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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: PathLengthFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:20 $
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5 # $Revision: 1.50 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use MoleculeFileIO;
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39 use FileIO::FingerprintsSDFileIO;
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40 use FileIO::FingerprintsTextFileIO;
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41 use FileIO::FingerprintsFPFileIO;
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42 use AtomTypes::AtomicInvariantsAtomTypes;
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43 use AtomTypes::FunctionalClassAtomTypes;
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44 use Fingerprints::PathLengthFingerprints;
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45
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46 my($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 GeneratePathLengthFingerprints($FileIndex);
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84 }
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85 }
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86 print "\n$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 GeneratePathLengthFingerprints {
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97 my($FileIndex) = @_;
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98 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $PathLengthFingerprints, $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 $PathLengthFingerprints = GenerateMoleculeFingerprints($Molecule);
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124 if (!$PathLengthFingerprints) {
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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, $PathLengthFingerprints, $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, $NewFPFileIO) = (undef) x 3;
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216
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217 # Setup common parameters for fingerprints file IO objects...
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218 #
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219 %FingerprintsFileIOParams = ();
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220 if ($OptionsInfo{Mode} =~ /^PathLengthBits$/i) {
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221 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder});
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222 }
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223 elsif ($OptionsInfo{Mode} =~ /^PathLengthCount$/i) {
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224 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
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225 }
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226
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227 if ($OptionsInfo{SDOutput}) {
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228 $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
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229 print "Generating SD file $NewFPSDFile...\n";
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230 $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
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231 $NewFPSDFileIO->Open();
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232 }
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233
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234 if ($OptionsInfo{FPOutput}) {
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235 $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
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236 print "Generating FP file $NewFPFile...\n";
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237 $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
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238 $NewFPFileIO->Open();
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239 }
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240
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241 if ($OptionsInfo{TextOutput}) {
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242 my($ColLabelsRef);
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243
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244 $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
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245 $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
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246
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247 print "Generating text file $NewFPTextFile...\n";
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248 $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
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249 $NewFPTextFileIO->Open();
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250 }
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251
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252 return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
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253 }
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254
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255 # Write fingerpritns and other data to appropriate output files...
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256 #
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257 sub WriteDataToOutputFiles {
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258 my($FileIndex, $CmpdCount, $Molecule, $PathLengthFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
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259 my($DataFieldLabelAndValuesRef);
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260
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261 $DataFieldLabelAndValuesRef = undef;
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262 if ($NewFPTextFileIO || $NewFPFileIO) {
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263 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
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264 }
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265
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266 if ($NewFPSDFileIO) {
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267 my($CmpdString);
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268
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269 $CmpdString = $Molecule->GetInputMoleculeString();
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270 $NewFPSDFileIO->WriteFingerprints($PathLengthFingerprints, $CmpdString);
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271 }
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272
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273 if ($NewFPTextFileIO) {
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274 my($ColValuesRef);
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275
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276 $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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277 $NewFPTextFileIO->WriteFingerprints($PathLengthFingerprints, $ColValuesRef);
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278 }
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279
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280 if ($NewFPFileIO) {
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281 my($CompoundID);
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282
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283 $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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284 $NewFPFileIO->WriteFingerprints($PathLengthFingerprints, $CompoundID);
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285 }
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286 }
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287
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288 # Generate approriate column labels for FPText output file...
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289 #
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290 sub SetupFPTextFileCoulmnLabels {
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291 my($FileIndex) = @_;
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292 my($Line, @ColLabels);
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293
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294 @ColLabels = ();
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295 if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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296 push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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297 }
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298 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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299 push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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300 }
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301 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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302 push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}};
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303 }
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304 elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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305 push @ColLabels, $OptionsInfo{CompoundIDLabel};
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306 }
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307 # Add fingerprints label...
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308 push @ColLabels, $OptionsInfo{FingerprintsLabel};
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309
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310 return \@ColLabels;
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311 }
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312
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313 # Generate column values FPText output file..
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314 #
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315 sub SetupFPTextFileCoulmnValues {
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316 my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
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317 my(@ColValues);
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318
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319 @ColValues = ();
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320 if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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321 push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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322 }
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323 elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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324 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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325 }
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326 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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327 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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328 }
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329 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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330 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
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331 }
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332
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333 return \@ColValues;
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334 }
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335
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336 # Generate compound ID for FP and FPText output files..
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337 #
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338 sub SetupCmpdIDForOutputFiles {
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339 my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
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340 my($CmpdID);
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341
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342 $CmpdID = '';
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343 if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
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344 my($MolName);
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345 $MolName = $Molecule->GetName();
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346 $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
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347 }
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348 elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
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349 $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
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350 }
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351 elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
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352 my($SpecifiedDataField);
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353 $SpecifiedDataField = $OptionsInfo{CompoundID};
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354 $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
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355 }
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356 elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
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357 $CmpdID = $Molecule->GetName();
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358 }
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359 return $CmpdID;
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360 }
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361
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362 # Generate fingerprints for molecule...
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363 #
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364 sub GenerateMoleculeFingerprints {
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365 my($Molecule) = @_;
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366 my($PathLengthFingerprints);
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367
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368 if ($OptionsInfo{KeepLargestComponent}) {
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369 $Molecule->KeepLargestComponent();
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370 }
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371 if ($OptionsInfo{IgnoreHydrogens}) {
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372 $Molecule->DeleteHydrogens();
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373 }
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374
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375 if ($OptionsInfo{DetectAromaticity}) {
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376 if (!$Molecule->DetectRings()) {
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|
|
377 return undef;
|
|
|
378 }
|
|
|
379 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
|
|
|
380 $Molecule->DetectAromaticity();
|
|
|
381 }
|
|
|
382
|
|
|
383 $PathLengthFingerprints = undef;
|
|
|
384 if ($OptionsInfo{Mode} =~ /^PathLengthBits$/i) {
|
|
|
385 $PathLengthFingerprints = GeneratePathLengthBitsFingerprints($Molecule);
|
|
|
386 }
|
|
|
387 elsif ($OptionsInfo{Mode} =~ /^PathLengthCount$/i) {
|
|
|
388 $PathLengthFingerprints = GeneratePathLengthCountFingerprints($Molecule);
|
|
|
389 }
|
|
|
390 else {
|
|
|
391 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n";
|
|
|
392 }
|
|
|
393
|
|
|
394 return $PathLengthFingerprints;
|
|
|
395 }
|
|
|
396
|
|
|
397 # Generate pathlength bits finerprints for molecule...
|
|
|
398 #
|
|
|
399 sub GeneratePathLengthBitsFingerprints {
|
|
|
400 my($Molecule) = @_;
|
|
|
401 my($PathLengthFingerprints);
|
|
|
402
|
|
|
403 $PathLengthFingerprints = new Fingerprints::PathLengthFingerprints('Molecule' => $Molecule, 'Type' => 'PathLengthBits', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'NumOfBitsToSetPerPath' => $OptionsInfo{NumOfBitsToSetPerPath}, 'Size' => $OptionsInfo{Size}, 'MinLength' => $OptionsInfo{MinPathLength}, 'MaxLength' => $OptionsInfo{MaxPathLength}, 'AllowRings' => $OptionsInfo{AllowRings}, 'AllowSharedBonds' => $OptionsInfo{AllowSharedBonds}, 'UseBondSymbols' => $OptionsInfo{UseBondSymbols}, 'UseUniquePaths' => $OptionsInfo{UseUniquePaths}, 'UsePerlCoreRandom' => $OptionsInfo{UsePerlCoreRandom});
|
|
|
404
|
|
|
405 # Set atom identifier type...
|
|
|
406 SetAtomIdentifierTypeValuesToUse($PathLengthFingerprints);
|
|
|
407
|
|
|
408 # Generate fingerprints...
|
|
|
409 $PathLengthFingerprints->GenerateFingerprints();
|
|
|
410
|
|
|
411 # Make sure fingerprints generation is successful...
|
|
|
412 if (!$PathLengthFingerprints->IsFingerprintsGenerationSuccessful()) {
|
|
|
413 return undef;
|
|
|
414 }
|
|
|
415
|
|
|
416 if ($OptionsInfo{Fold}) {
|
|
|
417 my($CheckSizeValue) = 0;
|
|
|
418 $PathLengthFingerprints->FoldFingerprintsBySize($OptionsInfo{FoldedSize}, $CheckSizeValue);
|
|
|
419 }
|
|
|
420
|
|
|
421 return $PathLengthFingerprints;
|
|
|
422 }
|
|
|
423
|
|
|
424 # Generate pathlength count finerprints for molecule...
|
|
|
425 #
|
|
|
426 sub GeneratePathLengthCountFingerprints {
|
|
|
427 my($Molecule) = @_;
|
|
|
428 my($PathLengthFingerprints);
|
|
|
429
|
|
|
430 $PathLengthFingerprints = new Fingerprints::PathLengthFingerprints('Molecule' => $Molecule, 'Type' => 'PathLengthCount', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'MinLength' => $OptionsInfo{MinPathLength}, 'MaxLength' => $OptionsInfo{MaxPathLength}, 'AllowRings' => $OptionsInfo{AllowRings}, 'AllowSharedBonds' => $OptionsInfo{AllowSharedBonds}, 'UseBondSymbols' => $OptionsInfo{UseBondSymbols}, 'UseUniquePaths' => $OptionsInfo{UseUniquePaths});
|
|
|
431
|
|
|
432 # Set atom identifier type...
|
|
|
433 SetAtomIdentifierTypeValuesToUse($PathLengthFingerprints);
|
|
|
434
|
|
|
435 # Generate fingerprints...
|
|
|
436 $PathLengthFingerprints->GenerateFingerprints();
|
|
|
437
|
|
|
438 # Make sure fingerprints generation is successful...
|
|
|
439 if (!$PathLengthFingerprints->IsFingerprintsGenerationSuccessful()) {
|
|
|
440 return undef;
|
|
|
441 }
|
|
|
442 return $PathLengthFingerprints;
|
|
|
443 }
|
|
|
444
|
|
|
445 # Set atom identifier type to use for generating path strings...
|
|
|
446 #
|
|
|
447 sub SetAtomIdentifierTypeValuesToUse {
|
|
|
448 my($PathLengthFingerprints) = @_;
|
|
|
449
|
|
|
450 if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
451 $PathLengthFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
|
|
|
452 }
|
|
|
453 elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
454 $PathLengthFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
|
|
|
455 }
|
|
|
456 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
457 # Nothing to do for now...
|
|
|
458 }
|
|
|
459 else {
|
|
|
460 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
461 }
|
|
|
462 }
|
|
|
463
|
|
|
464 # Retrieve information about SD files...
|
|
|
465 #
|
|
|
466 sub RetrieveSDFilesInfo {
|
|
|
467 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
|
|
|
468
|
|
|
469 %SDFilesInfo = ();
|
|
|
470 @{$SDFilesInfo{FileOkay}} = ();
|
|
|
471 @{$SDFilesInfo{OutFileRoot}} = ();
|
|
|
472 @{$SDFilesInfo{SDOutFileNames}} = ();
|
|
|
473 @{$SDFilesInfo{FPOutFileNames}} = ();
|
|
|
474 @{$SDFilesInfo{TextOutFileNames}} = ();
|
|
|
475 @{$SDFilesInfo{AllDataFieldsRef}} = ();
|
|
|
476 @{$SDFilesInfo{CommonDataFieldsRef}} = ();
|
|
|
477
|
|
|
478 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
|
|
|
479 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
|
|
|
480
|
|
|
481 FILELIST: for $Index (0 .. $#SDFilesList) {
|
|
|
482 $SDFile = $SDFilesList[$Index];
|
|
|
483
|
|
|
484 $SDFilesInfo{FileOkay}[$Index] = 0;
|
|
|
485 $SDFilesInfo{OutFileRoot}[$Index] = '';
|
|
|
486 $SDFilesInfo{SDOutFileNames}[$Index] = '';
|
|
|
487 $SDFilesInfo{FPOutFileNames}[$Index] = '';
|
|
|
488 $SDFilesInfo{TextOutFileNames}[$Index] = '';
|
|
|
489
|
|
|
490 $SDFile = $SDFilesList[$Index];
|
|
|
491 if (!(-e $SDFile)) {
|
|
|
492 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
|
|
|
493 next FILELIST;
|
|
|
494 }
|
|
|
495 if (!CheckFileType($SDFile, "sd sdf")) {
|
|
|
496 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
|
|
|
497 next FILELIST;
|
|
|
498 }
|
|
|
499
|
|
|
500 if ($CheckDataField) {
|
|
|
501 # Make sure data field exists in SD file..
|
|
|
502 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
|
|
|
503
|
|
|
504 @CmpdLines = ();
|
|
|
505 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
506 $CmpdString = ReadCmpdString(\*SDFILE);
|
|
|
507 close SDFILE;
|
|
|
508 @CmpdLines = split "\n", $CmpdString;
|
|
|
509 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
510 $SpecifiedDataField = $OptionsInfo{CompoundID};
|
|
|
511 if (!exists $DataFieldValues{$SpecifiedDataField}) {
|
|
|
512 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
|
|
|
513 next FILELIST;
|
|
|
514 }
|
|
|
515 }
|
|
|
516
|
|
|
517 $AllDataFieldsRef = '';
|
|
|
518 $CommonDataFieldsRef = '';
|
|
|
519 if ($CollectDataFields) {
|
|
|
520 my($CmpdCount);
|
|
|
521 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
522 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
|
|
|
523 close SDFILE;
|
|
|
524 }
|
|
|
525
|
|
|
526 # Setup output file names...
|
|
|
527 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
528 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
|
|
|
529
|
|
|
530 $TextOutFileExt = "csv";
|
|
|
531 if ($Options{outdelim} =~ /^tab$/i) {
|
|
|
532 $TextOutFileExt = "tsv";
|
|
|
533 }
|
|
|
534 $SDOutFileExt = $FileExt;
|
|
|
535 $FPOutFileExt = "fpf";
|
|
|
536
|
|
|
537 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
|
|
|
538 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
539 if ($RootFileName && $RootFileExt) {
|
|
|
540 $FileName = $RootFileName;
|
|
|
541 }
|
|
|
542 else {
|
|
|
543 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
544 }
|
|
|
545 $OutFileRoot = $FileName;
|
|
|
546 }
|
|
|
547 else {
|
|
|
548 $OutFileRoot = "${FileName}PathLengthFP";
|
|
|
549 }
|
|
|
550
|
|
|
551 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
|
|
|
552 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
|
|
|
553 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
|
|
|
554
|
|
|
555 if ($OptionsInfo{SDOutput}) {
|
|
|
556 if ($SDFile =~ /$NewSDFileName/i) {
|
|
|
557 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
|
|
|
558 print "Specify a different name using \"-r --root\" option or use default name.\n";
|
|
|
559 next FILELIST;
|
|
|
560 }
|
|
|
561 }
|
|
|
562
|
|
|
563 if (!$OptionsInfo{OverwriteFiles}) {
|
|
|
564 # Check SD, FP and text outout files...
|
|
|
565 if ($OptionsInfo{SDOutput}) {
|
|
|
566 if (-e $NewSDFileName) {
|
|
|
567 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
|
|
|
568 next FILELIST;
|
|
|
569 }
|
|
|
570 }
|
|
|
571 if ($OptionsInfo{FPOutput}) {
|
|
|
572 if (-e $NewFPFileName) {
|
|
|
573 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
|
|
|
574 next FILELIST;
|
|
|
575 }
|
|
|
576 }
|
|
|
577 if ($OptionsInfo{TextOutput}) {
|
|
|
578 if (-e $NewTextFileName) {
|
|
|
579 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
|
|
|
580 next FILELIST;
|
|
|
581 }
|
|
|
582 }
|
|
|
583 }
|
|
|
584
|
|
|
585 $SDFilesInfo{FileOkay}[$Index] = 1;
|
|
|
586
|
|
|
587 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
|
|
|
588 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
|
|
|
589 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
|
|
|
590 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
|
|
|
591
|
|
|
592 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
|
|
|
593 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
|
|
|
594 }
|
|
|
595 }
|
|
|
596
|
|
|
597 # Process option values...
|
|
|
598 sub ProcessOptions {
|
|
|
599 %OptionsInfo = ();
|
|
|
600
|
|
|
601 $OptionsInfo{Mode} = $Options{mode};
|
|
|
602 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
|
|
|
603 $OptionsInfo{PathMode} = $Options{pathmode};
|
|
|
604
|
|
|
605 ProcessAtomIdentifierTypeOptions();
|
|
|
606
|
|
|
607 $OptionsInfo{BitsOrder} = $Options{bitsorder};
|
|
|
608 $OptionsInfo{BitStringFormat} = $Options{bitstringformat};
|
|
|
609
|
|
|
610 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
|
|
|
611 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
|
|
|
612 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
|
|
|
613
|
|
|
614 my(@SpecifiedDataFields);
|
|
|
615 @SpecifiedDataFields = ();
|
|
|
616
|
|
|
617 @{$OptionsInfo{SpecifiedDataFields}} = ();
|
|
|
618 $OptionsInfo{CompoundID} = '';
|
|
|
619
|
|
|
620 if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
|
|
|
621 if ($Options{compoundidmode} =~ /^DataField$/i) {
|
|
|
622 if (!$Options{compoundid}) {
|
|
|
623 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
|
|
|
624 }
|
|
|
625 $OptionsInfo{CompoundID} = $Options{compoundid};
|
|
|
626 }
|
|
|
627 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
628 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
|
|
|
629 }
|
|
|
630 }
|
|
|
631 elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
|
|
|
632 if (!$Options{datafields}) {
|
|
|
633 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
|
|
|
634 }
|
|
|
635 @SpecifiedDataFields = split /\,/, $Options{datafields};
|
|
|
636 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
|
|
|
637 }
|
|
|
638
|
|
|
639 if ($Options{atomidentifiertype} !~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
640 if ($Options{detectaromaticity} =~ /^No$/i) {
|
|
|
641 die "Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. No value is only allowed during AtomicInvariantsAtomTypes value for \"-a, --AtomIdentifierType\" \n";
|
|
|
642 }
|
|
|
643 }
|
|
|
644 $OptionsInfo{DetectAromaticity} = ($Options{detectaromaticity} =~ /^Yes$/i) ? 1 : 0;
|
|
|
645
|
|
|
646 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
|
|
|
647
|
|
|
648 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'PathLengthFingerprints';
|
|
|
649
|
|
|
650 my($Size, $MinSize, $MaxSize);
|
|
|
651 $MinSize = 32;
|
|
|
652 $MaxSize = 2**32;
|
|
|
653 $Size = $Options{size};
|
|
|
654 if (!(IsPositiveInteger($Size) && $Size >= $MinSize && $Size <= $MaxSize && IsNumberPowerOfNumber($Size, 2))) {
|
|
|
655 die "Error: Invalid size value, $Size, for \"-s, --size\" option. Allowed values: power of 2, >= minimum size of $MinSize, and <= maximum size of $MaxSize.\n";
|
|
|
656 }
|
|
|
657 $OptionsInfo{Size} = $Size;
|
|
|
658
|
|
|
659 $OptionsInfo{Fold} = ($Options{fold} =~ /^Yes$/i) ? 1 : 0;
|
|
|
660 my($FoldedSize);
|
|
|
661 $FoldedSize = $Options{foldedsize};
|
|
|
662 if ($Options{fold} =~ /^Yes$/i) {
|
|
|
663 if (!(IsPositiveInteger($FoldedSize) && $FoldedSize < $Size && IsNumberPowerOfNumber($FoldedSize, 2))) {
|
|
|
664 die "Error: Invalid folded size value, $FoldedSize, for \"--FoldedSize\" option. Allowed values: power of 2, >= minimum size of $MinSize, and < size value of $Size.\n";
|
|
|
665 }
|
|
|
666 }
|
|
|
667 $OptionsInfo{FoldedSize} = $FoldedSize;
|
|
|
668
|
|
|
669 $OptionsInfo{IgnoreHydrogens} = ($Options{ignorehydrogens} =~ /^Yes$/i) ? 1 : 0;
|
|
|
670 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
|
|
|
671
|
|
|
672 my($MinPathLength, $MaxPathLength);
|
|
|
673 $MinPathLength = $Options{minpathlength};
|
|
|
674 $MaxPathLength = $Options{maxpathlength};
|
|
|
675 if (!IsPositiveInteger($MinPathLength)) {
|
|
|
676 die "Error: Invalid path length value, $MinPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n";
|
|
|
677 }
|
|
|
678 if (!IsPositiveInteger($MaxPathLength)) {
|
|
|
679 die "Error: Invalid path length value, $MaxPathLength, for \"--MinPathLength\" option. Allowed values: > 0\n";
|
|
|
680 }
|
|
|
681 if ($MinPathLength >= $MaxPathLength) {
|
|
|
682 die "Error: Invalid minimum and maximum path length values, $MinPathLength and $MaxPathLength, for \"--MinPathLength\" and \"--MaxPathLength\"options. Allowed values: minimum path length value must be smaller than maximum path length value.\n";
|
|
|
683 }
|
|
|
684 $OptionsInfo{MinPathLength} = $MinPathLength;
|
|
|
685 $OptionsInfo{MaxPathLength} = $MaxPathLength;
|
|
|
686
|
|
|
687 my($NumOfBitsToSetPerPath);
|
|
|
688 $NumOfBitsToSetPerPath = $Options{numofbitstosetperpath};
|
|
|
689 if (!IsPositiveInteger($MaxPathLength)) {
|
|
|
690 die "Error: Invalid value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: > 0\n";
|
|
|
691 }
|
|
|
692 if ($NumOfBitsToSetPerPath >= $Size) {
|
|
|
693 die "Error: Invalid value, $NumOfBitsToSetPerPath, for \"-n, --NumOfBitsToSetPerPath\" option. Allowed values: It must be less than the size, $Size, of the fingerprint bit-string.\n";
|
|
|
694 }
|
|
|
695 $OptionsInfo{NumOfBitsToSetPerPath} = $NumOfBitsToSetPerPath;
|
|
|
696
|
|
|
697 $OptionsInfo{Output} = $Options{output};
|
|
|
698 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
|
|
|
699 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
|
|
|
700 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
|
|
|
701
|
|
|
702 $OptionsInfo{OutDelim} = $Options{outdelim};
|
|
|
703 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
704
|
|
|
705 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
706 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
707
|
|
|
708 $OptionsInfo{UseBondSymbols} = ($Options{usebondsymbols} =~ /^Yes$/i) ? 1 : 0;
|
|
|
709
|
|
|
710 $OptionsInfo{UsePerlCoreRandom} = ($Options{useperlcorerandom} =~ /^Yes$/i) ? 1 : 0;
|
|
|
711
|
|
|
712 $OptionsInfo{UseUniquePaths} = ($Options{useuniquepaths} =~ /^Yes$/i) ? 1 : 0;
|
|
|
713
|
|
|
714 $OptionsInfo{VectorStringFormat} = $Options{vectorstringformat};
|
|
|
715
|
|
|
716 # Setup parameters used during generation of fingerprints by PathLengthFingerprints class...
|
|
|
717 my($AllowRings, $AllowSharedBonds);
|
|
|
718 $AllowRings = 1;
|
|
|
719 $AllowSharedBonds = 1;
|
|
|
720 MODE: {
|
|
|
721 if ($Options{pathmode} =~ /^AtomPathsWithoutRings$/i) { $AllowSharedBonds = 0; $AllowRings = 0; last MODE;}
|
|
|
722 if ($Options{pathmode} =~ /^AtomPathsWithRings$/i) { $AllowSharedBonds = 0; $AllowRings = 1; last MODE;}
|
|
|
723 if ($Options{pathmode} =~ /^AllAtomPathsWithoutRings$/i) { $AllowSharedBonds = 1; $AllowRings = 0; last MODE;}
|
|
|
724 if ($Options{pathmode} =~ /^AllAtomPathsWithRings$/i) { $AllowSharedBonds = 1; $AllowRings = 1; last MODE;}
|
|
|
725 die "Error: ProcessOptions: mode value, $Options{pathmode}, is not supported.\n";
|
|
|
726 }
|
|
|
727 $OptionsInfo{AllowRings} = $AllowRings;
|
|
|
728 $OptionsInfo{AllowSharedBonds} = $AllowSharedBonds;
|
|
|
729 }
|
|
|
730
|
|
|
731 # Process atom identifier type and related options...
|
|
|
732 #
|
|
|
733 sub ProcessAtomIdentifierTypeOptions {
|
|
|
734
|
|
|
735 $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
|
|
|
736
|
|
|
737 if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
738 ProcessAtomicInvariantsToUseOption();
|
|
|
739 }
|
|
|
740 elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
741 ProcessFunctionalClassesToUse();
|
|
|
742 }
|
|
|
743 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
744 # Nothing to do for now...
|
|
|
745 }
|
|
|
746 else {
|
|
|
747 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
748 }
|
|
|
749 }
|
|
|
750
|
|
|
751 # Process specified atomic invariants to use...
|
|
|
752 #
|
|
|
753 sub ProcessAtomicInvariantsToUseOption {
|
|
|
754 my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
|
|
|
755
|
|
|
756 @{$OptionsInfo{AtomicInvariantsToUse}} = ();
|
|
|
757 if (IsEmpty($Options{atomicinvariantstouse})) {
|
|
|
758 die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
|
|
|
759 }
|
|
|
760 $AtomSymbolSpecified = 0;
|
|
|
761 @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
|
|
|
762 for $AtomicInvariant (@AtomicInvariantsWords) {
|
|
|
763 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
|
|
|
764 die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
|
|
|
765 }
|
|
|
766 if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
|
|
|
767 $AtomSymbolSpecified = 1;
|
|
|
768 }
|
|
|
769 push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
|
|
|
770 }
|
|
|
771 if (!$AtomSymbolSpecified) {
|
|
|
772 die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
|
|
|
773 }
|
|
|
774 }
|
|
|
775
|
|
|
776 # Process specified functional classes invariants to use...
|
|
|
777 #
|
|
|
778 sub ProcessFunctionalClassesToUse {
|
|
|
779 my($FunctionalClass, @FunctionalClassesToUseWords);
|
|
|
780
|
|
|
781 @{$OptionsInfo{FunctionalClassesToUse}} = ();
|
|
|
782 if (IsEmpty($Options{functionalclassestouse})) {
|
|
|
783 die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
|
|
|
784 }
|
|
|
785 @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
|
|
|
786 for $FunctionalClass (@FunctionalClassesToUseWords) {
|
|
|
787 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
|
|
|
788 die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
|
|
|
789 }
|
|
|
790 push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
|
|
|
791 }
|
|
|
792 }
|
|
|
793
|
|
|
794 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
795 sub SetupScriptUsage {
|
|
|
796
|
|
|
797 # Retrieve all the options...
|
|
|
798 %Options = ();
|
|
|
799
|
|
|
800 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
|
|
|
801
|
|
|
802 $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
|
|
|
803 $Options{atomicinvariantstouse} = 'AS';
|
|
|
804
|
|
|
805 $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
|
|
|
806
|
|
|
807 $Options{bitsorder} = 'Ascending';
|
|
|
808 $Options{bitstringformat} = 'HexadecimalString';
|
|
|
809
|
|
|
810 $Options{compoundidmode} = 'LabelPrefix';
|
|
|
811 $Options{compoundidlabel} = 'CompoundID';
|
|
|
812 $Options{datafieldsmode} = 'CompoundID';
|
|
|
813 $Options{detectaromaticity} = 'Yes';
|
|
|
814
|
|
|
815 $Options{filter} = 'Yes';
|
|
|
816
|
|
|
817 $Options{fold} = 'No';
|
|
|
818 $Options{foldedsize} = 256;
|
|
|
819
|
|
|
820 $Options{ignorehydrogens} = 'Yes';
|
|
|
821 $Options{keeplargestcomponent} = 'Yes';
|
|
|
822
|
|
|
823 $Options{mode} = 'PathLengthBits';
|
|
|
824 $Options{pathmode} = 'AllAtomPathsWithRings';
|
|
|
825
|
|
|
826 $Options{minpathlength} = 1;
|
|
|
827 $Options{maxpathlength} = 8;
|
|
|
828
|
|
|
829 $Options{numofbitstosetperpath} = 1;
|
|
|
830
|
|
|
831 $Options{output} = 'text';
|
|
|
832 $Options{outdelim} = 'comma';
|
|
|
833 $Options{quote} = 'yes';
|
|
|
834
|
|
|
835 $Options{size} = 1024;
|
|
|
836
|
|
|
837 $Options{usebondsymbols} = 'yes';
|
|
|
838 $Options{useperlcorerandom} = 'yes';
|
|
|
839 $Options{useuniquepaths} = 'yes';
|
|
|
840
|
|
|
841 $Options{vectorstringformat} = 'IDsAndValuesString';
|
|
|
842
|
|
|
843 if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "detectaromaticity=s", "filter|f=s", "fingerprintslabel=s", "fold=s", "foldedsize=i", "help|h", "ignorehydrogens|i=s", "keeplargestcomponent|k=s", "mode|m=s", "minpathlength=i", "maxpathlength=i", "numofbitstosetperpath|n=i", "outdelim=s", "output=s", "overwrite|o", "pathmode|p=s", "quote|q=s", "root|r=s", "size|s=i", "usebondsymbols|u=s", "useperlcorerandom=s", "useuniquepaths=s", "vectorstringformat|v=s", "workingdir|w=s")) {
|
|
|
844 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
845 }
|
|
|
846 if ($Options{workingdir}) {
|
|
|
847 if (! -d $Options{workingdir}) {
|
|
|
848 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
849 }
|
|
|
850 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
851 }
|
|
|
852 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
|
|
|
853 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
|
|
|
854 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
|
|
|
855 }
|
|
|
856 if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
857 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
858 }
|
|
|
859 if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) {
|
|
|
860 die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n";
|
|
|
861 }
|
|
|
862 if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) {
|
|
|
863 die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n";
|
|
|
864 }
|
|
|
865 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
866 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
867 }
|
|
|
868 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
|
|
|
869 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
|
|
|
870 }
|
|
|
871 if ($Options{detectaromaticity} !~ /^(Yes|No)$/i) {
|
|
|
872 die "Error: The value specified, $Options{detectaromaticity}, for option \"--DetectAromaticity\" is not valid. Allowed values: Yes or No\n";
|
|
|
873 }
|
|
|
874 if ($Options{filter} !~ /^(Yes|No)$/i) {
|
|
|
875 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
|
|
|
876 }
|
|
|
877 if ($Options{fold} !~ /^(Yes|No)$/i) {
|
|
|
878 die "Error: The value specified, $Options{fold}, for option \"--fold\" is not valid. Allowed values: Yes or No\n";
|
|
|
879 }
|
|
|
880 if (!IsPositiveInteger($Options{foldedsize})) {
|
|
|
881 die "Error: The value specified, $Options{foldedsize}, for option \"--FoldedSize\" is not valid. Allowed values: > 0 \n";
|
|
|
882 }
|
|
|
883 if ($Options{ignorehydrogens} !~ /^(Yes|No)$/i) {
|
|
|
884 die "Error: The value specified, $Options{ignorehydrogens}, for option \"-i, --IgnoreHydrogens\" is not valid. Allowed values: Yes or No\n";
|
|
|
885 }
|
|
|
886 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
|
|
|
887 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
|
|
|
888 }
|
|
|
889 if ($Options{mode} !~ /^(PathLengthBits|PathLengthCount)$/i) {
|
|
|
890 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: PathLengthBits or PathLengthCount\n";
|
|
|
891 }
|
|
|
892 if (!IsPositiveInteger($Options{minpathlength})) {
|
|
|
893 die "Error: The value specified, $Options{minpathlength}, for option \"--MinPathLength\" is not valid. Allowed values: > 0 \n";
|
|
|
894 }
|
|
|
895 if (!IsPositiveInteger($Options{numofbitstosetperpath})) {
|
|
|
896 die "Error: The value specified, $Options{NumOfBitsToSetPerPath}, for option \"--NumOfBitsToSetPerPath\" is not valid. Allowed values: > 0 \n";
|
|
|
897 }
|
|
|
898 if (!IsPositiveInteger($Options{maxpathlength})) {
|
|
|
899 die "Error: The value specified, $Options{maxpathlength}, for option \"--MaxPathLength\" is not valid. Allowed values: > 0 \n";
|
|
|
900 }
|
|
|
901 if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
|
|
|
902 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
|
|
|
903 }
|
|
|
904 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
905 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
906 }
|
|
|
907 if ($Options{pathmode} !~ /^(AtomPathsWithoutRings|AtomPathsWithRings|AllAtomPathsWithoutRings|AllAtomPathsWithRings)$/i) {
|
|
|
908 die "Error: The value specified, $Options{pathmode}, for option \"-m, --PathMode\" is not valid. Allowed values: AtomPathsWithoutRings, AtomPathsWithRings, AllAtomPathsWithoutRings or AllAtomPathsWithRings\n";
|
|
|
909 }
|
|
|
910 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
911 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
912 }
|
|
|
913 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
|
|
|
914 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
|
|
|
915 }
|
|
|
916
|
|
|
917 if (!IsPositiveInteger($Options{size})) {
|
|
|
918 die "Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n";
|
|
|
919 }
|
|
|
920 if ($Options{usebondsymbols} !~ /^(Yes|No)$/i) {
|
|
|
921 die "Error: The value specified, $Options{usebondsymbols}, for option \"-u, --UseBondSymbols\" is not valid. Allowed values: Yes or No\n";
|
|
|
922 }
|
|
|
923 if ($Options{useperlcorerandom} !~ /^(Yes|No)$/i) {
|
|
|
924 die "Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n";
|
|
|
925 }
|
|
|
926 if ($Options{useuniquepaths} !~ /^(Yes|No)$/i) {
|
|
|
927 die "Error: The value specified, $Options{useuniquepaths}, for option \"--UseUniquePaths\" is not valid. Allowed values: Yes or No\n";
|
|
|
928 }
|
|
|
929 if ($Options{vectorstringformat} !~ /^(IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
|
|
|
930 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
|
|
|
931 }
|
|
|
932 }
|
|
|
933
|
|
|
934 __END__
|
|
|
935
|
|
|
936 =head1 NAME
|
|
|
937
|
|
|
938 PathLengthFingerprints.pl - Generate atom path length based fingerprints for SD files
|
|
|
939
|
|
|
940 =head1 SYNOPSIS
|
|
|
941
|
|
|
942 PathLengthFingerprints.pl SDFile(s)...
|
|
|
943
|
|
|
944 PathLengthFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
|
|
|
945 [B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes>]
|
|
|
946 [B<--AtomicInvariantsToUse> I<"AtomicInvariant1,AtomicInvariant2...">]
|
|
|
947 [B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
|
|
|
948 [B<--BitsOrder> I<Ascending | Descending>] [B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>]
|
|
|
949 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
|
|
|
950 [B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>]
|
|
|
951 [B<--DataFields> I<"FieldLabel1,FieldLabel2,... ">] [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>]
|
|
|
952 [B<--DetectAromaticity> I<Yes | No>] [B<-f, --Filter> I<Yes | No>] [B<--FingerprintsLabel> I<text>]
|
|
|
953 [B<--fold> I<Yes | No>] [B<--FoldedSize> I<number>] [B<-h, --help>]
|
|
|
954 [B<-i, --IgnoreHydrogens> I<Yes | No>] [B<-k, --KeepLargestComponent> I<Yes | No>]
|
|
|
955 [B<-m, --mode> I<PathLengthBits | PathLengthCount>]
|
|
|
956 [B<--MinPathLength> I<number>] [B<--MaxPathLength> I<number>] [B<-n, --NumOfBitsToSetPerPath> I<number>]
|
|
|
957 [B<--OutDelim> I<comma | tab | semicolon>]
|
|
|
958 [B<--output> I<SD | FP | text | all>] [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
|
|
|
959 [B<-p, --PathMode> I<AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings>]
|
|
|
960 [B<-s, --size> I<number>] [B<-u, --UseBondSymbols> I<Yes | No>] [B<--UsePerlCoreRandom> I<Yes | No>]
|
|
|
961 [B<--UseUniquePaths> I<Yes | No>] [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
|
|
|
962 [B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>]
|
|
|
963 [B<-w, --WorkingDir> dirname] SDFile(s)...
|
|
|
964
|
|
|
965 =head1 DESCRIPTION
|
|
|
966
|
|
|
967 Generate atom path length fingerprints for I<SDFile(s)> and create appropriate SD, FP or
|
|
|
968 CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to
|
|
|
969 molecular fingerprints.
|
|
|
970
|
|
|
971 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
|
|
|
972 and I<.sd>. All other file names are ignored. All the SD files in a current directory
|
|
|
973 can be specified either by I<*.sdf> or the current directory name.
|
|
|
974
|
|
|
975 The current release of MayaChemTools supports generation of path length fingerprints
|
|
|
976 corresponding to following B<-a, --AtomIdentifierTypes>:
|
|
|
977
|
|
|
978 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
979 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
980 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
981
|
|
|
982 Based on the values specified for B<-p, --PathMode>, B<--MinPathLength> and B<--MaxPathLength>,
|
|
|
983 all appropriate atom paths are generated for each atom in the molecule and collected in a list and
|
|
|
984 the list is filtered to remove any structurally duplicate paths as indicated by the value of
|
|
|
985 B<--UseUniquePaths> option.
|
|
|
986
|
|
|
987 For each atom path in the filtered atom paths list, an atom path string is created using value of
|
|
|
988 B<-a, --AtomIdentifierType> and specified values to use for a particular atom identifier type.
|
|
|
989 Value of B<-u, --UseBondSymbols> controls whether bond order symbols are used during generation
|
|
|
990 of atom path string. For each atom path, only lexicographically smaller atom path strings are kept.
|
|
|
991
|
|
|
992 For I<PathLengthBits> value of B<-m, --mode> option, each atom path is hashed to a 32 bit unsigned
|
|
|
993 integer key using B<TextUtil::HashCode> function. Using the hash key as a seed for a random number
|
|
|
994 generator, a random integer value between 0 and B<--Size> is used to set corresponding bits
|
|
|
995 in the fingerprint bit-vector string. Value of B<--NumOfBitsToSetPerPath> option controls the number
|
|
|
996 of time a random number is generated to set corresponding bits.
|
|
|
997
|
|
|
998 For I< PathLengthCount> value of B<-m, --mode> option, the number of times an atom path appears
|
|
|
999 is tracked and a fingerprints count-string corresponding to count of atom paths is generated.
|
|
|
1000
|
|
|
1001 Example of I<SD> file containing path length fingerprints string data:
|
|
|
1002
|
|
|
1003 ... ...
|
|
|
1004 ... ...
|
|
|
1005 $$$$
|
|
|
1006 ... ...
|
|
|
1007 ... ...
|
|
|
1008 ... ...
|
|
|
1009 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
1010 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1011 ... ...
|
|
|
1012 2 3 1 0 0 0 0
|
|
|
1013 ... ...
|
|
|
1014 M END
|
|
|
1015 > <CmpdID>
|
|
|
1016 Cmpd1
|
|
|
1017
|
|
|
1018 > <PathLengthFingerprints>
|
|
|
1019 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLengt
|
|
|
1020 h1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a49913991a66
|
|
|
1021 03130b0a19e8051c89184414953800cc2151082844a201042800130860308e8204d4028
|
|
|
1022 00831048940e44281c00060449a5000ac80c894114e006321264401600846c050164462
|
|
|
1023 08190410805000304a10205b0100e04c0038ba0fad0209c0ca8b1200012268b61c0026a
|
|
|
1024 aa0660a11014a011d46
|
|
|
1025
|
|
|
1026 $$$$
|
|
|
1027 ... ...
|
|
|
1028 ... ...
|
|
|
1029
|
|
|
1030 Example of I<FP> file containing path length fingerprints string data:
|
|
|
1031
|
|
|
1032 #
|
|
|
1033 # Package = MayaChemTools 7.4
|
|
|
1034 # ReleaseDate = Oct 21, 2010
|
|
|
1035 #
|
|
|
1036 # TimeStamp = Mon Mar 7 15:14:01 2011
|
|
|
1037 #
|
|
|
1038 # FingerprintsStringType = FingerprintsBitVector
|
|
|
1039 #
|
|
|
1040 # Description = PathLengthBits:AtomicInvariantsAtomTypes:MinLength1:...
|
|
|
1041 # Size = 1024
|
|
|
1042 # BitStringFormat = HexadecimalString
|
|
|
1043 # BitsOrder = Ascending
|
|
|
1044 #
|
|
|
1045 Cmpd1 9c8460989ec8a49913991a6603130b0a19e8051c89184414953800cc21510...
|
|
|
1046 Cmpd2 000000249400840040100042011001001980410c000000001010088001120...
|
|
|
1047 ... ...
|
|
|
1048 ... ..
|
|
|
1049
|
|
|
1050 Example of CSV I<Text> file containing pathlength fingerprints string data:
|
|
|
1051
|
|
|
1052 "CompoundID","PathLengthFingerprints"
|
|
|
1053 "Cmpd1","FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes
|
|
|
1054 :MinLength1:MaxLength8;1024;HexadecimalString;Ascending;9c8460989ec8a4
|
|
|
1055 9913991a6603130b0a19e8051c89184414953800cc2151082844a20104280013086030
|
|
|
1056 8e8204d402800831048940e44281c00060449a5000ac80c894114e006321264401..."
|
|
|
1057 ... ...
|
|
|
1058 ... ...
|
|
|
1059
|
|
|
1060 The current release of MayaChemTools generates the following types of path length
|
|
|
1061 fingerprints bit-vector and vector strings:
|
|
|
1062
|
|
|
1063 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
1064 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
1065 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
1066 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
1067 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
1068 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
1069
|
|
|
1070 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
1071 th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
|
|
|
1072 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
|
|
|
1073 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
|
|
|
1074 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
|
|
|
1075 6ea05280140069c780290c43
|
|
|
1076
|
|
|
1077 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
1078 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
1079 C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
|
|
|
1080 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
1081 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
1082 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
|
|
|
1083
|
|
|
1084 FingerprintsVector;PathLengthCount:DREIDINGAtomTypes:MinLength1:MaxLen
|
|
|
1085 gth8;410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_
|
|
|
1086 1 N_3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3
|
|
|
1087 1 C_3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C
|
|
|
1088 _RF_ 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C
|
|
|
1089 _2O_3 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R ...
|
|
|
1090
|
|
|
1091 FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
|
|
|
1092 h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
|
|
|
1093 O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
|
|
|
1094 aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
|
|
|
1095 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
|
|
|
1096 sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
|
|
|
1097
|
|
|
1098 FingerprintsVector;PathLengthCount:FunctionalClassAtomTypes:MinLength1
|
|
|
1099 :MaxLength8;404;NumericalValues;IDsAndValuesPairsString;Ar 22 Ar.HBA 1
|
|
|
1100 HBA 2 HBA.HBD 3 HBD 1 Hal 1 NI 1 None 10 Ar.HBA:Ar 2 Ar.HBANone 1 Ar:
|
|
|
1101 Ar 21 ArAr 2 ArHBD 1 ArHal 1 ArNone 2 HBA.HBDNI 1 HBA.HBDNone 2 HBA=NI
|
|
|
1102 1 HBA=None 1 HBDNone 1 NINone 1 NoneNone 7 Ar.HBA:Ar:Ar 2 Ar.HBA:ArAr
|
|
|
1103 1 Ar.HBA:ArNone 1 Ar.HBANoneNone 1 Ar:Ar.HBA:Ar 1 Ar:Ar.HBANone 2 ...
|
|
|
1104
|
|
|
1105 FingerprintsVector;PathLengthCount:MMFF94AtomTypes:MinLength1:MaxLengt
|
|
|
1106 h8;463;NumericalValues;IDsAndValuesPairsString;C5A 2 C5B 2 C=ON 1 CB 1
|
|
|
1107 8 COO 1 CR 9 F 1 N5 1 NC=O 1 O=CN 1 O=CO 1 OC=O 1 OR 2 C5A:C5B 2 C5A:N
|
|
|
1108 5 2 C5ACB 1 C5ACR 1 C5B:C5B 1 C5BC=ON 1 C5BCB 1 C=ON=O=CN 1 C=ONNC=O 1
|
|
|
1109 CB:CB 18 CBF 1 CBNC=O 1 COO=O=CO 1 COOCR 1 COOOC=O 1 CRCR 7 CRN5 1 CR
|
|
|
1110 OR 2 C5A:C5B:C5B 2 C5A:C5BC=ON 1 C5A:C5BCB 1 C5A:N5:C5A 1 C5A:N5CR ...
|
|
|
1111
|
|
|
1112 FingerprintsVector;PathLengthCount:SLogPAtomTypes:MinLength1:MaxLength
|
|
|
1113 8;518;NumericalValues;IDsAndValuesPairsString;C1 5 C10 1 C11 1 C14 1 C
|
|
|
1114 18 14 C20 4 C21 2 C22 1 C5 2 CS 2 F 1 N11 1 N4 1 O10 1 O2 3 O9 1 C10C1
|
|
|
1115 1 C10N11 1 C11C1 2 C11C21 1 C14:C18 2 C14F 1 C18:C18 10 C18:C20 4 C18
|
|
|
1116 :C22 2 C1C5 1 C1CS 4 C20:C20 1 C20:C21 1 C20:N11 1 C20C20 2 C21:C21 1
|
|
|
1117 C21:N11 1 C21C5 1 C22N4 1 C5=O10 1 C5=O9 1 C5N4 1 C5O2 1 CSO2 2 C10...
|
|
|
1118
|
|
|
1119 FingerprintsVector;PathLengthCount:SYBYLAtomTypes:MinLength1:MaxLength
|
|
|
1120 8;412;NumericalValues;IDsAndValuesPairsString;C.2 2 C.3 9 C.ar 22 F 1
|
|
|
1121 N.am 1 N.ar 1 O.2 1 O.3 2 O.co2 2 C.2=O.2 1 C.2=O.co2 1 C.2C.3 1 C.2C.
|
|
|
1122 ar 1 C.2N.am 1 C.2O.co2 1 C.3C.3 7 C.3C.ar 1 C.3N.ar 1 C.3O.3 2 C.ar:C
|
|
|
1123 .ar 21 C.ar:N.ar 2 C.arC.ar 2 C.arF 1 C.arN.am 1 C.2C.3C.3 1 C.2C.ar:C
|
|
|
1124 .ar 2 C.2N.amC.ar 1 C.3C.2=O.co2 1 C.3C.2O.co2 1 C.3C.3C.3 5 C.3C.3...
|
|
|
1125
|
|
|
1126 FingerprintsVector;PathLengthCount:TPSAAtomTypes:MinLength1:MaxLength8
|
|
|
1127 ;331;NumericalValues;IDsAndValuesPairsString;N21 1 N7 1 None 34 O3 2 O
|
|
|
1128 4 3 N21:None 2 N21None 1 N7None 2 None:None 21 None=O3 2 NoneNone 13 N
|
|
|
1129 oneO4 3 N21:None:None 2 N21:NoneNone 2 N21NoneNone 1 N7None:None 2 N7N
|
|
|
1130 one=O3 1 N7NoneNone 1 None:N21:None 1 None:N21None 2 None:None:None 20
|
|
|
1131 None:NoneNone 12 NoneN7None 1 NoneNone=O3 2 NoneNoneNone 8 NoneNon...
|
|
|
1132
|
|
|
1133 FingerprintsVector;PathLengthCount:UFFAtomTypes:MinLength1:MaxLength8;
|
|
|
1134 410;NumericalValues;IDsAndValuesPairsString;C_2 2 C_3 9 C_R 22 F_ 1 N_
|
|
|
1135 3 1 N_R 1 O_2 2 O_3 3 C_2=O_2 2 C_2C_3 1 C_2C_R 1 C_2N_3 1 C_2O_3 1 C_
|
|
|
1136 3C_3 7 C_3C_R 1 C_3N_R 1 C_3O_3 2 C_R:C_R 21 C_R:N_R 2 C_RC_R 2 C_RF_
|
|
|
1137 1 C_RN_3 1 C_2C_3C_3 1 C_2C_R:C_R 2 C_2N_3C_R 1 C_3C_2=O_2 1 C_3C_2O_3
|
|
|
1138 1 C_3C_3C_3 5 C_3C_3C_R 2 C_3C_3N_R 1 C_3C_3O_3 4 C_3C_R:C_R 1 C_3...
|
|
|
1139
|
|
|
1140 =head1 OPTIONS
|
|
|
1141
|
|
|
1142 =over 4
|
|
|
1143
|
|
|
1144 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
|
|
|
1145
|
|
|
1146 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
1147 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
1148 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
1149 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
|
|
|
1150
|
|
|
1151 The supported aromaticity model names along with model specific control parameters
|
|
|
1152 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
|
|
|
1153 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
|
|
|
1154 this file during class instantiation and makes it available to method B<DetectAromaticity>
|
|
|
1155 for detecting aromaticity corresponding to a specific model.
|
|
|
1156
|
|
|
1157 This option is ignored during I<No> value of B<--DetectAromaticity> option.
|
|
|
1158
|
|
|
1159 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
|
|
|
1160
|
|
|
1161 Specify atom identifier type to use for assignment of atom types to hydrogen and/or
|
|
|
1162 non-hydrogen atoms during calculation of atom types fingerprints. Possible values in the
|
|
|
1163 current release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
1164 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
1165 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
|
|
|
1166
|
|
|
1167 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
|
|
|
1168
|
|
|
1169 Specify atom identifier type to use during generation of atom path strings
|
|
|
1170 corresponding to path length fingerprints. Possible values in the current release are:
|
|
|
1171 I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
1172 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
1173 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
|
|
|
1174
|
|
|
1175 =item B<--AtomicInvariantsToUse> I<"AtomicInvariant1,AtomicInvariant2...">
|
|
|
1176
|
|
|
1177 This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1178 option. It's a list of comma separated valid atomic invariant atom types.
|
|
|
1179
|
|
|
1180 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB,
|
|
|
1181 H, Ar, RA, FC, MN, SM>. Default value: I<AS>.
|
|
|
1182
|
|
|
1183 The atomic invariants abbreviations correspond to:
|
|
|
1184
|
|
|
1185 AS = Atom symbol corresponding to element symbol
|
|
|
1186
|
|
|
1187 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
1188 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
1189 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
1190 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1191 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1192 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1193 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
1194 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
1195 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
1196 FC<+n/-n> = Formal charge assigned to atom
|
|
|
1197 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
1198 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
1199 3 (triplet)
|
|
|
1200
|
|
|
1201 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
1202
|
|
|
1203 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
1204
|
|
|
1205 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
1206 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
1207
|
|
|
1208 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
1209 are also allowed:
|
|
|
1210
|
|
|
1211 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
1212 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
1213 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
1214 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
1215 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1216 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1217 H : NumOfImplicitAndExplicitHydrogens
|
|
|
1218 Ar : Aromatic
|
|
|
1219 RA : RingAtom
|
|
|
1220 FC : FormalCharge
|
|
|
1221 MN : MassNumber
|
|
|
1222 SM : SpinMultiplicity
|
|
|
1223
|
|
|
1224 Examples:
|
|
|
1225
|
|
|
1226 B<Benzene>: Using value of I<AS> for B<--AtomicInvariantsToUse>, I<Yes> for B<UseBondSymbols>,
|
|
|
1227 and I< AllAtomPathsWithRings> for B<-p, --PathMode>, atom path strings generated are:
|
|
|
1228
|
|
|
1229 C C:C C:C:C C:C:C:C C:C:C:C:C C:C:C:C:C:C C:C:C:C:C:C:C
|
|
|
1230
|
|
|
1231 And using I<AS,X,BO> for B<--AtomicInvariantsToUse> generates following atom path
|
|
|
1232 strings:
|
|
|
1233
|
|
|
1234 C.X2.BO3 C.X2.BO3:C.X2.BO3 C.X2.BO3:C.X2.BO3:C.X2.BO3
|
|
|
1235 C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
|
|
|
1236 C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
|
|
|
1237 C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
|
|
|
1238 C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3:C.X2.BO3
|
|
|
1239
|
|
|
1240 B<Urea>: Using value of I<AS> for B<--AtomicInvariantsToUse>, I<Yes> for B<UseBondSymbols>,
|
|
|
1241 and I< AllAtomPathsWithRings> for B<-p, --PathMode>, atom path strings are:
|
|
|
1242
|
|
|
1243 C N O C=O CN NC=O NCN
|
|
|
1244
|
|
|
1245 And using I<AS,X,BO> for B<--AtomicInvariantsToUse> generates following atom path
|
|
|
1246 strings:
|
|
|
1247
|
|
|
1248 C.X3.BO4 N.X1.BO1 O.X1.BO2 C.X3.BO4=O.X1.BO2
|
|
|
1249 C.X3.BO4N.X1.BO1 N.X1.BO1C.X3.BO4=O.X1.BO2
|
|
|
1250 N.X1.BO1C.X3.BO4N.X1.BO1
|
|
|
1251
|
|
|
1252 =item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">
|
|
|
1253
|
|
|
1254 This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1255 option. It's a list of comma separated valid functional classes.
|
|
|
1256
|
|
|
1257 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1258 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
|
|
|
1259
|
|
|
1260 The functional class abbreviations correspond to:
|
|
|
1261
|
|
|
1262 HBD: HydrogenBondDonor
|
|
|
1263 HBA: HydrogenBondAcceptor
|
|
|
1264 PI : PositivelyIonizable
|
|
|
1265 NI : NegativelyIonizable
|
|
|
1266 Ar : Aromatic
|
|
|
1267 Hal : Halogen
|
|
|
1268 H : Hydrophobic
|
|
|
1269 RA : RingAtom
|
|
|
1270 CA : ChainAtom
|
|
|
1271
|
|
|
1272 Functional class atom type specification for an atom corresponds to:
|
|
|
1273
|
|
|
1274 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
1275
|
|
|
1276 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1277 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1278
|
|
|
1279 HydrogenBondDonor: NH, NH2, OH
|
|
|
1280 HydrogenBondAcceptor: N[!H], O
|
|
|
1281 PositivelyIonizable: +, NH2
|
|
|
1282 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1283
|
|
|
1284 =item B<--BitsOrder> I<Ascending | Descending>
|
|
|
1285
|
|
|
1286 Bits order to use during generation of fingerprints bit-vector string for I<PathLengthBits> value of
|
|
|
1287 B<-m, --mode> option. Possible values: I<Ascending, Descending>. Default: I<Ascending>.
|
|
|
1288
|
|
|
1289 I<Ascending> bit order which corresponds to first bit in each byte as the lowest bit as
|
|
|
1290 opposed to the highest bit.
|
|
|
1291
|
|
|
1292 Internally, bits are stored in I<Ascending> order using Perl vec function. Regardless
|
|
|
1293 of machine order, big-endian or little-endian, vec function always considers first
|
|
|
1294 string byte as the lowest byte and first bit within each byte as the lowest bit.
|
|
|
1295
|
|
|
1296 =item B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>
|
|
|
1297
|
|
|
1298 Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
1299 B<--output> used during I<PathLengthBits> value of B<-m, --mode> option. Possible
|
|
|
1300 values: I<BinaryString, HexadecimalString>. Default value: I<HexadecimalString>.
|
|
|
1301
|
|
|
1302 I<BinaryString> corresponds to an ASCII string containing 1s and 0s. I<HexadecimalString>
|
|
|
1303 contains bit values in ASCII hexadecimal format.
|
|
|
1304
|
|
|
1305 Examples:
|
|
|
1306
|
|
|
1307 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
1308 th1:MaxLength8;1024;BinaryString;Ascending;001000010011010101011000110
|
|
|
1309 0100010101011000101001011100110001000010001001101000001001001001001000
|
|
|
1310 0010110100000111001001000001001010100100100000000011000000101001011100
|
|
|
1311 0010000001000101010100000100111100110111011011011000000010110111001101
|
|
|
1312 0101100011000000010001000011000010100011101100001000001000100000000...
|
|
|
1313
|
|
|
1314 FingerprintsBitVector;PathLengthBits:AtomicInvariantsAtomTypes:MinLeng
|
|
|
1315 th1:MaxLength8;1024;HexadecimalString;Ascending;48caa1315d82d91122b029
|
|
|
1316 42861c9409a4208182d12015509767bd0867653604481a8b1288000056090583603078
|
|
|
1317 9cedae54e26596889ab121309800900490515224208421502120a0dd9200509723ae89
|
|
|
1318 00024181b86c0122821d4e4880c38620dab280824b455404009f082003d52c212b4e6d
|
|
|
1319 6ea05280140069c780290c43
|
|
|
1320
|
|
|
1321 =item B<--CompoundID> I<DataFieldName or LabelPrefixString>
|
|
|
1322
|
|
|
1323 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
|
|
|
1324
|
|
|
1325 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
|
|
|
1326 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
|
|
1327 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
|
|
|
1328 look like Cmpd<Number>.
|
|
|
1329
|
|
|
1330 Examples for I<DataField> value of B<--CompoundIDMode>:
|
|
|
1331
|
|
|
1332 MolID
|
|
|
1333 ExtReg
|
|
|
1334
|
|
|
1335 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
|
|
|
1336
|
|
|
1337 Compound
|
|
|
1338
|
|
|
1339 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
1340 instead of default value of Cmpd<Number>.
|
|
|
1341
|
|
|
1342 =item B<--CompoundIDLabel> I<text>
|
|
|
1343
|
|
|
1344 Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value
|
|
|
1345 of B<--DataFieldsMode> option. Default: I<CompoundID>.
|
|
|
1346
|
|
|
1347 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
1348
|
|
|
1349 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
|
|
|
1350 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value;
|
|
|
1351 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination
|
|
|
1352 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
1353
|
|
|
1354 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
1355 Default: I<LabelPrefix>.
|
|
|
1356
|
|
|
1357 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
|
|
|
1358 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
1359 values are replaced with sequential compound IDs.
|
|
|
1360
|
|
|
1361 This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
|
|
|
1362
|
|
|
1363 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,... ">
|
|
|
1364
|
|
|
1365 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
1366 with generated fingerprints for I<text | all> values of B<--output> option.
|
|
|
1367
|
|
|
1368 This is only used for I<Specify> value of B<--DataFieldsMode> option.
|
|
|
1369
|
|
|
1370 Examples:
|
|
|
1371
|
|
|
1372 Extreg
|
|
|
1373 MolID,CompoundName
|
|
|
1374
|
|
|
1375 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
|
|
|
1376
|
|
|
1377 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
|
|
|
1378 with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD
|
|
|
1379 data field; transfer SD data files common to all compounds; extract specified data fields;
|
|
|
1380 generate a compound ID using molname line, a compound prefix, or a combination of both.
|
|
|
1381 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
|
|
|
1382
|
|
|
1383 =item B<--DetectAromaticity> I<Yes | No>
|
|
|
1384
|
|
|
1385 Detect aromaticity before generating fingerprints. Possible values: I<Yes or No>.
|
|
|
1386 Default value: I<Yes>.
|
|
|
1387
|
|
|
1388 I<No> B<--DetectAromaticity> forces usage of atom and bond aromaticity values
|
|
|
1389 from I<SDFile(s)> and skips the step which detects and assigns aromaticity.
|
|
|
1390
|
|
|
1391 I<No> B<--DetectAromaticity> value is only allowed uring I<AtomicInvariantsAtomTypes>
|
|
|
1392 value of B<-a, --AtomIdentifierType> options; for all possible values B<-a, --AtomIdentifierType>
|
|
|
1393 values, it must be I<Yes>.
|
|
|
1394
|
|
|
1395 =item B<-f, --Filter> I<Yes | No>
|
|
|
1396
|
|
|
1397 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
|
|
|
1398 Default value: I<Yes>.
|
|
|
1399
|
|
|
1400 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
1401 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
1402
|
|
|
1403 =item B<--FingerprintsLabel> I<text>
|
|
|
1404
|
|
|
1405 SD data label or text file column label to use for fingerprints string in output SD or
|
|
|
1406 CSV/TSV text file(s) specified by B<--output>. Default value: I<PathLenghFingerprints>.
|
|
|
1407
|
|
|
1408 =item B<--fold> I<Yes | No>
|
|
|
1409
|
|
|
1410 Fold fingerprints to increase bit density during I<PathLengthBits> value of
|
|
|
1411 B<-m, --mode> option. Possible values: I<Yes or No>. Default value: I<No>.
|
|
|
1412
|
|
|
1413 =item B<--FoldedSize> I<number>
|
|
|
1414
|
|
|
1415 Size of folded fingerprint during I<PathLengthBits> value of B<-m, --mode> option. Default
|
|
|
1416 value: I<256>. Valid values correspond to any positive integer which is less than
|
|
|
1417 B<-s, --size> and meets the criteria for its value.
|
|
|
1418
|
|
|
1419 Examples:
|
|
|
1420
|
|
|
1421 128
|
|
|
1422 512
|
|
|
1423
|
|
|
1424 =item B<-h, --help>
|
|
|
1425
|
|
|
1426 Print this help message
|
|
|
1427
|
|
|
1428 =item B<-i, --IgnoreHydrogens> I<Yes | No>
|
|
|
1429
|
|
|
1430 Ignore hydrogens during fingerprints generation. Possible values: I<Yes or No>.
|
|
|
1431 Default value: I<Yes>.
|
|
|
1432
|
|
|
1433 For I<yes> value of B<-i, --IgnoreHydrogens>, any explicit hydrogens are also used for
|
|
|
1434 generation of atoms path lengths and fingerprints; implicit hydrogens are still ignored.
|
|
|
1435
|
|
|
1436 =item B<-k, --KeepLargestComponent> I<Yes | No>
|
|
|
1437
|
|
|
1438 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
1439 I<Yes or No>. Default value: I<Yes>.
|
|
|
1440
|
|
|
1441 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
1442 in two different ways: use all connected components or just the largest connected
|
|
|
1443 component. By default, all atoms except for the largest connected component are
|
|
|
1444 deleted before generation of fingerprints.
|
|
|
1445
|
|
|
1446 =item B<-m, --mode> I<PathLengthBits | PathLengthCount>
|
|
|
1447
|
|
|
1448 Specify type of path length fingerprints to generate for molecules in I<SDFile(s)>. Possible
|
|
|
1449 values: I<PathLengthBits, PathLengthCount>. Default value: I<PathLengthBits>.
|
|
|
1450
|
|
|
1451 For I<PathLengthBits> value of B<-m, --mode> option, a fingerprint bit-vector string containing
|
|
|
1452 zeros and ones is generated and for I<PathLengthCount> value, a fingerprint vector string
|
|
|
1453 corresponding to number of atom paths is generated.
|
|
|
1454
|
|
|
1455 =item B<--MinPathLength> I<number>
|
|
|
1456
|
|
|
1457 Minimum atom path length to include in fingerprints. Default value: I<1>. Valid values:
|
|
|
1458 positive integers and less than B<--MaxPathLength>. Path length of 1 correspond to
|
|
|
1459 a path containing only one atom.
|
|
|
1460
|
|
|
1461 =item B<--MaxPathLength> I<number>
|
|
|
1462
|
|
|
1463 Maximum atom path length to include in fingerprints. Default value: I<8>. Valid values:
|
|
|
1464 positive integers and greater than B<--MinPathLength>.
|
|
|
1465
|
|
|
1466 =item B<-n, --NumOfBitsToSetPerPath> I<number>
|
|
|
1467
|
|
|
1468 Number of bits to set per path during generation of fingerprints bit-vector string for I<PathLengthBits>
|
|
|
1469 value of B<-m, --mode> option. Default value: I<1>. Valid values: positive integers.
|
|
|
1470
|
|
|
1471 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
1472
|
|
|
1473 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
|
|
|
1474 Default value: I<comma>.
|
|
|
1475
|
|
|
1476 =item B<--output> I<SD | FP | text | all>
|
|
|
1477
|
|
|
1478 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>.
|
|
|
1479
|
|
|
1480 =item B<-o, --overwrite>
|
|
|
1481
|
|
|
1482 Overwrite existing files.
|
|
|
1483
|
|
|
1484 =item B<-p, --PathMode> I<AtomPathsWithoutRings | AtomPathsWithRings | AllAtomPathsWithoutRings | AllAtomPathsWithRings>
|
|
|
1485
|
|
|
1486 Specify type of atom paths to use for generating pathlength fingerprints for molecules in
|
|
|
1487 I<SDFile(s)>. Possible values:I<AtomPathsWithoutRings, AtomPathsWithRings,
|
|
|
1488 AllAtomPathsWithoutRings, AllAtomPathsWithRings>. Default value: I<AllAtomPathsWithRings>.
|
|
|
1489
|
|
|
1490 For molecules with no rings, first two and last two options are equivalent and generate
|
|
|
1491 same set of atom paths starting from each atom with length between B<--MinPathLength>
|
|
|
1492 and B<--MaxPathLength>. However, all these four options can result in the same set of
|
|
|
1493 final atom paths for molecules containing fused, bridged or spiro rings.
|
|
|
1494
|
|
|
1495 For molecules containing rings, atom paths starting from each atom can be traversed in
|
|
|
1496 four different ways:
|
|
|
1497
|
|
|
1498 I<AtomPathsWithoutRings> - Atom paths containing no rings and without sharing of bonds
|
|
|
1499 in traversed paths.
|
|
|
1500
|
|
|
1501 I<AtomPathsWithRings> - Atom paths containing rings and without any sharing of bonds in
|
|
|
1502 traversed paths.
|
|
|
1503
|
|
|
1504 I<AllAtomPathsWithoutRings> - All possible atom paths containing no rings and without any
|
|
|
1505 sharing of bonds in traversed paths.
|
|
|
1506
|
|
|
1507 I<AllAtomPathsWithRings> - All possible atom paths containing rings and with sharing of
|
|
|
1508 bonds in traversed paths.
|
|
|
1509
|
|
|
1510 Atom path traversal is terminated at the ring atom.
|
|
|
1511
|
|
|
1512 Based on values specified for for B<-p, --PathMode>, B<--MinPathLength> and
|
|
|
1513 B<--MaxPathLength>, all appropriate atom paths are generated for each atom in the molecule
|
|
|
1514 and collected in a list.
|
|
|
1515
|
|
|
1516 For each atom path in the filtered atom paths list, an atom path string is created using value of
|
|
|
1517 B<-a, --AtomIdentifierType> and specified values to use for a particular atom identifier type.
|
|
|
1518 Value of B<-u, --UseBondSymbols> controls whether bond order symbols are used during generation
|
|
|
1519 of atom path string. Atom symbol corresponds to element symbol and characters used to represent
|
|
|
1520 bond order are: I<1 - None; 2 - '='; 3 - '#'; 1.5 or aromatic - ':'; others: bond order value>. By default,
|
|
|
1521 bond symbols are included in atom path strings. Exclusion of bond symbols in atom path strings
|
|
|
1522 results in fingerprints which correspond purely to atom paths without considering bonds.
|
|
|
1523
|
|
|
1524 B<UseUniquePaths> controls the removal of structurally duplicate atom path strings are removed
|
|
|
1525 from the list.
|
|
|
1526
|
|
|
1527 For I<PathLengthBits> value of B<-m, --mode> option, each atom path is hashed to a 32 bit unsigned
|
|
|
1528 integer key using B<TextUtil::HashCode> function. Using the hash key as a seed for a random number
|
|
|
1529 generator, a random integer value between 0 and B<--Size> is used to set corresponding bits
|
|
|
1530 in the fingerprint bit-vector string. Value of B<--NumOfBitsToSetPerPaths> option controls the number
|
|
|
1531 of time a random number is generated to set corresponding bits.
|
|
|
1532
|
|
|
1533 For I< PathLengthCount> value of B<-m, --mode> option, the number of times an atom path appears
|
|
|
1534 is tracked and a fingerprints count-string corresponding to count of atom paths is generated.
|
|
|
1535
|
|
|
1536 For molecule containing rings, combination of B<-p, --PathMode> and B<--UseBondSymbols> allows
|
|
|
1537 generation of up to 8 different types of atom path length strings:
|
|
|
1538
|
|
|
1539 AllowSharedBonds AllowRings UseBondSymbols
|
|
|
1540
|
|
|
1541 0 0 1 - AtomPathsNoCyclesWithBondSymbols
|
|
|
1542 0 1 1 - AtomPathsWithCyclesWithBondSymbols
|
|
|
1543
|
|
|
1544 1 0 1 - AllAtomPathsNoCyclesWithBondSymbols
|
|
|
1545 1 1 1 - AllAtomPathsWithCyclesWithBondSymbols
|
|
|
1546 [ DEFAULT ]
|
|
|
1547
|
|
|
1548 0 0 0 - AtomPathsNoCyclesNoBondSymbols
|
|
|
1549 0 1 0 - AtomPathsWithCyclesNoBondSymbols
|
|
|
1550
|
|
|
1551 1 0 0 - AllAtomPathsNoCyclesNoBondSymbols
|
|
|
1552 1 1 0 - AllAtomPathsWithCyclesNoWithBondSymbols
|
|
|
1553
|
|
|
1554 Default atom path length fingerprints generation for molecules containing rings with
|
|
|
1555 I<AllAtomPathsWithRings> value for B<-p, --PathMode>, I<Yes> value for B<--UseBondSymbols>,
|
|
|
1556 I<2> value for B<--MinPathLength> and I<8> value for B<--MaxPathLength> is the most time
|
|
|
1557 consuming. Combinations of other options can substantially speed up fingerprint generation
|
|
|
1558 for molecules containing complex ring systems.
|
|
|
1559
|
|
|
1560 Additionally, value for option B<-a, --AtomIdentifierType> in conjunction with corresponding specified
|
|
|
1561 values for atom types changes the nature of atom path length strings and the fingerprints.
|
|
|
1562
|
|
|
1563 =item B<-q, --quote> I<Yes | No>
|
|
|
1564
|
|
|
1565 Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
1566 I<Yes or No>. Default value: I<Yes>.
|
|
|
1567
|
|
|
1568 =item B<-r, --root> I<RootName>
|
|
|
1569
|
|
|
1570 New file name is generated using the root: <Root>.<Ext>. Default for new file
|
|
|
1571 names: <SDFileName><PathLengthFP>.<Ext>. The file type determines <Ext> value.
|
|
|
1572 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
|
1573 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
1574
|
|
|
1575 =item B<-s, --size> I<number>
|
|
|
1576
|
|
|
1577 Size of fingerprints. Default value: I<1024>. Valid values correspond to any positive
|
|
|
1578 integer which satisfies the following criteria: power of 2, >= 32 and <= 2 ** 32.
|
|
|
1579
|
|
|
1580 Examples:
|
|
|
1581
|
|
|
1582 256
|
|
|
1583 512
|
|
|
1584 2048
|
|
|
1585
|
|
|
1586 =item B<-u, --UseBondSymbols> I<Yes | No>
|
|
|
1587
|
|
|
1588 Specify whether to use bond symbols for atom paths during generation of atom path strings.
|
|
|
1589 Possible values: I<Yes or No>. Default value: I<Yes>.
|
|
|
1590
|
|
|
1591 I<No> value option for B<-u, --UseBondSymbols> allows the generation of fingerprints corresponding
|
|
|
1592 purely to atoms disregarding all bonds.
|
|
|
1593
|
|
|
1594 =item B<--UsePerlCoreRandom> I<Yes | No>
|
|
|
1595
|
|
|
1596 Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function
|
|
|
1597 during random number generation for setting bits in fingerprints bit-vector strings. Possible
|
|
|
1598 values: I<Yes or No>. Default value: I<Yes>.
|
|
|
1599
|
|
|
1600 I<No> value option for B<--UsePerlCoreRandom> allows the generation of fingerprints
|
|
|
1601 bit-vector strings which are same across different platforms.
|
|
|
1602
|
|
|
1603 The random number generator implemented in MayaChemTools is a variant of
|
|
|
1604 linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].
|
|
|
1605 It is also referred to as Lehmer random number generator or Park-Miller
|
|
|
1606 random number generator.
|
|
|
1607
|
|
|
1608 Unlike Perl's core random number generator function rand, the random number
|
|
|
1609 generator implemented in MayaChemTools, MathUtil::random, generates consistent
|
|
|
1610 random values across different platforms for a specific random seed and leads
|
|
|
1611 to generation of portable fingerprints bit-vector strings.
|
|
|
1612
|
|
|
1613 =item B<--UseUniquePaths> I<Yes | No>
|
|
|
1614
|
|
|
1615 Specify whether to use structurally unique atom paths during generation of atom path strings.
|
|
|
1616 Possible values: I<Yes or No>. Default value: I<Yes>.
|
|
|
1617
|
|
|
1618 I<No> value option for B<--UseUniquePaths> allows usage of all atom paths generated by
|
|
|
1619 B<-p, --PathMode> option value for generation of atom path strings leading to duplicate
|
|
|
1620 path count during I<PathLengthCount> value of B<-m, --mode> option. It doesn't change fingerprint
|
|
|
1621 string generated during I<PathLengthBits> value of B<-m, --mode>.
|
|
|
1622
|
|
|
1623 For example, during I<AllAtomPathsWithRings> value of B<-p, --PathMode> option, benzene has
|
|
|
1624 12 linear paths of length 2 and 12 cyclic paths length of 7, but only 6 linear paths of length 2 and
|
|
|
1625 1 cyclic path of length 7 are structurally unique.
|
|
|
1626
|
|
|
1627 =item B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>
|
|
|
1628
|
|
|
1629 Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
1630 B<--output> used during I<PathLengthCount> value of B<-m, --mode> option. Possible
|
|
|
1631 values: I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
1632 ValuesAndIDsPairsString>. Defaultvalue: I<IDsAndValuesString>.
|
|
|
1633
|
|
|
1634 Examples:
|
|
|
1635
|
|
|
1636 FingerprintsVector;PathLengthCount:AtomicInvariantsAtomTypes:MinLength
|
|
|
1637 1:MaxLength8;432;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3 2
|
|
|
1638 C.X2.BO2.H2 4 C.X2.BO3.H1 14 C.X3.BO3.H1 3 C.X3.BO4 10 F.X1.BO1 1 N.X
|
|
|
1639 2.BO2.H1 1 N.X3.BO3 1 O.X1.BO1.H1 3 O.X1.BO2 2 C.X1.BO1.H3C.X3.BO3.H1
|
|
|
1640 2 C.X2.BO2.H2C.X2.BO2.H2 1 C.X2.BO2.H2C.X3.BO3.H1 4 C.X2.BO2.H2C.X3.BO
|
|
|
1641 4 1 C.X2.BO2.H2N.X3.BO3 1 C.X2.BO3.H1:C.X2.BO3.H1 10 C.X2.BO3.H1:C....
|
|
|
1642
|
|
|
1643 FingerprintsVector;PathLengthCount:EStateAtomTypes:MinLength1:MaxLengt
|
|
|
1644 h8;454;NumericalValues;IDsAndValuesPairsString;aaCH 14 aasC 8 aasN 1 d
|
|
|
1645 O 2 dssC 2 sCH3 2 sF 1 sOH 3 ssCH2 4 ssNH 1 sssCH 3 aaCH:aaCH 10 aaCH:
|
|
|
1646 aasC 8 aasC:aasC 3 aasC:aasN 2 aasCaasC 2 aasCdssC 1 aasCsF 1 aasCssNH
|
|
|
1647 1 aasCsssCH 1 aasNssCH2 1 dO=dssC 2 dssCsOH 1 dssCssCH2 1 dssCssNH 1
|
|
|
1648 sCH3sssCH 2 sOHsssCH 2 ssCH2ssCH2 1 ssCH2sssCH 4 aaCH:aaCH:aaCH 6 a...
|
|
|
1649
|
|
|
1650 =item B<-w, --WorkingDir> I<DirName>
|
|
|
1651
|
|
|
1652 Location of working directory. Default: current directory.
|
|
|
1653
|
|
|
1654 =back
|
|
|
1655
|
|
|
1656 =head1 EXAMPLES
|
|
|
1657
|
|
|
1658 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
1659 through 8 in hexadecimal bit-vector string format of size 1024 and create a
|
|
|
1660 SamplePLFPHex.csv file containing sequential compound IDs along with fingerprints
|
|
|
1661 bit-vector strings data, type:
|
|
|
1662
|
|
|
1663 % PathLengthFingerprints.pl -o -r SamplePLFPHex Sample.sdf
|
|
|
1664
|
|
|
1665 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
1666 through 8 in hexadecimal bit-vector string format of size 1024 and create SamplePLFPHex.sdf,
|
|
|
1667 SamplePLFPHex.fpf, and SamplePLFPHex.csv files containing sequential compound IDs
|
|
|
1668 in CSV file along with fingerprints bit-vector strings data, type:
|
|
|
1669
|
|
|
1670 % PathLengthFingerprints.pl --output all -o -r SamplePLFPHex Sample.sdf
|
|
|
1671
|
|
|
1672 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
1673 through 8 in binary bit-vector string format of size 1024 and create a
|
|
|
1674 SamplePLFPBin.csv file containing sequential compound IDs along with fingerprints
|
|
|
1675 bit-vector strings data, type:
|
|
|
1676
|
|
|
1677 % PathLengthFingerprints.pl --BitStringFormat BinaryString --size 2048
|
|
|
1678 -o -r SamplePLFPBin Sample.sdf
|
|
|
1679
|
|
|
1680 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
1681 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
1682 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1683
|
|
|
1684 % PathLengthFingerprints.pl -m PathLengthCount -o -r SamplePLFPCount
|
|
|
1685 Sample.sdf
|
|
|
1686
|
|
|
1687 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
1688 length 1 through 8 in IDsAndValuesString format using E-state atom types and
|
|
|
1689 create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
|
|
|
1690 vector strings data, type:
|
|
|
1691
|
|
|
1692 % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType
|
|
|
1693 EStateAtomTypes -o -r SamplePLFPCount Sample.sdf
|
|
|
1694
|
|
|
1695 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
1696 length 1 through 8 in IDsAndValuesString format using SLogP atom types and
|
|
|
1697 create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
|
|
|
1698 vector strings data, type:
|
|
|
1699
|
|
|
1700 % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType
|
|
|
1701 SLogPAtomTypes -o -r SamplePLFPCount Sample.sdf
|
|
|
1702
|
|
|
1703 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
1704 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
1705 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1706
|
|
|
1707 % PathLengthFingerprints.pl -m PathLengthCount --VectorStringFormat
|
|
|
1708 ValuesAndIDsPairsString -o -r SamplePLFPCount Sample.sdf
|
|
|
1709
|
|
|
1710 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
1711 length 1 through 8 in IDsAndValuesString format using AS,X,BO as atomic invariants and
|
|
|
1712 create a SamplePLFPCount.csv file containing sequential compound IDs along with fingerprints
|
|
|
1713 vector strings data, type:
|
|
|
1714
|
|
|
1715 % PathLengthFingerprints.pl -m PathLengthCount --AtomIdentifierType
|
|
|
1716 AtomicInvariantsAtomTypes --AtomicInvariantsToUse "AS,X,BO" -o
|
|
|
1717 -r SamplePLFPCount Sample.sdf
|
|
|
1718
|
|
|
1719 To generate path length fingerprints corresponding to count of all paths from
|
|
|
1720 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
1721 containing compound IDs from MolName line along with fingerprints vector strings data, type:
|
|
|
1722
|
|
|
1723 % PathLengthFingerprints.pl -m PathLengthCount --UseUniquePaths No
|
|
|
1724 -o --CompoundIDMode MolName -r SamplePLFPCount --UseUniquePaths No
|
|
|
1725 Sample.sdf
|
|
|
1726
|
|
|
1727 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
1728 through 8 in hexadecimal bit-vector string format of size 512 after folding and create
|
|
|
1729 SamplePLFPHex.sdf, SamplePLFPHex.fpf, and SamplePLFPHex.sdf files containing sequential
|
|
|
1730 compound IDs along with fingerprints bit-vector strings data, type:
|
|
|
1731
|
|
|
1732 % PathLengthFingerprints.pl --output all --Fold Yes --FoldedSize 512
|
|
|
1733 -o -r SamplePLFPHex Sample.sdf
|
|
|
1734
|
|
|
1735 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
1736 through 8 containing no rings and without sharing of bonds in hexadecimal bit-vector
|
|
|
1737 string format of size 1024 and create a SamplePLFPHex.csv file containing sequential
|
|
|
1738 compound IDs along with fingerprints bit-vector strings data and all data fields, type:
|
|
|
1739
|
|
|
1740 % PathLengthFingerprints.pl -p AtomPathsWithoutRings --DataFieldsMode All
|
|
|
1741 -o -r SamplePLFPHex Sample.sdf
|
|
|
1742
|
|
|
1743 To generate path length fingerprints corresponding to all unique paths from length 1
|
|
|
1744 through 8 containing rings and without sharing of bonds in hexadecimal bit-vector
|
|
|
1745 string format of size 1024 and create a SamplePLFPHex.tsv file containing compound IDs
|
|
|
1746 derived from combination of molecule name line and an explicit compound prefix
|
|
|
1747 along with fingerprints bit-vector strings data and all data fields, type:
|
|
|
1748
|
|
|
1749 % PathLengthFingerprints.pl -p AtomPathsWithRings --DataFieldsMode
|
|
|
1750 CompoundID --CompoundIDMode MolnameOrLabelPrefix --CompoundID Cmpd
|
|
|
1751 --CompoundIDLabel MolID --FingerprintsLabel PathLengthFP --OutDelim Tab
|
|
|
1752 -r SamplePLFPHex -o Sample.sdf
|
|
|
1753
|
|
|
1754 To generate path length fingerprints corresponding to count of all unique paths from
|
|
|
1755 length 1 through 8 in IDsAndValuesString format and create a SamplePLFPCount.csv file
|
|
|
1756 containing sequential compound IDs along with fingerprints vector strings data using
|
|
|
1757 aromaticity specified in SD file, type:
|
|
|
1758
|
|
|
1759 % PathLengthFingerprints.pl -m PathLengthCount --DetectAromaticity No
|
|
|
1760 -o -r SamplePLFPCount Sample.sdf
|
|
|
1761
|
|
|
1762 To generate path length fingerprints corresponding to all unique paths from length 2
|
|
|
1763 through 6 in hexadecimal bit-vector string format of size 1024 and create a
|
|
|
1764 SamplePLFPHex.csv file containing sequential compound IDs along with fingerprints
|
|
|
1765 bit-vector strings data, type:
|
|
|
1766
|
|
|
1767 % PathLengthFingerprints.pl --MinPathLength 2 --MaxPathLength 6
|
|
|
1768 -o -r SamplePLFPHex Sample.sdf
|
|
|
1769
|
|
|
1770 =head1 AUTHOR
|
|
|
1771
|
|
|
1772 Manish Sud <msud@san.rr.com>
|
|
|
1773
|
|
|
1774 =head1 SEE ALSO
|
|
|
1775
|
|
|
1776 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
1777 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
|
|
|
1778 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
1779 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
1780
|
|
|
1781 =head1 COPYRIGHT
|
|
|
1782
|
|
|
1783 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1784
|
|
|
1785 This file is part of MayaChemTools.
|
|
|
1786
|
|
|
1787 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1788 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1789 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1790 any later version.
|
|
|
1791
|
|
|
1792 =cut
|
