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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: TopologicalAtomPairsFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:22 $
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5 # $Revision: 1.34 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use MoleculeFileIO;
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39 use FileIO::FingerprintsSDFileIO;
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40 use FileIO::FingerprintsTextFileIO;
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41 use FileIO::FingerprintsFPFileIO;
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42 use AtomTypes::AtomicInvariantsAtomTypes;
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43 use AtomTypes::FunctionalClassAtomTypes;
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44 use Fingerprints::TopologicalAtomPairsFingerprints;
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45
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46 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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47
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48 # Autoflush STDOUT
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49 $| = 1;
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50
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51 # Starting message...
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52 $ScriptName = basename($0);
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53 print "\n$ScriptName: Starting...\n\n";
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54 $StartTime = new Benchmark;
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55
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56 # Get the options and setup script...
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57 SetupScriptUsage();
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58 if ($Options{help} || @ARGV < 1) {
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59 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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60 }
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61
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62 my(@SDFilesList);
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63 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
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64
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65 # Process options...
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66 print "Processing options...\n";
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67 my(%OptionsInfo);
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68 ProcessOptions();
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69
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70 # Setup information about input files...
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71 print "Checking input SD file(s)...\n";
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72 my(%SDFilesInfo);
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73 RetrieveSDFilesInfo();
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74
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75 # Process input files..
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76 my($FileIndex);
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77 if (@SDFilesList > 1) {
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78 print "\nProcessing SD files...\n";
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79 }
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80 for $FileIndex (0 .. $#SDFilesList) {
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81 if ($SDFilesInfo{FileOkay}[$FileIndex]) {
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82 print "\nProcessing file $SDFilesList[$FileIndex]...\n";
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83 GenerateTopologicalAtomPairsFingerprints($FileIndex);
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84 }
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85 }
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86 print "\n$ScriptName:Done...\n\n";
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87
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88 $EndTime = new Benchmark;
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89 $TotalTime = timediff ($EndTime, $StartTime);
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90 print "Total time: ", timestr($TotalTime), "\n";
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91
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92 ###############################################################################
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93
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94 # Generate fingerprints for a SD file...
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95 #
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96 sub GenerateTopologicalAtomPairsFingerprints {
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97 my($FileIndex) = @_;
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98 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $TopologicalAtomPairsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
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99
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100 $SDFile = $SDFilesList[$FileIndex];
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101
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102 # Setup output files...
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103 #
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104 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = SetupAndOpenOutputFiles($FileIndex);
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105
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106 $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile);
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107 $MoleculeFileIO->Open();
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108
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109 $CmpdCount = 0;
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110 $IgnoredCmpdCount = 0;
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111
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112 COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) {
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113 $CmpdCount++;
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114
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115 # Filter compound data before calculating fingerprints...
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116 if ($OptionsInfo{Filter}) {
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117 if (CheckAndFilterCompound($CmpdCount, $Molecule)) {
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118 $IgnoredCmpdCount++;
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119 next COMPOUND;
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120 }
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121 }
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122
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123 $TopologicalAtomPairsFingerprints = GenerateMoleculeFingerprints($Molecule);
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124 if (!$TopologicalAtomPairsFingerprints) {
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125 $IgnoredCmpdCount++;
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126 ProcessIgnoredCompound('FingerprintsGenerationFailed', $CmpdCount, $Molecule);
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127 next COMPOUND;
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128 }
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129
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130 WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $TopologicalAtomPairsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
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131 }
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132 $MoleculeFileIO->Close();
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133
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134 if ($NewFPSDFileIO) {
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135 $NewFPSDFileIO->Close();
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136 }
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137 if ($NewFPTextFileIO) {
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138 $NewFPTextFileIO->Close();
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139 }
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140 if ($NewFPFileIO) {
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141 $NewFPFileIO->Close();
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142 }
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143
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144 WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount);
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145 }
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146
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147 # Process compound being ignored due to problems in fingerprints geneation...
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148 #
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149 sub ProcessIgnoredCompound {
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150 my($Mode, $CmpdCount, $Molecule) = @_;
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151 my($CmpdID, $DataFieldLabelAndValuesRef);
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152
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153 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
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154 $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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155
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156 MODE: {
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157 if ($Mode =~ /^ContainsNonElementalData$/i) {
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158 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n";
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159 next MODE;
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160 }
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161
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162 if ($Mode =~ /^ContainsNoElementalData$/i) {
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163 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n";
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164 next MODE;
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165 }
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166
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167 if ($Mode =~ /^FingerprintsGenerationFailed$/i) {
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168 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
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169 next MODE;
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170 }
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171 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
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172 }
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173 }
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174
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175 # Check and filter compounds....
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176 #
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177 sub CheckAndFilterCompound {
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178 my($CmpdCount, $Molecule) = @_;
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179 my($ElementCount, $NonElementCount);
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180
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181 ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements();
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182
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183 if ($NonElementCount) {
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184 ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule);
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185 return 1;
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186 }
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187
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188 if (!$ElementCount) {
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189 ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule);
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190 return 1;
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191 }
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192
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193 return 0;
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194 }
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195
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196 # Write out compounds fingerprints generation summary statistics...
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197 #
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198 sub WriteFingerprintsGenerationSummaryStatistics {
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199 my($CmpdCount, $IgnoredCmpdCount) = @_;
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200 my($ProcessedCmpdCount);
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201
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202 $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount;
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203
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204 print "\nNumber of compounds: $CmpdCount\n";
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205 print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n";
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206 print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n";
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207 }
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208
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209 # Open output files...
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210 #
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211 sub SetupAndOpenOutputFiles {
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212 my($FileIndex) = @_;
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213 my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams);
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214
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215 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3;
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216
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217 # Setup common parameters for fingerprints file IO objects...
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218 #
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219 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
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220
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221 if ($OptionsInfo{SDOutput}) {
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222 $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
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223 print "Generating SD file $NewFPSDFile...\n";
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224 $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
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225 $NewFPSDFileIO->Open();
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226 }
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227
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228 if ($OptionsInfo{FPOutput}) {
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229 $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
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230 print "Generating FP file $NewFPFile...\n";
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231 $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
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232 $NewFPFileIO->Open();
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233 }
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234
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235 if ($OptionsInfo{TextOutput}) {
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236 my($ColLabelsRef);
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237
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238 $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
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239 $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
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240
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241 print "Generating text file $NewFPTextFile...\n";
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242 $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
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243 $NewFPTextFileIO->Open();
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244 }
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245
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246 return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
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247 }
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248
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249 # Write fingerpritns and other data to appropriate output files...
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250 #
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251 sub WriteDataToOutputFiles {
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252 my($FileIndex, $CmpdCount, $Molecule, $TopologicalAtomPairsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
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253 my($DataFieldLabelAndValuesRef);
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254
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255 $DataFieldLabelAndValuesRef = undef;
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256 if ($NewFPTextFileIO || $NewFPFileIO) {
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257 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
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258 }
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259
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260 if ($NewFPSDFileIO) {
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261 my($CmpdString);
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262
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263 $CmpdString = $Molecule->GetInputMoleculeString();
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264 $NewFPSDFileIO->WriteFingerprints($TopologicalAtomPairsFingerprints, $CmpdString);
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265 }
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266
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267 if ($NewFPTextFileIO) {
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268 my($ColValuesRef);
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269
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270 $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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271 $NewFPTextFileIO->WriteFingerprints($TopologicalAtomPairsFingerprints, $ColValuesRef);
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272 }
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273
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274 if ($NewFPFileIO) {
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275 my($CompoundID);
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276
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277 $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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278 $NewFPFileIO->WriteFingerprints($TopologicalAtomPairsFingerprints, $CompoundID);
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279 }
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280 }
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281
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282 # Generate approriate column labels for FPText output file...
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283 #
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284 sub SetupFPTextFileCoulmnLabels {
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285 my($FileIndex) = @_;
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286 my($Line, @ColLabels);
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287
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288 @ColLabels = ();
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289 if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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290 push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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291 }
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292 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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293 push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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294 }
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295 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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296 push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}};
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297 }
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298 elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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299 push @ColLabels, $OptionsInfo{CompoundIDLabel};
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300 }
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301 # Add fingerprints label...
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302 push @ColLabels, $OptionsInfo{FingerprintsLabel};
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303
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304 return \@ColLabels;
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305 }
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306
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307 # Generate column values FPText output file..
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308 #
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309 sub SetupFPTextFileCoulmnValues {
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310 my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
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311 my(@ColValues);
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312
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313 @ColValues = ();
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314 if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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315 push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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316 }
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317 elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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318 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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319 }
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320 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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321 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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322 }
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323 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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324 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
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325 }
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326
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327 return \@ColValues;
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328 }
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329
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330 # Generate compound ID for FP and FPText output files..
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331 #
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332 sub SetupCmpdIDForOutputFiles {
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333 my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
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334 my($CmpdID);
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335
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336 $CmpdID = '';
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337 if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
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338 my($MolName);
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339 $MolName = $Molecule->GetName();
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340 $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
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341 }
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342 elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
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343 $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
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344 }
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345 elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
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346 my($SpecifiedDataField);
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347 $SpecifiedDataField = $OptionsInfo{CompoundID};
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348 $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
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349 }
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350 elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
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351 $CmpdID = $Molecule->GetName();
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352 }
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353 return $CmpdID;
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354 }
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355
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356 # Generate fingerprints for molecule...
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357 #
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358 sub GenerateMoleculeFingerprints {
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359 my($Molecule) = @_;
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360 my($TopologicalAtomPairsFingerprints);
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361
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362 if ($OptionsInfo{KeepLargestComponent}) {
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363 $Molecule->KeepLargestComponent();
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364 }
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365 if (!$Molecule->DetectRings()) {
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366 return undef;
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367 }
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368 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
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369 $Molecule->DetectAromaticity();
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370
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371 $TopologicalAtomPairsFingerprints = new Fingerprints::TopologicalAtomPairsFingerprints('Molecule' => $Molecule, 'MinDistance' => $OptionsInfo{MinDistance}, 'MaxDistance' => $OptionsInfo{MaxDistance}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
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372 SetAtomIdentifierTypeValuesToUse($TopologicalAtomPairsFingerprints);
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373
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374 # Generate fingerprints...
|
|
|
375 $TopologicalAtomPairsFingerprints->GenerateFingerprints();
|
|
|
376
|
|
|
377 # Make sure fingerprints generation is successful...
|
|
|
378 if (!$TopologicalAtomPairsFingerprints->IsFingerprintsGenerationSuccessful()) {
|
|
|
379 return undef;
|
|
|
380 }
|
|
|
381
|
|
|
382 return $TopologicalAtomPairsFingerprints;
|
|
|
383 }
|
|
|
384
|
|
|
385 # Set atom identifier type to use for generating fingerprints...
|
|
|
386 #
|
|
|
387 sub SetAtomIdentifierTypeValuesToUse {
|
|
|
388 my($TopologicalAtomPairsFingerprints) = @_;
|
|
|
389
|
|
|
390 if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
391 $TopologicalAtomPairsFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
|
|
|
392 }
|
|
|
393 elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
394 $TopologicalAtomPairsFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
|
|
|
395 }
|
|
|
396 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
397 # Nothing to do for now...
|
|
|
398 }
|
|
|
399 else {
|
|
|
400 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
401 }
|
|
|
402 }
|
|
|
403
|
|
|
404 # Retrieve information about SD files...
|
|
|
405 #
|
|
|
406 sub RetrieveSDFilesInfo {
|
|
|
407 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
|
|
|
408
|
|
|
409 %SDFilesInfo = ();
|
|
|
410 @{$SDFilesInfo{FileOkay}} = ();
|
|
|
411 @{$SDFilesInfo{OutFileRoot}} = ();
|
|
|
412 @{$SDFilesInfo{SDOutFileNames}} = ();
|
|
|
413 @{$SDFilesInfo{FPOutFileNames}} = ();
|
|
|
414 @{$SDFilesInfo{TextOutFileNames}} = ();
|
|
|
415 @{$SDFilesInfo{AllDataFieldsRef}} = ();
|
|
|
416 @{$SDFilesInfo{CommonDataFieldsRef}} = ();
|
|
|
417
|
|
|
418 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
|
|
|
419 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
|
|
|
420
|
|
|
421 FILELIST: for $Index (0 .. $#SDFilesList) {
|
|
|
422 $SDFile = $SDFilesList[$Index];
|
|
|
423
|
|
|
424 $SDFilesInfo{FileOkay}[$Index] = 0;
|
|
|
425 $SDFilesInfo{OutFileRoot}[$Index] = '';
|
|
|
426 $SDFilesInfo{SDOutFileNames}[$Index] = '';
|
|
|
427 $SDFilesInfo{FPOutFileNames}[$Index] = '';
|
|
|
428 $SDFilesInfo{TextOutFileNames}[$Index] = '';
|
|
|
429
|
|
|
430 $SDFile = $SDFilesList[$Index];
|
|
|
431 if (!(-e $SDFile)) {
|
|
|
432 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
|
|
|
433 next FILELIST;
|
|
|
434 }
|
|
|
435 if (!CheckFileType($SDFile, "sd sdf")) {
|
|
|
436 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
|
|
|
437 next FILELIST;
|
|
|
438 }
|
|
|
439
|
|
|
440 if ($CheckDataField) {
|
|
|
441 # Make sure data field exists in SD file..
|
|
|
442 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
|
|
|
443
|
|
|
444 @CmpdLines = ();
|
|
|
445 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
446 $CmpdString = ReadCmpdString(\*SDFILE);
|
|
|
447 close SDFILE;
|
|
|
448 @CmpdLines = split "\n", $CmpdString;
|
|
|
449 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
450 $SpecifiedDataField = $OptionsInfo{CompoundID};
|
|
|
451 if (!exists $DataFieldValues{$SpecifiedDataField}) {
|
|
|
452 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
|
|
|
453 next FILELIST;
|
|
|
454 }
|
|
|
455 }
|
|
|
456
|
|
|
457 $AllDataFieldsRef = '';
|
|
|
458 $CommonDataFieldsRef = '';
|
|
|
459 if ($CollectDataFields) {
|
|
|
460 my($CmpdCount);
|
|
|
461 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
462 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
|
|
|
463 close SDFILE;
|
|
|
464 }
|
|
|
465
|
|
|
466 # Setup output file names...
|
|
|
467 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
468 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
|
|
|
469
|
|
|
470 $TextOutFileExt = "csv";
|
|
|
471 if ($Options{outdelim} =~ /^tab$/i) {
|
|
|
472 $TextOutFileExt = "tsv";
|
|
|
473 }
|
|
|
474 $SDOutFileExt = $FileExt;
|
|
|
475 $FPOutFileExt = "fpf";
|
|
|
476
|
|
|
477 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
|
|
|
478 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
479 if ($RootFileName && $RootFileExt) {
|
|
|
480 $FileName = $RootFileName;
|
|
|
481 }
|
|
|
482 else {
|
|
|
483 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
484 }
|
|
|
485 $OutFileRoot = $FileName;
|
|
|
486 }
|
|
|
487 else {
|
|
|
488 $OutFileRoot = "${FileName}TopologicalAtomPairsFP";
|
|
|
489 }
|
|
|
490
|
|
|
491 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
|
|
|
492 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
|
|
|
493 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
|
|
|
494
|
|
|
495 if ($OptionsInfo{SDOutput}) {
|
|
|
496 if ($SDFile =~ /$NewSDFileName/i) {
|
|
|
497 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
|
|
|
498 print "Specify a different name using \"-r --root\" option or use default name.\n";
|
|
|
499 next FILELIST;
|
|
|
500 }
|
|
|
501 }
|
|
|
502
|
|
|
503 if (!$OptionsInfo{OverwriteFiles}) {
|
|
|
504 # Check SD and text outout files...
|
|
|
505 if ($OptionsInfo{SDOutput}) {
|
|
|
506 if (-e $NewSDFileName) {
|
|
|
507 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
|
|
|
508 next FILELIST;
|
|
|
509 }
|
|
|
510 }
|
|
|
511 if ($OptionsInfo{FPOutput}) {
|
|
|
512 if (-e $NewFPFileName) {
|
|
|
513 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
|
|
|
514 next FILELIST;
|
|
|
515 }
|
|
|
516 }
|
|
|
517 if ($OptionsInfo{TextOutput}) {
|
|
|
518 if (-e $NewTextFileName) {
|
|
|
519 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
|
|
|
520 next FILELIST;
|
|
|
521 }
|
|
|
522 }
|
|
|
523 }
|
|
|
524
|
|
|
525 $SDFilesInfo{FileOkay}[$Index] = 1;
|
|
|
526
|
|
|
527 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
|
|
|
528 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
|
|
|
529 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
|
|
|
530 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
|
|
|
531
|
|
|
532 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
|
|
|
533 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
|
|
|
534 }
|
|
|
535 }
|
|
|
536
|
|
|
537 # Process option values...
|
|
|
538 sub ProcessOptions {
|
|
|
539 %OptionsInfo = ();
|
|
|
540
|
|
|
541 ProcessAtomIdentifierTypeOptions();
|
|
|
542
|
|
|
543 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
|
|
|
544
|
|
|
545 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
|
|
|
546 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
|
|
|
547 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
|
|
|
548
|
|
|
549 my(@SpecifiedDataFields);
|
|
|
550 @SpecifiedDataFields = ();
|
|
|
551
|
|
|
552 @{$OptionsInfo{SpecifiedDataFields}} = ();
|
|
|
553 $OptionsInfo{CompoundID} = '';
|
|
|
554
|
|
|
555 if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
|
|
|
556 if ($Options{compoundidmode} =~ /^DataField$/i) {
|
|
|
557 if (!$Options{compoundid}) {
|
|
|
558 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
|
|
|
559 }
|
|
|
560 $OptionsInfo{CompoundID} = $Options{compoundid};
|
|
|
561 }
|
|
|
562 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
563 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
|
|
|
564 }
|
|
|
565 }
|
|
|
566 elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
|
|
|
567 if (!$Options{datafields}) {
|
|
|
568 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
|
|
|
569 }
|
|
|
570 @SpecifiedDataFields = split /\,/, $Options{datafields};
|
|
|
571 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
|
|
|
572 }
|
|
|
573
|
|
|
574 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
|
|
|
575
|
|
|
576 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'TopologicalAtomPairsFingerprints';
|
|
|
577
|
|
|
578 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
|
|
|
579
|
|
|
580 $OptionsInfo{MinDistance} = $Options{mindistance};
|
|
|
581 $OptionsInfo{MaxDistance} = $Options{maxdistance};
|
|
|
582
|
|
|
583 $OptionsInfo{Output} = $Options{output};
|
|
|
584 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
|
|
|
585 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
|
|
|
586 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
|
|
|
587
|
|
|
588 $OptionsInfo{OutDelim} = $Options{outdelim};
|
|
|
589 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
590
|
|
|
591 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
592 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
593
|
|
|
594 $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat};
|
|
|
595 }
|
|
|
596
|
|
|
597 # Process atom identifier type and related options...
|
|
|
598 #
|
|
|
599 sub ProcessAtomIdentifierTypeOptions {
|
|
|
600
|
|
|
601 $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
|
|
|
602
|
|
|
603 if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
604 ProcessAtomicInvariantsToUseOption();
|
|
|
605 }
|
|
|
606 elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
607 ProcessFunctionalClassesToUse();
|
|
|
608 }
|
|
|
609 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
610 # Nothing to do for now...
|
|
|
611 }
|
|
|
612 else {
|
|
|
613 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
614 }
|
|
|
615 }
|
|
|
616
|
|
|
617 # Process specified atomic invariants to use...
|
|
|
618 #
|
|
|
619 sub ProcessAtomicInvariantsToUseOption {
|
|
|
620 my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
|
|
|
621
|
|
|
622 @{$OptionsInfo{AtomicInvariantsToUse}} = ();
|
|
|
623 if (IsEmpty($Options{atomicinvariantstouse})) {
|
|
|
624 die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
|
|
|
625 }
|
|
|
626 $AtomSymbolSpecified = 0;
|
|
|
627 @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
|
|
|
628 for $AtomicInvariant (@AtomicInvariantsWords) {
|
|
|
629 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
|
|
|
630 die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
|
|
|
631 }
|
|
|
632 if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
|
|
|
633 $AtomSymbolSpecified = 1;
|
|
|
634 }
|
|
|
635 push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
|
|
|
636 }
|
|
|
637 if (!$AtomSymbolSpecified) {
|
|
|
638 die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
|
|
|
639 }
|
|
|
640 }
|
|
|
641
|
|
|
642 # Process specified functional classes invariants to use...
|
|
|
643 #
|
|
|
644 sub ProcessFunctionalClassesToUse {
|
|
|
645 my($FunctionalClass, @FunctionalClassesToUseWords);
|
|
|
646
|
|
|
647 @{$OptionsInfo{FunctionalClassesToUse}} = ();
|
|
|
648 if (IsEmpty($Options{functionalclassestouse})) {
|
|
|
649 die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
|
|
|
650 }
|
|
|
651 @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
|
|
|
652 for $FunctionalClass (@FunctionalClassesToUseWords) {
|
|
|
653 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
|
|
|
654 die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
|
|
|
655 }
|
|
|
656 push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
|
|
|
657 }
|
|
|
658 }
|
|
|
659
|
|
|
660 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
661 sub SetupScriptUsage {
|
|
|
662
|
|
|
663 # Retrieve all the options...
|
|
|
664 %Options = ();
|
|
|
665
|
|
|
666 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
|
|
|
667
|
|
|
668 $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
|
|
|
669 $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC';
|
|
|
670
|
|
|
671 $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
|
|
|
672
|
|
|
673 $Options{compoundidmode} = 'LabelPrefix';
|
|
|
674 $Options{compoundidlabel} = 'CompoundID';
|
|
|
675 $Options{datafieldsmode} = 'CompoundID';
|
|
|
676
|
|
|
677 $Options{filter} = 'Yes';
|
|
|
678
|
|
|
679 $Options{keeplargestcomponent} = 'Yes';
|
|
|
680
|
|
|
681 $Options{mindistance} = 1;
|
|
|
682 $Options{maxdistance} = 10;
|
|
|
683
|
|
|
684 $Options{output} = 'text';
|
|
|
685 $Options{outdelim} = 'comma';
|
|
|
686 $Options{quote} = 'yes';
|
|
|
687
|
|
|
688 $Options{vectorstringformat} = 'IDsAndValuesString';
|
|
|
689
|
|
|
690 if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "mindistance=s", "maxdistance=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "vectorstringformat|v=s", "workingdir|w=s")) {
|
|
|
691 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
692 }
|
|
|
693 if ($Options{workingdir}) {
|
|
|
694 if (! -d $Options{workingdir}) {
|
|
|
695 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
696 }
|
|
|
697 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
698 }
|
|
|
699 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
|
|
|
700 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
|
|
|
701 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
|
|
|
702 }
|
|
|
703 if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
704 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
705 }
|
|
|
706 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
707 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
708 }
|
|
|
709 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
|
|
|
710 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
|
|
|
711 }
|
|
|
712 if ($Options{filter} !~ /^(Yes|No)$/i) {
|
|
|
713 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
|
|
|
714 }
|
|
|
715 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
|
|
|
716 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
|
|
|
717 }
|
|
|
718 if (!IsPositiveInteger($Options{mindistance})) {
|
|
|
719 die "Error: The value specified, $Options{mindistance}, for option \"--MinDistance\" is not valid. Allowed values: > 0 \n";
|
|
|
720 }
|
|
|
721 if (!IsPositiveInteger($Options{maxdistance})) {
|
|
|
722 die "Error: The value specified, $Options{maxdistance}, for option \"--MaxDistance\" is not valid. Allowed values: > 0 \n";
|
|
|
723 }
|
|
|
724 if ($Options{mindistance} > $Options{maxdistance}) {
|
|
|
725 die "Error: The value specified, specified, $Options{mindistance}, for option \"--MinDistance\" must be less than the value specified, $Options{maxdistance}, for option \"--MaxDistance\" \n";
|
|
|
726 }
|
|
|
727 if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
|
|
|
728 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
|
|
|
729 }
|
|
|
730 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
731 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
732 }
|
|
|
733 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
734 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
735 }
|
|
|
736 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
|
|
|
737 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
|
|
|
738 }
|
|
|
739 if ($Options{vectorstringformat} !~ /^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
|
|
|
740 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
|
|
|
741 }
|
|
|
742 }
|
|
|
743
|
|
|
744 __END__
|
|
|
745
|
|
|
746 =head1 NAME
|
|
|
747
|
|
|
748 TopologicalAtomPairsFingerprints.pl - Generate topological atom pairs fingerprints for SD files
|
|
|
749
|
|
|
750 =head1 SYNOPSIS
|
|
|
751
|
|
|
752 TopologicalAtomPairsFingerprints.pl SDFile(s)...
|
|
|
753
|
|
|
754 TopologicalAtomPairsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
|
|
|
755 [B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes>]
|
|
|
756 [B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">]
|
|
|
757 [B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
|
|
|
758 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
|
|
|
759 [B<--CompoundIDMode>] [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">]
|
|
|
760 [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] [B<-f, --Filter> I<Yes | No>]
|
|
|
761 [B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>]
|
|
|
762 [B<--MinDistance> I<number>] [B<--MaxDistance> I<number>]
|
|
|
763 [B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD | FP | text | all>] [B<-o, --overwrite>]
|
|
|
764 [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
|
|
|
765 [B<-v, --VectorStringFormat> I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>]
|
|
|
766 [B<-w, --WorkingDir> dirname] SDFile(s)...
|
|
|
767
|
|
|
768 =head1 DESCRIPTION
|
|
|
769
|
|
|
770 Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] for I<SDFile(s)> and create
|
|
|
771 appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to
|
|
|
772 molecular fingerprints.
|
|
|
773
|
|
|
774 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
|
|
|
775 and I<.sd>. All other file names are ignored. All the SD files in a current directory
|
|
|
776 can be specified either by I<*.sdf> or the current directory name.
|
|
|
777
|
|
|
778 The current release of MayaChemTools supports generation of topological atom pairs
|
|
|
779 corresponding to following B<-a, --AtomIdentifierTypes>:
|
|
|
780
|
|
|
781 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
782 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
783 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
784
|
|
|
785 Based on the values specified for B<-a, --AtomIdentifierType> and B<--AtomicInvariantsToUse>,
|
|
|
786 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
|
|
|
787 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
|
|
|
788 pairs within B<--MinDistance> and B<--MaxDistance> are identified and counted. An atom pair
|
|
|
789 identifier is generated for each unique atom pair; the format of the atom pair identifier is:
|
|
|
790
|
|
|
791 <AtomType1>-D<n>-<AtomType2>
|
|
|
792
|
|
|
793 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
|
|
|
794 D: Distance between atom1 and atom2
|
|
|
795
|
|
|
796 where AtomType1 <= AtomType2
|
|
|
797
|
|
|
798 The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
|
|
|
799 topological atom pairs fingerprints of the molecule.
|
|
|
800
|
|
|
801 Example of I<SD> file containing topological atom pairs fingerprints string data:
|
|
|
802
|
|
|
803 ... ...
|
|
|
804 ... ...
|
|
|
805 $$$$
|
|
|
806 ... ...
|
|
|
807 ... ...
|
|
|
808 ... ...
|
|
|
809 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
810 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
811 ... ...
|
|
|
812 2 3 1 0 0 0 0
|
|
|
813 ... ...
|
|
|
814 M END
|
|
|
815 > <CmpdID>
|
|
|
816 Cmpd1
|
|
|
817
|
|
|
818 > <TopologicalAtomPairsFingerprints>
|
|
|
819 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi
|
|
|
820 stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H
|
|
|
821 3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.H1
|
|
|
822 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-C.X2...;
|
|
|
823 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
824 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
|
|
|
825
|
|
|
826 $$$$
|
|
|
827 ... ...
|
|
|
828 ... ...
|
|
|
829
|
|
|
830 Example of I<FP> file containing topological atom pairs fingerprints string data:
|
|
|
831
|
|
|
832 #
|
|
|
833 # Package = MayaChemTools 7.4
|
|
|
834 # Release Date = Oct 21, 2010
|
|
|
835 #
|
|
|
836 # TimeStamp = Fri Mar 11 15:04:36 2011
|
|
|
837 #
|
|
|
838 # FingerprintsStringType = FingerprintsVector
|
|
|
839 #
|
|
|
840 # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi...
|
|
|
841 # VectorStringFormat = IDsAndValuesString
|
|
|
842 # VectorValuesType = NumericalValues
|
|
|
843 #
|
|
|
844 Cmpd1 223;C.X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2...;1 1...
|
|
|
845 Cmpd2 128;C.X1.BO1.H3-D1-C.X2.BO2.H2 C.X1.BO1.H3-D1-C.X3.BO4...;1 1...
|
|
|
846 ... ...
|
|
|
847 ... ..
|
|
|
848
|
|
|
849 Example of CSV I<Text> file containing topological atom pairs fingerprints string data:
|
|
|
850
|
|
|
851 "CompoundID","TopologicalAtomPairsFingerprints"
|
|
|
852 "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy
|
|
|
853 pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C
|
|
|
854 .X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X
|
|
|
855 3.BO3.H1C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1...;
|
|
|
856 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
857 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
|
|
|
858 ... ...
|
|
|
859 ... ...
|
|
|
860
|
|
|
861 The current release of MayaChemTools generates the following types of topological atom pairs
|
|
|
862 fingerprints vector strings:
|
|
|
863
|
|
|
864 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
865 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
866 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
867 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
868 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
869 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
|
|
|
870
|
|
|
871 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
872 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
|
|
|
873 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
|
|
|
874 C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
|
|
|
875 .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
|
|
|
876 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...
|
|
|
877
|
|
|
878 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
|
|
|
879 :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
|
|
|
880 1-C_R C_2-D1-N_3 C_2-D1-O_2 C_2-D1-O_3 C_3-D1-C_3 C_3-D1-C_R C_3-D1-N_
|
|
|
881 R C_3-D1-O_3 C_R-D1-C_R C_R-D1-F_ C_R-D1-N_3 C_R-D1-N_R C_2-D2-C_3 C_2
|
|
|
882 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
|
|
|
883 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...
|
|
|
884
|
|
|
885 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
|
|
|
886 axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
|
|
|
887 D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
|
|
|
888 aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
|
|
|
889 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
|
|
|
890 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...
|
|
|
891
|
|
|
892 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
893 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
|
|
|
894 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
|
|
|
895 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
|
|
|
896 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
|
|
|
897 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
|
|
|
898
|
|
|
899 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
|
|
|
900 axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
|
|
|
901 C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
|
|
|
902 CB 1 C=ON-D1-NC=O 1 C=ON-D1-O=CN 1 CB-D1-CB 18 CB-D1-F 1 CB-D1-NC=O 1
|
|
|
903 COO-D1-CR 1 COO-D1-O=CO 1 COO-D1-OC=O 1 CR-D1-CR 7 CR-D1-N5 1 CR-D1-OR
|
|
|
904 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...
|
|
|
905
|
|
|
906 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
|
|
|
907 xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
|
|
|
908 -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
|
|
|
909 C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
|
|
|
910 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
|
|
|
911 C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...
|
|
|
912
|
|
|
913 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
|
|
|
914 xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
|
|
|
915 .2-D1-C.ar 1 C.2-D1-N.am 1 C.2-D1-O.2 1 C.2-D1-O.co2 2 C.3-D1-C.3 7 C.
|
|
|
916 3-D1-C.ar 1 C.3-D1-N.ar 1 C.3-D1-O.3 2 C.ar-D1-C.ar 23 C.ar-D1-F 1 C.a
|
|
|
917 r-D1-N.am 1 C.ar-D1-N.ar 2 C.2-D2-C.3 1 C.2-D2-C.ar 3 C.3-D2-C.3 5 C.3
|
|
|
918 -D2-C.ar 5 C.3-D2-N.ar 2 C.3-D2-O.3 4 C.3-D2-O.co2 2 C.ar-D2-C.ar 2...
|
|
|
919
|
|
|
920 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
|
|
|
921 Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
|
|
|
922 -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
|
|
|
923 D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
|
|
|
924 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
|
|
|
925 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...
|
|
|
926
|
|
|
927 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
|
|
|
928 istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
|
|
|
929 -D1-C_R 1 C_2-D1-N_3 1 C_2-D1-O_2 2 C_2-D1-O_3 1 C_3-D1-C_3 7 C_3-D1-C
|
|
|
930 _R 1 C_3-D1-N_R 1 C_3-D1-O_3 2 C_R-D1-C_R 23 C_R-D1-F_ 1 C_R-D1-N_3 1
|
|
|
931 C_R-D1-N_R 2 C_2-D2-C_3 1 C_2-D2-C_R 3 C_3-D2-C_3 5 C_3-D2-C_R 5 C_3-D
|
|
|
932 2-N_R 2 C_3-D2-O_2 1 C_3-D2-O_3 5 C_R-D2-C_R 28 C_R-D2-F_ 2 C_R-D2-...
|
|
|
933
|
|
|
934 =head1 OPTIONS
|
|
|
935
|
|
|
936 =over 4
|
|
|
937
|
|
|
938 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
|
|
|
939
|
|
|
940 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
941 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
942 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
943 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
|
|
|
944
|
|
|
945 The supported aromaticity model names along with model specific control parameters
|
|
|
946 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
|
|
|
947 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
|
|
|
948 this file during class instantiation and makes it available to method B<DetectAromaticity>
|
|
|
949 for detecting aromaticity corresponding to a specific model.
|
|
|
950
|
|
|
951 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
|
|
|
952
|
|
|
953 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
|
|
|
954 atoms during calculation of topological atom pairs fingerprints. Possible values in the current
|
|
|
955 release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
956 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
957 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
|
|
|
958
|
|
|
959 =item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">
|
|
|
960
|
|
|
961 This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
962 option. It's a list of comma separated valid atomic invariant atom types.
|
|
|
963
|
|
|
964 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB,
|
|
|
965 H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>.
|
|
|
966
|
|
|
967 The atomic invariants abbreviations correspond to:
|
|
|
968
|
|
|
969 AS = Atom symbol corresponding to element symbol
|
|
|
970
|
|
|
971 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
972 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
973 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
974 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
975 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
976 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
977 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
978 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
979 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
980 FC<+n/-n> = Formal charge assigned to atom
|
|
|
981 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
982 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
983 3 (triplet)
|
|
|
984
|
|
|
985 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
986
|
|
|
987 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
988
|
|
|
989 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
990 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
991
|
|
|
992 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
993 are also allowed:
|
|
|
994
|
|
|
995 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
996 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
997 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
998 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
999 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1000 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1001 H : NumOfImplicitAndExplicitHydrogens
|
|
|
1002 Ar : Aromatic
|
|
|
1003 RA : RingAtom
|
|
|
1004 FC : FormalCharge
|
|
|
1005 MN : MassNumber
|
|
|
1006 SM : SpinMultiplicity
|
|
|
1007
|
|
|
1008 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
|
|
|
1009 atom types.
|
|
|
1010
|
|
|
1011 =item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">
|
|
|
1012
|
|
|
1013 This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1014 option. It's a list of comma separated valid functional classes.
|
|
|
1015
|
|
|
1016 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1017 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
|
|
|
1018
|
|
|
1019 The functional class abbreviations correspond to:
|
|
|
1020
|
|
|
1021 HBD: HydrogenBondDonor
|
|
|
1022 HBA: HydrogenBondAcceptor
|
|
|
1023 PI : PositivelyIonizable
|
|
|
1024 NI : NegativelyIonizable
|
|
|
1025 Ar : Aromatic
|
|
|
1026 Hal : Halogen
|
|
|
1027 H : Hydrophobic
|
|
|
1028 RA : RingAtom
|
|
|
1029 CA : ChainAtom
|
|
|
1030
|
|
|
1031 Functional class atom type specification for an atom corresponds to:
|
|
|
1032
|
|
|
1033 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
1034
|
|
|
1035 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1036 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1037
|
|
|
1038 HydrogenBondDonor: NH, NH2, OH
|
|
|
1039 HydrogenBondAcceptor: N[!H], O
|
|
|
1040 PositivelyIonizable: +, NH2
|
|
|
1041 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1042
|
|
|
1043 =item B<--CompoundID> I<DataFieldName or LabelPrefixString>
|
|
|
1044
|
|
|
1045 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
|
|
|
1046
|
|
|
1047 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
|
|
|
1048 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
|
|
1049 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
|
|
|
1050 look like Cmpd<Number>.
|
|
|
1051
|
|
|
1052 Examples for I<DataField> value of B<--CompoundIDMode>:
|
|
|
1053
|
|
|
1054 MolID
|
|
|
1055 ExtReg
|
|
|
1056
|
|
|
1057 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
|
|
|
1058
|
|
|
1059 Compound
|
|
|
1060
|
|
|
1061 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
1062 instead of default value of Cmpd<Number>.
|
|
|
1063
|
|
|
1064 =item B<--CompoundIDLabel> I<text>
|
|
|
1065
|
|
|
1066 Specify compound ID column label for CSV/TSV text file(s) used during I<CompoundID> value
|
|
|
1067 of B<--DataFieldsMode> option. Default value: I<CompoundID>.
|
|
|
1068
|
|
|
1069 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
1070
|
|
|
1071 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
|
|
|
1072 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value;
|
|
|
1073 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination
|
|
|
1074 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
1075
|
|
|
1076 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
1077 Default value: I<LabelPrefix>.
|
|
|
1078
|
|
|
1079 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
|
|
|
1080 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
1081 values are replaced with sequential compound IDs.
|
|
|
1082
|
|
|
1083 This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
|
|
|
1084
|
|
|
1085 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,...">
|
|
|
1086
|
|
|
1087 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
1088 with generated fingerprints for I<text | both> values of B<--output> option.
|
|
|
1089
|
|
|
1090 This is only used for I<Specify> value of B<--DataFieldsMode> option.
|
|
|
1091
|
|
|
1092 Examples:
|
|
|
1093
|
|
|
1094 Extreg
|
|
|
1095 MolID,CompoundName
|
|
|
1096
|
|
|
1097 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
|
|
|
1098
|
|
|
1099 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
|
|
|
1100 with generated fingerprints for I<text | both> values of B<--output> option: transfer all SD
|
|
|
1101 data field; transfer SD data files common to all compounds; extract specified data fields;
|
|
|
1102 generate a compound ID using molname line, a compound prefix, or a combination of both.
|
|
|
1103 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
|
|
|
1104
|
|
|
1105 =item B<-f, --Filter> I<Yes | No>
|
|
|
1106
|
|
|
1107 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
|
|
|
1108 Default value: I<Yes>.
|
|
|
1109
|
|
|
1110 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
1111 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
1112
|
|
|
1113 =item B<--FingerprintsLabel> I<text>
|
|
|
1114
|
|
|
1115 SD data label or text file column label to use for fingerprints string in output SD or
|
|
|
1116 CSV/TSV text file(s) specified by B<--output>. Default value: I<TopologicalAtomPairsFingerprints>.
|
|
|
1117
|
|
|
1118 =item B<-h, --help>
|
|
|
1119
|
|
|
1120 Print this help message.
|
|
|
1121
|
|
|
1122 =item B<-k, --KeepLargestComponent> I<Yes | No>
|
|
|
1123
|
|
|
1124 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
1125 I<Yes or No>. Default value: I<Yes>.
|
|
|
1126
|
|
|
1127 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
1128 in two different ways: use all connected components or just the largest connected
|
|
|
1129 component. By default, all atoms except for the largest connected component are
|
|
|
1130 deleted before generation of fingerprints.
|
|
|
1131
|
|
|
1132 =item B<--MinDistance> I<number>
|
|
|
1133
|
|
|
1134 Minimum bond distance between atom pairs for generating topological atom pairs. Default value:
|
|
|
1135 I<1>. Valid values: positive integers and less than B<--MaxDistance>.
|
|
|
1136
|
|
|
1137 =item B<--MaxDistance> I<number>
|
|
|
1138
|
|
|
1139 Maximum bond distance between atom pairs for generating topological atom pairs. Default value:
|
|
|
1140 I<10>. Valid values: positive integers and greater than B<--MinDistance>.
|
|
|
1141
|
|
|
1142 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
1143
|
|
|
1144 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
|
|
|
1145 Default value: I<comma>
|
|
|
1146
|
|
|
1147 =item B<--output> I<SD | FP | text | all>
|
|
|
1148
|
|
|
1149 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>.
|
|
|
1150
|
|
|
1151 =item B<-o, --overwrite>
|
|
|
1152
|
|
|
1153 Overwrite existing files.
|
|
|
1154
|
|
|
1155 =item B<-q, --quote> I<Yes | No>
|
|
|
1156
|
|
|
1157 Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
1158 I<Yes or No>. Default value: I<Yes>.
|
|
|
1159
|
|
|
1160 =item B<-r, --root> I<RootName>
|
|
|
1161
|
|
|
1162 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
1163 <SDFileName><TopologicalAtomPairsFP>.<Ext>. The file type determines <Ext> value.
|
|
|
1164 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
|
1165 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
1166
|
|
|
1167 =item B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>
|
|
|
1168
|
|
|
1169 Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
1170 B<--output> option. Possible values: I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
1171 ValuesAndIDsPairsString>. Default value: I<IDsAndValuesString>.
|
|
|
1172
|
|
|
1173 Examples:
|
|
|
1174
|
|
|
1175 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
1176 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
1177 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
1178 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
1179 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
1180 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
|
|
|
1181
|
|
|
1182 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
1183 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
|
|
|
1184 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
|
|
|
1185 C.X3.BO3.H1 4 C.X2.BO2.H2-D1-C.X3.BO4 1 C.X2.BO2.H2-D1-N.X3.BO3 1 C.X2
|
|
|
1186 .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
|
|
|
1187 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...
|
|
|
1188
|
|
|
1189
|
|
|
1190 =item B<-w, --WorkingDir> I<DirName>
|
|
|
1191
|
|
|
1192 Location of working directory. Default value: current directory.
|
|
|
1193
|
|
|
1194 =back
|
|
|
1195
|
|
|
1196 =head1 EXAMPLES
|
|
|
1197
|
|
|
1198 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1199 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1200 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1201
|
|
|
1202 % TopologicalAtomPairsFingerprints.pl -r SampleTAPFP -o Sample.sdf
|
|
|
1203
|
|
|
1204 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1205 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
|
|
|
1206 SampleTAPFP.fpf and SampleTAPFP.csv files containing sequential compound IDs in CSV file along
|
|
|
1207 with fingerprints vector strings data, type:
|
|
|
1208
|
|
|
1209 % TopologicalAtomPairsFingerprints.pl --output all -r SampleTAPFP
|
|
|
1210 -o Sample.sdf
|
|
|
1211
|
|
|
1212 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1213 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1214 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1215
|
|
|
1216 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
1217 -r SampleTAPFP -o Sample.sdf
|
|
|
1218
|
|
|
1219 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1220 10 using E-state types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1221 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1222
|
|
|
1223 % TopologicalAtomPairsFingerprints.pl -a EStateAtomTypes
|
|
|
1224 -r SampleTAPFP -o Sample.sdf
|
|
|
1225
|
|
|
1226 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1227 10 using DREIDING atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1228 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1229
|
|
|
1230 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
1231 -r SampleTAPFP -o Sample.sdf
|
|
|
1232
|
|
|
1233 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1234 10 using functional class atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1235 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1236
|
|
|
1237 % TopologicalAtomPairsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
1238 -r SampleTAPFP -o Sample.sdf
|
|
|
1239
|
|
|
1240 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1241 10 using MMFF94 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1242 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1243
|
|
|
1244 % TopologicalAtomPairsFingerprints.pl -a MMFF94AtomTypes
|
|
|
1245 -r SampleTAPFP -o Sample.sdf
|
|
|
1246
|
|
|
1247 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1248 10 using SLogP atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1249 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1250
|
|
|
1251 % TopologicalAtomPairsFingerprints.pl -a SLogPAtomTypes
|
|
|
1252 -r SampleTAPFP -o Sample.sdf
|
|
|
1253
|
|
|
1254 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1255 10 using SYBYL atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1256 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1257
|
|
|
1258 % TopologicalAtomPairsFingerprints.pl -a SYBYLAtomTypes
|
|
|
1259 -r SampleTAPFP -o Sample.sdf
|
|
|
1260
|
|
|
1261 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1262 10 using TPSA atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1263 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1264
|
|
|
1265 % TopologicalAtomPairsFingerprints.pl -a TPSAAtomTypes
|
|
|
1266 -r SampleTAPFP -o Sample.sdf
|
|
|
1267
|
|
|
1268 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1269 10 using UFF atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1270 file containing sequential compound IDs along with fingerprints vector strings data, type:
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|
|
1271
|
|
|
1272 % TopologicalAtomPairsFingerprints.pl -a UFFAtomTypes
|
|
|
1273 -r SampleTAPFP -o Sample.sdf
|
|
|
1274
|
|
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1275 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1276 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTAPFP.csv
|
|
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1277 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1278
|
|
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1279 % TopologicalAtomPairsFingerprints.pl --VectorStringFormat
|
|
|
1280 IDsAndValuesPairsString -r SampleTAPFP -o Sample.sdf
|
|
|
1281
|
|
|
1282 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1283 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1284 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1285
|
|
|
1286 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1287 --MinDistance 1 --MaxDistance 6 -r SampleTAPFP -o Sample.sdf
|
|
|
1288
|
|
|
1289 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1290 10 using only AS,X atomic invariants atom types in IDsAndValuesString format and create a
|
|
|
1291 SampleTAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
|
|
|
1292 data, type:
|
|
|
1293
|
|
|
1294 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1295 --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6
|
|
|
1296 -r SampleTAPFP -o Sample.sdf
|
|
|
1297
|
|
|
1298 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1299 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1300 file containing compound ID from molecule name line along with fingerprints vector strings
|
|
|
1301 data, type:
|
|
|
1302
|
|
|
1303 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1304 --DataFieldsMode CompoundID -CompoundIDMode MolName
|
|
|
1305 -r SampleTAPFP -o Sample.sdf
|
|
|
1306
|
|
|
1307 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1308 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1309 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
1310 data, type:
|
|
|
1311
|
|
|
1312 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1313 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
|
|
|
1314 Mol_ID -r SampleTAPFP -o Sample.sdf
|
|
|
1315
|
|
|
1316 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1317 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1318 file containing compound ID using combination of molecule name line and an explicit compound
|
|
|
1319 prefix along with fingerprints vector strings data, type:
|
|
|
1320
|
|
|
1321 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1322 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
1323 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTAPFP -o Sample.sdf
|
|
|
1324
|
|
|
1325 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1326 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1327 file containing specific data fields columns along with fingerprints vector strings
|
|
|
1328 data, type:
|
|
|
1329
|
|
|
1330 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1331 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTAPFP
|
|
|
1332 -o Sample.sdf
|
|
|
1333
|
|
|
1334 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1335 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
|
|
|
1336 file containing common data fields columns along with fingerprints vector strings
|
|
|
1337 data, type:
|
|
|
1338
|
|
|
1339 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1340 --DataFieldsMode Common -r SampleTAPFP -o Sample.sdf
|
|
|
1341
|
|
|
1342 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
|
|
|
1343 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
|
|
|
1344 SampleTAPFP.fpf and SampleTAPFP.csv files containing all data fields columns in CSV file along
|
|
|
1345 with fingerprints data, type:
|
|
|
1346
|
|
|
1347 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1348 --DataFieldsMode All --output all -r SampleTAPFP
|
|
|
1349 -o Sample.sdf
|
|
|
1350
|
|
|
1351 =head1 AUTHOR
|
|
|
1352
|
|
|
1353 Manish Sud <msud@san.rr.com>
|
|
|
1354
|
|
|
1355 =head1 SEE ALSO
|
|
|
1356
|
|
|
1357 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
1358 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
|
|
|
1359 PathLengthFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
1360 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
1361
|
|
|
1362 =head1 COPYRIGHT
|
|
|
1363
|
|
|
1364 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1365
|
|
|
1366 This file is part of MayaChemTools.
|
|
|
1367
|
|
|
1368 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1369 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1370 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1371 any later version.
|
|
|
1372
|
|
|
1373 =cut
|
