: comma, tab, or semicolon. Default value: comma.
Specify what to extract from SDFile(s). Possible values: alldatafields, commondatafields, datafields, datafieldsbyvalue, datafieldsbyregex, datafieldbylist, datafielduniquebylist, datafieldnotbylist, molnames, randomcmpds, recordnum, recordnums, recordrange, 2dcmpdrecords, 3dcmpdrecords. 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.
For 3DCmpdRecords mode, only those compounds with at least one non-zero value for Z atomic coordinates are retrieved; however, during retrieval of compounds in 2DCmpdRecords mode, all Z atomic coordinates must be zero.
Number of compouds to extract during randomcmpds mode.
Delimiter for output CSV/TSV text file(s). Possible values: comma, tab, or semicolon Default value: comma
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.
Overwrite existing files.
Put quote around column values in output CSV/TSV text file(s). Possible values: yes or no. Default value: yes.
Record number, record numbers or range of records to extract during recordnum, recordnums and recordrange mode. Input value format is: <num>, <num1,num2,...> and <startnum, endnum> for recordnum, recordnums and recordrange modes recpectively. Default value: none.
Specify whether to ingnore case during datafieldsbyregex value of -m, --mode option. Possible values: yes or no. Default value: yes.
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.
Random number seed used for randomcmpds mode. Default:123456789.
Specify whether to write out structure data string to CSV/TSV text file(s). Possible values: yes or no. Default value: no.
The value of StrDataStringDelimiter option is used as a delimiter to join structure data lines into a structure data string.
This option is ignored during generation of SD file(s).
Delimiter for joining multiple stucture data lines into a string before writing to CSV/TSV text file(s). Possible values: any alphanumeric text. Default value: |.
This option is ignored during generation of SD file(s).
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: StrOnly or StrAndDataFields. Default value: StrOnly.
The value of StrDataStringDelimiter option is used as a delimiter to join structure data lines into a structure data string.
This option is ignored during generation of SD file(s).
Specify how to compare data field values during datafieldsbyvalue mode: Compare values using either numeric or string ((eq, le, ge) comparison operators. Possible values: Numeric or Alphanumeric. Defaule value: Numeric.
Number of criterion violations allowed for values specified during datafieldsbyvalue and datafieldsbyregex mode. Default value: 0.
Location of working directory. Default: current directory.
To retrieve all data fields from SD files and generate CSV text files, type:
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:
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:
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 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:
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 record numbers 10, 20 and 30 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:
FilterSDFiles.pl, InfoSDFiles.pl, SplitSDFiles.pl, MergeTextFilesWithSD.pl
Copyright (C) 2024 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.
