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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: AtomTypesFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:19 $
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5 # $Revision: 1.25 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use MoleculeFileIO;
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39 use FileIO::FingerprintsSDFileIO;
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40 use FileIO::FingerprintsTextFileIO;
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41 use FileIO::FingerprintsFPFileIO;
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42 use AtomTypes::AtomicInvariantsAtomTypes;
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43 use AtomTypes::FunctionalClassAtomTypes;
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44 use Fingerprints::AtomTypesFingerprints;
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45
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46 my($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 GenerateAtomTypesFingerprints($FileIndex);
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84 }
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85 }
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86 print "\n$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 GenerateAtomTypesFingerprints {
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97 my($FileIndex) = @_;
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98 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $AtomTypesFingerprints, $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 $AtomTypesFingerprints = GenerateMoleculeFingerprints($Molecule);
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124 if (!$AtomTypesFingerprints) {
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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, $AtomTypesFingerprints, $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} =~ /^AtomTypesBits$/i) {
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221 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsBitVectorString', 'BitStringFormat' => $OptionsInfo{BitStringFormat}, 'BitsOrder' => $OptionsInfo{BitsOrder});
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222 }
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223 elsif ($OptionsInfo{Mode} =~ /^AtomTypesCount$/i) {
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224 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
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225 }
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226
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227 if ($OptionsInfo{SDOutput}) {
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228 $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
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229 print "Generating SD file $NewFPSDFile...\n";
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230 $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
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231 $NewFPSDFileIO->Open();
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232 }
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233
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234 if ($OptionsInfo{FPOutput}) {
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235 $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
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236 print "Generating FP file $NewFPFile...\n";
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237 $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
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238 $NewFPFileIO->Open();
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239 }
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240
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241 if ($OptionsInfo{TextOutput}) {
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242 my($ColLabelsRef);
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243
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244 $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
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245 $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
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246
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247 print "Generating text file $NewFPTextFile...\n";
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248 $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
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249 $NewFPTextFileIO->Open();
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250 }
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251
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252 return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
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253 }
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254
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255 # Write fingerpritns and other data to appropriate output files...
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256 #
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257 sub WriteDataToOutputFiles {
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258 my($FileIndex, $CmpdCount, $Molecule, $AtomTypesFingerprints, $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 $NewFPSDFileIO->WriteFingerprints($AtomTypesFingerprints, $CmpdString);
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271 }
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272
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273 if ($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 $NewFPTextFileIO->WriteFingerprints($AtomTypesFingerprints, $ColValuesRef);
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278 }
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279
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280 if ($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 $NewFPFileIO->WriteFingerprints($AtomTypesFingerprints, $CompoundID);
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285 }
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286 }
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287
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288 # Generate approriate column labels for FPText output file...
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289 #
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290 sub SetupFPTextFileCoulmnLabels {
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291 my($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($AtomTypesFingerprints);
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367
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368 if ($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 $AtomTypesFingerprints = undef;
|
|
|
378 if ($OptionsInfo{Mode} =~ /^AtomTypesCount$/i) {
|
|
|
379 $AtomTypesFingerprints = new Fingerprints::AtomTypesFingerprints('Molecule' => $Molecule, 'Type' => 'AtomTypesCount', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'AtomTypesSetToUse' => $OptionsInfo{AtomTypesSetToUse}, 'IgnoreHydrogens' => $OptionsInfo{IgnoreHydrogens});
|
|
|
380
|
|
|
381 }
|
|
|
382 elsif ($OptionsInfo{Mode} =~ /^AtomTypesBits$/i) {
|
|
|
383 $AtomTypesFingerprints = new Fingerprints::AtomTypesFingerprints('Molecule' => $Molecule, 'Type' => 'AtomTypesBits', 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType}, 'AtomTypesSetToUse' => 'FixedSize', 'IgnoreHydrogens' => $OptionsInfo{IgnoreHydrogens});
|
|
|
384 }
|
|
|
385 else {
|
|
|
386 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AtomTypesCount or AtomTypesBits\n";
|
|
|
387 }
|
|
|
388
|
|
|
389 SetAtomIdentifierTypeValuesToUse($AtomTypesFingerprints);
|
|
|
390
|
|
|
391 # Generate atom types fingerprints...
|
|
|
392 $AtomTypesFingerprints->GenerateFingerprints();
|
|
|
393
|
|
|
394 # Make sure atom types fingerprints generation is successful...
|
|
|
395 if (!$AtomTypesFingerprints->IsFingerprintsGenerationSuccessful()) {
|
|
|
396 return undef;
|
|
|
397 }
|
|
|
398
|
|
|
399 return $AtomTypesFingerprints;
|
|
|
400 }
|
|
|
401
|
|
|
402 # Set atom identifier type to use for generating fingerprints...
|
|
|
403 #
|
|
|
404 sub SetAtomIdentifierTypeValuesToUse {
|
|
|
405 my($AtomTypesFingerprints) = @_;
|
|
|
406
|
|
|
407 if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
408 $AtomTypesFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
|
|
|
409 }
|
|
|
410 elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
411 $AtomTypesFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
|
|
|
412 }
|
|
|
413 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
414 # Nothing to do for now...
|
|
|
415 }
|
|
|
416 else {
|
|
|
417 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
418 }
|
|
|
419 }
|
|
|
420
|
|
|
421 # Retrieve information about SD files...
|
|
|
422 #
|
|
|
423 sub RetrieveSDFilesInfo {
|
|
|
424 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
|
|
|
425
|
|
|
426 %SDFilesInfo = ();
|
|
|
427 @{$SDFilesInfo{FileOkay}} = ();
|
|
|
428 @{$SDFilesInfo{OutFileRoot}} = ();
|
|
|
429 @{$SDFilesInfo{SDOutFileNames}} = ();
|
|
|
430 @{$SDFilesInfo{FPOutFileNames}} = ();
|
|
|
431 @{$SDFilesInfo{TextOutFileNames}} = ();
|
|
|
432 @{$SDFilesInfo{AllDataFieldsRef}} = ();
|
|
|
433 @{$SDFilesInfo{CommonDataFieldsRef}} = ();
|
|
|
434
|
|
|
435 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
|
|
|
436 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
|
|
|
437
|
|
|
438 FILELIST: for $Index (0 .. $#SDFilesList) {
|
|
|
439 $SDFile = $SDFilesList[$Index];
|
|
|
440
|
|
|
441 $SDFilesInfo{FileOkay}[$Index] = 0;
|
|
|
442 $SDFilesInfo{OutFileRoot}[$Index] = '';
|
|
|
443 $SDFilesInfo{SDOutFileNames}[$Index] = '';
|
|
|
444 $SDFilesInfo{FPOutFileNames}[$Index] = '';
|
|
|
445 $SDFilesInfo{TextOutFileNames}[$Index] = '';
|
|
|
446
|
|
|
447 $SDFile = $SDFilesList[$Index];
|
|
|
448 if (!(-e $SDFile)) {
|
|
|
449 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
|
|
|
450 next FILELIST;
|
|
|
451 }
|
|
|
452 if (!CheckFileType($SDFile, "sd sdf")) {
|
|
|
453 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
|
|
|
454 next FILELIST;
|
|
|
455 }
|
|
|
456
|
|
|
457 if ($CheckDataField) {
|
|
|
458 # Make sure data field exists in SD file..
|
|
|
459 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
|
|
|
460
|
|
|
461 @CmpdLines = ();
|
|
|
462 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
463 $CmpdString = ReadCmpdString(\*SDFILE);
|
|
|
464 close SDFILE;
|
|
|
465 @CmpdLines = split "\n", $CmpdString;
|
|
|
466 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
467 $SpecifiedDataField = $OptionsInfo{CompoundID};
|
|
|
468 if (!exists $DataFieldValues{$SpecifiedDataField}) {
|
|
|
469 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
|
|
|
470 next FILELIST;
|
|
|
471 }
|
|
|
472 }
|
|
|
473
|
|
|
474 $AllDataFieldsRef = '';
|
|
|
475 $CommonDataFieldsRef = '';
|
|
|
476 if ($CollectDataFields) {
|
|
|
477 my($CmpdCount);
|
|
|
478 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
479 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
|
|
|
480 close SDFILE;
|
|
|
481 }
|
|
|
482
|
|
|
483 # Setup output file names...
|
|
|
484 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
485 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
|
|
|
486
|
|
|
487 $TextOutFileExt = "csv";
|
|
|
488 if ($Options{outdelim} =~ /^tab$/i) {
|
|
|
489 $TextOutFileExt = "tsv";
|
|
|
490 }
|
|
|
491 $SDOutFileExt = $FileExt;
|
|
|
492 $FPOutFileExt = "fpf";
|
|
|
493
|
|
|
494 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
|
|
|
495 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
496 if ($RootFileName && $RootFileExt) {
|
|
|
497 $FileName = $RootFileName;
|
|
|
498 }
|
|
|
499 else {
|
|
|
500 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
501 }
|
|
|
502 $OutFileRoot = $FileName;
|
|
|
503 }
|
|
|
504 else {
|
|
|
505 $OutFileRoot = $FileName . 'AtomTypesFP';
|
|
|
506 }
|
|
|
507
|
|
|
508 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
|
|
|
509 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
|
|
|
510 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
|
|
|
511
|
|
|
512 if ($OptionsInfo{SDOutput}) {
|
|
|
513 if ($SDFile =~ /$NewSDFileName/i) {
|
|
|
514 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
|
|
|
515 print "Specify a different name using \"-r --root\" option or use default name.\n";
|
|
|
516 next FILELIST;
|
|
|
517 }
|
|
|
518 }
|
|
|
519
|
|
|
520 if (!$OptionsInfo{OverwriteFiles}) {
|
|
|
521 # Check SD and text outout files...
|
|
|
522 if ($OptionsInfo{SDOutput}) {
|
|
|
523 if (-e $NewSDFileName) {
|
|
|
524 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
|
|
|
525 next FILELIST;
|
|
|
526 }
|
|
|
527 }
|
|
|
528 if ($OptionsInfo{FPOutput}) {
|
|
|
529 if (-e $NewFPFileName) {
|
|
|
530 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
|
|
|
531 next FILELIST;
|
|
|
532 }
|
|
|
533 }
|
|
|
534 if ($OptionsInfo{TextOutput}) {
|
|
|
535 if (-e $NewTextFileName) {
|
|
|
536 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
|
|
|
537 next FILELIST;
|
|
|
538 }
|
|
|
539 }
|
|
|
540 }
|
|
|
541
|
|
|
542 $SDFilesInfo{FileOkay}[$Index] = 1;
|
|
|
543
|
|
|
544 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
|
|
|
545 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
|
|
|
546 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
|
|
|
547 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
|
|
|
548
|
|
|
549 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
|
|
|
550 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
|
|
|
551 }
|
|
|
552 }
|
|
|
553
|
|
|
554 # Process option values...
|
|
|
555 sub ProcessOptions {
|
|
|
556 %OptionsInfo = ();
|
|
|
557
|
|
|
558 $OptionsInfo{Mode} = $Options{mode};
|
|
|
559 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
|
|
|
560
|
|
|
561 ProcessAtomIdentifierTypeOptions();
|
|
|
562
|
|
|
563 my($AtomTypesSetToUse);
|
|
|
564 $AtomTypesSetToUse = '';
|
|
|
565 if ($Options{mode} =~ /^AtomTypesBits$/i) {
|
|
|
566 if ($Options{atomtypessettouse} && $Options{atomtypessettouse} !~ /^FixedSize$/) {
|
|
|
567 die "Error: The value specified, $Options{atomtypessettouse}, for option \"-e, --AtomTypesSetToUse\" is not valid. Allowed values for AtomTypesBits of \"-m, --mode\" option: FixedSize\n";
|
|
|
568 }
|
|
|
569 $AtomTypesSetToUse = 'FixedSize';
|
|
|
570 }
|
|
|
571 else {
|
|
|
572 if ($Options{atomidentifiertype} =~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes)$/i && $Options{atomtypessettouse} =~ /^FixedSize$/) {
|
|
|
573 die "Error: The value specified, $Options{atomtypessettouse}, for option \"-e, --AtomTypesSetToUse\" is not valid during \"AtomicInvariantsAtomTypes or FunctionalClassAtomTypes\" value of \"-a, --AtomIdentifierType\". Allowed values: ArbitrarySize\n";
|
|
|
574 }
|
|
|
575 if ($Options{atomidentifiertype} =~ /^TPSAAtomTypes$/i && $Options{atomtypessettouse} =~ /^ArbitrarySize$/) {
|
|
|
576 die "Error: The value specified, $Options{atomtypessettouse}, for option \"-e, --AtomTypesSetToUse\" is not valid during \"TPSAAtomTypes\" value of \"-a, --AtomIdentifierType\". Allowed values: FixedSize\n";
|
|
|
577 }
|
|
|
578 $AtomTypesSetToUse = $Options{atomtypessettouse} ? $Options{atomtypessettouse} : 'ArbitrarySize';
|
|
|
579 }
|
|
|
580 $OptionsInfo{AtomTypesSetToUse} = $AtomTypesSetToUse;
|
|
|
581
|
|
|
582 $OptionsInfo{BitsOrder} = $Options{bitsorder};
|
|
|
583 $OptionsInfo{BitStringFormat} = $Options{bitstringformat};
|
|
|
584
|
|
|
585 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
|
|
|
586 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
|
|
|
587 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
|
|
|
588
|
|
|
589 my(@SpecifiedDataFields);
|
|
|
590 @SpecifiedDataFields = ();
|
|
|
591
|
|
|
592 @{$OptionsInfo{SpecifiedDataFields}} = ();
|
|
|
593 $OptionsInfo{CompoundID} = '';
|
|
|
594
|
|
|
595 if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
|
|
|
596 if ($Options{compoundidmode} =~ /^DataField$/i) {
|
|
|
597 if (!$Options{compoundid}) {
|
|
|
598 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
|
|
|
599 }
|
|
|
600 $OptionsInfo{CompoundID} = $Options{compoundid};
|
|
|
601 }
|
|
|
602 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
603 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
|
|
|
604 }
|
|
|
605 }
|
|
|
606 elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
|
|
|
607 if (!$Options{datafields}) {
|
|
|
608 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
|
|
|
609 }
|
|
|
610 @SpecifiedDataFields = split /\,/, $Options{datafields};
|
|
|
611 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
|
|
|
612 }
|
|
|
613
|
|
|
614 $OptionsInfo{IgnoreHydrogens} = ($Options{ignorehydrogens} =~ /^Yes$/i) ? 1 : 0;
|
|
|
615
|
|
|
616 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'AtomTypesFingerprints';
|
|
|
617
|
|
|
618 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
|
|
|
619
|
|
|
620 if ($Options{fingerprintslabelmode} =~ /^FingerprintsLabelWithIDs$/) {
|
|
|
621 if ($Options{mode} =~ /^(AtomTypesCount)$/i && $Options{atomtypessettouse} =~ /^FixedSize$/i) {
|
|
|
622 # Append atom types to the fingerprints label...
|
|
|
623 my($FixedSizeAtomTypesSetRef);
|
|
|
624 $FixedSizeAtomTypesSetRef = GetFixedSizeAtomTypesSet();
|
|
|
625
|
|
|
626 $OptionsInfo{FingerprintsLabel} .= "; AtomTypes: " . TextUtil::JoinWords($FixedSizeAtomTypesSetRef, " ", 0);
|
|
|
627 }
|
|
|
628 }
|
|
|
629 $OptionsInfo{FingerprintsLabelMode} = $Options{fingerprintslabelmode};
|
|
|
630
|
|
|
631 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
|
|
|
632
|
|
|
633 $OptionsInfo{Output} = $Options{output};
|
|
|
634 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
|
|
|
635 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
|
|
|
636 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
|
|
|
637
|
|
|
638 $OptionsInfo{OutDelim} = $Options{outdelim};
|
|
|
639 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
640
|
|
|
641 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
642 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
643
|
|
|
644 # Setup default vector string format...
|
|
|
645 my($VectorStringFormat);
|
|
|
646 $VectorStringFormat = '';
|
|
|
647 if ($Options{vectorstringformat}) {
|
|
|
648 $VectorStringFormat = $Options{vectorstringformat};
|
|
|
649 }
|
|
|
650 else {
|
|
|
651 $VectorStringFormat = ($Options{atomtypessettouse} =~ /^FixedSize$/) ? "ValuesString" : "IDsAndValuesString";
|
|
|
652 }
|
|
|
653 $OptionsInfo{VectorStringFormat} = $VectorStringFormat;
|
|
|
654 }
|
|
|
655
|
|
|
656 # Process atom identifier type and related options...
|
|
|
657 #
|
|
|
658 sub ProcessAtomIdentifierTypeOptions {
|
|
|
659
|
|
|
660 $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
|
|
|
661
|
|
|
662 if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
663 ProcessAtomicInvariantsToUseOption();
|
|
|
664 }
|
|
|
665 elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
666 ProcessFunctionalClassesToUse();
|
|
|
667 }
|
|
|
668 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
669 # Nothing to do for now...
|
|
|
670 }
|
|
|
671 else {
|
|
|
672 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
673 }
|
|
|
674 }
|
|
|
675
|
|
|
676 # Process specified atomic invariants to use...
|
|
|
677 #
|
|
|
678 sub ProcessAtomicInvariantsToUseOption {
|
|
|
679 my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
|
|
|
680
|
|
|
681 @{$OptionsInfo{AtomicInvariantsToUse}} = ();
|
|
|
682 if (IsEmpty($Options{atomicinvariantstouse})) {
|
|
|
683 die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
|
|
|
684 }
|
|
|
685 $AtomSymbolSpecified = 0;
|
|
|
686 @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
|
|
|
687 for $AtomicInvariant (@AtomicInvariantsWords) {
|
|
|
688 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
|
|
|
689 die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
|
|
|
690 }
|
|
|
691 if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
|
|
|
692 $AtomSymbolSpecified = 1;
|
|
|
693 }
|
|
|
694 push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
|
|
|
695 }
|
|
|
696 if (!$AtomSymbolSpecified) {
|
|
|
697 die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
|
|
|
698 }
|
|
|
699 }
|
|
|
700
|
|
|
701 # Process specified functional classes invariants to use...
|
|
|
702 #
|
|
|
703 sub ProcessFunctionalClassesToUse {
|
|
|
704 my($FunctionalClass, @FunctionalClassesToUseWords);
|
|
|
705
|
|
|
706 @{$OptionsInfo{FunctionalClassesToUse}} = ();
|
|
|
707 if (IsEmpty($Options{functionalclassestouse})) {
|
|
|
708 die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
|
|
|
709 }
|
|
|
710 @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
|
|
|
711 for $FunctionalClass (@FunctionalClassesToUseWords) {
|
|
|
712 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
|
|
|
713 die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
|
|
|
714 }
|
|
|
715 push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
|
|
|
716 }
|
|
|
717 }
|
|
|
718
|
|
|
719 # Get fixed size atom types set...
|
|
|
720 #
|
|
|
721 sub GetFixedSizeAtomTypesSet {
|
|
|
722 my($AtomTypesRef);
|
|
|
723
|
|
|
724 $AtomTypesRef = undef;
|
|
|
725
|
|
|
726 IDENTIFIERTYPE: {
|
|
|
727 if ($OptionsInfo{AtomIdentifierType} =~ /^DREIDINGAtomTypes$/i) {
|
|
|
728 $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? DREIDINGAtomTypes::GetAllPossibleDREIDINGNonHydrogenAtomTypes() : DREIDINGAtomTypes::GetAllPossibleDREIDINGAtomTypes();
|
|
|
729 last IDENTIFIERTYPE;
|
|
|
730 }
|
|
|
731
|
|
|
732 if ($OptionsInfo{AtomIdentifierType} =~ /^EStateAtomTypes$/i) {
|
|
|
733 $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? EStateAtomTypes::GetAllPossibleEStateNonHydrogenAtomTypes() : EStateAtomTypes::GetAllPossibleEStateAtomTypes();
|
|
|
734 last IDENTIFIERTYPE;
|
|
|
735 }
|
|
|
736
|
|
|
737 if ($OptionsInfo{AtomIdentifierType} =~ /^MMFF94AtomTypes$/i) {
|
|
|
738 $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? MMFF94AtomTypes::GetAllPossibleMMFF94NonHydrogenAtomTypes() : MMFF94AtomTypes::GetAllPossibleMMFF94AtomTypes();
|
|
|
739 last IDENTIFIERTYPE;
|
|
|
740 }
|
|
|
741
|
|
|
742 if ($OptionsInfo{AtomIdentifierType} =~ /^SLogPAtomTypes$/i) {
|
|
|
743 $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? SLogPAtomTypes::GetAllPossibleSLogPNonHydrogenAtomTypes() : SLogPAtomTypes::GetAllPossibleSLogPAtomTypes();
|
|
|
744 last IDENTIFIERTYPE;
|
|
|
745 }
|
|
|
746
|
|
|
747 if ($OptionsInfo{AtomIdentifierType} =~ /^SYBYLAtomTypes$/i) {
|
|
|
748 $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? SYBYLAtomTypes::GetAllPossibleSYBYLNonHydrogenAtomTypes() : SYBYLAtomTypes::GetAllPossibleSYBYLAtomTypes();
|
|
|
749 last IDENTIFIERTYPE;
|
|
|
750 }
|
|
|
751
|
|
|
752 if ($OptionsInfo{AtomIdentifierType} =~ /^TPSAAtomTypes$/i) {
|
|
|
753 $AtomTypesRef = TPSAAtomTypes::GetAllPossibleTPSAAtomTypes();
|
|
|
754 last IDENTIFIERTYPE;
|
|
|
755 }
|
|
|
756
|
|
|
757 if ($OptionsInfo{AtomIdentifierType} =~ /^UFFAtomTypes$/i) {
|
|
|
758 $AtomTypesRef = $OptionsInfo{IgnoreHydrogens} ? UFFAtomTypes::GetAllPossibleUFFNonHydrogenAtomTypes() : UFFAtomTypes::GetAllPossibleUFFAtomTypes();
|
|
|
759 last IDENTIFIERTYPE;
|
|
|
760 }
|
|
|
761 die "Error: GetFixedSizeAtomTypesSet: Atom types set for atom indentifier type, $OptionsInfo{AtomIdentifierType}, is not available...";
|
|
|
762 }
|
|
|
763
|
|
|
764 return $AtomTypesRef;
|
|
|
765 }
|
|
|
766
|
|
|
767 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
768 sub SetupScriptUsage {
|
|
|
769
|
|
|
770 # Retrieve all the options...
|
|
|
771 %Options = ();
|
|
|
772
|
|
|
773 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
|
|
|
774
|
|
|
775 $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
|
|
|
776 $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC';
|
|
|
777 $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
|
|
|
778
|
|
|
779 $Options{atomtypessettouse} = 'ArbitrarySize';
|
|
|
780
|
|
|
781 $Options{bitsorder} = 'Ascending';
|
|
|
782 $Options{bitstringformat} = 'BinaryString';
|
|
|
783
|
|
|
784 $Options{compoundidmode} = 'LabelPrefix';
|
|
|
785 $Options{compoundidlabel} = 'CompoundID';
|
|
|
786 $Options{datafieldsmode} = 'CompoundID';
|
|
|
787
|
|
|
788 $Options{filter} = 'Yes';
|
|
|
789
|
|
|
790 $Options{fingerprintslabelmode} = 'FingerprintsLabelOnly';
|
|
|
791 $Options{keeplargestcomponent} = 'Yes';
|
|
|
792
|
|
|
793 $Options{mode} = 'AtomTypesCount';
|
|
|
794
|
|
|
795 $Options{ignorehydrogens} = 'Yes';
|
|
|
796
|
|
|
797 $Options{quote} = 'yes';
|
|
|
798
|
|
|
799 $Options{output} = 'text';
|
|
|
800 $Options{outdelim} = 'comma';
|
|
|
801 $Options{quote} = 'yes';
|
|
|
802
|
|
|
803 $Options{vectorstringformat} = '';
|
|
|
804
|
|
|
805 if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "atomtypessettouse|e=s", "bitsorder=s", "bitstringformat|b=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabelmode=s", "fingerprintslabel=s", "help|h", "ignorehydrogens|i=s", "keeplargestcomponent|k=s", "mode|m=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "vectorstringformat|v=s", "workingdir|w=s")) {
|
|
|
806 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
807 }
|
|
|
808 if ($Options{workingdir}) {
|
|
|
809 if (! -d $Options{workingdir}) {
|
|
|
810 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
811 }
|
|
|
812 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
813 }
|
|
|
814 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
|
|
|
815 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
|
|
|
816 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
|
|
|
817 }
|
|
|
818 if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
819 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
820 }
|
|
|
821 if ($Options{atomtypessettouse} && $Options{atomtypessettouse} !~ /^(ArbitrarySize|FixedSize)$/) {
|
|
|
822 die "Error: The value specified, $Options{atomtypessettouse}, for option \"--AtomTypesSetToUse\" is not valid. Allowed values: ArbitrarySize or FixedSize\n";
|
|
|
823 }
|
|
|
824 if ($Options{bitsorder} !~ /^(Ascending|Descending)$/i) {
|
|
|
825 die "Error: The value specified, $Options{bitsorder}, for option \"--BitsOrder\" is not valid. Allowed values: Ascending or Descending\n";
|
|
|
826 }
|
|
|
827 if ($Options{bitstringformat} !~ /^(BinaryString|HexadecimalString)$/i) {
|
|
|
828 die "Error: The value specified, $Options{bitstringformat}, for option \"-b, --bitstringformat\" is not valid. Allowed values: BinaryString or HexadecimalString\n";
|
|
|
829 }
|
|
|
830 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
831 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
832 }
|
|
|
833 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
|
|
|
834 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
|
|
|
835 }
|
|
|
836 if ($Options{filter} !~ /^(Yes|No)$/i) {
|
|
|
837 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
|
|
|
838 }
|
|
|
839 if ($Options{fingerprintslabelmode} !~ /^(FingerprintsLabelOnly|FingerprintsLabelWithIDs)$/i) {
|
|
|
840 die "Error: The value specified, $Options{fingerprintslabelmode}, for option \"--FingerprintsLabelMode\" is not valid. Allowed values: FingerprintsLabelOnly or FingerprintsLabelWithIDs\n";
|
|
|
841 }
|
|
|
842 if ($Options{ignorehydrogens} !~ /^(Yes|No)$/i) {
|
|
|
843 die "Error: The value specified, $Options{ignorehydrogens}, for option \"-i, --IgnoreHydrogens\" is not valid. Allowed values: Yes or No\n";
|
|
|
844 }
|
|
|
845 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
|
|
|
846 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
|
|
|
847 }
|
|
|
848 if ($Options{mode} !~ /^(AtomTypesCount|AtomTypesBits)$/i) {
|
|
|
849 die "Error: The value specified, $Options{mode}, for option \"-m, --mode\" is not valid. Allowed values: AtomTypesCount, or AtomTypesBits\n";
|
|
|
850 }
|
|
|
851 if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
|
|
|
852 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
|
|
|
853 }
|
|
|
854 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
855 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
856 }
|
|
|
857 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
858 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
859 }
|
|
|
860 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
|
|
|
861 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not allowed with, semicolon value of \"--outdelim\" option: Fingerprints string use semicolon as delimiter for various data fields and must be quoted.\n";
|
|
|
862 }
|
|
|
863 if ($Options{vectorstringformat} && $Options{vectorstringformat} !~ /^(ValuesString|IDsAndValuesString|IDsAndValuesPairsString|ValuesAndIDsString|ValuesAndIDsPairsString)$/i) {
|
|
|
864 die "Error: The value specified, $Options{vectorstringformat}, for option \"-v, --VectorStringFormat\" is not valid. Allowed values: ValuesString, IDsAndValuesString, IDsAndValuesPairsString, ValuesAndIDsString or ValuesAndIDsPairsString\n";
|
|
|
865 }
|
|
|
866 }
|
|
|
867
|
|
|
868 __END__
|
|
|
869
|
|
|
870 =head1 NAME
|
|
|
871
|
|
|
872 AtomTypesFingerprints.pl - Generate atom types fingerprints for SD files
|
|
|
873
|
|
|
874 =head1 SYNOPSIS
|
|
|
875
|
|
|
876 AtomTypesFingerprints.pl SDFile(s)...
|
|
|
877
|
|
|
878 AtomTypesFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
|
|
|
879 [B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes |
|
|
|
880 DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>]
|
|
|
881 [B<--AtomicInvariantsToUse> I<"AtomicInvariant, AtomicInvariant...">]
|
|
|
882 [B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
|
|
|
883 [B<--AtomTypesSetToUse> I<ArbitrarySize | FixedSize>]
|
|
|
884 [B<--BitsOrder> I<Ascending | Descending>] [B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>]
|
|
|
885 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
|
|
|
886 [B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>]
|
|
|
887 [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">] [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>]
|
|
|
888 [B<-f, --Filter> I<Yes | No>] [B<--FingerprintsLabelMode> I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>] [B<--FingerprintsLabel> I<text>]
|
|
|
889 [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>]
|
|
|
890 [B<-m, --mode> I<AtomTypesCount | AtomTypesBits>] [B<-i, --IgnoreHydrogens> I<Yes | No>]
|
|
|
891 [B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD |FP | text | all>] [B<-o, --overwrite>]
|
|
|
892 [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>] [B<-s, --size> I<number>] [B<--ValuesPrecision> I<number>]
|
|
|
893 [B<-v, --VectorStringFormat> I<IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>]
|
|
|
894 [B<-w, --WorkingDir> I<DirName>]
|
|
|
895
|
|
|
896 =head1 DESCRIPTION
|
|
|
897
|
|
|
898 Generate atom types fingerprints for I<SDFile(s)> and create appropriate SD, FP or
|
|
|
899 CSV/TSV text file(s) containing fingerprints bit-vector or vector strings corresponding to
|
|
|
900 molecular fingerprints.
|
|
|
901
|
|
|
902 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
|
|
|
903 and I<.sd>. All other file names are ignored. All the SD files in a current directory
|
|
|
904 can be specified either by I<*.sdf> or the current directory name.
|
|
|
905
|
|
|
906 The current release of MayaChemTools supports generation of atom types fingerpritns
|
|
|
907 corresponding to following B<-a, --AtomIdentifierTypes>:
|
|
|
908
|
|
|
909 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
910 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
911 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
912
|
|
|
913 Based on the values specified for B<-a, --AtomIdentifierType> along with other specified
|
|
|
914 parameters such as B<--AtomicInvariantsToUse> and B<--FunctionalClassesToUse>, initial
|
|
|
915 atom types are assigned to all non-hydrogen atoms or all atoms in a molecule
|
|
|
916
|
|
|
917 Using the assigned atom types and specified B<-m, --Mode>, one of the following types of
|
|
|
918 fingerprints are generated:
|
|
|
919
|
|
|
920 AtomTypesCount - A vector containing count of atom types
|
|
|
921 AtomTypesBits - A bit vector indicating presence/absence of atom types
|
|
|
922
|
|
|
923 For I<AtomTypesCount> fingerprints, two types of atom types set size are allowed as
|
|
|
924 value of B<--AtomTypesSetToUse> option:
|
|
|
925
|
|
|
926 ArbitrarySize - Corresponds to only atom types detected in molecule
|
|
|
927 FixedSize - Corresponds to fixed number of atom types previously defined
|
|
|
928
|
|
|
929 For I<AtomTypesBits> fingerprints, only I<FixedSize> atom type set is allowed.
|
|
|
930
|
|
|
931 I<ArbitrarySize> corresponds to atom types detected in a molecule where as I<FixedSize> implies
|
|
|
932 a fix number of all possible atom types previously defined for a specific B<-a, --AtomIdentifierType>.
|
|
|
933
|
|
|
934 Fix number of all possible atom types for supported I<AtomIdentifierTypes> in current release
|
|
|
935 of MayaChemTools are:
|
|
|
936
|
|
|
937 AtomIdentifier Total TotalWithoutHydrogens
|
|
|
938
|
|
|
939 DREIDINGAtomTypes 37 34
|
|
|
940 EStateAtomTypes 109 87
|
|
|
941 MMFF94AtomTypes 212 171
|
|
|
942 SLogPAtomTypes 72 67
|
|
|
943 SYBYLAtomTypes 45 44
|
|
|
944 TPSAAtomTypes 47 47
|
|
|
945 UFFAtomTypes 126 124
|
|
|
946
|
|
|
947 The current release of MayaChemTools generates the following atom types fingerprints
|
|
|
948 bit-vector and vector strings:
|
|
|
949
|
|
|
950 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitraryS
|
|
|
951 ize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2
|
|
|
952 .BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1
|
|
|
953 O.X1.BO2;2 4 14 3 10 1 1 1 3 2
|
|
|
954
|
|
|
955 FingerprintsVector;AtomTypesCount:DREIDINGAtomTypes:ArbitrarySize;8;Nu
|
|
|
956 mericalValues;IDsAndValuesString;C_2 C_3 C_R F_ N_3 N_R O_2 O_3;2 9 22
|
|
|
957 1 1 1 2 3
|
|
|
958
|
|
|
959 FingerprintsVector;AtomTypesCount:DREIDINGAtomTypes:FixedSize;34;Order
|
|
|
960 edNumericalValues;IDsAndValuesString;B_3 B_2 C_3 C_R C_2 C_1 N_3 N_R N
|
|
|
961 _2 N_1 O_3 O_R O_2 O_1 F_ Al3 Si3 P_3 S_3 Cl Ga3 Ge3 As3 Se3 Br In3 Sn
|
|
|
962 3 Sb3 Te3 I_ Na Ca Fe Zn;0 0 9 22 2 0 1 1 0 0 3 0 2 0 1 0 0 0 0 0 0 0
|
|
|
963 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
964
|
|
|
965 FingerprintsBitVector;AtomTypesBits:DREIDINGAtomTypes:FixedSize;34;Bin
|
|
|
966 aryString;Ascending;0011101100101010000000000000000000000000
|
|
|
967
|
|
|
968 FingerprintsVector;AtomTypesCount:EStateAtomTypes:ArbitrarySize;11;Num
|
|
|
969 ericalValues;IDsAndValuesString;aaCH aasC aasN dO dssC sCH3 sF sOH ssC
|
|
|
970 H2 ssNH sssCH;14 8 1 2 2 2 1 3 4 1 3
|
|
|
971
|
|
|
972 FingerprintsVector;AtomTypesCount:EStateAtomTypes:FixedSize;87;Ordered
|
|
|
973 NumericalValues;IDsAndValuesString;sLi ssBe ssssBem sBH2 ssBH sssB sss
|
|
|
974 sBm sCH3 dCH2 ssCH2 tCH dsCH aaCH sssCH ddC tsC dssC aasC aaaC ssssC s
|
|
|
975 NH3p sNH2 ssNH2p dNH ssNH aaNH tN sssNHp dsN aaN sssN ddsN aasN ss...;
|
|
|
976 0 0 0 0 0 0 0 2 0 4 0 0 14 3 0 0 2 8 0 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 3 2 0 0
|
|
|
977 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
|
|
|
978
|
|
|
979 FingerprintsBitVector;AtomTypesBits:EStateAtomTypes:FixedSize;87;Binar
|
|
|
980 yString;Ascending;0000000101001100110000001000000010110000100000000000
|
|
|
981 000000000000000000000000000000000000
|
|
|
982
|
|
|
983 FingerprintsVector;AtomTypesCount:FunctionalClassAtomTypes:ArbitrarySi
|
|
|
984 ze;8;NumericalValues;IDsAndValuesString;Ar Ar.HBA HBA HBA.HBD HBD Hal
|
|
|
985 NI None;22 1 2 3 1 1 1 10
|
|
|
986
|
|
|
987 FingerprintsVector;AtomTypesCount:MMFF94AtomTypes:ArbitrarySize;13;Num
|
|
|
988 ericalValues;IDsAndValuesString;C5A C5B C=ON CB COO CR F N5 NC=O O=CN
|
|
|
989 O=CO OC=O OR;2 2 1 18 1 9 1 1 1 1 1 1 2
|
|
|
990
|
|
|
991 FingerprintsVector;AtomTypesCount:MMFF94AtomTypes:FixedSize;171;Ordere
|
|
|
992 dNumericalValues;IDsAndValuesString;CR C=C CSP2 C=O C=N CGD C=OR C=ON
|
|
|
993 CONN COO COON COOO C=OS C=S C=SN CSO2 CS=O CSS C=P CSP =C= OR OC=O OC=
|
|
|
994 C OC=N OC=S ONO2 ON=O OSO3 OSO2 OSO OS=O -OS OPO3 OPO2 OPO -OP -O-...;
|
|
|
995 9 0 0 0 0 0 0 1 0 1 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
996 0 0 0 0 1 0 1 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
997 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 18 0 0 0 0 0 0 0 0 ...
|
|
|
998
|
|
|
999 FingerprintsBitVector;AtomTypesBits:MMFF94AtomTypes:FixedSize;171;Bina
|
|
|
1000 ryString;Ascending;100000010100000000000110000000000000000101000000100
|
|
|
1001 0100000000000000000000000000000000000000000100000000000000000000000000
|
|
|
1002 0000000011000000000000000001000000000000000000000000000
|
|
|
1003
|
|
|
1004 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:ArbitrarySize;16;Nume
|
|
|
1005 ricalValues;IDsAndValuesString;C1 C10 C11 C14 C18 C20 C21 C22 C5 CS F
|
|
|
1006 N11 N4 O10 O2 O9;5 1 1 1 14 4 2 1 2 2 1 1 1 1 3 1
|
|
|
1007
|
|
|
1008 FingerprintsVector;AtomTypesCount:SLogPAtomTypes:FixedSize;67;OrderedN
|
|
|
1009 umericalValues;IDsAndValuesString;C1 C2 C3 C4 C5 C6 C7 C8 C9 C10 C11 C
|
|
|
1010 12 C13 C14 C15 C16 C17 C18 C19 C20 C21 C22 C23 C24 C25 C26 C27 CS N1 N
|
|
|
1011 2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N12 N13 N14 NS O1 O2 O3 O4 O5 O6 O7 O8
|
|
|
1012 O9 O10 O11 O12 OS F Cl Br I Hal P S1 S2 S3 Me1 Me2;5 0 0 0 2 0 0 0 0 1
|
|
|
1013 1 0 0 1 0 0 0 14 0 4 2 1 0 0 0 0 0 2 0 0 0 1 0 0 0 0 0 0 1 0 0 0 0...
|
|
|
1014
|
|
|
1015 FingerprintsBitVector;AtomTypesBits:SLogPAtomTypes:FixedSize;67;Binary
|
|
|
1016 String;Ascending;10001000011001000101110000010001000000100000100000011
|
|
|
1017 0001000000000000000
|
|
|
1018
|
|
|
1019 FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:ArbitrarySize;9;Numer
|
|
|
1020 icalValues;IDsAndValuesString;C.2 C.3 C.ar F N.am N.ar O.2 O.3 O.co2;2
|
|
|
1021 9 22 1 1 1 1 2 2
|
|
|
1022
|
|
|
1023 FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:FixedSize;44;OrderedN
|
|
|
1024 umericalValues;IDsAndValuesString;C.3 C.2 C.1 C.ar C.cat N.3 N.2 N.1 N
|
|
|
1025 .ar N.am N.pl3 N.4 O.3 O.2 O.co2 S.3 S.2 S.o S.o2 P.3 F Cl Br I ANY HA
|
|
|
1026 L HET Li Na Mg Al Si K Ca Cr.th Cr.oh Mn Fe Co.oh Cu Zn Se Mo Sn;9 2 0
|
|
|
1027 22 0 0 0 0 1 1 0 0 2 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1028 0 0 0 0 0 0 0
|
|
|
1029
|
|
|
1030 FingerprintsBitVector;AtomTypesBits:SYBYLAtomTypes:FixedSize;44;Binary
|
|
|
1031 String;Ascending;110100001100111000001000000000000000000000000000
|
|
|
1032
|
|
|
1033 FingerprintsVector;AtomTypesCount:TPSAAtomTypes:FixedSize;47;OrderedNu
|
|
|
1034 mericalValues;IDsAndValuesString;N1 N2 N3 N4 N5 N6 N7 N8 N9 N10 N11 N1
|
|
|
1035 2 N13 N14 N15 N16 N17 N18 N19 N20 N21 N22 N23 N24 N25 N26 N O1 O2 O3 O
|
|
|
1036 4 O5 O6 O S1 S2 S3 S4 S5 S6 S7 S P1 P2 P3 P4 P;0 0 0 0 0 0 1 0 0 0 0 0
|
|
|
1037 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 2 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1038
|
|
|
1039 FingerprintsBitVector;AtomTypesBits:TPSAAtomTypes:FixedSize;47;BinaryS
|
|
|
1040 tring;Ascending;000000100000000000001000000001100000000000000000
|
|
|
1041
|
|
|
1042 FingerprintsVector;AtomTypesCount:UFFAtomTypes:ArbitrarySize;8;Numeric
|
|
|
1043 alValues;IDsAndValuesString;C_2 C_3 C_R F_ N_3 N_R O_2 O_3;2 9 22 1 1
|
|
|
1044 1 2 3
|
|
|
1045
|
|
|
1046 FingerprintsVector;AtomTypesCount:UFFAtomTypes;124;OrderedNumerical
|
|
|
1047 Values;IDsAndValuesString;He4+4 Li Be3+2 B_3 B_2 C_3 C_R C_2 C_1 N_3 N_
|
|
|
1048 R N_2 N_1 O_3 O_3_z O_R O_2 O_1 F_ Ne4+4 Na Mg3+2 Al3 Si3 P_3+3 P_3+5 P
|
|
|
1049 _3+q S_3+2 S_3+4 S_3+6 S_R S_2 Cl Ar4+4 K_ Ca6+2 Sc3+3 Ti3+4 Ti6+4 V_3+
|
|
|
1050 ;0 0 0 0 0 12 0 3 0 3 0 1 0 2 0 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1051 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ...
|
|
|
1052
|
|
|
1053 FingerprintsVector;AtomTypesCount:UFFAtomTypes:FixedSize;124;OrderedNu
|
|
|
1054 mericalValues;IDsAndValuesString;He4+4 Li Be3+2 B_3 B_2 C_3 C_R C_2 C_
|
|
|
1055 1 N_3 N_R N_2 N_1 O_3 O_3_z O_R O_2 O_1 F_ Ne4+4 Na Mg3+2 Al3 Si3 P_3+
|
|
|
1056 3 P_3+5 P_3+q S_3+2 S_3+4 S_3+6 S_R S_2 Cl Ar4+4 K_ Ca6+2 Sc3+3 Ti...;
|
|
|
1057 0 0 0 0 0 9 22 2 0 1 1 0 0 3 0 0 2 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1058 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1059 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...
|
|
|
1060
|
|
|
1061 FingerprintsBitVector;AtomTypesBits:UFFAtomTypes:FixedSize;124;BinaryS
|
|
|
1062 tring;Ascending;000001110110010010100000000000000000000000000000000000
|
|
|
1063 0000000000000000000000000000000000000000000000000000000000000000000000
|
|
|
1064
|
|
|
1065 =head1 OPTIONS
|
|
|
1066
|
|
|
1067 =over 4
|
|
|
1068
|
|
|
1069 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
|
|
|
1070
|
|
|
1071 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
1072 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
1073 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
1074 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
|
|
|
1075
|
|
|
1076 The supported aromaticity model names along with model specific control parameters
|
|
|
1077 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
|
|
|
1078 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
|
|
|
1079 this file during class instantiation and makes it available to method B<DetectAromaticity>
|
|
|
1080 for detecting aromaticity corresponding to a specific model.
|
|
|
1081
|
|
|
1082 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
|
|
|
1083
|
|
|
1084 Specify atom identifier type to use for assignment of atom types to hydrogen and/or
|
|
|
1085 non-hydrogen atoms during calculation of atom types fingerprints. Possible values in the
|
|
|
1086 current release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
1087 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
1088 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
|
|
|
1089
|
|
|
1090 =item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">
|
|
|
1091
|
|
|
1092 This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1093 option. It's a list of comma separated valid atomic invariant atom types.
|
|
|
1094
|
|
|
1095 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB,
|
|
|
1096 H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>.
|
|
|
1097
|
|
|
1098 The atomic invariants abbreviations correspond to:
|
|
|
1099
|
|
|
1100 AS = Atom symbol corresponding to element symbol
|
|
|
1101
|
|
|
1102 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
1103 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
1104 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
1105 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1106 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1107 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1108 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
1109 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
1110 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
1111 FC<+n/-n> = Formal charge assigned to atom
|
|
|
1112 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
1113 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
1114 3 (triplet)
|
|
|
1115
|
|
|
1116 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
1117
|
|
|
1118 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
1119
|
|
|
1120 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
1121 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
1122
|
|
|
1123 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
1124 are also allowed:
|
|
|
1125
|
|
|
1126 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
1127 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
1128 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
1129 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
1130 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1131 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1132 H : NumOfImplicitAndExplicitHydrogens
|
|
|
1133 Ar : Aromatic
|
|
|
1134 RA : RingAtom
|
|
|
1135 FC : FormalCharge
|
|
|
1136 MN : MassNumber
|
|
|
1137 SM : SpinMultiplicity
|
|
|
1138
|
|
|
1139 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
|
|
|
1140 atom types.
|
|
|
1141
|
|
|
1142 =item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">
|
|
|
1143
|
|
|
1144 This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1145 option. It's a list of comma separated valid functional classes.
|
|
|
1146
|
|
|
1147 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1148 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
|
|
|
1149
|
|
|
1150 The functional class abbreviations correspond to:
|
|
|
1151
|
|
|
1152 HBD: HydrogenBondDonor
|
|
|
1153 HBA: HydrogenBondAcceptor
|
|
|
1154 PI : PositivelyIonizable
|
|
|
1155 NI : NegativelyIonizable
|
|
|
1156 Ar : Aromatic
|
|
|
1157 Hal : Halogen
|
|
|
1158 H : Hydrophobic
|
|
|
1159 RA : RingAtom
|
|
|
1160 CA : ChainAtom
|
|
|
1161
|
|
|
1162 Functional class atom type specification for an atom corresponds to:
|
|
|
1163
|
|
|
1164 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
1165
|
|
|
1166 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1167 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1168
|
|
|
1169 HydrogenBondDonor: NH, NH2, OH
|
|
|
1170 HydrogenBondAcceptor: N[!H], O
|
|
|
1171 PositivelyIonizable: +, NH2
|
|
|
1172 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1173
|
|
|
1174
|
|
|
1175 =item B<--AtomTypesSetToUse> I<ArbitrarySize | FixedSize>
|
|
|
1176
|
|
|
1177 Atom types set size to use during generation of atom types fingerprints.
|
|
|
1178
|
|
|
1179 Possible values for I<AtomTypesCount> values of B<-m, --mode> option: I<ArbitrarySize |
|
|
|
1180 FixedSize>; Default value: I<ArbitrarySize>.
|
|
|
1181
|
|
|
1182 Possible values for I<AtomTypesBits> value of B<-m, --mode> option: I<FixedSize>;
|
|
|
1183 Default value: I<FixedSize>.
|
|
|
1184
|
|
|
1185 I<FixedSize> value is not supported for I<AtomicInvariantsAtomTypes> value of
|
|
|
1186 B<-a, --AtomIdentifierType> option.
|
|
|
1187
|
|
|
1188 I<ArbitrarySize> corresponds to only atom types detected in molecule; I<FixedSize> corresponds
|
|
|
1189 to fixed number of previously defined atom types for specified B<-a, --AtomIdentifierType>.
|
|
|
1190
|
|
|
1191 =item B<--BitsOrder> I<Ascending | Descending>
|
|
|
1192
|
|
|
1193 Bits order to use during generation of fingerprints bit-vector string for I<AtomTypesBits> value of
|
|
|
1194 =item B<--BitsOrder> I<Ascending | Descending>
|
|
|
1195
|
|
|
1196 Bits order to use during generation of fingerprints bit-vector string for I<AtomTypesBits> value of
|
|
|
1197 B<-m, --mode> option. Possible values: I<Ascending, Descending>. Default: I<Ascending>.
|
|
|
1198
|
|
|
1199 I<Ascending> bit order which corresponds to first bit in each byte as the lowest bit as
|
|
|
1200 opposed to the highest bit.
|
|
|
1201
|
|
|
1202 Internally, bits are stored in I<Ascending> order using Perl vec function. Regardless
|
|
|
1203 of machine order, big-endian or little-endian, vec function always considers first
|
|
|
1204 string byte as the lowest byte and first bit within each byte as the lowest bit.
|
|
|
1205
|
|
|
1206 =item B<-b, --BitStringFormat> I<BinaryString | HexadecimalString>
|
|
|
1207
|
|
|
1208 Format of fingerprints bit-vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
1209 B<--output> used during I<AtomTypesBits> value of B<-m, --mode> option. Possible
|
|
|
1210 values: I<BinaryString, HexadecimalString>. Default value: I<BinaryString>.
|
|
|
1211
|
|
|
1212 I<BinaryString> corresponds to an ASCII string containing 1s and 0s. I<HexadecimalString>
|
|
|
1213 contains bit values in ASCII hexadecimal format.
|
|
|
1214
|
|
|
1215 Examples:
|
|
|
1216
|
|
|
1217 FingerprintsBitVector;AtomTypesBits:DREIDINGAtomTypes;34;BinaryString;
|
|
|
1218 Ascending;0010101010101000000000000000000000000000
|
|
|
1219
|
|
|
1220 FingerprintsBitVector;AtomTypesBits:MMFF94AtomTypes;171;BinaryString;
|
|
|
1221 Ascending;1000010101000000000001100000000000000001010000101000000000000
|
|
|
1222 00000000000000000000000000000000000001000000000000000000000000000000000
|
|
|
1223 0000000000000000000000000000000000000000000
|
|
|
1224
|
|
|
1225 =item B<--CompoundID> I<DataFieldName or LabelPrefixString>
|
|
|
1226
|
|
|
1227 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
|
|
|
1228
|
|
|
1229 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
|
|
|
1230 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
|
|
1231 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
|
|
|
1232 look like Cmpd<Number>.
|
|
|
1233
|
|
|
1234 Examples for I<DataField> value of B<--CompoundIDMode>:
|
|
|
1235
|
|
|
1236 MolID
|
|
|
1237 ExtReg
|
|
|
1238
|
|
|
1239 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
|
|
|
1240
|
|
|
1241 Compound
|
|
|
1242
|
|
|
1243 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
1244 instead of default value of Cmpd<Number>.
|
|
|
1245
|
|
|
1246 =item B<--CompoundIDLabel> I<text>
|
|
|
1247
|
|
|
1248 Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value
|
|
|
1249 of B<--DataFieldsMode> option. Default: I<CompoundID>.
|
|
|
1250
|
|
|
1251 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
1252
|
|
|
1253 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
|
|
|
1254 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value;
|
|
|
1255 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination
|
|
|
1256 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
1257
|
|
|
1258 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
1259 Default: I<LabelPrefix>.
|
|
|
1260
|
|
|
1261 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
|
|
|
1262 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
1263 values are replaced with sequential compound IDs.
|
|
|
1264
|
|
|
1265 This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
|
|
|
1266
|
|
|
1267 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,...">
|
|
|
1268
|
|
|
1269 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
1270 with generated fingerprints for I<text | all> values of B<--output> option.
|
|
|
1271
|
|
|
1272 This is only used for I<Specify> value of B<--DataFieldsMode> option.
|
|
|
1273
|
|
|
1274 Examples:
|
|
|
1275
|
|
|
1276 Extreg
|
|
|
1277 MolID,CompoundName
|
|
|
1278
|
|
|
1279 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
|
|
|
1280
|
|
|
1281 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
|
|
|
1282 with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD
|
|
|
1283 data field; transfer SD data files common to all compounds; extract specified data fields;
|
|
|
1284 generate a compound ID using molname line, a compound prefix, or a combination of both.
|
|
|
1285 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
|
|
|
1286
|
|
|
1287 =item B<-f, --Filter> I<Yes | No>
|
|
|
1288
|
|
|
1289 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
|
|
|
1290 Default value: I<Yes>.
|
|
|
1291
|
|
|
1292 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
1293 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
1294
|
|
|
1295 =item B<--FingerprintsLabelMode> I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>
|
|
|
1296
|
|
|
1297 Specify how fingerprints label is generated in conjunction with B<--FingerprintsLabel> option value:
|
|
|
1298 use fingerprints label generated only by B<--FingerprintsLabel> option value or append atom type
|
|
|
1299 value IDs to B<--FingerprintsLabel> option value.
|
|
|
1300
|
|
|
1301 Possible values: I<FingerprintsLabelOnly | FingerprintsLabelWithIDs>. Default value:
|
|
|
1302 I<FingerprintsLabelOnly>.
|
|
|
1303
|
|
|
1304 This option is only used for I<FixedSize> value of B<-e, --AtomTypesSetToUse> option during
|
|
|
1305 generation of I<AtomTypesCount> fingerprints and ignored for I<AtomTypesBits>.
|
|
|
1306
|
|
|
1307 Atom type IDs appended to B<--FingerprintsLabel> value during I<FingerprintsLabelWithIDs>
|
|
|
1308 values of B<--FingerprintsLabelMode> correspond to fixed number of previously defined
|
|
|
1309 atom types.
|
|
|
1310
|
|
|
1311 =item B<--FingerprintsLabel> I<text>
|
|
|
1312
|
|
|
1313 SD data label or text file column label to use for fingerprints string in output SD or
|
|
|
1314 CSV/TSV text file(s) specified by B<--output>. Default value: I<AtomTypesFingerprints>.
|
|
|
1315
|
|
|
1316 =item B<-h, --help>
|
|
|
1317
|
|
|
1318 Print this help message.
|
|
|
1319
|
|
|
1320 =item B<-i, --IgnoreHydrogens> I<Yes | No>
|
|
|
1321
|
|
|
1322 Ignore hydrogens during fingerprints generation. Possible values: I<Yes or No>.
|
|
|
1323 Default value: I<Yes>.
|
|
|
1324
|
|
|
1325 For I<yes> value of B<-i, --IgnoreHydrogens>, any explicit hydrogens are also used for
|
|
|
1326 generation of atom type fingerprints; implicit hydrogens are still ignored.
|
|
|
1327
|
|
|
1328 =item B<-k, --KeepLargestComponent> I<Yes | No>
|
|
|
1329
|
|
|
1330 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
1331 I<Yes or No>. Default value: I<Yes>.
|
|
|
1332
|
|
|
1333 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
1334 in two different ways: use all connected components or just the largest connected
|
|
|
1335 component. By default, all atoms except for the largest connected component are
|
|
|
1336 deleted before generation of fingerprints.
|
|
|
1337
|
|
|
1338 =item B<-m, --mode> I<AtomTypesCount | AtomTypesBits>
|
|
|
1339
|
|
|
1340 Specify type of atom types fingerprints to generate for molecules in I<SDFile(s)>.
|
|
|
1341 Possible values: I<AtomTypesCount or AtomTypesBits>. Default value: I<AtomTypesCount>.
|
|
|
1342
|
|
|
1343 For I<AtomTypesCount> values of B<-m, --mode> option, a fingerprint vector string is generated.
|
|
|
1344 The vector string corresponding to I<AtomTypesCount> contains count of atom types.
|
|
|
1345
|
|
|
1346 For I<AtomTypesBits> value of B<-m, --mode> option, a fingerprint bit-vector string containing
|
|
|
1347 zeros and ones indicating presence or absence of atom types is generated.
|
|
|
1348
|
|
|
1349 For I<AtomTypesCount> atom types fingerprints, two types of atom types set size can be specified
|
|
|
1350 using B<-a, --AtomTypesSetToUse> option: I<ArbitrarySize or FixedSize>. I<ArbitrarySize> corrresponds
|
|
|
1351 to only atom types detected in molecule; I<FixedSize> corresponds to fixed number of atom types
|
|
|
1352 previously defined.
|
|
|
1353
|
|
|
1354 For I<AtomTypesBits> atom types fingeprints, only I<FixedSize> is allowed.
|
|
|
1355
|
|
|
1356 Combination of B<-m, --Mode> and B<--AtomTypesSetToUse> along with B<-a, --AtomtomIdentifierType>
|
|
|
1357 allows generation of following different atom types fingerprints:
|
|
|
1358
|
|
|
1359 Mode AtomIdentifierType AtomTypesSetToUse
|
|
|
1360
|
|
|
1361 AtomTypesCount AtomicInvariantsAtomTypes ArbitrarySize [ Default ]
|
|
|
1362
|
|
|
1363 AtomTypesCount DREIDINGAtomTypes ArbitrarySize
|
|
|
1364 AtomTypesCount DREIDINGAtomTypes FixedSize
|
|
|
1365 AtomTypesBits DREIDINGAtomTypes FixedSize
|
|
|
1366
|
|
|
1367 AtomTypesCount EStateAtomTypes ArbitrarySize
|
|
|
1368 AtomTypesCount EStateAtomTypes FixedSize
|
|
|
1369 AtomTypesBits EStateAtomTypes FixedSize
|
|
|
1370
|
|
|
1371 AtomTypesCount FunctionalClassAtomTypes ArbitrarySize
|
|
|
1372
|
|
|
1373 AtomTypesCount MMFF94AtomTypes ArbitrarySize
|
|
|
1374 AtomTypesCount MMFF94AtomTypes FixedSize
|
|
|
1375 AtomTypesBits MMFF94AtomTypes FixedSize
|
|
|
1376
|
|
|
1377 AtomTypesCount SLogPAtomTypes ArbitrarySize
|
|
|
1378 AtomTypesCount SLogPAtomTypes FixedSize
|
|
|
1379 AtomTypesBits SLogPAtomTypes FixedSize
|
|
|
1380
|
|
|
1381 AtomTypesCount SYBYLAtomTypes ArbitrarySize
|
|
|
1382 AtomTypesCount SYBYLAtomTypes FixedSize
|
|
|
1383 AtomTypesBits SYBYLAtomTypes FixedSize
|
|
|
1384
|
|
|
1385 AtomTypesCount TPSAAtomTypes FixedSize
|
|
|
1386 AtomTypesBits TPSAAtomTypes FixedSize
|
|
|
1387
|
|
|
1388 AtomTypesCount UFFAtomTypes ArbitrarySize
|
|
|
1389 AtomTypesCount UFFAtomTypes FixedSize
|
|
|
1390 AtomTypesBits UFFAtomTypes FixedSize
|
|
|
1391
|
|
|
1392 The default is to generate I<AtomicInvariantAtomTypes> fingeprints corresponding to I<ArbitrarySize> as
|
|
|
1393 value of B<--AtomTypesSetToUse> option.
|
|
|
1394
|
|
|
1395 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
1396
|
|
|
1397 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
|
|
|
1398 Default value: I<comma>.
|
|
|
1399
|
|
|
1400 =item B<--output> I<SD | FP | text | all>
|
|
|
1401
|
|
|
1402 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>.
|
|
|
1403
|
|
|
1404 =item B<-o, --overwrite>
|
|
|
1405
|
|
|
1406 Overwrite existing files.
|
|
|
1407
|
|
|
1408 =item B<-q, --quote> I<Yes | No>
|
|
|
1409
|
|
|
1410 Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
1411 I<Yes or No>. Default value: I<Yes>.
|
|
|
1412
|
|
|
1413 =item B<-r, --root> I<RootName>
|
|
|
1414
|
|
|
1415 New file name is generated using the root: <Root>.<Ext>. Default for new file
|
|
|
1416 names: <SDFileName><AtomTypesFP>.<Ext>. The file type determines <Ext> value.
|
|
|
1417 The sdf, fpf, csv, and tsv <Ext> values are used for SD, FP, comma/semicolon, and tab
|
|
|
1418 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
1419
|
|
|
1420 =item B<-v, --VectorStringFormat> I<ValuesString | IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString>
|
|
|
1421
|
|
|
1422 Format of fingerprints vector string data in output SD, FP or CSV/TSV text file(s) specified by
|
|
|
1423 B<--output> used during <AtomTypesCount> value of B<-m, --mode> option. Possible values:
|
|
|
1424 I<ValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
1425 ValuesAndIDsPairsString>.
|
|
|
1426
|
|
|
1427 Default value during I<ArbitrarySize> value of B<-e, --AtomTypesSetToUse>
|
|
|
1428 option: I<IDsAndValuesString>. Default value during I<FixedSize> value of
|
|
|
1429 B<-e, --AtomTypesSetToUse> option: I<ValuesString>.
|
|
|
1430
|
|
|
1431 Example of I<SD> file containing atom types fingerprints string data:
|
|
|
1432
|
|
|
1433 ... ...
|
|
|
1434 ... ...
|
|
|
1435 $$$$
|
|
|
1436 ... ...
|
|
|
1437 ... ...
|
|
|
1438 ... ...
|
|
|
1439 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
1440 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1441 ... ...
|
|
|
1442 2 3 1 0 0 0 0
|
|
|
1443 ... ...
|
|
|
1444 M END
|
|
|
1445 > <CmpdID>
|
|
|
1446 Cmpd1
|
|
|
1447
|
|
|
1448 > <AtomTypesFingerprints>
|
|
|
1449 FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:ArbitrarySi
|
|
|
1450 ze;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.H2 C.X2.B
|
|
|
1451 O3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.BO1.H1 O.
|
|
|
1452 X1.BO2;2 4 14 3 10 1 1 1 3 2
|
|
|
1453
|
|
|
1454 $$$$
|
|
|
1455 ... ...
|
|
|
1456 ... ...
|
|
|
1457
|
|
|
1458 Example of I<FP> file containing atom types fingerprints string data:
|
|
|
1459
|
|
|
1460 #
|
|
|
1461 # Package = MayaChemTools 7.4
|
|
|
1462 # Release Date = Oct 21, 2010
|
|
|
1463 #
|
|
|
1464 # TimeStamp = Fri Mar 11 14:28:07 2011
|
|
|
1465 #
|
|
|
1466 # FingerprintsStringType = FingerprintsVector
|
|
|
1467 #
|
|
|
1468 # Description = AtomTypesCount:AtomicInvariantsAtomTypes:ArbitrarySize
|
|
|
1469 # VectorStringFormat = IDsAndValuesString
|
|
|
1470 # VectorValuesType = NumericalValues
|
|
|
1471 #
|
|
|
1472 Cmpd1 10;C.X1.BO1.H3 C.X2.BO2.H2 C.X2.BO3.H1 C.X3.BO3.H1 C.X3.BO4 F...
|
|
|
1473 Cmpd2 9;C.X1.BO1.H3 C.X2.BO2.H2 C.X3.BO3.H1 C.X3.BO4 N.X1.BO1.H2 N....
|
|
|
1474 ... ...
|
|
|
1475 ... ..
|
|
|
1476
|
|
|
1477 Example of CSV I<Text> file atom types containing fingerprints string data:
|
|
|
1478
|
|
|
1479 "CompoundID","AtomTypesFingerprints"
|
|
|
1480 "Cmpd1","FingerprintsVector;AtomTypesCount:AtomicInvariantsAtomTypes:Ar
|
|
|
1481 bitrarySize;10;NumericalValues;IDsAndValuesString;C.X1.BO1.H3 C.X2.BO2.
|
|
|
1482 H2 C.X2.BO3.H1 C.X3.BO3.H1 C.X3.BO4 F.X1.BO1 N.X2.BO2.H1 N.X3.BO3 O.X1.
|
|
|
1483 BO1.H1 O.X1.BO2;2 4 14 3 10 1 1 1 3 2"
|
|
|
1484 O.X1.BO2;3 3 6 3 1 1 2 2 2"
|
|
|
1485 ... ...
|
|
|
1486 ... ...
|
|
|
1487
|
|
|
1488 Examples:
|
|
|
1489
|
|
|
1490 FingerprintsVector;AtomTypesCount:EStateAtomTypes:ArbitrarySize;11;Num
|
|
|
1491 ericalValues;IDsAndValuesString;aaCH aasC aasN dO dssC sCH3 sF sOH ssC
|
|
|
1492 H2 ssNH sssCH;14 8 1 2 2 2 1 3 4 1 3
|
|
|
1493
|
|
|
1494 FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:ArbitrarySize;9;Numer
|
|
|
1495 icalValues;IDsAndValuesString;C.2 C.3 C.ar F N.am N.ar O.2 O.3 O.co2;2
|
|
|
1496 9 22 1 1 1 1 2 2
|
|
|
1497
|
|
|
1498 FingerprintsVector;AtomTypesCount:SYBYLAtomTypes:FixedSize;44;OrderedN
|
|
|
1499 umericalValues;IDsAndValuesString;C.3 C.2 C.1 C.ar C.cat N.3 N.2 N.1 N
|
|
|
1500 .ar N.am N.pl3 N.4 O.3 O.2 O.co2 S.3 S.2 S.o S.o2 P.3 F Cl Br I ANY HA
|
|
|
1501 L HET Li Na Mg Al Si K Ca Cr.th Cr.oh Mn Fe Co.oh Cu Zn Se Mo Sn;9 2 0
|
|
|
1502 22 0 0 0 0 1 1 0 0 2 1 2 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
1503 0 0 0 0 0 0 0
|
|
|
1504
|
|
|
1505 =item B<-w, --WorkingDir> I<DirName>
|
|
|
1506
|
|
|
1507 Location of working directory. Default: current directory.
|
|
|
1508
|
|
|
1509 =back
|
|
|
1510
|
|
|
1511 =head1 EXAMPLES
|
|
|
1512
|
|
|
1513 To generate atomic invariants atom types count fingerprints of arbitrary size in vector
|
|
|
1514 string format and create a SampleATFP.csv file containing sequential compound IDs along
|
|
|
1515 with fingerprints vector strings data, type:
|
|
|
1516
|
|
|
1517 % AtomTypesFingerprints.pl -r SampleATFP -o Sample.sdf
|
|
|
1518
|
|
|
1519 To generate functional class atom types count fingerprints of arbitrary size in vector
|
|
|
1520 string format and create a SampleATFP.csv file containing sequential compound IDs along
|
|
|
1521 with fingerprints vector strings data, type:
|
|
|
1522
|
|
|
1523 % AtomTypesFingerprints.pl -m AtomTypesCount -a FunctionalClassAtomTypes
|
|
|
1524 -r SampleATFP -o Sample.sdf
|
|
|
1525
|
|
|
1526 To generate E-state atom types count fingerprints of arbitrary size in vector string
|
|
|
1527 format and create a SampleATFP.csv file containing sequential compound IDs along
|
|
|
1528 with fingerprints vector strings data, type:
|
|
|
1529
|
|
|
1530 % AtomTypesFingerprints.pl -m AtomTypesCount -a EStateAtomTypes
|
|
|
1531 --AtomTypesSetToUse ArbitrarySize -r SampleATFP -o Sample.sdf
|
|
|
1532
|
|
|
1533 To generate E-state atom types count fingerprints of fixed size in vector string
|
|
|
1534 with IDsAndValues format and create a SampleATFP.csv file containing sequential
|
|
|
1535 compound IDs along with fingerprints vector strings data, type:
|
|
|
1536
|
|
|
1537 % AtomTypesFingerprints.pl -m AtomTypesCount -a EStateAtomTypes
|
|
|
1538 --AtomTypesSetToUse FixedSize -v IDsAndValuesString
|
|
|
1539 -r SampleATFP -o Sample.sdf
|
|
|
1540
|
|
|
1541 To generate E-state atom types bits fingerprints of fixed size in bit-vector string
|
|
|
1542 format and create a SampleATFP.csv file containing sequential compound IDs along
|
|
|
1543 with fingerprints vector strings data, type:
|
|
|
1544
|
|
|
1545 % AtomTypesFingerprints.pl -m AtomTypesBits -a EStateAtomTypes
|
|
|
1546 --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf
|
|
|
1547
|
|
|
1548 To generate MMFF94 atom types count fingerprints of arbitrary size in vector string
|
|
|
1549 format and create a SampleATFP.csv file containing sequential compound IDs along
|
|
|
1550 with fingerprints vector strings data, type:
|
|
|
1551
|
|
|
1552 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1553 --AtomTypesSetToUse ArbitrarySize -r SampleATFP -o Sample.sdf
|
|
|
1554
|
|
|
1555 To generate MMFF94 atom types count fingerprints of fixed size in vector string
|
|
|
1556 format and create a SampleATFP.csv file containing sequential compound IDs along
|
|
|
1557 with fingerprints vector strings data, type:
|
|
|
1558
|
|
|
1559 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1560 --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf
|
|
|
1561
|
|
|
1562 To generate MMFF94 atom types count fingerprints of fixed size in vector string
|
|
|
1563 with IDsAndValues format and create a SampleATFP.csv file containing sequential
|
|
|
1564 compound IDs along with fingerprints vector strings data, type:
|
|
|
1565
|
|
|
1566 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1567 --AtomTypesSetToUse FixedSize -v IDsAndValuesString
|
|
|
1568 -r SampleATFP -o Sample.sdf
|
|
|
1569
|
|
|
1570 To generate MMFF94 atom types bits fingerprints of fixed size in bit-vector string
|
|
|
1571 format and create a SampleATFP.csv file containing sequential compound IDs along
|
|
|
1572 with fingerprints vector strings data, type:
|
|
|
1573
|
|
|
1574 % AtomTypesFingerprints.pl -m AtomTypesBits -a MMFF94AtomTypes
|
|
|
1575 --AtomTypesSetToUse FixedSize -r SampleATFP -o Sample.sdf
|
|
|
1576
|
|
|
1577 To generate MMFF94 atom types count fingerprints of arbitrary size in vector string
|
|
|
1578 format and create a SampleATFP.csv file containing compound ID from molecule
|
|
|
1579 name line along with fingerprints vector strings data, type
|
|
|
1580
|
|
|
1581 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1582 --DataFieldsMode CompoundID --CompoundIDMode MolName
|
|
|
1583 -r SampleATFP -o Sample.sdf
|
|
|
1584
|
|
|
1585 To generate MMFF94 atom types count fingerprints of arbitrary size in vector string
|
|
|
1586 format and create a SampleATFP.csv file containing compound IDs using specified
|
|
|
1587 data field along with fingerprints vector strings data, type:
|
|
|
1588
|
|
|
1589 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1590 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
|
|
|
1591 Mol_ID -r SampleATFP -o Sample.sdf
|
|
|
1592
|
|
|
1593 To generate MMFF94 atom types count fingerprints of arbitrary size in vector string
|
|
|
1594 format and create a SampleATFP.csv file containing compound ID using combination
|
|
|
1595 of molecule name line and an explicit compound prefix along with fingerprints vector
|
|
|
1596 strings data, type:
|
|
|
1597
|
|
|
1598 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1599 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
|
|
|
1600 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleATFP -o Sample.sdf
|
|
|
1601
|
|
|
1602 To generate MMFF94 atom types count fingerprints of arbitrary size in vector string
|
|
|
1603 format and create a SampleATFP.csv file containing specific data fields columns along
|
|
|
1604 with fingerprints vector strings data, type:
|
|
|
1605
|
|
|
1606 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1607 --DataFieldsMode Specify --DataFields Mol_ID -r SampleATFP
|
|
|
1608 -o Sample.sdf
|
|
|
1609
|
|
|
1610 To generate MMFF94 atom types count fingerprints of arbitrary size in vector string
|
|
|
1611 format and create a SampleATFP.csv file containing common data fields columns along
|
|
|
1612 with fingerprints vector strings data, type:
|
|
|
1613
|
|
|
1614 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1615 --DataFieldsMode Common -r SampleATFP -o Sample.sdf
|
|
|
1616
|
|
|
1617 To generate MMFF94 atom types count fingerprints of arbitrary size in vector string
|
|
|
1618 format and create SampleATFP.sdf, SampleATFP.fpf and SampleATFP.csv files containing
|
|
|
1619 all data fields columns in CSV file along with fingerprints vector strings data, type:
|
|
|
1620
|
|
|
1621 % AtomTypesFingerprints.pl -m AtomTypesCount -a MMFF94AtomTypes
|
|
|
1622 --DataFieldsMode All --output all -r SampleATFP -o Sample.sdf
|
|
|
1623
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|
|
1624 =head1 AUTHOR
|
|
|
1625
|
|
|
1626 Manish Sud <msud@san.rr.com>
|
|
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1627
|
|
|
1628 =head1 SEE ALSO
|
|
|
1629
|
|
|
1630 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
|
|
|
1631 ExtendedConnectivityFingerprints.pl, MACCSKeysFingeprints.pl, PathLengthFingerprints.pl,
|
|
|
1632 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
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|
|
1633 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
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|
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1634
|
|
|
1635 =head1 COPYRIGHT
|
|
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1636
|
|
|
1637 Copyright (C) 2015 Manish Sud. All rights reserved.
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1638
|
|
|
1639 This file is part of MayaChemTools.
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|
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1640
|
|
|
1641 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1642 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1643 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1644 any later version.
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|
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1645
|
|
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1646 =cut
|
