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15 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>&nbsp;|&nbsp;<a href="./../pdf/ExtractFromSDFiles.pdf" title="PDF US Letter Size">PDF</a>&nbsp;|&nbsp;<a href="./../pdfgreen/ExtractFromSDFiles.pdf" title="PDF US Letter Size with narrow margins: www.changethemargins.com">PDFGreen</a>&nbsp;|&nbsp;<a href="./../pdfa4/ExtractFromSDFiles.pdf" title="PDF A4 Size">PDFA4</a>&nbsp;|&nbsp;<a href="./../pdfa4green/ExtractFromSDFiles.pdf" title="PDF A4 Size with narrow margins: www.changethemargins.com">PDFA4Green</a></td></tr>
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18 <p>
19 </p>
20 <h2>NAME</h2>
21 <p>ExtractFromSDFiles.pl - Extract specific data from SDFile(s)</p>
22 <p>
23 </p>
24 <h2>SYNOPSIS</h2>
25 <p>ExtractFromSDFiles.pl SDFile(s)...</p>
26 <p>ExtractFromSDFiles.pl [<strong>-h, --help</strong>]
27 [<strong>-d, --datafields</strong> &quot;fieldlabel,...&quot; | &quot;fieldlabel,value,criteria...&quot; | &quot;fieldlabel,value,value...&quot;]
28 [<strong>--datafieldsfile</strong> filename] [<strong>--indelim</strong> comma | tab | semicolon] [<strong>-m, --mode</strong> alldatafields |
29 commondatafields | | datafieldnotbylist | datafields | datafieldsbyvalue | datafieldsbyregex | datafieldbylist |
30 datafielduniquebylist | molnames | randomcmpds | recordnum | recordnums | recordrange | 2dcmpdrecords |
31 3dcmpdrecords ] [<strong>-n, --numofcmpds</strong> number] [<strong>--outdelim</strong> comma | tab | semicolon]
32 [<strong>--output</strong> SD | text | both] [<strong>-o, --overwrite</strong>] [<strong>-q, --quote</strong> yes | no]
33 [<strong>--record</strong> recnum | startrecnum,endrecnum] <strong>--RegexIgnoreCase</strong> <em>yes or no</em>
34 [<strong>-r, --root</strong> rootname] [<strong>-s, --seed</strong> number] [<strong>--StrDataString</strong> yes | no]
35 [<strong>--StrDataStringDelimiter</strong> text] [<strong>--StrDataStringMode</strong> StrOnly | StrAndDataFields]
36 [<strong>--ValueComparisonMode</strong> <em>Numeric | Alphanumeric</em>]
37 [<strong>-v, --violations-</strong> number] [<strong>-w, --workingdir</strong> dirname] SDFile(s)...</p>
38 <p>
39 </p>
40 <h2>DESCRIPTION</h2>
41 <p>Extract specific data from <em>SDFile(s)</em> and generate appropriate SD or CSV/TSV text
42 file(s). The structure data from SDFile(s) is not transferred to CSV/TSV text file(s).
43 Multiple SDFile names are separated by spaces. The valid file extensions are <em>.sdf</em>
44 and <em>.sd</em>. All other file names are ignored. All the SD files in a current directory
45 can be specified either by <em>*.sdf</em> or the current directory name.</p>
46 <p>
47 </p>
48 <h2>OPTIONS</h2>
49 <dl>
50 <dt><strong><strong>-h, --help</strong></strong></dt>
51 <dd>
52 <p>Print this help message.</p>
53 </dd>
54 <dt><strong><strong>-d, --datafields</strong> <em>&quot;fieldlabel,...&quot; | &quot;fieldlabel,value,criteria...&quot; | &quot;fieldlabel,value,value,...&quot;</em></strong></dt>
55 <dd>
56 <p>This value is mode specific. In general, it's a list of comma separated data field labels
57 and associated mode specific values.</p>
58 <p>For <em>datafields</em> mode, input value format is: <em>fieldlabel,...</em>. Examples:</p>
59 <div class="OptionsBox">
60 Extreg
61 <br/> Extreg,CompoundName,ID</div>
62 <p>For <em>datafieldsbyvalue</em> mode, input value format contains these triplets:
63 <em>fieldlabel,value, criteria...</em>. Possible values for criteria: <em>le, ge or eq</em>.
64 The values of <strong>--ValueComparisonMode</strong> indicates whether values are
65 compared numerical or string comarison operators. Default is to consider
66 data field values as numerical values and use numerical comparison operators.
67 Examples:</p>
68 <div class="OptionsBox">
69 MolWt,450,le
70 <br/> MolWt,450,le,LogP,5,le,SumNumNO,10,le,SumNHOH,5,le</div>
71 <p>For <em>datafieldsbyregex</em> mode, input value format contains these triplets:
72 <em>fieldlabel,regex, criteria...</em>. <em>regex</em> corresponds to any valid regular expression
73 and is used to match the values for specified <em>fieldlabel</em>. Possible values for criteria:
74 <em>eq or ne</em>. During <em>eq</em> and <em>ne</em> values, data field label value is matched with
75 regular expression using =~ and !~ respectively. <strong>--RegexIgnoreCase</strong> option
76 value is used to determine whether to ignore letter upper/lower case during
77 regular expression match. Examples:</p>
78 <div class="OptionsBox">
79 Name,ol,eq
80 <br/> Name,'^pat',ne</div>
81 <p>For <em>datafieldbylist</em> and <em>datafielduniquebylist</em> mode, input value format is:
82 <em>fieldlabel,value1,value2...</em>. This is equivalent to <em>datafieldsbyvalue</em> mode with
83 this input value format:<em>fieldlabel,value1,eq,fieldlabel,value2,eq,...</em>. For
84 <em>datafielduniquebylist</em> mode, only unique compounds identified by first occurrence
85 of <em>value</em> associated with <em>fieldlabel</em> in <em>SDFile(s)</em> are kept; any subsequent compounds
86 are simply ignored.</p>
87 <p>For <em>datafieldnotbylist</em> mode, input value format is: <em>fieldlabel,value1,value2...</em>. In this
88 mode, the script behaves exactly opposite of <em>datafieldbylist</em> mode, and only those compounds
89 are extracted whose data field values don't match any specified data field value.</p>
90 </dd>
91 <dt><strong><strong>--datafieldsfile</strong> <em>filename</em></strong></dt>
92 <dd>
93 <p>Filename which contains various mode specific values. This option provides a way
94 to specify mode specific values in a file instead of entering them on the command
95 line using <strong>-d --datafields</strong>.</p>
96 <p>For <em>datafields</em> mode, input file lines contain comma delimited field labels:
97 <em>fieldlabel,...</em>. Example:</p>
98 <div class="OptionsBox">
99 Line 1:MolId
100 <br/> Line 2:&quot;Extreg&quot;,CompoundName,ID</div>
101 <p>For <em>datafieldsbyvalue</em> mode, input file lines contains these comma separated triplets:
102 <em>fieldlabel,value, criteria</em>. Possible values for criteria: <em>le, ge or eq</em>. Examples:</p>
103 <div class="OptionsBox">
104 Line 1:MolWt,450,le</div>
105 <div class="OptionsBox">
106 Line 1:&quot;MolWt&quot;,450,le,&quot;LogP&quot;,5,le,&quot;SumNumNO&quot;,10,le,&quot;SumNHOH&quot;,5,le</div>
107 <div class="OptionsBox">
108 Line 1:MolWt,450,le
109 <br/> Line 2:&quot;LogP&quot;,5,le
110 <br/> Line 3:&quot;SumNumNO&quot;,10,le
111 <br/> Line 4: SumNHOH,5,le</div>
112 <p>For <em>datafieldbylist</em> and <em>datafielduniquebylist</em> mode, input file line format is:</p>
113 <div class="OptionsBox">
114 Line 1:fieldlabel;
115 <br/> Subsequent lines:value1,value2...</div>
116 <p>For <em>datafieldbylist</em>, <em>datafielduniquebylist</em>, and <em>datafieldnotbylist</em> mode, input file
117 line format is:</p>
118 <div class="OptionsBox">
119 Line 1:fieldlabel;
120 <br/> Subsequent lines:value1,value2...</div>
121 <p>For <em>datafielduniquebylist</em> mode, only unique compounds identified by first occurrence
122 of <em>value</em> associated with <em>fieldlabel</em> in <em>SDFile(s)</em> are kept; any subsequent compounds
123 are simply ignored. Example:</p>
124 <div class="OptionsBox">
125 Line 1: MolID
126 <br/> Subsequent Lines:
127 <br/> 907508
128 <br/> 832291,4642
129 <br/> &quot;1254&quot;,&quot;907303&quot;</div>
130 </dd>
131 <dt><strong><strong>--indelim</strong> <em>comma | tab | semicolon</em></strong></dt>
132 <dd>
133 <p>Delimiter used to specify text values for <strong>-d --datafields</strong> and <strong>--datafieldsfile</strong> options.
134 Possible values: <em>comma, tab, or semicolon</em>. Default value: <em>comma</em>.</p>
135 </dd>
136 <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>
137 <dd>
138 <p>Specify what to extract from <em>SDFile(s)</em>. Possible values: <em>alldatafields, commondatafields,
139 datafields, datafieldsbyvalue, datafieldsbyregex, datafieldbylist, datafielduniquebylist, datafieldnotbylist,
140 molnames, randomcmpds, recordnum, recordnums, recordrange, 2dcmpdrecords, 3dcmpdrecords</em>.
141 Default value: <em>alldatafields</em>.</p>
142 <p>For <em>alldatafields</em> and <em>molnames</em> mode, only a CSV/TSV text file is generated; for all
143 other modes, however, a SD file is generated by default - you can change the behavior to genereate
144 text file using <em>--output</em> option.</p>
145 <p>For <em>3DCmpdRecords</em> mode, only those compounds with at least one non-zero value for Z atomic coordinates
146 are retrieved; however, during retrieval of compounds in <em>2DCmpdRecords</em> mode, all Z atomic coordinates must
147 be zero.</p>
148 </dd>
149 <dt><strong><strong>-n, --numofcmpds</strong> <em>number</em></strong></dt>
150 <dd>
151 <p>Number of compouds to extract during <em>randomcmpds</em> mode.</p>
152 </dd>
153 <dt><strong><strong>--outdelim</strong> <em>comma | tab | semicolon</em></strong></dt>
154 <dd>
155 <p>Delimiter for output CSV/TSV text file(s). Possible values: <em>comma, tab, or semicolon</em>
156 Default value: <em>comma</em></p>
157 </dd>
158 <dt><strong><strong>--output</strong> <em>SD | text | both</em></strong></dt>
159 <dd>
160 <p>Type of output files to generate. Possible values: <em>SD, text, or both</em>. Default value: <em>SD</em>. For
161 <em>alldatafields</em> and <em>molnames</em> mode, this option is ingored and only a CSV/TSV text file is generated.</p>
162 </dd>
163 <dt><strong><strong>-o, --overwrite</strong></strong></dt>
164 <dd>
165 <p>Overwrite existing files.</p>
166 </dd>
167 <dt><strong><strong>-q, --quote</strong> <em>yes | no</em></strong></dt>
168 <dd>
169 <p>Put quote around column values in output CSV/TSV text file(s). Possible values:
170 <em>yes or no</em>. Default value: <em>yes</em>.</p>
171 </dd>
172 <dt><strong><strong>--record</strong> <em>recnum | recnums | startrecnum,endrecnum</em></strong></dt>
173 <dd>
174 <p>Record number, record numbers or range of records to extract during <em>recordnum</em>, <em>recordnums</em>
175 and <em>recordrange</em> mode. Input value format is: &lt;num&gt;, &lt;num1,num2,...&gt; and &lt;startnum, endnum&gt;
176 for <em>recordnum</em>, <em>recordnums</em> and <em>recordrange</em> modes recpectively. Default value: none.</p>
177 </dd>
178 <dt><strong><strong>--RegexIgnoreCase</strong> <em>yes or no</em></strong></dt>
179 <dd>
180 <p>Specify whether to ingnore case during <em>datafieldsbyregex</em> value of <strong>-m, --mode</strong> option.
181 Possible values: <em>yes or no</em>. Default value: <em>yes</em>.</p>
182 </dd>
183 <dt><strong><strong>-r, --root</strong> <em>rootname</em></strong></dt>
184 <dd>
185 <p>New file name is generated using the root: &lt;Root&gt;.&lt;Ext&gt;. Default for new file
186 names: &lt;SDFileName&gt;&lt;mode&gt;.&lt;Ext&gt;. The file type determines &lt;Ext&gt; value.
187 The sdf, csv, and tsv &lt;Ext&gt; values are used for SD, comma/semicolon, and tab
188 delimited text files respectively.This option is ignored for multiple input files.</p>
189 </dd>
190 <dt><strong><strong>-s, --seed</strong> <em>number</em></strong></dt>
191 <dd>
192 <p>Random number seed used for <em>randomcmpds</em> mode. Default:123456789.</p>
193 </dd>
194 <dt><strong><strong>--StrDataString</strong> <em>yes | no</em></strong></dt>
195 <dd>
196 <p>Specify whether to write out structure data string to CSV/TSV text file(s). Possible values:
197 <em>yes or no</em>. Default value: <em>no</em>.</p>
198 <p>The value of <strong>StrDataStringDelimiter</strong> option is used as a delimiter to join structure
199 data lines into a structure data string.</p>
200 <p>This option is ignored during generation of SD file(s).</p>
201 </dd>
202 <dt><strong><strong>--StrDataStringDelimiter</strong> <em>text</em></strong></dt>
203 <dd>
204 <p>Delimiter for joining multiple stucture data lines into a string before writing to CSV/TSV text
205 file(s). Possible values: <em>any alphanumeric text</em>. Default value: <em>|</em>.</p>
206 <p>This option is ignored during generation of SD file(s).</p>
207 </dd>
208 <dt><strong><strong>--StrDataStringMode</strong> <em>StrOnly | StrAndDataFields</em></strong></dt>
209 <dd>
210 <p>Specify whether to include SD data fields and values along with the structure data into structure
211 data string before writing it out to CSV/TSV text file(s). Possible values: <em>StrOnly or StrAndDataFields</em>.
212 Default value: <em>StrOnly</em>.</p>
213 <p>The value of <strong>StrDataStringDelimiter</strong> option is used as a delimiter to join structure
214 data lines into a structure data string.</p>
215 <p>This option is ignored during generation of SD file(s).</p>
216 </dd>
217 <dt><strong><strong>--ValueComparisonMode</strong> <em>Numeric | Alphanumeric</em></strong></dt>
218 <dd>
219 <p>Specify how to compare data field values during <em>datafieldsbyvalue</em> mode: Compare
220 values using either numeric or string ((eq, le, ge) comparison operators. Possible values:
221 <em>Numeric or Alphanumeric</em>. Defaule value: <em>Numeric</em>.</p>
222 </dd>
223 <dt><strong><strong>-v, --violations</strong> <em>number</em></strong></dt>
224 <dd>
225 <p>Number of criterion violations allowed for values specified during <em>datafieldsbyvalue</em>
226 and <em>datafieldsbyregex</em> mode. Default value: <em>0</em>.</p>
227 </dd>
228 <dt><strong><strong>-w, --workingdir</strong> <em>dirname</em></strong></dt>
229 <dd>
230 <p>Location of working directory. Default: current directory.</p>
231 </dd>
232 </dl>
233 <p>
234 </p>
235 <h2>EXAMPLES</h2>
236 <p>To retrieve all data fields from SD files and generate CSV text files, type:</p>
237 <div class="ExampleBox">
238 % ExtractFromSDFiles.pl -o Sample.sdf
239 <br/>% ExtractFromSDFiles.pl -o *.sdf</div>
240 <p>To retrieve all data fields from SD file and generate CSV text files containing
241 a column with structure data as a string with | as line delimiter, type:</p>
242 <div class="ExampleBox">
243 % ExtractFromSDFiles.pl --StrDataString Yes -o Sample.sdf</div>
244 <p>To retrieve MOL_ID data fileld from SD file and generate CSV text files containing
245 a column with structure data along with all data fields as a string with | as line
246 delimiter, type:</p>
247 <div class="ExampleBox">
248 % ExtractFromSDFiles.pl -m datafields -d &quot;Mol_ID&quot; --StrDataString Yes
249 --StrDataStringMode StrAndDataFields --StrDataStringDelimiter &quot;|&quot;
250 --output text -o Sample.sdf</div>
251 <p>To retrieve common data fields which exists for all the compounds in
252 a SD file and generate a TSV text file NewSample.tsv, type:</p>
253 <div class="ExampleBox">
254 % ExtractFromSDFiles.pl -m commondatafields --outdelim tab -r NewSample
255 --output Text -o Sample.sdf</div>
256 <p>To retrieve MolId, ExtReg, and CompoundName data field from a SD file and generate a
257 CSV text file NewSample.csv, type:</p>
258 <div class="ExampleBox">
259 % ExtractFromSDFiles.pl -m datafields -d &quot;Mol_ID,MolWeight,
260 CompoundName&quot; -r NewSample --output Text -o Sample.sdf</div>
261 <p>To retrieve compounds from a SD which meet a specific set of criteria - MolWt &lt;= 450,
262 LogP &lt;= 5 and SumNO &lt; 10 - from a SD file and generate a new SD file NewSample.sdf,
263 type:</p>
264 <div class="ExampleBox">
265 % ExtractFromSDFiles.pl -m datafieldsbyvalue -d &quot;MolWt,450,le,LogP
266 ,5,le,SumNO,10&quot; -r NewSample -o Sample.sdf</div>
267 <p>To retrive compounds from a SD file with a specific set of values for MolID and
268 generate a new SD file NewSample.sdf, type:</p>
269 <div class="ExampleBox">
270 % ExtractFromSDFiles.pl -m datafieldbylist -d &quot;Mol_ID,159,4509,4619&quot;
271 -r NewSample -o Sample.sdf</div>
272 <p>To retrive compounds from a SD file with values for MolID not on a list of specified
273 values and generate a new SD file NewSample.sdf, type:</p>
274 <div class="ExampleBox">
275 % ExtractFromSDFiles.pl -m datafieldnotbylist -d &quot;Mol_ID,159,4509,4619&quot;
276 -r NewSample -o Sample.sdf</div>
277 <p>To retrive 10 random compounds from a SD file and generate a new SD file RandomSample.sdf, type:</p>
278 <div class="ExampleBox">
279 % ExtractFromSDFiles.pl -m randomcmpds -n 10 -r RandomSample
280 -o Sample.sdf</div>
281 <p>To retrive compound record number 10 from a SD file and generate a new SD file NewSample.sdf, type:</p>
282 <div class="ExampleBox">
283 % ExtractFromSDFiles.pl -m recordnum --record 10 -r NewSample
284 -o Sample.sdf</div>
285 <p>To retrive compound record numbers 10, 20 and 30 from a SD file and generate a new SD file
286 NewSample.sdf, type:</p>
287 <div class="ExampleBox">
288 % ExtractFromSDFiles.pl -m recordnums --record 10,20,30 -r NewSample
289 -o Sample.sdf</div>
290 <p>To retrive compound records between 10 to 20 from SD file and generate a new SD
291 file NewSample.sdf, type:</p>
292 <div class="ExampleBox">
293 % ExtractFromSDFiles.pl -m recordrange --record 10,20 -r NewSample
294 -o Sample.sdf</div>
295 <p>
296 </p>
297 <h2>AUTHOR</h2>
298 <p><a href="mailto:msud@san.rr.com">Manish Sud</a></p>
299 <p>
300 </p>
301 <h2>SEE ALSO</h2>
302 <p><a href="./FilterSDFiles.html">FilterSDFiles.pl</a>,&nbsp<a href="./InfoSDFiles.html">InfoSDFiles.pl</a>,&nbsp<a href="./SplitSDFiles.html">SplitSDFiles.pl</a>,&nbsp<a href="./MergeTextFilesWithSD.html">MergeTextFilesWithSD.pl</a>
303 </p>
304 <p>
305 </p>
306 <h2>COPYRIGHT</h2>
307 <p>Copyright (C) 2015 Manish Sud. All rights reserved.</p>
308 <p>This file is part of MayaChemTools.</p>
309 <p>MayaChemTools is free software; you can redistribute it and/or modify it under
310 the terms of the GNU Lesser General Public License as published by the Free
311 Software Foundation; either version 3 of the License, or (at your option)
312 any later version.</p>
313 <p>&nbsp</p><p>&nbsp</p><div class="DocNav">
314 <table width="100%" border=0 cellpadding=0 cellspacing=2>
315 <tr align="left" valign="top"><td width="33%" align="left"><a href="./ExtractFromPDBFiles.html" title="ExtractFromPDBFiles.html">Previous</a>&nbsp;&nbsp;<a href="./index.html" title="Table of Contents">TOC</a>&nbsp;&nbsp;<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>
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