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1 #!/usr/bin/perl -w
2 #
3 # $RCSfile: ElementalAnalysisSDFiles.pl,v $
4 # $Date: 2015/02/28 20:46:19 $
5 # $Revision: 1.24 $
6 #
7 # Author: Manish Sud <msud@san.rr.com>
8 #
9 # Copyright (C) 2015 Manish Sud. All rights reserved.
10 #
11 # This file is part of MayaChemTools.
12 #
13 # MayaChemTools is free software; you can redistribute it and/or modify it under
14 # the terms of the GNU Lesser General Public License as published by the Free
15 # Software Foundation; either version 3 of the License, or (at your option) any
16 # later version.
17 #
18 # MayaChemTools is distributed in the hope that it will be useful, but without
19 # any warranty; without even the implied warranty of merchantability of fitness
20 # for a particular purpose. See the GNU Lesser General Public License for more
21 # details.
22 #
23 # You should have received a copy of the GNU Lesser General Public License
24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or
25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,
26 # Boston, MA, 02111-1307, USA.
27 #
28
29 use strict;
30 use FindBin; use lib "$FindBin::Bin/../lib";
31 use Getopt::Long;
32 use File::Basename;
33 use Text::ParseWords;
34 use Benchmark;
35 use FileUtil;
36 use SDFileUtil;
37 use TextUtil;
38 use MolecularFormula;
39 use FileIO::SDFileIO;
40 use Molecule;
41
42 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
43
44 # Autoflush STDOUT
45 $| = 1;
46
47 # Starting message...
48 $ScriptName = basename($0);
49 print "\n$ScriptName: Starting...\n\n";
50 $StartTime = new Benchmark;
51
52 # Get the options and setup script...
53 SetupScriptUsage();
54 if ($Options{help} || @ARGV < 1) {
55 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
56 }
57
58 my(@SDFilesList);
59 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
60
61 print "Processing options...\n";
62 my(%OptionsInfo);
63 ProcessOptions();
64
65 print "Checking input SD file(s)...\n";
66 my(%SDFilesInfo);
67 RetrieveSDFilesInfo();
68
69 # Generate output files...
70 my($FileIndex);
71 if (@SDFilesList > 1) {
72 print "\nProcessing SD files...\n";
73 }
74 for $FileIndex (0 .. $#SDFilesList) {
75 if ($SDFilesInfo{FileOkay}[$FileIndex]) {
76 print "\nProcessing file $SDFilesList[$FileIndex]...\n";
77 PerformElementalAnalysis($FileIndex);
78 }
79 }
80 print "\n$ScriptName:Done...\n\n";
81
82 $EndTime = new Benchmark;
83 $TotalTime = timediff ($EndTime, $StartTime);
84 print "Total time: ", timestr($TotalTime), "\n";
85
86 ###############################################################################
87
88 # Perform analysis...
89 sub PerformElementalAnalysis {
90 my($Index) = @_;
91 my($SDFile, $NewSDFile, $KeyDataFieldName, $CmpdCount, $CurrentFormula, $FormulaFieldName, $CmpdString, $Value, $CalculationType, $CalculatedValue, $ErrorMsg, $Status, $ElementsRef, $ElementCompositionRef, $Molecule, @CalculatedValues, @CmpdLines, %DataFieldValuesMap);
92
93 $SDFile = $SDFilesList[$Index];
94 $NewSDFile = $SDFilesInfo{OutFile}[$Index];
95
96 print "Generating new SD file $NewSDFile...\n";
97 open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
98 open SDFILE, "$SDFile" or die "Error: Can't open $SDFile: $! \n";
99
100
101 $CmpdCount = 0;
102 $FormulaFieldName = $SDFilesInfo{FormulaFieldName}[$Index];
103
104 COMPOUND: while ($CmpdString = ReadCmpdString(\*SDFILE)) {
105 $CmpdCount++;
106 @CmpdLines = split "\n", $CmpdString;
107 %DataFieldValuesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
108
109 @CalculatedValues = ();
110 for $Value (@{$OptionsInfo{SpecifiedCalculations}}) {
111 push @CalculatedValues, '';
112 }
113
114 $CurrentFormula = undef;
115
116 if ($OptionsInfo{UseStructureData}) {
117 $Molecule = FileIO::SDFileIO::ParseMoleculeString($CmpdString);
118 $CurrentFormula = $Molecule->GetMolecularFormula();
119 }
120 else {
121 if (!exists $DataFieldValuesMap{$FormulaFieldName}) {
122 $ErrorMsg = "Ignoring compound record $CmpdCount: Formula field $FormulaFieldName not found";
123 PrintErrorMsg($CmpdString, $ErrorMsg);
124 WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
125 next COMPOUND;
126 }
127
128 # Make sure it's a valid molecular formula...
129 $CurrentFormula = $DataFieldValuesMap{$FormulaFieldName};
130 if ($OptionsInfo{CheckFormula}) {
131 ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($CurrentFormula);
132 if (!$Status) {
133 $ErrorMsg = "Ignoring compound record $CmpdCount: Formula field value $CurrentFormula is not valid: $ErrorMsg";
134 PrintErrorMsg($CmpdString, $ErrorMsg);
135 WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues);
136 next COMPOUND;
137 }
138 }
139 }
140
141 # Calculate appropriate values and write 'em out...
142 @CalculatedValues = ();
143 for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
144 if ($CalculationType =~ /^ElementalAnalysis$/i) {
145 ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($CurrentFormula);
146 $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
147 }
148 elsif ($CalculationType =~ /^MolecularWeight$/i) {
149 $CalculatedValue = MolecularFormula::CalculateMolecularWeight($CurrentFormula);
150 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
151 }
152 elsif ($CalculationType =~ /^ExactMass$/i) {
153 $CalculatedValue = MolecularFormula::CalculateExactMass($CurrentFormula);
154 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
155 }
156 else {
157 $CalculatedValue = '';
158 }
159 push @CalculatedValues, $CalculatedValue;
160 }
161 WriteNewCompoundRecord($Index, \*NEWSDFILE, \@CmpdLines, \@CalculatedValues, $CurrentFormula);
162 }
163 close NEWSDFILE;
164 close SDFILE;
165 }
166
167 # Write out compound record with calculated values...
168 sub WriteNewCompoundRecord {
169 my($Index, $SDFileRef, $CmpdLinesRef, $CalculatedValuesRef, $MolecularFormula) = @_;
170
171 # Write out compound lines except the last line which contains $$$$...
172 my($LineIndex);
173 for $LineIndex (0 .. ($#{$CmpdLinesRef} - 1)) {
174 print $SDFileRef "$CmpdLinesRef->[$LineIndex]\n";
175 }
176
177 # Write out calculated values...
178 my($CalcIndex, $FieldName, $FieldValue);
179 for $CalcIndex (0 .. $#{$OptionsInfo{SpecifiedCalculations}}) {
180 $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{$OptionsInfo{SpecifiedCalculations}[$CalcIndex]};
181 $FieldValue = $CalculatedValuesRef->[$CalcIndex];
182 print $SDFileRef "> <$FieldName>\n$FieldValue\n\n";
183 }
184
185 if ($OptionsInfo{UseStructureData} && $OptionsInfo{WriteOutFormula} && defined($MolecularFormula)) {
186 $FieldName = $SDFilesInfo{ValueFieldNamesMap}[$Index]{MolecularFormula};
187 $FieldValue = $MolecularFormula;
188 print $SDFileRef "> <$FieldName>\n$FieldValue\n\n";
189 }
190
191 print $SDFileRef "\$\$\$\$\n";
192 }
193
194 # Print out error message...
195 sub PrintErrorMsg {
196 my($CmpdString, $ErrorMsg) = @_;
197
198 if ($OptionsInfo{DetailLevel} >= 2 ) {
199 print "$ErrorMsg:\n$CmpdString\n";
200 }
201 elsif ($OptionsInfo{DetailLevel} >= 1) {
202 print "$ErrorMsg\n";
203 }
204 }
205
206 # Retrieve information about input SD files...
207 sub RetrieveSDFilesInfo {
208 my($Index, $SDFile, $FileDir, $FileName, $FileExt, $OutFileRoot, $OutFile, $FormulaFieldName, $Value, $FieldName, $NewFieldName, $Count);
209
210 my(%NewValueFieldNames) = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass', MolecularFormula => 'MolecularFormula');
211 if (@{$OptionsInfo{SpecifiedValueFieldNames}}) {
212 for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueFieldNames}}; $Index +=2) {
213 $Value = $OptionsInfo{SpecifiedValueFieldNames}[$Index];
214 $FieldName = $OptionsInfo{SpecifiedValueFieldNames}[$Index + 1];
215 if (exists $NewValueFieldNames{$Value}) {
216 $NewValueFieldNames{$Value} = $FieldName;
217 }
218 }
219 }
220
221 %SDFilesInfo = ();
222
223 @{$SDFilesInfo{FileOkay}} = ();
224 @{$SDFilesInfo{OutFile}} = ();
225 @{$SDFilesInfo{FormulaFieldName}} = ();
226 @{$SDFilesInfo{ValueFieldNamesMap}} = ();
227
228 FILELIST: for $Index (0 .. $#SDFilesList) {
229 $SDFile = $SDFilesList[$Index];
230
231 $SDFilesInfo{FileOkay}[$Index] = 0;
232 $SDFilesInfo{OutFile}[$Index] = '';
233 $SDFilesInfo{FormulaFieldName}[$Index] = '';
234
235 %{$SDFilesInfo{ValueFieldNamesMap}[$Index]} = ();
236
237 if (!(-e $SDFile)) {
238 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
239 next FILELIST;
240 }
241 if (!CheckFileType($SDFile, "sd sdf")) {
242 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
243 next FILELIST;
244 }
245 $FileDir = ""; $FileName = ""; $FileExt = "";
246 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
247 if ($Options{root} && (@SDFilesList == 1)) {
248 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
249 if ($RootFileName && $RootFileExt) {
250 $FileName = $RootFileName;
251 }
252 else {
253 $FileName = $Options{root};
254 }
255 $OutFileRoot = $FileName;
256 }
257 else {
258 $OutFileRoot = $FileName . "ElementalAnalysis";
259 }
260
261 $OutFile = $OutFileRoot . ".$FileExt";
262 if (lc($OutFile) eq lc($SDFile)) {
263 warn "Warning: Ignoring file $SDFile:Output file name, $OutFile, is same as input SD file name, $SDFile\n";
264 next FILELIST;
265 }
266 if (!$Options{overwrite}) {
267 if (-e $OutFile) {
268 warn "Warning: Ignoring file $SDFile: The file $OutFile already exists\n";
269 next FILELIST;
270 }
271 }
272 # Get data field names and values...
273 my($CmpdString, $FieldName, @CmpdLines, @DataFieldNames, %DataFieldNamesMap);
274 @DataFieldNames = ();
275 if (!open(SDFILE, "$SDFile")) {
276 warn "Warning: Ignoring file $SDFile: Couldn't open it: $! \n";
277 next FILELIST;
278 }
279 $CmpdString = ReadCmpdString(\*SDFILE);
280 close SDFILE;
281
282 @CmpdLines = split "\n", $CmpdString;
283 @DataFieldNames = GetCmpdDataHeaderLabels(\@CmpdLines);
284 %DataFieldNamesMap = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
285
286 # Setup formula field name...
287 $FormulaFieldName = '';
288 if ($OptionsInfo{UseDataField}) {
289 if ($OptionsInfo{SpecifiedFormulaFieldName}) {
290 $FormulaFieldName = $OptionsInfo{SpecifiedFormulaFieldName};
291 }
292 else {
293 FIELDNAME: for $FieldName (@DataFieldNames) {
294 if ($FieldName =~ /Formula/i) {
295 $FormulaFieldName = $FieldName;
296 last FIELDNAME;
297 }
298 }
299 if (!$FormulaFieldName) {
300 warn "Warning: Ignoring file $SDFile: Data field label containing the word Formula doesn't exist\n";
301 next FILELIST;
302 }
303 }
304 }
305 $SDFilesInfo{FileOkay}[$Index] = 1;
306 $SDFilesInfo{OutFile}[$Index] = $OutFile;
307 $SDFilesInfo{FormulaFieldName}[$Index] = $FormulaFieldName;
308
309 # Setup value data field names for calculated values...
310 for $Value (keys %NewValueFieldNames) {
311 $FieldName = $NewValueFieldNames{$Value};
312
313 # Make sure it doesn't already exists...
314 $Count = 1;
315 $NewFieldName = $FieldName;
316 while (exists $DataFieldNamesMap{$NewFieldName}) {
317 $Count++;
318 $NewFieldName = $FieldName . $Count;
319 }
320 $SDFilesInfo{ValueFieldNamesMap}[$Index]{$Value} = $NewFieldName;
321 }
322 }
323 }
324
325 # Process option values...
326 sub ProcessOptions {
327 %OptionsInfo = ();
328
329 $OptionsInfo{Mode} = $Options{mode};
330 $OptionsInfo{FormulaMode} = $Options{formulamode};
331
332 $OptionsInfo{WriteOutFormula} = ($Options{formulaout} =~ /^Yes$/i) ? 1 : 0;
333
334 $OptionsInfo{UseStructureData} = ($Options{formulamode} =~ /^StructureData$/i) ? 1 : 0;
335 $OptionsInfo{UseDataField} = ($Options{formulamode} =~ /^DataField$/i) ? 1 : 0;
336
337 $OptionsInfo{Fast} = defined $Options{fast} ? $Options{fast} : undef;
338
339 $OptionsInfo{DetailLevel} = $Options{detail};
340 $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
341 $OptionsInfo{Precision} = $Options{precision};
342
343 $OptionsInfo{Overwrite} = defined $Options{overwrite} ? $Options{overwrite} : undef;
344
345 $OptionsInfo{FormulaField} = defined $Options{formulafield} ? $Options{formulafield} : undef;
346 $OptionsInfo{SpecifiedFormulaFieldName} = "";
347
348 if (defined $Options{formulafield}) {
349 $OptionsInfo{SpecifiedFormulaFieldName} = $Options{formulafield};
350 }
351 # Setup what to calculate...
352 @{$OptionsInfo{SpecifiedCalculations}} = ();
353 if ($Options{mode} =~ /^All$/i) {
354 @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
355 }
356 else {
357 my($Mode, $ModeValue, @SpecifiedModeValues);
358 $Mode = $Options{mode};
359 $Mode =~ s/ //g;
360 @SpecifiedModeValues = split /\,/, $Mode;
361 for $ModeValue (@SpecifiedModeValues) {
362 if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
363 if ($ModeValue =~ /^All$/i) {
364 die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
365 }
366 else {
367 die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
368 }
369 }
370 push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
371 }
372 }
373
374 $OptionsInfo{ValueFieldNames} = defined $Options{valuefieldnames} ? $Options{valuefieldnames} : undef;
375 @{$OptionsInfo{SpecifiedValueFieldNames}} = ();
376
377 if ($Options{valuefieldnames}) {
378 my($Value, $Label, @ValueLabels);
379 @ValueLabels = split /\,/, $Options{valuefieldnames};
380 if (@ValueLabels % 2) {
381 die "Error: The value specified, $Options{valuefieldnames}, for option \"-v --valuefieldnames\" is not valid: It must contain even number of comma delimited values\n";
382 }
383 my($Index);
384 for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
385 $Value = $ValueLabels[$Index];
386 $Value =~ s/ //g;
387 $Label = $ValueLabels[$Index + 1];
388 if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass|MolecularFormula)$/i) {
389 die "Error: The value specified, $Value, using option \"-v --valuefieldnames\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, ExactMass, or MolecularFormula\n";
390 }
391 push @{$OptionsInfo{SpecifiedValueFieldNames}}, ($Value, $Label);
392 }
393 }
394 }
395
396 # Setup script usage and retrieve command line arguments specified using various options...
397 sub SetupScriptUsage {
398
399 # Retrieve all the options...
400 %Options = ();
401 $Options{detail} = 1;
402 $Options{formulamode} = "DataField";
403 $Options{formulaout} = "No";
404 $Options{mode} = "All";
405 $Options{precision} = 2;
406
407 if (!GetOptions(\%Options, "detail|d=i", "fast", "formulafield=s", "formulamode|f=s", "formulaout=s", "mode|m=s", "help|h", "overwrite|o", "precision|p=i", "root|r=s", "valuefieldnames|v=s", "workingdir|w=s")) {
408 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
409 }
410 if ($Options{workingdir}) {
411 if (! -d $Options{workingdir}) {
412 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
413 }
414 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
415 }
416 if (!IsPositiveInteger($Options{detail})) {
417 die "Error: The value specified, $Options{detail}, for option \"-d --detail\" is not valid. Allowed values: > 0\n";
418 }
419 if ($Options{formulamode} !~ /^(StructureData|DataField)$/i) {
420 die "Error: The value specified, $Options{formulamode}, for option \"-f, --formulamode\" is not valid. Allowed values: StructureData or DataField \n";
421 }
422 if ($Options{formulaout} !~ /^(Yes|No)$/i) {
423 die "Error: The value specified, $Options{formulaout}, for option \"--formulaout\" is not valid. Allowed values: Yes or No \n";
424 }
425 if (!IsPositiveInteger($Options{precision})) {
426 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
427 }
428 }
429
430 __END__
431
432 =head1 NAME
433
434 ElementalAnalysisSDFiles.pl - Perform elemental analysis using formula data field in SDFile(s)
435
436 =head1 SYNOPSIS
437
438 ElementalAnalysisSDFiles.pl SDFile(s)...
439
440 ElementalAnalysisSDFiles.pl [B<-d, --detail> infolevel] [B<--fast>]
441 [B<--formulafield> SD data field name] [B<-f, --formulamode> I<DataField | StructureData>]
442 [B<--formulaout> yes or no] [B<-m, --mode> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"]
443 [B<-h, --help>] [B<-o, --overwrite>] [B<-r, --root> rootname]
444 [B<-v --valuefieldnames> Name, Label, [Name, Label,...]] [B<-w, --workingdir> dirname] SDFile(s)...
445
446 =head1 DESCRIPTION
447
448 Perform elemental analysis using molecular formula specified by a data field name or generated
449 from structure data in I<SDFile(s)>.
450
451 In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
452 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
453 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
454 D and T, are not supported.
455
456 The file names are separated by space.The valid file extensions are I<.sdf> and I<.sd>.
457 All other file names are ignored. All the SD files in a current directory can be specified
458 either by I<*.sdf> or the current directory name.
459
460 =head1 OPTIONS
461
462 =over 4
463
464 =item B<-d, --detail> I<infolevel>
465
466 Level of information to print about compound records being ignored. Default: I<1>. Possible
467 values: I<1, 2 or 3>.
468
469 =item B<--fast>
470
471 In this mode, the formula data field specified using B<-f, --formulafield> option is assumed
472 to contain valid molecular formula data and initial formula validation check is skipped.
473
474 =item B<--formulafield> I<SD data field name>
475
476 I<SDFile(s)> data field name containing molecular formulas used for performing
477 elemental analysis during I<DataField> value of B<-f, --formulamode> option.
478 Default value: I<SD data field containing the word formula in its name>.
479
480 This option is ignore during I<StructureData> value of B<-f, --formulamode> option.
481
482 =item B<-f, --formulamode> I<DataField | StructureData>
483
484 Specify source of molecular formula used for performing elemental analysis: retrieve
485 formula using I<SDFile(s)> data field name or generate formula from structure. Possible
486 values: I<DataField or StructureData>. Default value: I<DataField>.
487
488 =item B<--formulaout> I<yes or no>
489
490 Specify whether to write out formula to SD file during I<StructureData> value of
491 B<-f, --formulamode> option. Possible values: I<Yes or No>. Default: I<No>.
492
493 =item B<-m, --mode> I<All | "ElementalAnalysis,[MolecularWeight,ExactMass]">
494
495 Specify what values to calculate using molecular formula data field or structure data from
496 I<SDFile(s)>: calculate all supported values or specify a comma delimited list of values.
497 Possible values: I<All | "ElementalAnalysis, [MolecularWeight, ExactMass]">. Default: I<All>
498
499 =item B<-h, --help>
500
501 Print this help message.
502
503 =item B<-o, --overwrite>
504
505 Overwrite existing files.
506
507 =item B<-p, --precision> I<number>
508
509 Precision of calculated values in the output file. Default: up to I<2> decimal places.
510 Valid values: positive integers.
511
512 =item B<-r, --root> I<rootname>
513
514 New SD file name is generated using the root: <Root>.<Ext>. Default new file
515 name: <InitialSDFileName>ElementalAnalysis.<Ext>. This option is ignored for multiple
516 input files.
517
518 =item B<-v --valuefieldnames> I<Name,Label,[Name,Label,...]>
519
520 Specify SD data field names to use for calculated values. In general, it's a comma delimited
521 list of value name and SD field name pairs. Supported value names: I<ElementalAnalysis,
522 MolecularWeight, ExactMass, and MolecularFormula>. Default labels: I<ElementalAnalysis,
523 MolecularWeight, ExactMass, and MolecularFormula>.
524
525 I<MolecularFormula> label is only used during I<StructureData> value of
526 B<-f, --formulamode> option.
527
528 =item B<-w, --workingdir> I<dirname>
529
530 Location of working directory. Default: current directory.
531
532 =back
533
534 =head1 EXAMPLES
535
536 To perform elemental analysis, calculate molecular weight and exact mass using SD
537 field name value with the word Formula in its name and generate a new SD file
538 NewSample1.sdf, type:
539
540 % ElementalAnalysisSDFiles.pl -o -r NewSample1 Sample1.sdf
541
542 To perform elemental analysis, calculate molecular weight and exact mass using
543 structure data in SD file and generate a new SD file NewSample1.sdf, type:
544
545 % ElementalAnalysisSDFiles.pl --formulamode StructureData -o
546 -r NewSample1 Sample1.sdf
547
548 To perform elemental analysis using formulas in SD field name Formula, use field name
549 Analysis for calculated data, and generate a new SD file NewSample1.sdf, type:
550
551 % ElementalAnalysisSDFiles.pl --m ElementalAnalysis --formulafield
552 Formula --valuefieldnames "ElementalAnalysis,Analysis" -o
553 -r NewSample1 Sample1.sdf
554
555 To calculate molecular weight, using formulas in SD field name Formula, with four decimal
556 precision and generate a new SD file NewSample1.sdf, type
557
558 % ElementalAnalysisSDFiles.pl --m MolecularWeight --formulafield
559 Formula --precision 4 -o -r NewSample1 Sample1.sdf
560
561 =head1 AUTHOR
562
563 Manish Sud <msud@san.rr.com>
564
565 =head1 SEE ALSO
566
567 AnalyzeSDFilesData.pl, InfoSDFiles.pl, ExtractFromSDFiles.pl
568
569 =head1 COPYRIGHT
570
571 Copyright (C) 2015 Manish Sud. All rights reserved.
572
573 This file is part of MayaChemTools.
574
575 MayaChemTools is free software; you can redistribute it and/or modify it under
576 the terms of the GNU Lesser General Public License as published by the Free
577 Software Foundation; either version 3 of the License, or (at your option)
578 any later version.
579
580 =cut