annotate bin/TopologicalAtomTorsionsFingerprints.pl @ 3:90ea638ce878 draft default tip

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author deepakjadmin
date Wed, 20 Jan 2016 09:11:59 -0500
parents 2abf0d43254d
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1
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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: TopologicalAtomTorsionsFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:22 $
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5 # $Revision: 1.32 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use MoleculeFileIO;
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39 use FileIO::FingerprintsSDFileIO;
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40 use FileIO::FingerprintsTextFileIO;
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41 use FileIO::FingerprintsFPFileIO;
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42 use AtomTypes::AtomicInvariantsAtomTypes;
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43 use AtomTypes::FunctionalClassAtomTypes;
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44 use Fingerprints::TopologicalAtomTorsionsFingerprints;
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45
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46 my($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 GenerateTopologicalAtomTorsionsFingerprints($FileIndex);
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84 }
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85 }
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86 print "\n$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 GenerateTopologicalAtomTorsionsFingerprints {
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97 my($FileIndex) = @_;
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98 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $TopologicalAtomTorsionsFingerprints, $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 $TopologicalAtomTorsionsFingerprints = GenerateMoleculeFingerprints($Molecule);
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124 if (!$TopologicalAtomTorsionsFingerprints) {
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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, $TopologicalAtomTorsionsFingerprints, $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, $TopologicalAtomTorsionsFingerprints, $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 $NewFPSDFileIO->WriteFingerprints($TopologicalAtomTorsionsFingerprints, $CmpdString);
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265 }
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266
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267 if ($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 $NewFPTextFileIO->WriteFingerprints($TopologicalAtomTorsionsFingerprints, $ColValuesRef);
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272 }
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273
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274 if ($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 $NewFPFileIO->WriteFingerprints($TopologicalAtomTorsionsFingerprints, $CompoundID);
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279 }
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280 }
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281
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282 # Generate approriate column labels for FPText output file...
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283 #
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284 sub SetupFPTextFileCoulmnLabels {
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285 my($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($TopologicalAtomTorsionsFingerprints);
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361
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362 if ($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 $TopologicalAtomTorsionsFingerprints = new Fingerprints::TopologicalAtomTorsionsFingerprints('Molecule' => $Molecule, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
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372 SetAtomIdentifierTypeValuesToUse($TopologicalAtomTorsionsFingerprints);
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373
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374 # Generate fingerprints...
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375 $TopologicalAtomTorsionsFingerprints->GenerateFingerprints();
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376
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377 # Make sure fingerprints generation is successful...
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378 if (!$TopologicalAtomTorsionsFingerprints->IsFingerprintsGenerationSuccessful()) {
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379 return undef;
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380 }
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381
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382 return $TopologicalAtomTorsionsFingerprints;
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383 }
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384
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385 # Set atom identifier type to use for generating fingerprints...
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386 #
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387 sub SetAtomIdentifierTypeValuesToUse {
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388 my($TopologicalAtomTorsionsFingerprints) = @_;
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389
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390 if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
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391 $TopologicalAtomTorsionsFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
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392 }
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393 elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
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394 $TopologicalAtomTorsionsFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
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395 }
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diff changeset
396 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
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deepakjadmin
parents:
diff changeset
397 # Nothing to do for now...
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deepakjadmin
parents:
diff changeset
398 }
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deepakjadmin
parents:
diff changeset
399 else {
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deepakjadmin
parents:
diff changeset
400 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
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deepakjadmin
parents:
diff changeset
401 }
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deepakjadmin
parents:
diff changeset
402 }
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deepakjadmin
parents:
diff changeset
403
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deepakjadmin
parents:
diff changeset
404 # Retrieve information about SD files...
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deepakjadmin
parents:
diff changeset
405 #
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deepakjadmin
parents:
diff changeset
406 sub RetrieveSDFilesInfo {
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deepakjadmin
parents:
diff changeset
407 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
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deepakjadmin
parents:
diff changeset
408
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deepakjadmin
parents:
diff changeset
409 %SDFilesInfo = ();
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deepakjadmin
parents:
diff changeset
410 @{$SDFilesInfo{FileOkay}} = ();
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deepakjadmin
parents:
diff changeset
411 @{$SDFilesInfo{OutFileRoot}} = ();
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deepakjadmin
parents:
diff changeset
412 @{$SDFilesInfo{SDOutFileNames}} = ();
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deepakjadmin
parents:
diff changeset
413 @{$SDFilesInfo{FPOutFileNames}} = ();
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deepakjadmin
parents:
diff changeset
414 @{$SDFilesInfo{TextOutFileNames}} = ();
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deepakjadmin
parents:
diff changeset
415 @{$SDFilesInfo{AllDataFieldsRef}} = ();
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deepakjadmin
parents:
diff changeset
416 @{$SDFilesInfo{CommonDataFieldsRef}} = ();
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deepakjadmin
parents:
diff changeset
417
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deepakjadmin
parents:
diff changeset
418 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
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parents:
diff changeset
419 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
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deepakjadmin
parents:
diff changeset
420
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deepakjadmin
parents:
diff changeset
421 FILELIST: for $Index (0 .. $#SDFilesList) {
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deepakjadmin
parents:
diff changeset
422 $SDFile = $SDFilesList[$Index];
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deepakjadmin
parents:
diff changeset
423
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deepakjadmin
parents:
diff changeset
424 $SDFilesInfo{FileOkay}[$Index] = 0;
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deepakjadmin
parents:
diff changeset
425 $SDFilesInfo{OutFileRoot}[$Index] = '';
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deepakjadmin
parents:
diff changeset
426 $SDFilesInfo{SDOutFileNames}[$Index] = '';
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deepakjadmin
parents:
diff changeset
427 $SDFilesInfo{FPOutFileNames}[$Index] = '';
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deepakjadmin
parents:
diff changeset
428 $SDFilesInfo{TextOutFileNames}[$Index] = '';
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deepakjadmin
parents:
diff changeset
429
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deepakjadmin
parents:
diff changeset
430 $SDFile = $SDFilesList[$Index];
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deepakjadmin
parents:
diff changeset
431 if (!(-e $SDFile)) {
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deepakjadmin
parents:
diff changeset
432 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
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deepakjadmin
parents:
diff changeset
433 next FILELIST;
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deepakjadmin
parents:
diff changeset
434 }
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deepakjadmin
parents:
diff changeset
435 if (!CheckFileType($SDFile, "sd sdf")) {
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deepakjadmin
parents:
diff changeset
436 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
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deepakjadmin
parents:
diff changeset
437 next FILELIST;
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deepakjadmin
parents:
diff changeset
438 }
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deepakjadmin
parents:
diff changeset
439
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deepakjadmin
parents:
diff changeset
440 if ($CheckDataField) {
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deepakjadmin
parents:
diff changeset
441 # Make sure data field exists in SD file..
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deepakjadmin
parents:
diff changeset
442 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
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deepakjadmin
parents:
diff changeset
443
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deepakjadmin
parents:
diff changeset
444 @CmpdLines = ();
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deepakjadmin
parents:
diff changeset
445 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
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deepakjadmin
parents:
diff changeset
446 $CmpdString = ReadCmpdString(\*SDFILE);
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deepakjadmin
parents:
diff changeset
447 close SDFILE;
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deepakjadmin
parents:
diff changeset
448 @CmpdLines = split "\n", $CmpdString;
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deepakjadmin
parents:
diff changeset
449 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
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deepakjadmin
parents:
diff changeset
450 $SpecifiedDataField = $OptionsInfo{CompoundID};
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deepakjadmin
parents:
diff changeset
451 if (!exists $DataFieldValues{$SpecifiedDataField}) {
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deepakjadmin
parents:
diff changeset
452 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
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deepakjadmin
parents:
diff changeset
453 next FILELIST;
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deepakjadmin
parents:
diff changeset
454 }
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deepakjadmin
parents:
diff changeset
455 }
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deepakjadmin
parents:
diff changeset
456
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deepakjadmin
parents:
diff changeset
457 $AllDataFieldsRef = '';
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deepakjadmin
parents:
diff changeset
458 $CommonDataFieldsRef = '';
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deepakjadmin
parents:
diff changeset
459 if ($CollectDataFields) {
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deepakjadmin
parents:
diff changeset
460 my($CmpdCount);
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deepakjadmin
parents:
diff changeset
461 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
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deepakjadmin
parents:
diff changeset
462 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
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deepakjadmin
parents:
diff changeset
463 close SDFILE;
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deepakjadmin
parents:
diff changeset
464 }
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deepakjadmin
parents:
diff changeset
465
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deepakjadmin
parents:
diff changeset
466 # Setup output file names...
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deepakjadmin
parents:
diff changeset
467 $FileDir = ""; $FileName = ""; $FileExt = "";
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deepakjadmin
parents:
diff changeset
468 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
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deepakjadmin
parents:
diff changeset
469
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deepakjadmin
parents:
diff changeset
470 $TextOutFileExt = "csv";
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deepakjadmin
parents:
diff changeset
471 if ($Options{outdelim} =~ /^tab$/i) {
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deepakjadmin
parents:
diff changeset
472 $TextOutFileExt = "tsv";
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deepakjadmin
parents:
diff changeset
473 }
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deepakjadmin
parents:
diff changeset
474 $SDOutFileExt = $FileExt;
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deepakjadmin
parents:
diff changeset
475 $FPOutFileExt = "fpf";
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deepakjadmin
parents:
diff changeset
476
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deepakjadmin
parents:
diff changeset
477 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
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deepakjadmin
parents:
diff changeset
478 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
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deepakjadmin
parents:
diff changeset
479 if ($RootFileName && $RootFileExt) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
480 $FileName = $RootFileName;
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deepakjadmin
parents:
diff changeset
481 }
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deepakjadmin
parents:
diff changeset
482 else {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
483 $FileName = $OptionsInfo{OutFileRoot};
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deepakjadmin
parents:
diff changeset
484 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
485 $OutFileRoot = $FileName;
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deepakjadmin
parents:
diff changeset
486 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
487 else {
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deepakjadmin
parents:
diff changeset
488 $OutFileRoot = "${FileName}TopologicalAtomTorsionsFP";
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deepakjadmin
parents:
diff changeset
489 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
490
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deepakjadmin
parents:
diff changeset
491 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
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deepakjadmin
parents:
diff changeset
492 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
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deepakjadmin
parents:
diff changeset
493 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
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deepakjadmin
parents:
diff changeset
494
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deepakjadmin
parents:
diff changeset
495 if ($OptionsInfo{SDOutput}) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
496 if ($SDFile =~ /$NewSDFileName/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
497 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
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deepakjadmin
parents:
diff changeset
498 print "Specify a different name using \"-r --root\" option or use default name.\n";
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deepakjadmin
parents:
diff changeset
499 next FILELIST;
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deepakjadmin
parents:
diff changeset
500 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
501 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
502
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deepakjadmin
parents:
diff changeset
503 if (!$OptionsInfo{OverwriteFiles}) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
504 # Check SD and text outout files...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
505 if ($OptionsInfo{SDOutput}) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
506 if (-e $NewSDFileName) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
507 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
508 next FILELIST;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
509 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
510 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
511 if ($OptionsInfo{FPOutput}) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
512 if (-e $NewFPFileName) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
513 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
514 next FILELIST;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
515 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
516 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
517 if ($OptionsInfo{TextOutput}) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
518 if (-e $NewTextFileName) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
519 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
520 next FILELIST;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
521 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
522 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
523 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
524
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deepakjadmin
parents:
diff changeset
525 $SDFilesInfo{FileOkay}[$Index] = 1;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
526
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
527 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
528 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
529 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
530 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
531
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deepakjadmin
parents:
diff changeset
532 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
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deepakjadmin
parents:
diff changeset
533 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
534 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
535 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
536
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
537 # Process option values...
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deepakjadmin
parents:
diff changeset
538 sub ProcessOptions {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
539 %OptionsInfo = ();
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
540
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
541 ProcessAtomIdentifierTypeOptions();
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
542
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deepakjadmin
parents:
diff changeset
543 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
544
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deepakjadmin
parents:
diff changeset
545 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
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deepakjadmin
parents:
diff changeset
546 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
547 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
548
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
549 my(@SpecifiedDataFields);
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
550 @SpecifiedDataFields = ();
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
551
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
552 @{$OptionsInfo{SpecifiedDataFields}} = ();
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
553 $OptionsInfo{CompoundID} = '';
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
554
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
555 if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
556 if ($Options{compoundidmode} =~ /^DataField$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
557 if (!$Options{compoundid}) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
558 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
559 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
560 $OptionsInfo{CompoundID} = $Options{compoundid};
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
561 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
562 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
563 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
564 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
565 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
566 elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
567 if (!$Options{datafields}) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
568 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
569 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
570 @SpecifiedDataFields = split /\,/, $Options{datafields};
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
571 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
572 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
573
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
574 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
575
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deepakjadmin
parents:
diff changeset
576 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'TopologicalAtomTorsionsFingerprints';
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
577
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
578 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
579
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
580 $OptionsInfo{Output} = $Options{output};
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
581 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
582 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
583 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
584
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
585 $OptionsInfo{OutDelim} = $Options{outdelim};
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
586 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
587
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
588 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
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589 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
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diff changeset
590
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diff changeset
591 $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat};
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592 }
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diff changeset
593
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parents:
diff changeset
594 # Process atom identifier type and related options...
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parents:
diff changeset
595 #
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diff changeset
596 sub ProcessAtomIdentifierTypeOptions {
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597
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diff changeset
598 $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
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parents:
diff changeset
599
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diff changeset
600 if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
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diff changeset
601 ProcessAtomicInvariantsToUseOption();
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diff changeset
602 }
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diff changeset
603 elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
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604 ProcessFunctionalClassesToUse();
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diff changeset
605 }
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606 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
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parents:
diff changeset
607 # Nothing to do for now...
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diff changeset
608 }
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diff changeset
609 else {
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610 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
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611 }
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diff changeset
612 }
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613
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diff changeset
614 # Process specified atomic invariants to use...
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parents:
diff changeset
615 #
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616 sub ProcessAtomicInvariantsToUseOption {
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617 my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
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618
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619 @{$OptionsInfo{AtomicInvariantsToUse}} = ();
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620 if (IsEmpty($Options{atomicinvariantstouse})) {
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621 die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
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622 }
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623 $AtomSymbolSpecified = 0;
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624 @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
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diff changeset
625 for $AtomicInvariant (@AtomicInvariantsWords) {
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626 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
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diff changeset
627 die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
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628 }
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629 if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
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diff changeset
630 $AtomSymbolSpecified = 1;
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parents:
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631 }
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632 push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
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633 }
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parents:
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634 if (!$AtomSymbolSpecified) {
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parents:
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635 die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
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parents:
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636 }
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637 }
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638
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parents:
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639 # Process specified functional classes invariants to use...
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parents:
diff changeset
640 #
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parents:
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641 sub ProcessFunctionalClassesToUse {
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642 my($FunctionalClass, @FunctionalClassesToUseWords);
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parents:
diff changeset
643
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parents:
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644 @{$OptionsInfo{FunctionalClassesToUse}} = ();
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parents:
diff changeset
645 if (IsEmpty($Options{functionalclassestouse})) {
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parents:
diff changeset
646 die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
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parents:
diff changeset
647 }
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parents:
diff changeset
648 @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
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parents:
diff changeset
649 for $FunctionalClass (@FunctionalClassesToUseWords) {
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parents:
diff changeset
650 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
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parents:
diff changeset
651 die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
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parents:
diff changeset
652 }
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parents:
diff changeset
653 push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
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parents:
diff changeset
654 }
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parents:
diff changeset
655 }
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parents:
diff changeset
656
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parents:
diff changeset
657 # Setup script usage and retrieve command line arguments specified using various options...
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parents:
diff changeset
658 sub SetupScriptUsage {
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parents:
diff changeset
659
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parents:
diff changeset
660 # Retrieve all the options...
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parents:
diff changeset
661 %Options = ();
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diff changeset
662
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663 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
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parents:
diff changeset
664
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665 $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
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diff changeset
666 $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC';
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diff changeset
667
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diff changeset
668 $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
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parents:
diff changeset
669
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diff changeset
670 $Options{compoundidmode} = 'LabelPrefix';
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diff changeset
671 $Options{compoundidlabel} = 'CompoundID';
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diff changeset
672 $Options{datafieldsmode} = 'CompoundID';
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parents:
diff changeset
673
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diff changeset
674 $Options{filter} = 'Yes';
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parents:
diff changeset
675
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diff changeset
676 $Options{keeplargestcomponent} = 'Yes';
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parents:
diff changeset
677
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diff changeset
678 $Options{output} = 'text';
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parents:
diff changeset
679 $Options{outdelim} = 'comma';
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parents:
diff changeset
680 $Options{quote} = 'yes';
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parents:
diff changeset
681
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parents:
diff changeset
682 $Options{vectorstringformat} = 'IDsAndValuesString';
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parents:
diff changeset
683
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parents:
diff changeset
684 if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "vectorstringformat|v=s", "workingdir|w=s")) {
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parents:
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685 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
2abf0d43254d Uploaded
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parents:
diff changeset
686 }
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parents:
diff changeset
687 if ($Options{workingdir}) {
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parents:
diff changeset
688 if (! -d $Options{workingdir}) {
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deepakjadmin
parents:
diff changeset
689 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
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deepakjadmin
parents:
diff changeset
690 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
691 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
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deepakjadmin
parents:
diff changeset
692 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
693 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
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parents:
diff changeset
694 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
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parents:
diff changeset
695 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
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parents:
diff changeset
696 }
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parents:
diff changeset
697 if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
698 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
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parents:
diff changeset
699 }
2abf0d43254d Uploaded
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parents:
diff changeset
700 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
701 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
2abf0d43254d Uploaded
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parents:
diff changeset
702 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
703 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
704 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
2abf0d43254d Uploaded
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parents:
diff changeset
705 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
706 if ($Options{filter} !~ /^(Yes|No)$/i) {
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deepakjadmin
parents:
diff changeset
707 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
708 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
709 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
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deepakjadmin
parents:
diff changeset
710 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
711 }
2abf0d43254d Uploaded
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parents:
diff changeset
712 if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
713 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
714 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
715 if ($Options{quote} !~ /^(Yes|No)$/i) {
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deepakjadmin
parents:
diff changeset
716 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
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parents:
diff changeset
717 }
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
718 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
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deepakjadmin
parents:
diff changeset
719 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
2abf0d43254d Uploaded
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parents:
diff changeset
720 }
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parents:
diff changeset
721 if ($Options{vectorstringformat} !~ /^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
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deepakjadmin
parents:
diff changeset
722 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
723 }
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deepakjadmin
parents:
diff changeset
724 }
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deepakjadmin
parents:
diff changeset
725
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deepakjadmin
parents:
diff changeset
726 __END__
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deepakjadmin
parents:
diff changeset
727
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deepakjadmin
parents:
diff changeset
728 =head1 NAME
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deepakjadmin
parents:
diff changeset
729
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deepakjadmin
parents:
diff changeset
730 TopologicalAtomTorsionsFingerprints.pl - Generate topological atom torsions fingerprints for SD files
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
731
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deepakjadmin
parents:
diff changeset
732 =head1 SYNOPSIS
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
733
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deepakjadmin
parents:
diff changeset
734 TopologicalAtomTorsionsFingerprints.pl SDFile(s)...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
735
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deepakjadmin
parents:
diff changeset
736 TopologicalAtomTorsionsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
737 [B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes>]
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deepakjadmin
parents:
diff changeset
738 [B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">]
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
739 [B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
740 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
741 [B<--CompoundIDMode>] [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">]
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
742 [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] [B<-f, --Filter> I<Yes | No>]
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deepakjadmin
parents:
diff changeset
743 [B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>]
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deepakjadmin
parents:
diff changeset
744 [B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD | FP | text | all>] [B<-o, --overwrite>]
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
745 [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] [B<-v, --VectorStringFormat>]
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
746 [B<-w, --WorkingDir> dirname] SDFile(s)...
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deepakjadmin
parents:
diff changeset
747
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deepakjadmin
parents:
diff changeset
748 =head1 DESCRIPTION
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deepakjadmin
parents:
diff changeset
749
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deepakjadmin
parents:
diff changeset
750 Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for I<SDFile(s)> and create
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
751 appropriate SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
752 molecular fingerprints.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
753
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
754 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
755 and I<.sd>. All other file names are ignored. All the SD files in a current directory
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
756 can be specified either by I<*.sdf> or the current directory name.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
757
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deepakjadmin
parents:
diff changeset
758 The current release of MayaChemTools supports generation of topological atom torsions
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
759 fingerprints corresponding to following B<-a, --AtomIdentifierTypes>:
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deepakjadmin
parents:
diff changeset
760
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deepakjadmin
parents:
diff changeset
761 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
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deepakjadmin
parents:
diff changeset
762 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
763 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
764
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
765 Based on the values specified for B<-a, --AtomIdentifierType> and B<--AtomicInvariantsToUse>,
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
766 initial atom types are assigned to all non-hydrogen atoms in a molecule. All unique atom torsions
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
767 are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
768
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
769 <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
770
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
771 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
772
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
773 where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
774
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
775 The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
776 topological atom torsions fingerprints of the molecule.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
777
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
778 Example of I<SD> file containing topological atom torsions fingerprints string data:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
779
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
780 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
781 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
782 $$$$
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
783 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
784 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
785 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
786 41 44 0 0 0 0 0 0 0 0999 V2000
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
787 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
788 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
789 2 3 1 0 0 0 0
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
790 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
791 M END
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
792 > <CmpdID>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
793 Cmpd1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
794
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
795 > <TopologicalAtomTorsionsFingerprints>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
796 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
797 ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
798 X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
799 2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
800 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
801
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
802 $$$$
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
803 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
804 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
805
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
806 Example of I<FP> file containing topological atom torsions fingerprints string data:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
807
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
808 #
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
809 # Package = MayaChemTools 7.4
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
810 # Release Date = Oct 21, 2010
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
811 #
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
812 # TimeStamp = Fri Mar 11 15:17:20 2011
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
813 #
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
814 # FingerprintsStringType = FingerprintsVector
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
815 #
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
816 # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
817 # VectorStringFormat = IDsAndValuesString
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
818 # VectorValuesType = NumericalValues
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
819 #
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
820 Cmpd1 33;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.X3.BO4...;2 2 1 1 2 2 ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
821 Cmpd2 23;C.X1.BO1.H3-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2...;2 2 1 5 ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
822 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
823 ... ..
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
824
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
825 Example of CSV I<Text> file containing topological atom torsions fingerprints string data:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
826
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
827 "CompoundID","TopologicalAtomTorsionsFingerprints"
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
828 "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
829 mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
830 X3.BO4-C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
831 .X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3....;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
832 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
833 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
834 ... ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
835
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
836 The current release of MayaChemTools generates the following types of topological atom torsions
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
837 fingerprints vector strings:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
838
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
839 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
840 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
841 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
842 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
843 ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
844
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
845 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
846 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
847 .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
848 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
849 O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
850 O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
851
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
852 FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
853 calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
854 _R-C_3 C_2-C_R-C_R-C_R C_2-C_R-C_R-N_R C_2-N_3-C_R-C_R C_3-C_3-C_2-O_2
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
855 C_3-C_3-C_2-O_3 C_3-C_3-C_3-C_3 C_3-C_3-C_3-N_R C_3-C_3-C_3-O_3 C_...;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
856 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
857
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
858 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
859 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
860 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
861 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
862 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
863
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
864 FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
865 ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
866 Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
867 -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
868 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
869
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
870 FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
871 lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
872 B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
873 A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
874 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
875 1 1 2 1 1 3 1 3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
876
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
877 FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
878 Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
879 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
880 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
881 C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
882 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
883
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
884 FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
885 Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
886 -C.ar-C.ar-C.3 1 C.2-C.ar-C.ar-C.ar 2 C.2-C.ar-C.ar-N.ar 1 C.2-N.am-C.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
887 ar-C.ar 2 C.3-C.3-C.2-O.co2 2 C.3-C.3-C.3-C.3 3 C.3-C.3-C.3-N.ar 1 C.3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
888 -C.3-C.3-O.3 3 C.3-C.3-C.ar-C.ar 2 C.3-C.3-C.ar-N.ar 2 C.3-C.3-N.ar-C.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
889 ar 2 C.3-C.ar-C.ar-C.ar 1 C.3-C.ar-N.ar-C.3 1 C.3-C.ar-N.ar-C.ar 1 ...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
890
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
891 FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
892 lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
893 None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
894 None-None 44 None-None-None-O3 3 None-None-None-O4 5
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
895
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
896 FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
897 lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
898 _R-C_R-C_3 1 C_2-C_R-C_R-C_R 2 C_2-C_R-C_R-N_R 1 C_2-N_3-C_R-C_R 2 C_3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
899 -C_3-C_2-O_2 1 C_3-C_3-C_2-O_3 1 C_3-C_3-C_3-C_3 3 C_3-C_3-C_3-N_R 1 C
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
900 _3-C_3-C_3-O_3 3 C_3-C_3-C_R-C_R 2 C_3-C_3-C_R-N_R 2 C_3-C_3-N_R-C_R 2
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
901 C_3-C_R-C_R-C_R 1 C_3-C_R-N_R-C_3 1 C_3-C_R-N_R-C_R 1 C_3-N_R-C_R-...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
902
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
903 =head1 OPTIONS
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
904
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
905 =over 4
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
906
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
907 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
908
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
909 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
910 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
911 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
912 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
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deepakjadmin
parents:
diff changeset
913
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deepakjadmin
parents:
diff changeset
914 The supported aromaticity model names along with model specific control parameters
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deepakjadmin
parents:
diff changeset
915 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
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deepakjadmin
parents:
diff changeset
916 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
917 this file during class instantiation and makes it available to method B<DetectAromaticity>
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deepakjadmin
parents:
diff changeset
918 for detecting aromaticity corresponding to a specific model.
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deepakjadmin
parents:
diff changeset
919
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parents:
diff changeset
920 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
921
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parents:
diff changeset
922 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
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deepakjadmin
parents:
diff changeset
923 atoms during calculation of topological atom torsions fingerprints. Possible values in the current
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
924 release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
925 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
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parents:
diff changeset
926 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
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parents:
diff changeset
927
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parents:
diff changeset
928 =item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">
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parents:
diff changeset
929
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parents:
diff changeset
930 This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType>
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deepakjadmin
parents:
diff changeset
931 option. It's a list of comma separated valid atomic invariant atom types.
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deepakjadmin
parents:
diff changeset
932
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parents:
diff changeset
933 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB,
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deepakjadmin
parents:
diff changeset
934 H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>.
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deepakjadmin
parents:
diff changeset
935
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parents:
diff changeset
936 The atomic invariants abbreviations correspond to:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
937
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parents:
diff changeset
938 AS = Atom symbol corresponding to element symbol
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
939
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parents:
diff changeset
940 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
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parents:
diff changeset
941 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
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deepakjadmin
parents:
diff changeset
942 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
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deepakjadmin
parents:
diff changeset
943 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
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deepakjadmin
parents:
diff changeset
944 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
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deepakjadmin
parents:
diff changeset
945 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
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deepakjadmin
parents:
diff changeset
946 H<n> = Number of implicit and explicit hydrogens for atom
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deepakjadmin
parents:
diff changeset
947 Ar = Aromatic annotation indicating whether atom is aromatic
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deepakjadmin
parents:
diff changeset
948 RA = Ring atom annotation indicating whether atom is a ring
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deepakjadmin
parents:
diff changeset
949 FC<+n/-n> = Formal charge assigned to atom
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parents:
diff changeset
950 MN<n> = Mass number indicating isotope other than most abundant isotope
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parents:
diff changeset
951 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
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parents:
diff changeset
952 3 (triplet)
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parents:
diff changeset
953
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parents:
diff changeset
954 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
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parents:
diff changeset
955
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parents:
diff changeset
956 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
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parents:
diff changeset
957
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parents:
diff changeset
958 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
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parents:
diff changeset
959 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
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deepakjadmin
parents:
diff changeset
960
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deepakjadmin
parents:
diff changeset
961 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
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deepakjadmin
parents:
diff changeset
962 are also allowed:
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diff changeset
963
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parents:
diff changeset
964 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
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parents:
diff changeset
965 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
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parents:
diff changeset
966 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
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parents:
diff changeset
967 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
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parents:
diff changeset
968 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
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parents:
diff changeset
969 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
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parents:
diff changeset
970 H : NumOfImplicitAndExplicitHydrogens
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parents:
diff changeset
971 Ar : Aromatic
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parents:
diff changeset
972 RA : RingAtom
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parents:
diff changeset
973 FC : FormalCharge
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parents:
diff changeset
974 MN : MassNumber
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parents:
diff changeset
975 SM : SpinMultiplicity
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parents:
diff changeset
976
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parents:
diff changeset
977 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
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deepakjadmin
parents:
diff changeset
978 atom types.
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diff changeset
979
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parents:
diff changeset
980 =item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">
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deepakjadmin
parents:
diff changeset
981
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parents:
diff changeset
982 This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType>
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deepakjadmin
parents:
diff changeset
983 option. It's a list of comma separated valid functional classes.
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deepakjadmin
parents:
diff changeset
984
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parents:
diff changeset
985 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
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deepakjadmin
parents:
diff changeset
986 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
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deepakjadmin
parents:
diff changeset
987
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deepakjadmin
parents:
diff changeset
988 The functional class abbreviations correspond to:
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deepakjadmin
parents:
diff changeset
989
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parents:
diff changeset
990 HBD: HydrogenBondDonor
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parents:
diff changeset
991 HBA: HydrogenBondAcceptor
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parents:
diff changeset
992 PI : PositivelyIonizable
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deepakjadmin
parents:
diff changeset
993 NI : NegativelyIonizable
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parents:
diff changeset
994 Ar : Aromatic
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diff changeset
995 Hal : Halogen
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parents:
diff changeset
996 H : Hydrophobic
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diff changeset
997 RA : RingAtom
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parents:
diff changeset
998 CA : ChainAtom
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deepakjadmin
parents:
diff changeset
999
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deepakjadmin
parents:
diff changeset
1000 Functional class atom type specification for an atom corresponds to:
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deepakjadmin
parents:
diff changeset
1001
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parents:
diff changeset
1002 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
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deepakjadmin
parents:
diff changeset
1003
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deepakjadmin
parents:
diff changeset
1004 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
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deepakjadmin
parents:
diff changeset
1005 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
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parents:
diff changeset
1006
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parents:
diff changeset
1007 HydrogenBondDonor: NH, NH2, OH
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deepakjadmin
parents:
diff changeset
1008 HydrogenBondAcceptor: N[!H], O
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deepakjadmin
parents:
diff changeset
1009 PositivelyIonizable: +, NH2
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deepakjadmin
parents:
diff changeset
1010 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
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deepakjadmin
parents:
diff changeset
1011
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parents:
diff changeset
1012 =item B<--CompoundID> I<DataFieldName or LabelPrefixString>
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deepakjadmin
parents:
diff changeset
1013
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parents:
diff changeset
1014 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
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deepakjadmin
parents:
diff changeset
1015
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deepakjadmin
parents:
diff changeset
1016 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
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deepakjadmin
parents:
diff changeset
1017 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
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deepakjadmin
parents:
diff changeset
1018 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1019 look like Cmpd<Number>.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1020
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deepakjadmin
parents:
diff changeset
1021 Examples for I<DataField> value of B<--CompoundIDMode>:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1022
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deepakjadmin
parents:
diff changeset
1023 MolID
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1024 ExtReg
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1025
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deepakjadmin
parents:
diff changeset
1026 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1027
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deepakjadmin
parents:
diff changeset
1028 Compound
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deepakjadmin
parents:
diff changeset
1029
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deepakjadmin
parents:
diff changeset
1030 The value specified above generates compound IDs which correspond to Compound<Number>
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deepakjadmin
parents:
diff changeset
1031 instead of default value of Cmpd<Number>.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1032
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deepakjadmin
parents:
diff changeset
1033 =item B<--CompoundIDLabel> I<text>
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deepakjadmin
parents:
diff changeset
1034
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deepakjadmin
parents:
diff changeset
1035 Specify compound ID column label for CSV/TSV text file(s) used during I<CompoundID> value
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1036 of B<--DataFieldsMode> option. Default value: I<CompoundID>.
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deepakjadmin
parents:
diff changeset
1037
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deepakjadmin
parents:
diff changeset
1038 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
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deepakjadmin
parents:
diff changeset
1039
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deepakjadmin
parents:
diff changeset
1040 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1041 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1042 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination
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deepakjadmin
parents:
diff changeset
1043 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
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deepakjadmin
parents:
diff changeset
1044
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deepakjadmin
parents:
diff changeset
1045 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
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deepakjadmin
parents:
diff changeset
1046 Default value: I<LabelPrefix>.
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deepakjadmin
parents:
diff changeset
1047
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deepakjadmin
parents:
diff changeset
1048 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
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deepakjadmin
parents:
diff changeset
1049 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
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deepakjadmin
parents:
diff changeset
1050 values are replaced with sequential compound IDs.
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deepakjadmin
parents:
diff changeset
1051
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deepakjadmin
parents:
diff changeset
1052 This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
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deepakjadmin
parents:
diff changeset
1053
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parents:
diff changeset
1054 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,...">
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deepakjadmin
parents:
diff changeset
1055
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deepakjadmin
parents:
diff changeset
1056 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
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deepakjadmin
parents:
diff changeset
1057 with generated fingerprints for I<text | all> values of B<--output> option.
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deepakjadmin
parents:
diff changeset
1058
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deepakjadmin
parents:
diff changeset
1059 This is only used for I<Specify> value of B<--DataFieldsMode> option.
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deepakjadmin
parents:
diff changeset
1060
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deepakjadmin
parents:
diff changeset
1061 Examples:
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deepakjadmin
parents:
diff changeset
1062
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deepakjadmin
parents:
diff changeset
1063 Extreg
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deepakjadmin
parents:
diff changeset
1064 MolID,CompoundName
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deepakjadmin
parents:
diff changeset
1065
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deepakjadmin
parents:
diff changeset
1066 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
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deepakjadmin
parents:
diff changeset
1067
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deepakjadmin
parents:
diff changeset
1068 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
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deepakjadmin
parents:
diff changeset
1069 with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD
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deepakjadmin
parents:
diff changeset
1070 data field; transfer SD data files common to all compounds; extract specified data fields;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1071 generate a compound ID using molname line, a compound prefix, or a combination of both.
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deepakjadmin
parents:
diff changeset
1072 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
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deepakjadmin
parents:
diff changeset
1073
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deepakjadmin
parents:
diff changeset
1074 =item B<-f, --Filter> I<Yes | No>
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deepakjadmin
parents:
diff changeset
1075
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deepakjadmin
parents:
diff changeset
1076 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
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deepakjadmin
parents:
diff changeset
1077 Default value: I<Yes>.
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deepakjadmin
parents:
diff changeset
1078
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deepakjadmin
parents:
diff changeset
1079 By default, compound data is checked before calculating fingerprints and compounds containing
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deepakjadmin
parents:
diff changeset
1080 atom data corresponding to non-element symbols or no atom data are ignored.
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deepakjadmin
parents:
diff changeset
1081
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deepakjadmin
parents:
diff changeset
1082 =item B<--FingerprintsLabel> I<text>
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deepakjadmin
parents:
diff changeset
1083
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deepakjadmin
parents:
diff changeset
1084 SD data label or text file column label to use for fingerprints string in output SD or
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deepakjadmin
parents:
diff changeset
1085 CSV/TSV text file(s) specified by B<--output>. Default value: I<TopologicalAtomTorsionsFingerprints>.
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deepakjadmin
parents:
diff changeset
1086
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deepakjadmin
parents:
diff changeset
1087 =item B<-h, --help>
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deepakjadmin
parents:
diff changeset
1088
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deepakjadmin
parents:
diff changeset
1089 Print this help message.
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deepakjadmin
parents:
diff changeset
1090
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deepakjadmin
parents:
diff changeset
1091 =item B<-k, --KeepLargestComponent> I<Yes | No>
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deepakjadmin
parents:
diff changeset
1092
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deepakjadmin
parents:
diff changeset
1093 Generate fingerprints for only the largest component in molecule. Possible values:
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deepakjadmin
parents:
diff changeset
1094 I<Yes or No>. Default value: I<Yes>.
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deepakjadmin
parents:
diff changeset
1095
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deepakjadmin
parents:
diff changeset
1096 For molecules containing multiple connected components, fingerprints can be generated
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deepakjadmin
parents:
diff changeset
1097 in two different ways: use all connected components or just the largest connected
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deepakjadmin
parents:
diff changeset
1098 component. By default, all atoms except for the largest connected component are
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deepakjadmin
parents:
diff changeset
1099 deleted before generation of fingerprints.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1100
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1101 =item B<--OutDelim> I<comma | tab | semicolon>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1102
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1103 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1104 Default value: I<comma>.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1105
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1106 =item B<--output> I<SD | FP | text | all>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1107
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1108 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1109
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1110 =item B<-o, --overwrite>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1111
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1112 Overwrite existing files.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1113
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1114 =item B<-q, --quote> I<Yes | No>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1115
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1116 Put quote around column values in output CSV/TSV text file(s). Possible values:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1117 I<Yes or No>. Default value: I<Yes>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1118
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1119 =item B<-r, --root> I<RootName>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1120
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1121 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1122 <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The file type determines <Ext> value.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1123 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1124 delimited text files, respectively.This option is ignored for multiple input files.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1125
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1126 =item B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1127
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1128 Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1129 B<--output> option. Possible values: I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1130 ValuesAndIDsPairsString>. Defaultvalue: I<IDsAndValuesString>.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1131
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1132 Examples:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1133
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1134 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1135 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1136 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1137 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1138 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1139
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1140 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1141 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1142 .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1143 2-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 1 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.B
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1144 O3.H1-O.X1.BO1.H1 1 C.X2.BO2.H2-C.X2.BO2.H2-N.X3.BO3-C.X3.BO4 2 C.X2.B
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1145 O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1146
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1147 =item B<-w, --WorkingDir> I<DirName>
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1148
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1149 Location of working directory. Default value: current directory.
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1150
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1151 =back
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1152
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1153 =head1 EXAMPLES
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1154
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1155 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1156 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1157 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1158
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1159 % TopologicalAtomTorsionsFingerprints.pl -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1160
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1161 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1162 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1163 files containing sequential compound IDs in CSV file along with fingerprints vector strings
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1164 data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1165
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1166 % TopologicalAtomTorsionsFingerprints.pl --output all -r SampleTATFP
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1167 -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1168
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1169 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1170 IDsAndValuesPairsString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1171 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1172
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1173 % TopologicalAtomTorsionsFingerprints.pl --VectorStringFormat
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1174 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1175
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1176 To generate topological atom torsions fingerprints using DREIDING atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1177 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1178 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1179
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1180 % TopologicalAtomTorsionsFingerprints.pl -a DREIDINGAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1181 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1182
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1183 To generate topological atom torsions fingerprints using E-state atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1184 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1185 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1186
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1187 % TopologicalAtomTorsionsFingerprints.pl -a EStateAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1188 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1189
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1190 To generate topological atom torsions fingerprints using functional class atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1191 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1192 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1193
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1194 % TopologicalAtomTorsionsFingerprints.pl -a FunctionalClassAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1195 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1196
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1197 To generate topological atom torsions fingerprints using MMFF94 atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1198 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1199 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1200
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1201 % TopologicalAtomTorsionsFingerprints.pl -a MMFF94AtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1202 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1203
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1204 To generate topological atom torsions fingerprints using SLogP atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1205 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1206 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1207
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1208 % TopologicalAtomTorsionsFingerprints.pl -a SLogPAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1209 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1210
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1211 To generate topological atom torsions fingerprints using SYBYL atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1212 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1213 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1214
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1215 % TopologicalAtomTorsionsFingerprints.pl -a SYBYLAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1216 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1217
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1218 To generate topological atom torsions fingerprints using TPSA atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1219 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1220 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1221
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1222 % TopologicalAtomTorsionsFingerprints.pl -a TPSAAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1223 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1224
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1225 To generate topological atom torsions fingerprints using UFF atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1226 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1227 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1228
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1229 % TopologicalAtomTorsionsFingerprints.pl -a UFFAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1230 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1231
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1232 To generate topological atom torsions fingerprints using only AS,X atomic invariants atom
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1233 types in IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1234 compound IDs along with fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1235
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1236 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1237 --AtomicInvariantsToUse "AS,X" -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1238
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1239 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1240 IDsAndValuesString format and create a SampleTATFP.csv file containing compoundID
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1241 from molecule name line along with fingerprints vector strings, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1242
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1243 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1244 --DataFieldsMode CompoundID -CompoundIDMode MolName
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1245 -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1246
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1247 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1248 IDsAndValuesString format and create a SampleTATFP.csv file containing compound IDs
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1249 using specified data field along with fingerprints vector strings, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1250
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1251 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1252 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1253 Mol_ID -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1254
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1255 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1256 IDsAndValuesString format and create a SampleTATFP.csv file containing compound ID
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1257 using combination of molecule name line and an explicit compound prefix along with
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1258 fingerprints vector strings data, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1259
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1260 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1261 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1262 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1263
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1264 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1265 IDsAndValuesString format and create a SampleTATFP.csv file containing specific data
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1266 fields columns along with fingerprints vector strings, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1267
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1268 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1269 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1270 -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1271
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1272 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1273 IDsAndValuesString format and create a SampleTATFP.csv file containing common
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1274 data fields columns along with fingerprints vector strings, type:
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1275
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1276 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1277 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1278
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1279 To generate topological atom torsions fingerprints using atomic invariants atom types in
2abf0d43254d Uploaded
deepakjadmin
parents:
diff changeset
1280 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
2abf0d43254d Uploaded
deepakjadmin
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1281 files containing all data fields columns in CSV file along with fingerprints data, type:
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1282
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1283 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
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1284 --DataFieldsMode All --output all -r SampleTATFP
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1285 -o Sample.sdf
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1286
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1287
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1288 =head1 AUTHOR
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1289
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1290 Manish Sud <msud@san.rr.com>
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1291
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1292 =head1 SEE ALSO
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1293
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1294 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
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1295 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
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1296 PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl,
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1297 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
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1298
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1299 =head1 COPYRIGHT
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1300
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1301 Copyright (C) 2015 Manish Sud. All rights reserved.
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1302
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1303 This file is part of MayaChemTools.
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1304
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1305 MayaChemTools is free software; you can redistribute it and/or modify it under
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1306 the terms of the GNU Lesser General Public License as published by the Free
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1307 Software Foundation; either version 3 of the License, or (at your option)
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1308 any later version.
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1309
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1310 =cut