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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: ExtendedConnectivityFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:19 $
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5 # $Revision: 1.37 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use MoleculeFileIO;
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39 use FileIO::FingerprintsSDFileIO;
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40 use FileIO::FingerprintsTextFileIO;
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41 use FileIO::FingerprintsFPFileIO;
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42 use AtomTypes::AtomicInvariantsAtomTypes;
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43 use AtomTypes::FunctionalClassAtomTypes;
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44 use Fingerprints::ExtendedConnectivityFingerprints;
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45
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46 my($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 GenerateExtendedConnectivityFingerprints($FileIndex);
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84 }
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85 }
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86 print "\n$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 GenerateExtendedConnectivityFingerprints {
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97 my($FileIndex) = @_;
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98 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $ExtendedConnectivityFingerprints, $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 $ExtendedConnectivityFingerprints = GenerateMoleculeFingerprints($Molecule);
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124 if (!$ExtendedConnectivityFingerprints) {
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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, $ExtendedConnectivityFingerprints, $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} =~ /^(ExtendedConnectivity|ExtendedConnectivityCount)$/i) {
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221 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
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222 }
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223 elsif ($OptionsInfo{Mode} =~ /^ExtendedConnectivityBits$/i) {
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224 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder});
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225 }
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226
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227 if ($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, $ExtendedConnectivityFingerprints, $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 $NewFPSDFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $CmpdString);
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271 }
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272
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273 if ($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 $NewFPTextFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $ColValuesRef);
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278 }
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279
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280 if ($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 $NewFPFileIO->WriteFingerprints($ExtendedConnectivityFingerprints, $CompoundID);
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285 }
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286 }
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287
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288 # Generate approriate column labels for FPText output file...
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289 #
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290 sub SetupFPTextFileCoulmnLabels {
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291 my($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($ExtendedConnectivityFingerprints);
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367
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368 if ($OptionsInfo{KeepLargestComponent}) {
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369 $Molecule->KeepLargestComponent();
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370 }
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371 if (!$Molecule->DetectRings()) {
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372 return undef;
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373 }
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374 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
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375 $Molecule->DetectAromaticity();
|
|
|
376
|
|
|
377 $ExtendedConnectivityFingerprints = undef;
|
|
|
378 if ($OptionsInfo{Mode} =~ /^(ExtendedConnectivity|ExtendedConnectivityCount)$/i ) {
|
|
|
379 $ExtendedConnectivityFingerprints = new Fingerprints::ExtendedConnectivityFingerprints('Type' => $OptionsInfo{Mode}, 'Molecule' => $Molecule, 'NeighborhoodRadius' => $OptionsInfo{NeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
|
|
|
380 }
|
|
|
381 elsif ($OptionsInfo{Mode} =~ /^ExtendedConnectivityBits$/i) {
|
|
|
382 $ExtendedConnectivityFingerprints = new Fingerprints::ExtendedConnectivityFingerprints('Type' => $OptionsInfo{Mode}, 'Molecule' => $Molecule, 'NeighborhoodRadius' => $OptionsInfo{NeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'Size' => $OptionsInfo{Size}, 'UsePerlCoreRandom' => $OptionsInfo{UsePerlCoreRandom});
|
|
|
383 }
|
|
|
384 else {
|
|
|
385 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity, ExtendedConnectivityCount or ExtendedConnectivityBits\n";
|
|
|
386 }
|
|
|
387 SetAtomIdentifierTypeValuesToUse($ExtendedConnectivityFingerprints);
|
|
|
388
|
|
|
389 # Generate fingerprints...
|
|
|
390 $ExtendedConnectivityFingerprints->GenerateFingerprints();
|
|
|
391
|
|
|
392 # Make sure fingerprints generation is successful...
|
|
|
393 if (!$ExtendedConnectivityFingerprints->IsFingerprintsGenerationSuccessful()) {
|
|
|
394 return undef;
|
|
|
395 }
|
|
|
396
|
|
|
397 return $ExtendedConnectivityFingerprints;
|
|
|
398 }
|
|
|
399
|
|
|
400 # Set atom identifier type to use for generating fingerprints...
|
|
|
401 #
|
|
|
402 sub SetAtomIdentifierTypeValuesToUse {
|
|
|
403 my($ExtendedConnectivityFingerprints) = @_;
|
|
|
404
|
|
|
405 if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
406 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
|
|
|
407 }
|
|
|
408 elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
409 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
|
|
|
410 }
|
|
|
411 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
412 # Nothing to do for now...
|
|
|
413 }
|
|
|
414 else {
|
|
|
415 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
416 }
|
|
|
417 }
|
|
|
418
|
|
|
419 # Retrieve information about SD files...
|
|
|
420 #
|
|
|
421 sub RetrieveSDFilesInfo {
|
|
|
422 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
|
|
|
423
|
|
|
424 %SDFilesInfo = ();
|
|
|
425 @{$SDFilesInfo{FileOkay}} = ();
|
|
|
426 @{$SDFilesInfo{OutFileRoot}} = ();
|
|
|
427 @{$SDFilesInfo{SDOutFileNames}} = ();
|
|
|
428 @{$SDFilesInfo{FPOutFileNames}} = ();
|
|
|
429 @{$SDFilesInfo{TextOutFileNames}} = ();
|
|
|
430 @{$SDFilesInfo{AllDataFieldsRef}} = ();
|
|
|
431 @{$SDFilesInfo{CommonDataFieldsRef}} = ();
|
|
|
432
|
|
|
433 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
|
|
|
434 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
|
|
|
435
|
|
|
436 FILELIST: for $Index (0 .. $#SDFilesList) {
|
|
|
437 $SDFile = $SDFilesList[$Index];
|
|
|
438
|
|
|
439 $SDFilesInfo{FileOkay}[$Index] = 0;
|
|
|
440 $SDFilesInfo{OutFileRoot}[$Index] = '';
|
|
|
441 $SDFilesInfo{SDOutFileNames}[$Index] = '';
|
|
|
442 $SDFilesInfo{FPOutFileNames}[$Index] = '';
|
|
|
443 $SDFilesInfo{TextOutFileNames}[$Index] = '';
|
|
|
444
|
|
|
445 $SDFile = $SDFilesList[$Index];
|
|
|
446 if (!(-e $SDFile)) {
|
|
|
447 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
|
|
|
448 next FILELIST;
|
|
|
449 }
|
|
|
450 if (!CheckFileType($SDFile, "sd sdf")) {
|
|
|
451 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
|
|
|
452 next FILELIST;
|
|
|
453 }
|
|
|
454
|
|
|
455 if ($CheckDataField) {
|
|
|
456 # Make sure data field exists in SD file..
|
|
|
457 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
|
|
|
458
|
|
|
459 @CmpdLines = ();
|
|
|
460 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
461 $CmpdString = ReadCmpdString(\*SDFILE);
|
|
|
462 close SDFILE;
|
|
|
463 @CmpdLines = split "\n", $CmpdString;
|
|
|
464 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
465 $SpecifiedDataField = $OptionsInfo{CompoundID};
|
|
|
466 if (!exists $DataFieldValues{$SpecifiedDataField}) {
|
|
|
467 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
|
|
|
468 next FILELIST;
|
|
|
469 }
|
|
|
470 }
|
|
|
471
|
|
|
472 $AllDataFieldsRef = '';
|
|
|
473 $CommonDataFieldsRef = '';
|
|
|
474 if ($CollectDataFields) {
|
|
|
475 my($CmpdCount);
|
|
|
476 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
477 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
|
|
|
478 close SDFILE;
|
|
|
479 }
|
|
|
480
|
|
|
481 # Setup output file names...
|
|
|
482 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
483 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
|
|
|
484
|
|
|
485 $TextOutFileExt = "csv";
|
|
|
486 if ($Options{outdelim} =~ /^tab$/i) {
|
|
|
487 $TextOutFileExt = "tsv";
|
|
|
488 }
|
|
|
489 $SDOutFileExt = $FileExt;
|
|
|
490 $FPOutFileExt = "fpf";
|
|
|
491
|
|
|
492 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
|
|
|
493 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
494 if ($RootFileName && $RootFileExt) {
|
|
|
495 $FileName = $RootFileName;
|
|
|
496 }
|
|
|
497 else {
|
|
|
498 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
499 }
|
|
|
500 $OutFileRoot = $FileName;
|
|
|
501 }
|
|
|
502 else {
|
|
|
503 $OutFileRoot = "${FileName}ExtendedConnectivityFP";
|
|
|
504 }
|
|
|
505
|
|
|
506 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
|
|
|
507 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
|
|
|
508 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
|
|
|
509
|
|
|
510 if ($OptionsInfo{SDOutput}) {
|
|
|
511 if ($SDFile =~ /$NewSDFileName/i) {
|
|
|
512 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
|
|
|
513 print "Specify a different name using \"-r --root\" option or use default name.\n";
|
|
|
514 next FILELIST;
|
|
|
515 }
|
|
|
516 }
|
|
|
517
|
|
|
518 if (!$OptionsInfo{OverwriteFiles}) {
|
|
|
519 # Check SD and text outout files...
|
|
|
520 if ($OptionsInfo{SDOutput}) {
|
|
|
521 if (-e $NewSDFileName) {
|
|
|
522 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
|
|
|
523 next FILELIST;
|
|
|
524 }
|
|
|
525 }
|
|
|
526 if ($OptionsInfo{FPOutput}) {
|
|
|
527 if (-e $NewFPFileName) {
|
|
|
528 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
|
|
|
529 next FILELIST;
|
|
|
530 }
|
|
|
531 }
|
|
|
532 if ($OptionsInfo{TextOutput}) {
|
|
|
533 if (-e $NewTextFileName) {
|
|
|
534 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
|
|
|
535 next FILELIST;
|
|
|
536 }
|
|
|
537 }
|
|
|
538 }
|
|
|
539
|
|
|
540 $SDFilesInfo{FileOkay}[$Index] = 1;
|
|
|
541
|
|
|
542 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
|
|
|
543 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
|
|
|
544 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
|
|
|
545 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
|
|
|
546
|
|
|
547 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
|
|
|
548 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
|
|
|
549 }
|
|
|
550 }
|
|
|
551
|
|
|
552 # Process option values...
|
|
|
553 sub ProcessOptions {
|
|
|
554 %OptionsInfo = ();
|
|
|
555
|
|
|
556 ProcessAtomIdentifierTypeOptions();
|
|
|
557
|
|
|
558 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
|
|
|
559
|
|
|
560 $OptionsInfo{BitsOrder} = $Options{bitsorder};
|
|
|
561 $OptionsInfo{BitStringFormat} = $Options{bitstringformat};
|
|
|
562
|
|
|
563 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
|
|
|
564 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
|
|
|
565 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
|
|
|
566
|
|
|
567 my(@SpecifiedDataFields);
|
|
|
568 @SpecifiedDataFields = ();
|
|
|
569
|
|
|
570 @{$OptionsInfo{SpecifiedDataFields}} = ();
|
|
|
571 $OptionsInfo{CompoundID} = '';
|
|
|
572
|
|
|
573 if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
|
|
|
574 if ($Options{compoundidmode} =~ /^DataField$/i) {
|
|
|
575 if (!$Options{compoundid}) {
|
|
|
576 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
|
|
|
577 }
|
|
|
578 $OptionsInfo{CompoundID} = $Options{compoundid};
|
|
|
579 }
|
|
|
580 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
581 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
|
|
|
582 }
|
|
|
583 }
|
|
|
584 elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
|
|
|
585 if (!$Options{datafields}) {
|
|
|
586 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
|
|
|
587 }
|
|
|
588 @SpecifiedDataFields = split /\,/, $Options{datafields};
|
|
|
589 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
|
|
|
590 }
|
|
|
591
|
|
|
592 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'ExtendedConnectivityFingerprints';
|
|
|
593
|
|
|
594 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
|
|
|
595
|
|
|
596 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
|
|
|
597
|
|
|
598 $OptionsInfo{Mode} = $Options{mode};
|
|
|
599
|
|
|
600 $OptionsInfo{NeighborhoodRadius} = $Options{neighborhoodradius};
|
|
|
601
|
|
|
602 $OptionsInfo{UsePerlCoreRandom} = ($Options{useperlcorerandom} =~ /^Yes$/i) ? 1 : 0;
|
|
|
603
|
|
|
604 $OptionsInfo{Output} = $Options{output};
|
|
|
605 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
|
|
|
606 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
|
|
|
607 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
|
|
|
608
|
|
|
609 $OptionsInfo{OutDelim} = $Options{outdelim};
|
|
|
610 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
611
|
|
|
612 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
613 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
614
|
|
|
615 my($Size, $MinSize, $MaxSize);
|
|
|
616 $MinSize = 32;
|
|
|
617 $MaxSize = 2**32;
|
|
|
618 $Size = $Options{size};
|
|
|
619 if (!(IsPositiveInteger($Size) && $Size >= $MinSize && $Size <= $MaxSize && IsNumberPowerOfNumber($Size, 2))) {
|
|
|
620 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";
|
|
|
621 }
|
|
|
622 $OptionsInfo{Size} = $Size;
|
|
|
623
|
|
|
624 # Setup default vector string format...
|
|
|
625 #
|
|
|
626 my($VectorStringFormat);
|
|
|
627 $VectorStringFormat = '';
|
|
|
628 if ($Options{vectorstringformat}) {
|
|
|
629 $VectorStringFormat = $Options{vectorstringformat};
|
|
|
630 }
|
|
|
631 else {
|
|
|
632 $VectorStringFormat = ($Options{mode} =~ /^ExtendedConnectivity$/) ? "ValuesString" : "IDsAndValuesString";
|
|
|
633 }
|
|
|
634 $OptionsInfo{VectorStringFormat} = $VectorStringFormat;
|
|
|
635 }
|
|
|
636
|
|
|
637 # Process atom identifier type and related options...
|
|
|
638 #
|
|
|
639 sub ProcessAtomIdentifierTypeOptions {
|
|
|
640
|
|
|
641 $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
|
|
|
642
|
|
|
643 if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
644 ProcessAtomicInvariantsToUseOption();
|
|
|
645 }
|
|
|
646 elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
647 ProcessFunctionalClassesToUse();
|
|
|
648 }
|
|
|
649 elsif ($Options{atomidentifiertype} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
650 # Nothing to do for now...
|
|
|
651 }
|
|
|
652 else {
|
|
|
653 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
654 }
|
|
|
655 }
|
|
|
656
|
|
|
657 # Process specified atomic invariants to use...
|
|
|
658 #
|
|
|
659 sub ProcessAtomicInvariantsToUseOption {
|
|
|
660 my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
|
|
|
661
|
|
|
662 @{$OptionsInfo{AtomicInvariantsToUse}} = ();
|
|
|
663 if (IsEmpty($Options{atomicinvariantstouse})) {
|
|
|
664 die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
|
|
|
665 }
|
|
|
666 $AtomSymbolSpecified = 0;
|
|
|
667 @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
|
|
|
668 for $AtomicInvariant (@AtomicInvariantsWords) {
|
|
|
669 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
|
|
|
670 die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
|
|
|
671 }
|
|
|
672 if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
|
|
|
673 $AtomSymbolSpecified = 1;
|
|
|
674 }
|
|
|
675 push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
|
|
|
676 }
|
|
|
677 if (!$AtomSymbolSpecified) {
|
|
|
678 die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
|
|
|
679 }
|
|
|
680 }
|
|
|
681
|
|
|
682 # Process specified functional classes invariants to use...
|
|
|
683 #
|
|
|
684 sub ProcessFunctionalClassesToUse {
|
|
|
685 my($FunctionalClass, @FunctionalClassesToUseWords);
|
|
|
686
|
|
|
687 @{$OptionsInfo{FunctionalClassesToUse}} = ();
|
|
|
688 if (IsEmpty($Options{functionalclassestouse})) {
|
|
|
689 die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
|
|
|
690 }
|
|
|
691 @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
|
|
|
692 for $FunctionalClass (@FunctionalClassesToUseWords) {
|
|
|
693 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
|
|
|
694 die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
|
|
|
695 }
|
|
|
696 push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
|
|
|
697 }
|
|
|
698 }
|
|
|
699
|
|
|
700 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
701 sub SetupScriptUsage {
|
|
|
702
|
|
|
703 # Retrieve all the options...
|
|
|
704 %Options = ();
|
|
|
705
|
|
|
706 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
|
|
|
707
|
|
|
708 $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
|
|
|
709 $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC,MN';
|
|
|
710 $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
|
|
|
711
|
|
|
712 $Options{bitsorder} = 'Ascending';
|
|
|
713 $Options{bitstringformat} = 'HexadecimalString';
|
|
|
714
|
|
|
715 $Options{compoundidmode} = 'LabelPrefix';
|
|
|
716 $Options{compoundidlabel} = 'CompoundID';
|
|
|
717 $Options{datafieldsmode} = 'CompoundID';
|
|
|
718
|
|
|
719 $Options{filter} = 'Yes';
|
|
|
720
|
|
|
721 $Options{keeplargestcomponent} = 'Yes';
|
|
|
722
|
|
|
723 $Options{mode} = 'ExtendedConnectivity';
|
|
|
724
|
|
|
725 $Options{neighborhoodradius} = 2;
|
|
|
726
|
|
|
727 $Options{useperlcorerandom} = 'yes';
|
|
|
728
|
|
|
729 $Options{output} = 'text';
|
|
|
730 $Options{outdelim} = 'comma';
|
|
|
731 $Options{quote} = 'yes';
|
|
|
732
|
|
|
733 $Options{size} = 1024;
|
|
|
734
|
|
|
735 $Options{vectorstringformat} = '';
|
|
|
736
|
|
|
737 if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "mode|m=s", "neighborhoodradius|n=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "size|s=i", "useperlcorerandom=s", "vectorstringformat|v=s", "workingdir|w=s")) {
|
|
|
738 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
739 }
|
|
|
740 if ($Options{workingdir}) {
|
|
|
741 if (! -d $Options{workingdir}) {
|
|
|
742 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
743 }
|
|
|
744 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
745 }
|
|
|
746 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
|
|
|
747 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
|
|
|
748 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
|
|
|
749 }
|
|
|
750 if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
751 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
752 }
|
|
|
753 if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) {
|
|
|
754 die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n";
|
|
|
755 }
|
|
|
756 if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) {
|
|
|
757 die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n";
|
|
|
758 }
|
|
|
759 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
760 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
761 }
|
|
|
762 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
|
|
|
763 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
|
|
|
764 }
|
|
|
765 if ($Options{filter} !~ /^(Yes|No)$/i) {
|
|
|
766 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
|
|
|
767 }
|
|
|
768 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
|
|
|
769 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
|
|
|
770 }
|
|
|
771 if ($Options{mode} !~ /^(ExtendedConnectivity|ExtendedConnectivityCount|ExtendedConnectivityBits)$/i) {
|
|
|
772 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: ExtendedConnectivity, ExtendedConnecticityCount, or ExtendedConnectivityBits\n";
|
|
|
773 }
|
|
|
774 if (!(IsInteger($Options{neighborhoodradius}) && ($Options{neighborhoodradius} >= 0))) {
|
|
|
775 die "Error: The value specified, $Options{neighborhoodradius}, for option \"-n, --NeighborhoodRadius\" is not valid. Allowed values: >= 0 \n";
|
|
|
776 }
|
|
|
777 if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
|
|
|
778 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
|
|
|
779 }
|
|
|
780 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
781 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
782 }
|
|
|
783 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
784 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
785 }
|
|
|
786 if (!IsPositiveInteger($Options{size})) {
|
|
|
787 die "Error: The value specified, $Options{size}, for option \"-s, --size\" is not valid. Allowed values: > 0 \n";
|
|
|
788 }
|
|
|
789 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
|
|
|
790 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
|
|
|
791 }
|
|
|
792 if ($Options{useperlcorerandom} !~ /^(Yes|No)$/i) {
|
|
|
793 die "Error: The value specified, $Options{useperlcorerandom}, for option \"--UsePerlCoreRandom\" is not valid. Allowed values: Yes or No\n";
|
|
|
794 }
|
|
|
795 if ($Options{vectorstringformat} && $Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
|
|
|
796 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
|
|
|
797 }
|
|
|
798 }
|
|
|
799
|
|
|
800 __END__
|
|
|
801
|
|
|
802 =head1 NAME
|
|
|
803
|
|
|
804 ExtendedConnectivityFingerprints.pl - Generate extended connectivity fingerprints for SD files
|
|
|
805
|
|
|
806 =head1 SYNOPSIS
|
|
|
807
|
|
|
808 ExtendedConnectivityFingerprints.pl SDFile(s)...
|
|
|
809
|
|
|
810 ExtendedConnectivityFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
|
|
|
811 [B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes>]
|
|
|
812 [B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">]
|
|
|
813 [B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
|
|
|
814 [B<--BitsOrder> I<Ascending | Descending>] [B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>]
|
|
|
815 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
|
|
|
816 [B<--CompoundIDMode>] [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">]
|
|
|
817 [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] [B<-f, --Filter> I<Yes | No>]
|
|
|
818 [B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>]
|
|
|
819 [B<-m, --mode> I<ExtendedConnectivity | ExtendedConnecticityCount | ExtendedConnecticityBits>]
|
|
|
820 [B<-n, --NeighborhoodRadius> I<number>] [B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD | FP | text | all>]
|
|
|
821 [B<-o, --overwrite>] [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] [B<-s, --size> I<number>]
|
|
|
822 [B<--UsePerlCoreRandom> I<Yes | No>]
|
|
|
823 [B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>]
|
|
|
824 [B<-w, --WorkingDir> dirname] SDFile(s)...
|
|
|
825
|
|
|
826 =head1 DESCRIPTION
|
|
|
827
|
|
|
828 Generate extended connectivity fingerprints [ Ref 48, Ref 52 ] for I<SDFile(s)> and create appropriate
|
|
|
829 SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to molecular fingerprints.
|
|
|
830
|
|
|
831 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
|
|
|
832 and I<.sd>. All other file names are ignored. All the SD files in a current directory
|
|
|
833 can be specified either by I<*.sdf> or the current directory name.
|
|
|
834
|
|
|
835 The current release of MayaChemTools supports generation of extended connectivity fingerprints
|
|
|
836 corresponding to following B<-a, --AtomIdentifierTypes>:
|
|
|
837
|
|
|
838 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
839 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
840 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
841
|
|
|
842 Based on values specified for B<-a, --AtomIdentifierType>, B<--AtomicInvariantsToUse>
|
|
|
843 and B<--FunctionalClassesToUse>, initial atom types are assigned to all non-hydrogen atoms in
|
|
|
844 a molecule and these atom types strings are converted into initial atom identifier integers using
|
|
|
845 B<TextUtil::HashCode> function. The duplicate atom identifiers are removed.
|
|
|
846
|
|
|
847 For B<-n, --NeighborhoodRadius> value of I<0>, the initial set of unique atom identifiers comprises
|
|
|
848 the molecule fingerprints. Otherwise, atom neighborhoods are generated for each non-hydrogen
|
|
|
849 atom up to specified B<-n, --NeighborhoodRadius> value. For each non-hydrogen central atom
|
|
|
850 at a specific radius, its neighbors at next radius level along with their bond orders and previously
|
|
|
851 calculated atom identifiers are collected which in turn are used to generate a new integer
|
|
|
852 atom identifier; the bond orders and atom identifier pairs list is first sorted by bond order
|
|
|
853 followed by atom identifiers to make these values graph invariant.
|
|
|
854
|
|
|
855 After integer atom identifiers have been generated for all non-hydrogen atoms at all specified
|
|
|
856 neighborhood radii, the duplicate integer atom identifiers corresponding to same hash code
|
|
|
857 value generated using B<TextUtil::HashCode> are tracked by keeping the atom identifiers at
|
|
|
858 lower radius. Additionally, all structurally duplicate integer atom identifiers at each specified
|
|
|
859 radius are also tracked by identifying equivalent atoms and bonds corresponding to substructures
|
|
|
860 used for generating atom identifier and keeping integer atom identifier with lowest value.
|
|
|
861
|
|
|
862 For I<ExtendedConnnectivity> value of fingerprints B<-m, --mode>, the duplicate identifiers are
|
|
|
863 removed from the list and the unique atom identifiers constitute the extended connectivity
|
|
|
864 fingerprints of a molecule.
|
|
|
865
|
|
|
866 For I<ExtendedConnnectivityCount> value of fingerprints B<-m, --mode>, the occurrence of each
|
|
|
867 unique atom identifiers appears is counted and the unique atom identifiers along with their
|
|
|
868 count constitute the extended connectivity fingerprints of a molecule.
|
|
|
869
|
|
|
870 For I<ExtendedConnectivityBits> value of fingerprints B<-m, --mode>, the unique atom identifiers
|
|
|
871 are used as a random number seed to generate a random integer value between 0 and B<--Size> which
|
|
|
872 in turn is used to set corresponding bits in the fingerprint bit-vector string.
|
|
|
873
|
|
|
874 Example of I<SD> file containing extended connectivity fingerprints string data:
|
|
|
875
|
|
|
876 ... ...
|
|
|
877 ... ...
|
|
|
878 $$$$
|
|
|
879 ... ...
|
|
|
880 ... ...
|
|
|
881 ... ...
|
|
|
882 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
883 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
884 ... ...
|
|
|
885 2 3 1 0 0 0 0
|
|
|
886 ... ...
|
|
|
887 M END
|
|
|
888 > <CmpdID>
|
|
|
889 Cmpd1
|
|
|
890
|
|
|
891 > <ExtendedConnectivityFingerprints>
|
|
|
892 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radiu
|
|
|
893 s2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391 66
|
|
|
894 6191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414087
|
|
|
895 99 49532520 64643108 79385615 96062769 273726379 564565671 855141035 90
|
|
|
896 6706094 988546669 1018231313 1032696425 1197507444 1331250018 133853...
|
|
|
897
|
|
|
898 $$$$
|
|
|
899 ... ...
|
|
|
900 ... ...
|
|
|
901
|
|
|
902 Example of I<FP> file containing extended connectivity fingerprints string data:
|
|
|
903
|
|
|
904 #
|
|
|
905 # Package = MayaChemTools 7.4
|
|
|
906 # Release Date = Oct 21, 2010
|
|
|
907 #
|
|
|
908 # TimeStamp = Fri Mar 11 14:43:57 2011
|
|
|
909 #
|
|
|
910 # FingerprintsStringType = FingerprintsVector
|
|
|
911 #
|
|
|
912 # Description = ExtendedConnectivity:AtomicInvariantsAtomTypes:Radius2
|
|
|
913 # VectorStringFormat = ValuesString
|
|
|
914 # VectorValuesType = AlphaNumericalValues
|
|
|
915 #
|
|
|
916 Cmpd1 60;73555770 333564680 352413391 666191900 1001270906 137167432...
|
|
|
917 Cmpd2 41;73555770 333564680 666191900 1142173602 1363635752 14814699...
|
|
|
918 ... ...
|
|
|
919 ... ..
|
|
|
920
|
|
|
921 Example of CSV I<Text> file containing extended connectivity fingerprints string data:
|
|
|
922
|
|
|
923 "CompoundID","ExtendedConnectivityFingerprints"
|
|
|
924 "Cmpd1","FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTy
|
|
|
925 pes:Radius2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352
|
|
|
926 413391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
927 2141408799 49532520 64643108 79385615 96062769 273726379 564565671 8551
|
|
|
928 41035 906706094 988546669 1018231313 1032696425 1197507444 13312500..."
|
|
|
929 ... ...
|
|
|
930 ... ...
|
|
|
931
|
|
|
932 The current release of MayaChemTools generates the following types of extended connectivity
|
|
|
933 fingerprints vector strings:
|
|
|
934
|
|
|
935 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
936 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
937 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
938 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
939 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
940 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
941
|
|
|
942 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
943 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
944 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
945 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
946 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
|
|
|
947 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
|
|
|
948
|
|
|
949 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
950 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
951 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
952 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
953 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
954 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
955
|
|
|
956 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
957 es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
|
|
|
958 0300000091000004000000020000100000000124008200020000000040020000000000
|
|
|
959 2080000000820040010020000000008040000000000080001000000000400000000000
|
|
|
960 4040000090000061010000000800200000000000001400000000020080000000000020
|
|
|
961 00008020200000408000
|
|
|
962
|
|
|
963 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
|
|
|
964 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
|
|
|
965 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
|
|
966 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
|
|
967 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
|
|
|
968 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
|
|
969
|
|
|
970 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
|
|
|
971 Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
|
|
|
972 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
|
|
|
973 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
|
|
|
974 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
|
|
|
975 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1
|
|
|
976
|
|
|
977 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
|
|
|
978 s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
|
|
|
979 0000000001000100000000001000000000000000000000000000000000101000000010
|
|
|
980 0000001000000000010000000000000000000000000000000000000000000000000100
|
|
|
981 0000000000001000000000000001000000000001001000000000000000000000000000
|
|
|
982 0000000000000000100000000000001000000000000000000000000000000000000...
|
|
|
983
|
|
|
984 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
|
|
|
985 lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
|
|
|
986 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
|
|
|
987 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
|
|
|
988 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
|
|
|
989 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...
|
|
|
990
|
|
|
991 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
992 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
993 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
994 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
995 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
996 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
|
|
|
997
|
|
|
998 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
|
|
|
999 haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
|
|
|
1000 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
|
|
|
1001 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
|
|
|
1002 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
|
|
|
1003 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...
|
|
|
1004
|
|
|
1005 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
|
|
|
1006 aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
|
|
|
1007 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
|
|
|
1008 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
|
|
|
1009 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
|
|
|
1010 41915747 679881756 721736571 794256218 908276640 992898760 10987549...
|
|
|
1011
|
|
|
1012 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
|
|
|
1013 aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
|
|
|
1014 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
|
|
|
1015 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
|
|
|
1016 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
|
|
|
1017 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...
|
|
|
1018
|
|
|
1019 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
|
|
|
1020 NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
|
|
|
1021 700688206 265614156 363161397 681332588 810600886 885767127 950172500
|
|
|
1022 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
|
|
|
1023 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
|
|
|
1024 654 256360355 279492740 291251259 317592700 333763396 972105960 101...
|
|
|
1025
|
|
|
1026 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
|
|
|
1027 umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
|
|
|
1028 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
|
|
|
1029 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
|
|
|
1030 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
|
|
|
1031 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...
|
|
|
1032
|
|
|
1033 =head1 OPTIONS
|
|
|
1034
|
|
|
1035 =over 4
|
|
|
1036
|
|
|
1037 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
|
|
|
1038
|
|
|
1039 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
1040 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
1041 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
1042 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
|
|
|
1043
|
|
|
1044 The supported aromaticity model names along with model specific control parameters
|
|
|
1045 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
|
|
|
1046 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
|
|
|
1047 this file during class instantiation and makes it available to method B<DetectAromaticity>
|
|
|
1048 for detecting aromaticity corresponding to a specific model.
|
|
|
1049
|
|
|
1050 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | FunctionalClassAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
|
|
|
1051
|
|
|
1052 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
|
|
|
1053 atoms during calculation of extended connectivity fingerprints [ Ref 48, Ref 52]. Possible values
|
|
|
1054 in the current release are: I<AtomicInvariantsAtomTypes, FunctionalClassAtomTypes,
|
|
|
1055 DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
1056 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
|
|
|
1057
|
|
|
1058 =item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">
|
|
|
1059
|
|
|
1060 This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1061 option. It's a list of comma separated valid atomic invariant atom types.
|
|
|
1062
|
|
|
1063 Possible values for atomic invarians are: I<AS, X, BO, LBO, SB, DB, TB,
|
|
|
1064 H, Ar, RA, FC, MN, SM>. Default value [ Ref 24 ]: I<AS,X,BO,H,FC,MN>.
|
|
|
1065
|
|
|
1066 The atomic invariants abbreviations correspond to:
|
|
|
1067
|
|
|
1068 AS = Atom symbol corresponding to element symbol
|
|
|
1069
|
|
|
1070 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
1071 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
1072 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
1073 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1074 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1075 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1076 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
1077 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
1078 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
1079 FC<+n/-n> = Formal charge assigned to atom
|
|
|
1080 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
1081 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
1082 3 (triplet)
|
|
|
1083
|
|
|
1084 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
1085
|
|
|
1086 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
1087
|
|
|
1088 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
1089 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
1090
|
|
|
1091 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
1092 are also allowed:
|
|
|
1093
|
|
|
1094 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
1095 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
1096 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
1097 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
1098 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1099 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1100 H : NumOfImplicitAndExplicitHydrogens
|
|
|
1101 Ar : Aromatic
|
|
|
1102 RA : RingAtom
|
|
|
1103 FC : FormalCharge
|
|
|
1104 MN : MassNumber
|
|
|
1105 SM : SpinMultiplicity
|
|
|
1106
|
|
|
1107 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
|
|
|
1108 atom types.
|
|
|
1109
|
|
|
1110 =item B<--BitsOrder> I<Ascending | Descending>
|
|
|
1111
|
|
|
1112 Bits order to use during generation of fingerprints bit-vector string for I<ExtendedConnectivityBits>
|
|
|
1113 value of B<-m, --mode> option. Possible values: I<Ascending, Descending>. Default: I<Ascending>.
|
|
|
1114
|
|
|
1115 I<Ascending> bit order which corresponds to first bit in each byte as the lowest bit as
|
|
|
1116 opposed to the highest bit.
|
|
|
1117
|
|
|
1118 Internally, bits are stored in I<Ascending> order using Perl vec function. Regardless
|
|
|
1119 of machine order, big-endian or little-endian, vec function always considers first
|
|
|
1120 string byte as the lowest byte and first bit within each byte as the lowest bit.
|
|
|
1121
|
|
|
1122 =item B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>
|
|
|
1123
|
|
|
1124 Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
1125 B<--output> used during I<ExtendedConnectivityBits> value of B<-m, --mode> option. Possible
|
|
|
1126 values: I<BinaryString, HexadecimalString>. Default value: I<BinaryString>.
|
|
|
1127
|
|
|
1128 I<BinaryString> corresponds to an ASCII string containing 1s and 0s. I<HexadecimalString>
|
|
|
1129 contains bit values in ASCII hexadecimal format.
|
|
|
1130
|
|
|
1131 Examples:
|
|
|
1132
|
|
|
1133 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
1134 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
1135 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
1136 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
1137 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
1138 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
1139
|
|
|
1140 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
|
|
|
1141 s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
|
|
|
1142 0000000001000100000000001000000000000000000000000000000000101000000010
|
|
|
1143 0000001000000000010000000000000000000000000000000000000000000000000100
|
|
|
1144 0000000000001000000000000001000000000001001000000000000000000000000000
|
|
|
1145 0000000000000000100000000000001000000000000000000000000000000000000...
|
|
|
1146
|
|
|
1147 =item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">
|
|
|
1148
|
|
|
1149 This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1150 option. It's a list of comma separated valid functional classes.
|
|
|
1151
|
|
|
1152 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1153 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
|
|
|
1154
|
|
|
1155 The functional class abbreviations correspond to:
|
|
|
1156
|
|
|
1157 HBD: HydrogenBondDonor
|
|
|
1158 HBA: HydrogenBondAcceptor
|
|
|
1159 PI : PositivelyIonizable
|
|
|
1160 NI : NegativelyIonizable
|
|
|
1161 Ar : Aromatic
|
|
|
1162 Hal : Halogen
|
|
|
1163 H : Hydrophobic
|
|
|
1164 RA : RingAtom
|
|
|
1165 CA : ChainAtom
|
|
|
1166
|
|
|
1167 Functional class atom type specification for an atom corresponds to:
|
|
|
1168
|
|
|
1169 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
1170
|
|
|
1171 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1172 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1173
|
|
|
1174 HydrogenBondDonor: NH, NH2, OH
|
|
|
1175 HydrogenBondAcceptor: N[!H], O
|
|
|
1176 PositivelyIonizable: +, NH2
|
|
|
1177 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1178
|
|
|
1179 =item B<--CompoundID> I<DataFieldName or LabelPrefixString>
|
|
|
1180
|
|
|
1181 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
|
|
|
1182
|
|
|
1183 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
|
|
|
1184 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
|
|
1185 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
|
|
|
1186 look like Cmpd<Number>.
|
|
|
1187
|
|
|
1188 Examples for I<DataField> value of B<--CompoundIDMode>:
|
|
|
1189
|
|
|
1190 MolID
|
|
|
1191 ExtReg
|
|
|
1192
|
|
|
1193 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
|
|
|
1194
|
|
|
1195 Compound
|
|
|
1196
|
|
|
1197 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
1198 instead of default value of Cmpd<Number>.
|
|
|
1199
|
|
|
1200 =item B<--CompoundIDLabel> I<text>
|
|
|
1201
|
|
|
1202 Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value
|
|
|
1203 of B<--DataFieldsMode> option. Default: I<CompoundID>.
|
|
|
1204
|
|
|
1205 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
1206
|
|
|
1207 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
|
|
|
1208 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value;
|
|
|
1209 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination
|
|
|
1210 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
1211
|
|
|
1212 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
1213 Default: I<LabelPrefix>.
|
|
|
1214
|
|
|
1215 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
|
|
|
1216 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
1217 values are replaced with sequential compound IDs.
|
|
|
1218
|
|
|
1219 This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
|
|
|
1220
|
|
|
1221 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,...">
|
|
|
1222
|
|
|
1223 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
1224 with generated fingerprints for I<text | all> values of B<--output> option.
|
|
|
1225
|
|
|
1226 This is only used for I<Specify> value of B<--DataFieldsMode> option.
|
|
|
1227
|
|
|
1228 Examples:
|
|
|
1229
|
|
|
1230 Extreg
|
|
|
1231 MolID,CompoundName
|
|
|
1232
|
|
|
1233 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
|
|
|
1234
|
|
|
1235 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
|
|
|
1236 with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD
|
|
|
1237 data field; transfer SD data files common to all compounds; extract specified data fields;
|
|
|
1238 generate a compound ID using molname line, a compound prefix, or a combination of both.
|
|
|
1239 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
|
|
|
1240
|
|
|
1241 =item B<-f, --Filter> I<Yes | No>
|
|
|
1242
|
|
|
1243 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
|
|
|
1244 Default value: I<Yes>.
|
|
|
1245
|
|
|
1246 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
1247 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
1248
|
|
|
1249 =item B<--FingerprintsLabel> I<text>
|
|
|
1250
|
|
|
1251 SD data label or text file column label to use for fingerprints string in output SD or
|
|
|
1252 CSV/TSV text file(s) specified by B<--output>. Default value: I<ExtendedConnectivityFingerprints>.
|
|
|
1253
|
|
|
1254 =item B<-h, --help>
|
|
|
1255
|
|
|
1256 Print this help message.
|
|
|
1257
|
|
|
1258 =item B<-k, --KeepLargestComponent> I<Yes | No>
|
|
|
1259
|
|
|
1260 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
1261 I<Yes or No>. Default value: I<Yes>.
|
|
|
1262
|
|
|
1263 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
1264 in two different ways: use all connected components or just the largest connected
|
|
|
1265 component. By default, all atoms except for the largest connected component are
|
|
|
1266 deleted before generation of fingerprints.
|
|
|
1267
|
|
|
1268 =item B<-m, --mode> I<ExtendedConnectivity | ExtendedConnectivityCount | ExtendedConnectivityBits>
|
|
|
1269
|
|
|
1270 Specify type of extended connectivity fingerprints to generate for molecules in I<SDFile(s)>.
|
|
|
1271 Possible values: I<ExtendedConnectivity, ExtendedConnecticityCount or
|
|
|
1272 ExtendedConnectivityBits>. Default value: I<ExtendedConnectivity>.
|
|
|
1273
|
|
|
1274 For I<ExtendedConnnectivity> value of fingerprints B<-m, --mode>, a fingerprint vector
|
|
|
1275 containing unique atom identifiers constitute the extended connectivity fingerprints
|
|
|
1276 of a molecule.
|
|
|
1277
|
|
|
1278 For I<ExtendedConnnectivityCount> value of fingerprints B<-m, --mode>, a fingerprint vector
|
|
|
1279 containing unique atom identifiers along with their count constitute the extended connectivity
|
|
|
1280 fingerprints of a molecule.
|
|
|
1281
|
|
|
1282 For I<ExtendedConnnectivityBits> value of fingerprints B<-m, --mode>, a fingerprint bit vector
|
|
|
1283 indicating presence/absence of structurally unique atom identifiers constitute the extended
|
|
|
1284 connectivity fingerprints of a molecule.
|
|
|
1285
|
|
|
1286 =item B<-n, --NeighborhoodRadius> I<number>
|
|
|
1287
|
|
|
1288 Atomic neighborhood radius for generating extended connectivity neighborhoods. Default
|
|
|
1289 value: I<2>. Valid values: >= 0. Neighborhood radius of zero correspond to just the list
|
|
|
1290 of non-hydrogen atoms.
|
|
|
1291
|
|
|
1292 Default value of I<2> for atomic neighborhood radius generates extended connectivity
|
|
|
1293 fingerprints corresponding to path length or diameter value of I<4> [ Ref 52b ].
|
|
|
1294
|
|
|
1295 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
1296
|
|
|
1297 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
|
|
|
1298 Default value: I<comma>.
|
|
|
1299
|
|
|
1300 =item B<--output> I<SD | FP | text | all>
|
|
|
1301
|
|
|
1302 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>.
|
|
|
1303
|
|
|
1304 =item B<-o, --overwrite>
|
|
|
1305
|
|
|
1306 Overwrite existing files.
|
|
|
1307
|
|
|
1308 =item B<-q, --quote> I<Yes | No>
|
|
|
1309
|
|
|
1310 Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
1311 I<Yes or No>. Default value: I<Yes>.
|
|
|
1312
|
|
|
1313 =item B<-r, --root> I<RootName>
|
|
|
1314
|
|
|
1315 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
1316 <SDFileName><ExtendedConnectivityFP>.<Ext>. The file type determines <Ext>
|
|
|
1317 value. The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
|
1318 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
1319
|
|
|
1320 =item B<-s, --size> I<number>
|
|
|
1321
|
|
|
1322 Size of bit-vector to use during generation of fingerprints bit-vector string for
|
|
|
1323 I<ExtendedConnectivityBits> value of B<-m, --mode>. Default value: I<1024>.
|
|
|
1324 Valid values correspond to any positive integer which satisfies the following criteria:
|
|
|
1325 power of 2, >= 32 and <= 2 ** 32.
|
|
|
1326
|
|
|
1327 Examples:
|
|
|
1328
|
|
|
1329 512
|
|
|
1330 1024
|
|
|
1331 2048
|
|
|
1332
|
|
|
1333 =item B<--UsePerlCoreRandom> I<Yes | No>
|
|
|
1334
|
|
|
1335 Specify whether to use Perl CORE::rand or MayaChemTools MathUtil::random function
|
|
|
1336 during random number generation for setting bits in fingerprints bit-vector strings. Possible
|
|
|
1337 values: I<Yes or No>. Default value: I<Yes>.
|
|
|
1338
|
|
|
1339 I<No> value option for B<--UsePerlCoreRandom> allows the generation of fingerprints
|
|
|
1340 bit-vector strings which are same across different platforms.
|
|
|
1341
|
|
|
1342 The random number generator implemented in MayaChemTools is a variant of
|
|
|
1343 linear congruential generator (LCG) as described by Miller et al. [ Ref 120 ].
|
|
|
1344 It is also referred to as Lehmer random number generator or Park-Miller
|
|
|
1345 random number generator.
|
|
|
1346
|
|
|
1347 Unlike Perl's core random number generator function rand, the random number
|
|
|
1348 generator implemented in MayaChemTools, MathUtil::random, generates consistent
|
|
|
1349 random values across different platforms for a specific random seed and leads
|
|
|
1350 to generation of portable fingerprints bit-vector strings.
|
|
|
1351
|
|
|
1352 =item B<-v, --VectorStringFormat> I<ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>
|
|
|
1353
|
|
|
1354 Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
1355 B<--output> used during <ExtendedConnectivityCount> value of B<-m, --mode> option. Possible
|
|
|
1356 values: I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
1357 ValuesAndIDsPairsString>.
|
|
|
1358
|
|
|
1359 Default value during <ExtendedConnectivityCount> value of B<-m, --mode> option:
|
|
|
1360 I<IDsAndValuesString>.
|
|
|
1361
|
|
|
1362 Default value during <ExtendedConnectivity> value of B<-m, --mode> option: I<ValuesString>.
|
|
|
1363
|
|
|
1364 Examples:
|
|
|
1365
|
|
|
1366 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
1367 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
1368 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
1369 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
1370 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
1371 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
1372
|
|
|
1373 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
1374 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
1375 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
1376 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
1377 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
|
|
|
1378 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
|
|
|
1379
|
|
|
1380 =item B<-w, --WorkingDir> I<DirName>
|
|
|
1381
|
|
|
1382 Location of working directory. Default: current directory.
|
|
|
1383
|
|
|
1384 =back
|
|
|
1385
|
|
|
1386 =head1 EXAMPLES
|
|
|
1387
|
|
|
1388 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1389 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
1390 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1391
|
|
|
1392 % ExtendedConnectivityFingerprints.pl -r SampleECAIFP -o Sample.sdf
|
|
|
1393
|
|
|
1394 To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
|
|
|
1395 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
1396 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1397
|
|
|
1398 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
|
|
|
1399 -r SampleECAIFP -o Sample.sdf
|
|
|
1400
|
|
|
1401 To generate extended connectivity bits fingerprints as hexadecimal bit-string corresponding to
|
|
|
1402 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
|
|
|
1403 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
|
|
|
1404 vector strings data, type:
|
|
|
1405
|
|
|
1406 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
|
|
|
1407 -r SampleECAIFP -o Sample.sdf
|
|
|
1408
|
|
|
1409 To generate extended connectivity bits fingerprints as binary bit-string corresponding to
|
|
|
1410 neighborhood radius up to 2 using atomic invariants atom types in vector string format and
|
|
|
1411 create a SampleECAIFP.csv file containing sequential compound IDs along with fingerprints
|
|
|
1412 vector strings data, type:
|
|
|
1413
|
|
|
1414 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityBits
|
|
|
1415 --BitStringFormat BinaryString -r SampleECAIFP -o Sample.sdf
|
|
|
1416
|
|
|
1417 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1418 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
|
|
|
1419 and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints
|
|
|
1420 vector strings data, type:
|
|
|
1421
|
|
|
1422 % ExtendedConnectivityFingerprints.pl --output all -r SampleECAIFP
|
|
|
1423 -o Sample.sdf
|
|
|
1424
|
|
|
1425 To generate extended connectivity count fingerprints corresponding to neighborhood radius up to
|
|
|
1426 2 using atomic invariants atom types in vector string format and create SampleECAIFP.sdf, SampleECAIFP.fpf
|
|
|
1427 and SampleECAIFP.csv files containing sequential compound IDs in CSV file along with fingerprints
|
|
|
1428 vector strings data, type:
|
|
|
1429
|
|
|
1430 % ExtendedConnectivityFingerprints.pl -m ExtendedConnectivityCount
|
|
|
1431 --output all -r SampleECAIFP -o Sample.sdf
|
|
|
1432
|
|
|
1433 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1434 2 using functional class atom types in vector string format and create a SampleECFCFP.csv file
|
|
|
1435 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1436
|
|
|
1437 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
1438 -r SampleECFCFP -o Sample.sdf
|
|
|
1439
|
|
|
1440 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1441 2 using DREIDING atom types in vector string format and create a SampleECFP.csv file
|
|
|
1442 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1443
|
|
|
1444 % ExtendedConnectivityFingerprints.pl -a DREIDINGAtomTypes
|
|
|
1445 -r SampleECFP -o Sample.sdf
|
|
|
1446
|
|
|
1447 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1448 2 using E-state atom types in vector string format and create a SampleECFP.csv file
|
|
|
1449 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1450
|
|
|
1451 % ExtendedConnectivityFingerprints.pl -a EStateAtomTypes
|
|
|
1452 -r SampleECFP -o Sample.sdf
|
|
|
1453
|
|
|
1454 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1455 2 using MMFF94 atom types in vector string format and create a SampleECFP.csv file
|
|
|
1456 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1457
|
|
|
1458 % ExtendedConnectivityFingerprints.pl -a MMFF94AtomTypes
|
|
|
1459 -r SampleECFP -o Sample.sdf
|
|
|
1460
|
|
|
1461 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1462 2 using SLogP atom types in vector string format and create a SampleECFP.csv file
|
|
|
1463 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1464
|
|
|
1465 % ExtendedConnectivityFingerprints.pl -a SLogPAtomTypes
|
|
|
1466 -r SampleECFP -o Sample.sdf
|
|
|
1467
|
|
|
1468 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1469 2 using SYBYL atom types in vector string format and create a SampleECFP.csv file
|
|
|
1470 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1471
|
|
|
1472 % ExtendedConnectivityFingerprints.pl -a SYBYLAtomTypes
|
|
|
1473 -r SampleECFP -o Sample.sdf
|
|
|
1474
|
|
|
1475 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1476 2 using TPSA atom types in vector string format and create a SampleECFP.csv file
|
|
|
1477 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1478
|
|
|
1479 % ExtendedConnectivityFingerprints.pl -a TPSAAtomTypes
|
|
|
1480 -r SampleECFP -o Sample.sdf
|
|
|
1481
|
|
|
1482 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1483 2 using UFF atom types in vector string format and create a SampleECFP.csv file
|
|
|
1484 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1485
|
|
|
1486 % ExtendedConnectivityFingerprints.pl -a UFFAtomTypes
|
|
|
1487 -r SampleECFP -o Sample.sdf
|
|
|
1488
|
|
|
1489 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1490 3 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
1491 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1492
|
|
|
1493 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes -n 3
|
|
|
1494 -r SampleECAIFP -o Sample.sdf
|
|
|
1495
|
|
|
1496 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1497 3 using functional class atom types in vector string format and create a SampleECFCFP.csv file
|
|
|
1498 containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1499
|
|
|
1500 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes -n 3
|
|
|
1501 -r SampleECFCFP -o Sample.sdf
|
|
|
1502
|
|
|
1503 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1504 2 using only AS,X atomic invariants atom types in vector string format and create a
|
|
|
1505 SampleECAIFP.csv file containing sequential compound IDs along with fingerprints vector
|
|
|
1506 strings data, type:
|
|
|
1507
|
|
|
1508 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1509 --AtomicInvariantsToUse "AS,X" -r SampleECAIFP -o Sample.sdf
|
|
|
1510
|
|
|
1511 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1512 2 using only HBD,HBA functional class atom types in vector string format and create a
|
|
|
1513 SampleECFCFP.csv file containing sequential compound IDs along with fingerprints vector
|
|
|
1514 strings data, type:
|
|
|
1515
|
|
|
1516 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
1517 --FunctionalClassesToUse "HBD,HBA" -r SampleECFCFP -o Sample.sdf
|
|
|
1518
|
|
|
1519 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1520 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.csv
|
|
|
1521 file containing compound ID from molecule name line along with fingerprints vector strings
|
|
|
1522 data, type:
|
|
|
1523
|
|
|
1524 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1525 --DataFieldsMode CompoundID -CompoundIDMode MolName
|
|
|
1526 -r SampleECAIFP -o Sample.sdf
|
|
|
1527
|
|
|
1528 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1529 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
|
|
|
1530 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
1531 data, type:
|
|
|
1532
|
|
|
1533 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
1534 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID Mol_ID
|
|
|
1535 -r SampleECFCFP -o Sample.sdf
|
|
|
1536
|
|
|
1537 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1538 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
|
|
|
1539 file containing compound ID using combination of molecule name line and an explicit compound
|
|
|
1540 prefix along with fingerprints vector strings data, type:
|
|
|
1541
|
|
|
1542 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1543 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
1544 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleECAIFP -o Sample.sdf
|
|
|
1545
|
|
|
1546 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1547 2 using functional class atom types in vector string format and create a SampleECFCFP.csv
|
|
|
1548 file containing specific data fields columns along with fingerprints vector strings
|
|
|
1549 data, type:
|
|
|
1550
|
|
|
1551 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
1552 --DataFieldsMode Specify --DataFields Mol_ID -r SampleECFCFP
|
|
|
1553 -o Sample.sdf
|
|
|
1554
|
|
|
1555 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1556 2 using atomic invariants atom types in vector string format and create a SampleECAIFP.tsv
|
|
|
1557 file containing common data fields columns along with fingerprints vector strings data, type:
|
|
|
1558
|
|
|
1559 % ExtendedConnectivityFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1560 --DataFieldsMode Common -r SampleECAIFP -o Sample.sdf
|
|
|
1561
|
|
|
1562 To generate extended connectivity fingerprints corresponding to neighborhood radius up to
|
|
|
1563 2 using functional class atom types in vector string format and create SampleECFCFP.sdf, SampleECFCFP.fpf
|
|
|
1564 and SampleECFCFP.csv files containing all data fields columns in CSV file along with fingerprints
|
|
|
1565 vector strings data, type:
|
|
|
1566
|
|
|
1567 % ExtendedConnectivityFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
1568 --DataFieldsMode All --output all -r SampleECFCFP
|
|
|
1569 -o Sample.sdf
|
|
|
1570
|
|
|
1571 =head1 AUTHOR
|
|
|
1572
|
|
|
1573 Manish Sud <msud@san.rr.com>
|
|
|
1574
|
|
|
1575 =head1 SEE ALSO
|
|
|
1576
|
|
|
1577 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
1578 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
1579 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
|
|
|
1580 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
1581
|
|
|
1582 =head1 COPYRIGHT
|
|
|
1583
|
|
|
1584 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1585
|
|
|
1586 This file is part of MayaChemTools.
|
|
|
1587
|
|
|
1588 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1589 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1590 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1591 any later version.
|
|
|
1592
|
|
|
1593 =cut
|
