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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: ElementalAnalysis.pl,v $
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4 # $Date: 2015/02/28 20:46:19 $
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5 # $Revision: 1.19 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use MolecularFormula;
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38
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39 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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40
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41 # Autoflush STDOUT
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42 $| = 1;
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43
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44 # Starting message...
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45 $ScriptName = basename($0);
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46 print "\n$ScriptName: Starting...\n\n";
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47 $StartTime = new Benchmark;
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48
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49 # Get the options and setup script...
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50 SetupScriptUsage();
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51 if ($Options{help}) {
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52 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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53 }
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54
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55 print "Processing options...\n";
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56 my(%OptionsInfo);
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57 ProcessOptions();
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58
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59 PerformElementalAnalysis();
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60
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61 print "\n$ScriptName:Done...\n\n";
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62
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63 $EndTime = new Benchmark;
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64 $TotalTime = timediff ($EndTime, $StartTime);
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65 print "Total time: ", timestr($TotalTime), "\n";
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66
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67 ###############################################################################
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68
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69 # Elemental analysis...
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70 sub PerformElementalAnalysis {
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71 my($Formula, $FormulaDataRef, $ValueLabel, $CalculationType, $CalculatedValue, $ElementsRef, $ElementCompositionRef, $Status, $ErrorMsg, @ValueLabels, @CalculatedValues);
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72
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73 print "Performing elemental analysis...\n";
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74
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75 if ($OptionsInfo{FileOutput}) {
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76 print "Generating file $OptionsInfo{OutFileName}...\n";
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77 open OUTFILE, ">$OptionsInfo{OutFileName}" or die "Couldn't open $OptionsInfo{OutFileName}: $!\n";
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78 }
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79
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80 # Setup value labels...
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81 @ValueLabels = ();
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82 if ($OptionsInfo{RowsOutput}) {
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83 push @ValueLabels, "Formula";
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84 }
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85 for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
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86 push @ValueLabels, $OptionsInfo{ValueLabelsMap}{$CalculationType};
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87 }
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88
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89 if ($OptionsInfo{RowsOutput}) {
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90 ListHeaderRowData(\@ValueLabels);
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91 }
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92
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93 # Go over specified properties...
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94 FORMULA: for $Formula (@{$OptionsInfo{SpecifiedFormulas}}) {
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95 if (!$OptionsInfo{RowsOutput}) {
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96 if ($OptionsInfo{FileOutput}) {
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97 print OUTFILE "\nPerforming elemental analysis using formula $Formula...\n\n";
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98 }
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99 else {
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100 print "\nPerforming elemental analysis using formula $Formula...\n\n";
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101 }
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102 }
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103 # Calculate appropriate values and write 'em out...
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104 if ($OptionsInfo{CheckFormula}) {
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105 ($Status, $ErrorMsg) = MolecularFormula::IsMolecularFormula($Formula);
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106 if (!$Status) {
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107 warn("Warning: Ignoring formula $Formula: It's not a valid value: $ErrorMsg\n");
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108 next FORMULA;
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109 }
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110 }
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111 @CalculatedValues = ();
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112 if ($OptionsInfo{RowsOutput}) {
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113 push @CalculatedValues, $Formula;
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114 }
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115 for $CalculationType (@{$OptionsInfo{SpecifiedCalculations}}) {
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116 if ($CalculationType =~ /^ElementalAnalysis$/i) {
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117 ($ElementsRef, $ElementCompositionRef) = MolecularFormula::CalculateElementalComposition($Formula);
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118 $CalculatedValue = (defined($ElementsRef) && defined($ElementCompositionRef)) ? MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $OptionsInfo{Precision}) : '';
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119 }
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120 elsif ($CalculationType =~ /^MolecularWeight$/i) {
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121 $CalculatedValue = MolecularFormula::CalculateMolecularWeight($Formula);
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122 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
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123 }
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124 elsif ($CalculationType =~ /^ExactMass$/i) {
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125 $CalculatedValue = MolecularFormula::CalculateExactMass($Formula);
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126 $CalculatedValue = (defined($CalculatedValue) && length($CalculatedValue)) ? (sprintf("%.$OptionsInfo{Precision}f", $CalculatedValue)) : "";
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127 }
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128 else {
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129 $CalculatedValue = '';
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130 }
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131 push @CalculatedValues, $CalculatedValue;
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132 }
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133 # List data...
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134 ListFormulaData(\@ValueLabels, \@CalculatedValues);
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135 }
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136 if ($OptionsInfo{FileOutput}) {
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137 close OUTFILE;
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138 }
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139 print "\n";
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140 }
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141
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142 # List calculated data values...
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143 sub ListFormulaData {
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144 my($DataLabelRef, $DataValueRef) = @_;
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145 my($Index, $Line, $Value);
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146
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147 if ($OptionsInfo{RowsOutput}) {
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148 $Line = '';
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149 # Format data...
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150 if ($OptionsInfo{OutQuote} || $Options{outdelim} !~ /^comma$/i) {
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151 $Line = JoinWords($DataValueRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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152 }
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153 else {
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154 # Always quote values containing commas...
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155 $Line = ($DataValueRef->[0] =~ /\,/) ? qq("$DataValueRef->[0]") : $DataValueRef->[0];
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156 for $Index (1 .. $#{$DataValueRef} ) {
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157 $Value = $DataValueRef->[$Index];
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158 if ($Value =~ /\,/) {
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159 $Value = qq("$Value");
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160 }
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161 $Line .= $OptionsInfo{OutDelim} . $Value;
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162 }
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163 }
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164 if ($OptionsInfo{FileOutput}) {
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165 print OUTFILE "$Line\n";
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166 }
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167 else {
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168 print "$Line\n";
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169 }
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170 }
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171 else {
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172 # Format and list data...
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173 $Line = '';
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174 for $Index (0 .. $#{$DataLabelRef} ) {
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175 $Line = $DataLabelRef->[$Index] . ': ' . $DataValueRef->[$Index];
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176 if ($OptionsInfo{FileOutput}) {
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177 print OUTFILE "$Line\n";
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178 }
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179 else {
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180 print "$Line\n";
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181 }
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182 }
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183 }
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184 }
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185
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186 # List calculated data for a formula...
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187 sub ListHeaderRowData {
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188 my($DataLabelRef) = @_;
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189 my($Line);
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190
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191 # Format data...
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192 $Line = JoinWords($DataLabelRef, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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193 $Line =~ s/\://g;
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194 # List data...
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195 if ($OptionsInfo{FileOutput}) {
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196 print OUTFILE "$Line\n";
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197 }
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198 else {
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199 print "$Line\n";
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200 }
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201 }
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202
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203 # Process option values...
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204 sub ProcessOptions {
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205 %OptionsInfo = ();
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206
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207 $OptionsInfo{Mode} = $Options{mode};
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208
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209 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /^tab$/i ) ? "\t" : (($Options{outdelim} =~ /^semicolon$/i) ? "\;" : "\,");
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210 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^yes$/i) ? 1 : 0;
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211
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212 $OptionsInfo{Output} = $Options{output};
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213 $OptionsInfo{OutputStyle} = $Options{outputstyle};
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214
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215 $OptionsInfo{RowsOutput} = ($Options{outputstyle} =~ /^FormulaRows$/i) ? 1 : 0;
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216 $OptionsInfo{FileOutput} = ($Options{output} =~ /^File$/i) ? 1 : 0;
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217 $OptionsInfo{CheckFormula} = $Options{fast} ? 0 : 1;
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218
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219 $OptionsInfo{Precision} = $Options{precision};
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220
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221 $OptionsInfo{OutFileRoot} = defined $Options{root} ? $Options{root} : undef;
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222 $OptionsInfo{ValueLabels} = defined $Options{valuelabels} ? $Options{valuelabels} : undef;
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223
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224 # Setup formulas...
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225 @{$OptionsInfo{SpecifiedFormulas}} = ();
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226 if (@ARGV >= 1) {
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227 push @{$OptionsInfo{SpecifiedFormulas}}, @ARGV;
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228 }
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229 else {
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230 # Setup mode specified default values...
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231 push @{$OptionsInfo{SpecifiedFormulas}}, 'H2O';
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232 }
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233
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234 # Setup what to calculate...
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235 @{$OptionsInfo{SpecifiedCalculations}} = ();
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236 if ($Options{mode} =~ /^All$/i) {
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237 @{$OptionsInfo{SpecifiedCalculations}} = qw(ElementalAnalysis MolecularWeight ExactMass);
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238 }
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239 else {
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240 my($Mode, $ModeValue, @SpecifiedModeValues);
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241 $Mode = $Options{mode};
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242 $Mode =~ s/ //g;
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243 @SpecifiedModeValues = split /\,/, $Mode;
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244 for $ModeValue (@SpecifiedModeValues) {
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245 if ($ModeValue !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
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246 if ($ModeValue =~ /^All$/i) {
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247 die "Error: All value for option \"-m --mode\" is not allowed with other valid values.\n";
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248 }
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249 else {
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250 die "Error: The value specified, $ModeValue, for option \"-m --mode\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
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251 }
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252 }
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253 push @{$OptionsInfo{SpecifiedCalculations}}, $ModeValue;
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254 }
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255 }
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256 my($Index, $Value, $Label);
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257 # Set up labels for calculated values...
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258 @{$OptionsInfo{SpecifiedValueLabels}} = ();
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259 if ($Options{valuelabels}) {
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260 my($Value, $Label, @ValueLabels);
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261 @ValueLabels = split /\,/, $Options{valuelabels};
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262 if (@ValueLabels % 2) {
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263 die "Error: The value specified, $Options{valuelabels}, for option \"-v --valuelabels\" is not valid: It must contain even number of comma delimited values\n";
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264 }
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265 for ($Index = 0; $Index < @ValueLabels; $Index +=2) {
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266 $Value = $ValueLabels[$Index];
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267 $Value =~ s/ //g;
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268 $Label = $ValueLabels[$Index + 1];
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269 if ($Value !~ /^(ElementalAnalysis|MolecularWeight|ExactMass)$/i) {
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270 die "Error: The value specified, $Value, using option \"-v --valuelabels\" is not valid. Allowed values: ElementalAnalysis, MolecularWeight, or ExactMass\n";
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271 }
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272 push @{$OptionsInfo{SpecifiedValueLabels}}, ($Value, $Label);
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273 }
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274 }
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275
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276 # Set up calculation type to label map...
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277 %{$OptionsInfo{ValueLabelsMap}} = (ElementalAnalysis => 'ElementalAnalysis', MolecularWeight => 'MolecularWeight', ExactMass => 'ExactMass');
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278 if (@{$OptionsInfo{SpecifiedValueLabels}}) {
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279 for ($Index = 0; $Index < @{$OptionsInfo{SpecifiedValueLabels}}; $Index +=2) {
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280 $Value = $OptionsInfo{SpecifiedValueLabels}[$Index];
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281 $Label = $OptionsInfo{SpecifiedValueLabels}[$Index + 1];
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282 if (exists $OptionsInfo{ValueLabelsMap}{$Value}) {
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283 $OptionsInfo{ValueLabelsMap}{$Value} = $Label;
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284 }
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285 }
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286 }
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287
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288 # Setup output file name...
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289 $OptionsInfo{OutFileName} = '';
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290 if ($OptionsInfo{FileOutput}) {
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291 my($OutFileRoot, $OutFileExt);
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292
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293 $OutFileRoot = '';
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294 $OutFileExt = "csv";
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295 if ($Options{outdelim} =~ /^tab$/i) {
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296 $OutFileExt = "tsv";
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297 }
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298 if ($Options{root}) {
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299 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($Options{root});
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300 if ($RootFileName && $RootFileExt) {
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301 $OutFileRoot = $RootFileName;
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302 }
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303 else {
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304 $OutFileRoot = $Options{root};
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305 }
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306 }
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307 else {
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308 $OutFileRoot = 'FormulasElementalAnalysis';
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309 }
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310 $OptionsInfo{OutFileName} = $OutFileRoot . '.' . $OutFileExt;
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311 if (!$Options{overwrite}) {
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312 if (-e $OptionsInfo{OutFileName}) {
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313 die "Error: Output file, $OptionsInfo{OutFileName}, already exists.\nUse \-o --overwrite\ option or specify a different name using \"-r --root\" option.\n";
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314 }
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315 }
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316 }
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317 }
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318
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319
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320 # Setup script usage and retrieve command line arguments specified using various options...
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321 sub SetupScriptUsage {
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322
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323 # Retrieve all the options...
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324 %Options = ();
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325 $Options{mode} = "All";
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326 $Options{outdelim} = "comma";
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327 $Options{output} = "STDOUT";
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328 $Options{outputstyle} = "FormulaBlock";
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329 $Options{precision} = 2;
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330 $Options{quote} = "yes";
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331
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332 if (!GetOptions(\%Options, "help|h", "fast", "mode|m=s", "outdelim=s", "output=s", "outputstyle=s", "overwrite|o", "precision=i", "quote|q=s", "root|r=s", "valuelabels|v=s", "workingdir|w=s")) {
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333 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
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334 }
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335 if ($Options{workingdir}) {
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336 if (! -d $Options{workingdir}) {
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337 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
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338 }
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339 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
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340 }
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341 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
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342 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
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343 }
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344 if ($Options{output} !~ /^(STDOUT|File)$/i) {
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345 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: STDOUT or File\n";
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346 }
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347 if ($Options{outputstyle} !~ /^(FormulaBlock|FormulaRows)$/i) {
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348 die "Error: The value specified, $Options{outputstyle}, for option \"--outputstyle\" is not valid. Allowed values: FormulaBlock or FormulaRows\n";
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349 }
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350 if (!IsPositiveInteger($Options{precision})) {
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351 die "Error: The value specified, $Options{precision}, for option \"-p --precision\" is not valid. Allowed values: > 0 \n";
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352 }
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353 if ($Options{quote} !~ /^(yes|no)$/i) {
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354 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: yes or no\n";
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355 }
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356 }
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357
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358 __END__
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359
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360 =head1 NAME
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361
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362 ElementalAnalysis.pl - Perform elemental analysis using specified formulas
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363
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364 =head1 SYNOPSIS
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365
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366 ElementalAnalysis.pl Formula(s)...
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367
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368 ElementalAnalysis.pl [B<-h, --help>]
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369 [B<-m, --mode> All | "ElementalAnalysis, [MolecularWeight, ExactMass]"]
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370 [B<--outdelim> comma | tab | semicolon]
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371 [B<--output> STDOUT | File] [B<--outputstyle> FormulaBlock | FormulaRows]
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372 [B<-o, --overwrite>] [B<--precision> number] [B<-q, --quote> yes | no] [B<-r, --root> rootname]
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373 [B<-v --valuelabels> [Name, Label, [Name, Label,...]]
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374 [B<-w, --workingdir> dirname] Formula(s)...
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375
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376 =head1 DESCRIPTION
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377
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378 Perform elemental analysis using molecular formula(s) specified on the command line.
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379
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380 In addition to straightforward molecular formulas - H2O, HCl, C3H7O2N -
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381 other supported variations are: Ca3(PO4)2, [PCl4]+, [Fe(CN)6]4-, C37H42N2O6+2, Na2CO3.10H2O,
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382 8H2S.46H2O, and so on. Charges are simply ignored. Isotope symbols in formulas specification, including
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383 D and T, are not supported.
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384
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385 =head1 PARAMETERS
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386
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387 =over 4
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388
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389 =item B<Formulas> I<Formula1 [Formula2...]>
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390
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391 I<Formulas> is a space delimited list of molecular formulas to use for elemental analysis.
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392
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393 Input value format is: I<Formula1 [Formula2 Formula3...]>. Default: I<H2O>.
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394 Examples:
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395
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396 HCl
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397 HCl, C3H7O2N
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398 H2O2 Ca3(PO4)2 [PCl4]+
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399
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400 =back
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401
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402 =head1 OPTIONS
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403
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404 =over 4
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405
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406 =item B<-h, --help>
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407
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408 Print this help message.
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409
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410 =item B<--fast>
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411
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412 In this mode, the specified formulas are considered valid and initial formula
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413 validation check is skipped.
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414
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415 =item B<-m, --mode> I<All | "ElementalAnalysis,[MolecularWeight,ExactMass]">
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416
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417 Specify what values to calculate using molecular formulas specified on command
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418 line: calculate all supported values or specify a comma delimited list of values. Possible
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419 values: I<All | "ElementalAnalysis, [MolecularWeight, ExactMass]">. Default: I<All>.
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420
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421 =item B<--outdelim> I<comma | tab | semicolon>
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422
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423 Output text file delimiter. Possible values: I<comma, tab, or semicolon>
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424 Default value: I<comma>.
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425
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426 =item B<--output> I<STDOUT | File>
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427
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428 List information at STDOUT or write it to a file. Possible values: I<STDOUT or File>. Default:
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429 I<STDOUT>. B<-r, --root> option is used to generate output file name.
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430
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431 =item B<--outputstyle> I<FormulaBlock | FormulaRows>
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432
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433 Specify how to list calculated values: add a new line for each property and present it as a block
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434 for each formula; or include all properties in one line and show it as a single line.
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435
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436 Possible values: I<FormulaBlock | FormulaRows>. Default: I<FormulaBlock>
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437
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438 An example for I<FormulaBlock> output style:
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439
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440 Formula: H2O
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441 ElementalAnalysis: H: H: 11.1898%; O: 88.8102%
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442 MolecularWeight: 18.0153
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443 ExactMass: 18.0106
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444 ... ...
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445 ... ...
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446 ... ...
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447
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448 Formula: H2O2
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449 ElementalAnalysis: H: 5.9265%; O: 94.0735%
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450 MolecularWeight: 34.0147
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451 ExactMass: 34.0055
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452 ... ...
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453 ... ...
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454 ... ...
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455
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456 An example for I<FormulaRows> output style:
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457
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458 Formula,ElementalAnalysis,MolecularWeight,ExactMass
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459 H2O,H: 11.1898%; O: 88.8102%,18.0153,18.0106
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460 H2O2,H: 5.9265%; O: 94.0735%,34.0147,34.0055
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461
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462 =item B<-o, --overwrite>
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463
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464 Overwrite existing files.
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465
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466 =item B<--precision> I<number>
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467
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468 Precision for listing numerical values. Default: up to I<4> decimal places.
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469 Valid values: positive integers.
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470
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471 =item B<-r, --root> I<rootname>
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472
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473 New text file name is generated using the root: <Root>.<Ext>. File name is only
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474 used during I<File> value of B<-o, --output> option.
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475
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476 Default file name: FormulsElementalAnalysis.<Ext>. The csv, and tsv
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477 <Ext> values are used for comma/semicolon, and tab delimited text files respectively.
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478
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479 =item B<-v --valuelabels> I<Name,Label,[Name,Label,...]>
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480
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481 Specify labels to use for calculated values. In general, it's a comma delimited
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482 list of value name and column label pairs. Supported value names: I<ElementalAnalysis,
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483 MolecularWeight, and ExactMass>. Default labels: I<ElementalAnalysis, MolecularWeight,
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484 and ExactMass>.
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485
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486 =item B<-w, --workingdir> I<dirname>
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487
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488 Location of working directory. Default: current directory.
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489
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490 =back
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491
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492 =head1 EXAMPLES
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493
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494 To perform elemental analysis, calculate molecular weight and exact mass for H2O,
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495 type:
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496
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497 % ElementalAnalysis.pl
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498
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499 To perform elemental analysis, calculate molecular weight and exact mass for
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500 Ca3(PO4)2 and [PCl4]+, type:
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501
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502 % ElementalAnalysis.pl "Ca3(PO4)2" "[PCl4]+"
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503
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504 To perform elemental analysis, use label analysis for calculated data, and generate a
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505 new CSV file ElementalAnalysis.csv for H2O and H2O2, type:
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506
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507 % ElementalAnalysis.pl --m ElementalAnalysis --output File
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508 --valuelabels "ElementalAnalysis,Analysis" -o -r ElementalAnalysis.csv
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509 H2O H2O2
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510
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511 To calculate molecular weight and exact mass with four decimal precision and
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512 generate a new CSV file WeightAndMass.csv with data rows for H2O and H2O2, type:
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513
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514 % ElementalAnalysis.pl --m "MolecularWeight,ExactMass" --output File
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515 --outputstyle FormulaRows -o -r WeightAndMass.csv
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516 H2O H2O2
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517
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518 =head1 AUTHOR
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519
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520 Manish Sud <msud@san.rr.com>
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521
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522 =head1 SEE ALSO
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523
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524 ElementalAnalysisSDFiles.pl, ElementalAnalysisTextFiles.pl
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525
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526 =head1 COPYRIGHT
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527
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528 Copyright (C) 2015 Manish Sud. All rights reserved.
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529
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530 This file is part of MayaChemTools.
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531
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532 MayaChemTools is free software; you can redistribute it and/or modify it under
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533 the terms of the GNU Lesser General Public License as published by the Free
|
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534 Software Foundation; either version 3 of the License, or (at your option)
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535 any later version.
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536
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537 =cut
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