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