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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: AtomNeighborhoodsFingerprints.pl,v $
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4 # $Date: 2015/02/28 20:46:19 $
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5 # $Revision: 1.31 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use MoleculeFileIO;
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39 use FileIO::FingerprintsSDFileIO;
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40 use FileIO::FingerprintsTextFileIO;
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41 use FileIO::FingerprintsFPFileIO;
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42 use AtomTypes::AtomicInvariantsAtomTypes;
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43 use AtomTypes::FunctionalClassAtomTypes;
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44 use Fingerprints::AtomNeighborhoodsFingerprints;
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45
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46 my($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 GenerateAtomNeighborhoodsFingerprints($FileIndex);
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84 }
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85 }
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86 print "\n$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 GenerateAtomNeighborhoodsFingerprints {
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97 my($FileIndex) = @_;
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98 my($CmpdCount, $IgnoredCmpdCount, $SDFile, $MoleculeFileIO, $Molecule, $AtomNeighborhoodsFingerprints, $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 $AtomNeighborhoodsFingerprints = GenerateMoleculeFingerprints($Molecule);
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124 if (!$AtomNeighborhoodsFingerprints) {
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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, $AtomNeighborhoodsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
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131 }
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132 $MoleculeFileIO->Close();
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133
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134 if ($NewFPSDFileIO) {
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135 $NewFPSDFileIO->Close();
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136 }
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137 if ($NewFPTextFileIO) {
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138 $NewFPTextFileIO->Close();
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139 }
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140 if ($NewFPFileIO) {
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141 $NewFPFileIO->Close();
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142 }
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143
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144 WriteFingerprintsGenerationSummaryStatistics($CmpdCount, $IgnoredCmpdCount);
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145 }
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146
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147 # Process compound being ignored due to problems in fingerprints geneation...
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148 #
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149 sub ProcessIgnoredCompound {
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150 my($Mode, $CmpdCount, $Molecule) = @_;
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151 my($CmpdID, $DataFieldLabelAndValuesRef);
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152
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153 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
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154 $CmpdID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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155
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156 MODE: {
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157 if ($Mode =~ /^ContainsNonElementalData$/i) {
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158 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n";
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159 next MODE;
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160 }
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161
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162 if ($Mode =~ /^ContainsNoElementalData$/i) {
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163 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n";
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164 next MODE;
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165 }
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166
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167 if ($Mode =~ /^FingerprintsGenerationFailed$/i) {
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168 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
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169 next MODE;
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170 }
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171 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Fingerprints generation didn't succeed...\n\n";
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172 }
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173 }
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174
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175 # Check and filter compounds....
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176 #
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177 sub CheckAndFilterCompound {
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178 my($CmpdCount, $Molecule) = @_;
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179 my($ElementCount, $NonElementCount);
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180
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181 ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements();
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182
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183 if ($NonElementCount) {
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184 ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule);
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185 return 1;
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186 }
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187
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188 if (!$ElementCount) {
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189 ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule);
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190 return 1;
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191 }
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192
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193 return 0;
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194 }
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195
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196 # Write out compounds fingerprints generation summary statistics...
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197 #
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198 sub WriteFingerprintsGenerationSummaryStatistics {
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199 my($CmpdCount, $IgnoredCmpdCount) = @_;
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200 my($ProcessedCmpdCount);
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201
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202 $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount;
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203
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204 print "\nNumber of compounds: $CmpdCount\n";
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205 print "Number of compounds processed successfully during fingerprints generation: $ProcessedCmpdCount\n";
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206 print "Number of compounds ignored during fingerprints generation: $IgnoredCmpdCount\n";
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207 }
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208
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209 # Open output files...
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210 #
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211 sub SetupAndOpenOutputFiles {
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212 my($FileIndex) = @_;
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213 my($NewFPSDFile, $NewFPFile, $NewFPTextFile, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO, %FingerprintsFileIOParams);
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214
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215 ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = (undef) x 3;
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216
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217 # Setup common parameters for fingerprints file IO objects...
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218 #
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219 %FingerprintsFileIOParams = ('Mode' => 'Write', 'Overwrite' => $OptionsInfo{OverwriteFiles}, 'FingerprintsStringMode' => 'FingerprintsVectorString', 'VectorStringFormat' => $OptionsInfo{VectorStringFormat});
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220
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221 if ($OptionsInfo{SDOutput}) {
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222 $NewFPSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
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223 print "Generating SD file $NewFPSDFile...\n";
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224 $NewFPSDFileIO = new FileIO::FingerprintsSDFileIO('Name' => $NewFPSDFile, %FingerprintsFileIOParams, 'FingerprintsFieldLabel' => $OptionsInfo{FingerprintsLabel});
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225 $NewFPSDFileIO->Open();
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226 }
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227
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228 if ($OptionsInfo{FPOutput}) {
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229 $NewFPFile = $SDFilesInfo{FPOutFileNames}[$FileIndex];
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230 print "Generating FP file $NewFPFile...\n";
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231 $NewFPFileIO = new FileIO::FingerprintsFPFileIO('Name' => $NewFPFile, %FingerprintsFileIOParams);
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232 $NewFPFileIO->Open();
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233 }
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234
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235 if ($OptionsInfo{TextOutput}) {
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236 my($ColLabelsRef);
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237
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238 $NewFPTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
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239 $ColLabelsRef = SetupFPTextFileCoulmnLabels($FileIndex);
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240
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241 print "Generating text file $NewFPTextFile...\n";
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242 $NewFPTextFileIO = new FileIO::FingerprintsTextFileIO('Name' => $NewFPTextFile, %FingerprintsFileIOParams, 'DataColLabels' => $ColLabelsRef, 'OutDelim' => $OptionsInfo{OutDelim}, 'OutQuote' => $OptionsInfo{OutQuote});
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243 $NewFPTextFileIO->Open();
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244 }
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245
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246 return ($NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO);
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247 }
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248
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249 # Write fingerpritns and other data to appropriate output files...
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250 #
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251 sub WriteDataToOutputFiles {
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252 my($FileIndex, $CmpdCount, $Molecule, $AtomNeighborhoodsFingerprints, $NewFPSDFileIO, $NewFPTextFileIO, $NewFPFileIO) = @_;
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253 my($DataFieldLabelAndValuesRef);
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254
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255 $DataFieldLabelAndValuesRef = undef;
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256 if ($NewFPTextFileIO || $NewFPFileIO) {
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257 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
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258 }
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259
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260 if ($NewFPSDFileIO) {
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261 my($CmpdString);
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262
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263 $CmpdString = $Molecule->GetInputMoleculeString();
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264 $NewFPSDFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $CmpdString);
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265 }
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266
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267 if ($NewFPTextFileIO) {
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268 my($ColValuesRef);
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269
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270 $ColValuesRef = SetupFPTextFileCoulmnValues($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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271 $NewFPTextFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $ColValuesRef);
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272 }
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273
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274 if ($NewFPFileIO) {
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275 my($CompoundID);
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276
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277 $CompoundID = SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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278 $NewFPFileIO->WriteFingerprints($AtomNeighborhoodsFingerprints, $CompoundID);
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279 }
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280 }
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281
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282 # Generate approriate column labels for FPText output file...
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283 #
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284 sub SetupFPTextFileCoulmnLabels {
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285 my($FileIndex) = @_;
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286 my($Line, @ColLabels);
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287
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288 @ColLabels = ();
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289 if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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290 push @ColLabels, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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291 }
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292 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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293 push @ColLabels, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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294 }
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295 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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296 push @ColLabels, @{$OptionsInfo{SpecifiedDataFields}};
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297 }
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298 elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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299 push @ColLabels, $OptionsInfo{CompoundIDLabel};
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300 }
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301 # Add fingerprints label...
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302 push @ColLabels, $OptionsInfo{FingerprintsLabel};
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303
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304 return \@ColLabels;
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305 }
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306
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307 # Generate column values FPText output file..
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308 #
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309 sub SetupFPTextFileCoulmnValues {
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310 my($FileIndex, $CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
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311 my(@ColValues);
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312
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313 @ColValues = ();
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314 if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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315 push @ColValues, SetupCmpdIDForOutputFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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316 }
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317 elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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318 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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319 }
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320 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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321 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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322 }
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323 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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324 @ColValues = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
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325 }
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326
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327 return \@ColValues;
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328 }
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329
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330 # Generate compound ID for FP and FPText output files..
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331 #
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332 sub SetupCmpdIDForOutputFiles {
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333 my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
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334 my($CmpdID);
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335
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336 $CmpdID = '';
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337 if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
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338 my($MolName);
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339 $MolName = $Molecule->GetName();
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340 $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
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341 }
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342 elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
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343 $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
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344 }
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345 elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
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346 my($SpecifiedDataField);
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347 $SpecifiedDataField = $OptionsInfo{CompoundID};
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348 $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
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349 }
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350 elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
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351 $CmpdID = $Molecule->GetName();
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352 }
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353 return $CmpdID;
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354 }
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355
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356 # Generate fingerprints for molecule...
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357 #
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358 sub GenerateMoleculeFingerprints {
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359 my($Molecule) = @_;
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360 my($AtomNeighborhoodsFingerprints);
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361
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362 if ($OptionsInfo{KeepLargestComponent}) {
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363 $Molecule->KeepLargestComponent();
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364 }
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365 if (!$Molecule->DetectRings()) {
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366 return undef;
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367 }
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368 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
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369 $Molecule->DetectAromaticity();
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370
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371 $AtomNeighborhoodsFingerprints = new Fingerprints::AtomNeighborhoodsFingerprints('Molecule' => $Molecule, 'MinNeighborhoodRadius' => $OptionsInfo{MinNeighborhoodRadius}, 'MaxNeighborhoodRadius' => $OptionsInfo{MaxNeighborhoodRadius}, 'AtomIdentifierType' => $OptionsInfo{AtomIdentifierType});
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372 SetAtomIdentifierTypeValuesToUse($AtomNeighborhoodsFingerprints);
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373
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374 # Generate fingerprints...
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|
375 $AtomNeighborhoodsFingerprints->GenerateFingerprints();
|
|
|
376
|
|
|
377 # Make sure fingerprints generation is successful...
|
|
|
378 if (!$AtomNeighborhoodsFingerprints->IsFingerprintsGenerationSuccessful()) {
|
|
|
379 return undef;
|
|
|
380 }
|
|
|
381
|
|
|
382 return $AtomNeighborhoodsFingerprints;
|
|
|
383 }
|
|
|
384
|
|
|
385 # Set atom identifier type to use for generating fingerprints...
|
|
|
386 #
|
|
|
387 sub SetAtomIdentifierTypeValuesToUse {
|
|
|
388 my($AtomNeighborhoodsFingerprints) = @_;
|
|
|
389
|
|
|
390 if ($OptionsInfo{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
391 $AtomNeighborhoodsFingerprints->SetAtomicInvariantsToUse(\@{$OptionsInfo{AtomicInvariantsToUse}});
|
|
|
392 }
|
|
|
393 elsif ($OptionsInfo{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
394 $AtomNeighborhoodsFingerprints->SetFunctionalClassesToUse(\@{$OptionsInfo{FunctionalClassesToUse}});
|
|
|
395 }
|
|
|
396 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
397 # Nothing to do for now...
|
|
|
398 }
|
|
|
399 else {
|
|
|
400 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
401 }
|
|
|
402 }
|
|
|
403
|
|
|
404 # Retrieve information about SD files...
|
|
|
405 #
|
|
|
406 sub RetrieveSDFilesInfo {
|
|
|
407 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $FPOutFileExt, $NewSDFileName, $NewFPFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
|
|
|
408
|
|
|
409 %SDFilesInfo = ();
|
|
|
410 @{$SDFilesInfo{FileOkay}} = ();
|
|
|
411 @{$SDFilesInfo{OutFileRoot}} = ();
|
|
|
412 @{$SDFilesInfo{SDOutFileNames}} = ();
|
|
|
413 @{$SDFilesInfo{FPOutFileNames}} = ();
|
|
|
414 @{$SDFilesInfo{TextOutFileNames}} = ();
|
|
|
415 @{$SDFilesInfo{AllDataFieldsRef}} = ();
|
|
|
416 @{$SDFilesInfo{CommonDataFieldsRef}} = ();
|
|
|
417
|
|
|
418 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
|
|
|
419 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
|
|
|
420
|
|
|
421 FILELIST: for $Index (0 .. $#SDFilesList) {
|
|
|
422 $SDFile = $SDFilesList[$Index];
|
|
|
423
|
|
|
424 $SDFilesInfo{FileOkay}[$Index] = 0;
|
|
|
425 $SDFilesInfo{OutFileRoot}[$Index] = '';
|
|
|
426 $SDFilesInfo{SDOutFileNames}[$Index] = '';
|
|
|
427 $SDFilesInfo{FPOutFileNames}[$Index] = '';
|
|
|
428 $SDFilesInfo{TextOutFileNames}[$Index] = '';
|
|
|
429
|
|
|
430 $SDFile = $SDFilesList[$Index];
|
|
|
431 if (!(-e $SDFile)) {
|
|
|
432 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
|
|
|
433 next FILELIST;
|
|
|
434 }
|
|
|
435 if (!CheckFileType($SDFile, "sd sdf")) {
|
|
|
436 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
|
|
|
437 next FILELIST;
|
|
|
438 }
|
|
|
439
|
|
|
440 if ($CheckDataField) {
|
|
|
441 # Make sure data field exists in SD file..
|
|
|
442 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
|
|
|
443
|
|
|
444 @CmpdLines = ();
|
|
|
445 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
446 $CmpdString = ReadCmpdString(\*SDFILE);
|
|
|
447 close SDFILE;
|
|
|
448 @CmpdLines = split "\n", $CmpdString;
|
|
|
449 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
450 $SpecifiedDataField = $OptionsInfo{CompoundID};
|
|
|
451 if (!exists $DataFieldValues{$SpecifiedDataField}) {
|
|
|
452 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
|
|
|
453 next FILELIST;
|
|
|
454 }
|
|
|
455 }
|
|
|
456
|
|
|
457 $AllDataFieldsRef = '';
|
|
|
458 $CommonDataFieldsRef = '';
|
|
|
459 if ($CollectDataFields) {
|
|
|
460 my($CmpdCount);
|
|
|
461 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
462 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
|
|
|
463 close SDFILE;
|
|
|
464 }
|
|
|
465
|
|
|
466 # Setup output file names...
|
|
|
467 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
468 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
|
|
|
469
|
|
|
470 $TextOutFileExt = "csv";
|
|
|
471 if ($Options{outdelim} =~ /^tab$/i) {
|
|
|
472 $TextOutFileExt = "tsv";
|
|
|
473 }
|
|
|
474 $SDOutFileExt = $FileExt;
|
|
|
475 $FPOutFileExt = "fpf";
|
|
|
476
|
|
|
477 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
|
|
|
478 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
479 if ($RootFileName && $RootFileExt) {
|
|
|
480 $FileName = $RootFileName;
|
|
|
481 }
|
|
|
482 else {
|
|
|
483 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
484 }
|
|
|
485 $OutFileRoot = $FileName;
|
|
|
486 }
|
|
|
487 else {
|
|
|
488 $OutFileRoot = "${FileName}AtomNeighborhoodsFP";
|
|
|
489 }
|
|
|
490
|
|
|
491 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
|
|
|
492 $NewFPFileName = "${OutFileRoot}.${FPOutFileExt}";
|
|
|
493 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
|
|
|
494
|
|
|
495 if ($OptionsInfo{SDOutput}) {
|
|
|
496 if ($SDFile =~ /$NewSDFileName/i) {
|
|
|
497 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
|
|
|
498 print "Specify a different name using \"-r --root\" option or use default name.\n";
|
|
|
499 next FILELIST;
|
|
|
500 }
|
|
|
501 }
|
|
|
502
|
|
|
503 if (!$OptionsInfo{OverwriteFiles}) {
|
|
|
504 # Check SD and text outout files...
|
|
|
505 if ($OptionsInfo{SDOutput}) {
|
|
|
506 if (-e $NewSDFileName) {
|
|
|
507 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
|
|
|
508 next FILELIST;
|
|
|
509 }
|
|
|
510 }
|
|
|
511 if ($OptionsInfo{FPOutput}) {
|
|
|
512 if (-e $NewFPFileName) {
|
|
|
513 warn "Warning: Ignoring file $SDFile: The file $NewFPFileName already exists\n";
|
|
|
514 next FILELIST;
|
|
|
515 }
|
|
|
516 }
|
|
|
517 if ($OptionsInfo{TextOutput}) {
|
|
|
518 if (-e $NewTextFileName) {
|
|
|
519 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
|
|
|
520 next FILELIST;
|
|
|
521 }
|
|
|
522 }
|
|
|
523 }
|
|
|
524
|
|
|
525 $SDFilesInfo{FileOkay}[$Index] = 1;
|
|
|
526
|
|
|
527 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
|
|
|
528 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
|
|
|
529 $SDFilesInfo{FPOutFileNames}[$Index] = $NewFPFileName;
|
|
|
530 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
|
|
|
531
|
|
|
532 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
|
|
|
533 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
|
|
|
534 }
|
|
|
535 }
|
|
|
536
|
|
|
537 # Process option values...
|
|
|
538 sub ProcessOptions {
|
|
|
539 %OptionsInfo = ();
|
|
|
540
|
|
|
541 ProcessAtomIdentifierTypeOptions();
|
|
|
542
|
|
|
543 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
|
|
|
544
|
|
|
545 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
|
|
|
546 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
|
|
|
547 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
|
|
|
548
|
|
|
549 my(@SpecifiedDataFields);
|
|
|
550 @SpecifiedDataFields = ();
|
|
|
551
|
|
|
552 @{$OptionsInfo{SpecifiedDataFields}} = ();
|
|
|
553 $OptionsInfo{CompoundID} = '';
|
|
|
554
|
|
|
555 if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
|
|
|
556 if ($Options{compoundidmode} =~ /^DataField$/i) {
|
|
|
557 if (!$Options{compoundid}) {
|
|
|
558 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
|
|
|
559 }
|
|
|
560 $OptionsInfo{CompoundID} = $Options{compoundid};
|
|
|
561 }
|
|
|
562 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
563 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
|
|
|
564 }
|
|
|
565 }
|
|
|
566 elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
|
|
|
567 if (!$Options{datafields}) {
|
|
|
568 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
|
|
|
569 }
|
|
|
570 @SpecifiedDataFields = split /\,/, $Options{datafields};
|
|
|
571 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
|
|
|
572 }
|
|
|
573
|
|
|
574 $OptionsInfo{FingerprintsLabel} = $Options{fingerprintslabel} ? $Options{fingerprintslabel} : 'AtomNeighborhoodsFingerprints';
|
|
|
575
|
|
|
576 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
|
|
|
577
|
|
|
578 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
|
|
|
579
|
|
|
580 $OptionsInfo{MinNeighborhoodRadius} = $Options{minneighborhoodradius};
|
|
|
581 $OptionsInfo{MaxNeighborhoodRadius} = $Options{maxneighborhoodradius};
|
|
|
582
|
|
|
583 $OptionsInfo{Output} = $Options{output};
|
|
|
584 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|All)$/i) ? 1 : 0;
|
|
|
585 $OptionsInfo{FPOutput} = ($Options{output} =~ /^(FP|All)$/i) ? 1 : 0;
|
|
|
586 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|All)$/i) ? 1 : 0;
|
|
|
587
|
|
|
588 $OptionsInfo{OutDelim} = $Options{outdelim};
|
|
|
589 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
590
|
|
|
591 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
592 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
593
|
|
|
594 $OptionsInfo{VectorStringFormat} = 'ValuesString';
|
|
|
595 }
|
|
|
596
|
|
|
597 # Process atom identifier type and related options...
|
|
|
598 #
|
|
|
599 sub ProcessAtomIdentifierTypeOptions {
|
|
|
600
|
|
|
601 $OptionsInfo{AtomIdentifierType} = $Options{atomidentifiertype};
|
|
|
602
|
|
|
603 if ($Options{atomidentifiertype} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
604 ProcessAtomicInvariantsToUseOption();
|
|
|
605 }
|
|
|
606 elsif ($Options{atomidentifiertype} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
607 ProcessFunctionalClassesToUse();
|
|
|
608 }
|
|
|
609 elsif ($OptionsInfo{AtomIdentifierType} =~ /^(DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
610 # Nothing to do for now...
|
|
|
611 }
|
|
|
612 else {
|
|
|
613 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
614 }
|
|
|
615 }
|
|
|
616
|
|
|
617 # Process specified atomic invariants to use...
|
|
|
618 #
|
|
|
619 sub ProcessAtomicInvariantsToUseOption {
|
|
|
620 my($AtomicInvariant, $AtomSymbolSpecified, @AtomicInvariantsWords);
|
|
|
621
|
|
|
622 @{$OptionsInfo{AtomicInvariantsToUse}} = ();
|
|
|
623 if (IsEmpty($Options{atomicinvariantstouse})) {
|
|
|
624 die "Error: Atomic invariants value specified using \"--AtomicInvariantsToUse\" option is empty\n";
|
|
|
625 }
|
|
|
626 $AtomSymbolSpecified = 0;
|
|
|
627 @AtomicInvariantsWords = split /\,/, $Options{atomicinvariantstouse};
|
|
|
628 for $AtomicInvariant (@AtomicInvariantsWords) {
|
|
|
629 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($AtomicInvariant)) {
|
|
|
630 die "Error: Atomic invariant specified, $AtomicInvariant, using \"--AtomicInvariantsToUse\" option is not valid...\n ";
|
|
|
631 }
|
|
|
632 if ($AtomicInvariant =~ /^(AS|AtomSymbol)$/i) {
|
|
|
633 $AtomSymbolSpecified = 1;
|
|
|
634 }
|
|
|
635 push @{$OptionsInfo{AtomicInvariantsToUse}}, $AtomicInvariant;
|
|
|
636 }
|
|
|
637 if (!$AtomSymbolSpecified) {
|
|
|
638 die "Error: Atomic invariant, AS or AtomSymbol, must be specified as using \"--AtomicInvariantsToUse\" option...\n ";
|
|
|
639 }
|
|
|
640 }
|
|
|
641
|
|
|
642 # Process specified functional classes invariants to use...
|
|
|
643 #
|
|
|
644 sub ProcessFunctionalClassesToUse {
|
|
|
645 my($FunctionalClass, @FunctionalClassesToUseWords);
|
|
|
646
|
|
|
647 @{$OptionsInfo{FunctionalClassesToUse}} = ();
|
|
|
648 if (IsEmpty($Options{functionalclassestouse})) {
|
|
|
649 die "Error: Functional classes value specified using \"--FunctionalClassesToUse\" option is empty\n";
|
|
|
650 }
|
|
|
651 @FunctionalClassesToUseWords = split /\,/, $Options{functionalclassestouse};
|
|
|
652 for $FunctionalClass (@FunctionalClassesToUseWords) {
|
|
|
653 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($FunctionalClass)) {
|
|
|
654 die "Error: Functional class specified, $FunctionalClass, using \"--FunctionalClassesToUse\" option is not valid...\n ";
|
|
|
655 }
|
|
|
656 push @{$OptionsInfo{FunctionalClassesToUse}}, $FunctionalClass;
|
|
|
657 }
|
|
|
658 }
|
|
|
659
|
|
|
660 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
661 sub SetupScriptUsage {
|
|
|
662
|
|
|
663 # Retrieve all the options...
|
|
|
664 %Options = ();
|
|
|
665
|
|
|
666 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
|
|
|
667
|
|
|
668 $Options{atomidentifiertype} = 'AtomicInvariantsAtomTypes';
|
|
|
669 $Options{atomicinvariantstouse} = 'AS,X,BO,H,FC';
|
|
|
670 $Options{functionalclassestouse} = 'HBD,HBA,PI,NI,Ar,Hal';
|
|
|
671
|
|
|
672 $Options{compoundidmode} = 'LabelPrefix';
|
|
|
673 $Options{compoundidlabel} = 'CompoundID';
|
|
|
674 $Options{datafieldsmode} = 'CompoundID';
|
|
|
675
|
|
|
676 $Options{filter} = 'Yes';
|
|
|
677
|
|
|
678 $Options{keeplargestcomponent} = 'Yes';
|
|
|
679
|
|
|
680 $Options{minneighborhoodradius} = 0;
|
|
|
681 $Options{maxneighborhoodradius} = 2;
|
|
|
682
|
|
|
683 $Options{output} = 'text';
|
|
|
684 $Options{outdelim} = 'comma';
|
|
|
685 $Options{quote} = 'yes';
|
|
|
686
|
|
|
687 if (!GetOptions(\%Options, "aromaticitymodel=s", "atomidentifiertype|a=s", "atomicinvariantstouse=s", "functionalclassestouse=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "fingerprintslabel=s", "help|h", "keeplargestcomponent|k=s", "minneighborhoodradius=s", "maxneighborhoodradius=s", "outdelim=s", "output=s", "overwrite|o", "quote|q=s", "root|r=s", "workingdir|w=s")) {
|
|
|
688 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
689 }
|
|
|
690 if ($Options{workingdir}) {
|
|
|
691 if (! -d $Options{workingdir}) {
|
|
|
692 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
693 }
|
|
|
694 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
695 }
|
|
|
696 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
|
|
|
697 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
|
|
|
698 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
|
|
|
699 }
|
|
|
700 if ($Options{atomidentifiertype} !~ /^(AtomicInvariantsAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|FunctionalClassAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
701 die "Error: The value specified, $Options{atomidentifiertype}, for option \"-a, --AtomIdentifierType\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes\n";
|
|
|
702 }
|
|
|
703 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
704 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
705 }
|
|
|
706 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
|
|
|
707 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
|
|
|
708 }
|
|
|
709 if ($Options{filter} !~ /^(Yes|No)$/i) {
|
|
|
710 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
|
|
|
711 }
|
|
|
712 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
|
|
|
713 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
|
|
|
714 }
|
|
|
715 if (!(IsInteger($Options{minneighborhoodradius}) && ($Options{minneighborhoodradius} >= 0))) {
|
|
|
716 die "Error: The value specified, $Options{minneighborhoodradius}, for option \"--MinNeighborhoodRadius\" is not valid. Allowed values: >= 0 \n";
|
|
|
717 }
|
|
|
718 if (!(IsInteger($Options{maxneighborhoodradius}) && ($Options{maxneighborhoodradius} >= 0))) {
|
|
|
719 die "Error: The value specified, $Options{maxneighborhoodradius}, for option \"--MaxNeighborhoodRadius\" is not valid. Allowed values: >= 0 \n";
|
|
|
720 }
|
|
|
721 if ($Options{minneighborhoodradius} > $Options{maxneighborhoodradius}) {
|
|
|
722 die "Error: The value specified, specified, $Options{minneighborhoodradius}, for option \"--MinNeighborhoodRadius\" must be less than the value specified, $Options{maxneighborhoodradius}, for option \"--MaxNeighborhoodRadius\" \n";
|
|
|
723 }
|
|
|
724 if ($Options{output} !~ /^(SD|FP|text|all)$/i) {
|
|
|
725 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, FP, text, or all\n";
|
|
|
726 }
|
|
|
727 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
728 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
729 }
|
|
|
730 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
731 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
732 }
|
|
|
733 if ($Options{outdelim} =~ /semicolon/i && $Options{quote} =~ /^No$/i) {
|
|
|
734 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";
|
|
|
735 }
|
|
|
736 }
|
|
|
737
|
|
|
738 __END__
|
|
|
739
|
|
|
740 =head1 NAME
|
|
|
741
|
|
|
742 AtomNeighborhoodsFingerprints.pl - Generate atom neighborhoods fingerprints for SD files
|
|
|
743
|
|
|
744 =head1 SYNOPSIS
|
|
|
745
|
|
|
746 AtomNeighborhoodsFingerprints.pl SDFile(s)...
|
|
|
747
|
|
|
748 AtomNeighborhoodsFingerprints.pl [B<--AromaticityModel> I<AromaticityModelType>]
|
|
|
749 [B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes |
|
|
|
750 DREIDINGAtomTypes | EStateAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>]
|
|
|
751 [B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">]
|
|
|
752 [B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">]
|
|
|
753 [B<--CompoundID> I<DataFieldName or LabelPrefixString>] [B<--CompoundIDLabel> I<text>]
|
|
|
754 [B<--CompoundIDMode>] [B<--DataFields> I<"FieldLabel1,FieldLabel2,...">]
|
|
|
755 [B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>] [B<-f, --Filter> I<Yes | No>]
|
|
|
756 [B<--FingerprintsLabel> I<text>] [B<-h, --help>] [B<-k, --KeepLargestComponent> I<Yes | No>]
|
|
|
757 [B<--MinNeighborhoodRadius> I<number>] [B<--MaxNeighborhoodRadius> I<number>]
|
|
|
758 [B<--OutDelim> I<comma | tab | semicolon>] [B<--output> I<SD | FP | text | all>] [B<-o, --overwrite>]
|
|
|
759 [B<-q, --quote> I<Yes | No>] [B<-r, --root> I<RootName>]
|
|
|
760 [B<-w, --WorkingDir> dirname] SDFile(s)...
|
|
|
761
|
|
|
762 =head1 DESCRIPTION
|
|
|
763
|
|
|
764 Generate atom neighborhoods fingerprints [ Ref 53-56, Ref 73 ] for I<SDFile(s)> and create appropriate
|
|
|
765 SD, FP or CSV/TSV text file(s) containing fingerprints vector strings corresponding to molecular fingerprints.
|
|
|
766
|
|
|
767 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
|
|
|
768 and I<.sd>. All other file names are ignored. All the SD files in a current directory
|
|
|
769 can be specified either by I<*.sdf> or the current directory name.
|
|
|
770
|
|
|
771 The current release of MayaChemTools supports generation of atom neighborhoods fingerprints
|
|
|
772 corresponding to following B<-a, --AtomIdentifierTypes>:
|
|
|
773
|
|
|
774 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
775 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
776 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
777
|
|
|
778 Based on the values specified for B<-a, --AtomIdentifierType> and B<--AtomicInvariantsToUse>,
|
|
|
779 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
|
|
|
780 around each non-hydrogen central atom corresponding to radii between specified values
|
|
|
781 B<--MinNeighborhoodRadius> and B<--MaxNeighborhoodRadius>, unique atom types at
|
|
|
782 each radii level are counted and an atom neighborhood identifier is generated.
|
|
|
783
|
|
|
784 The format of an atom neighborhood identifier around a central non-hydrogen atom at a
|
|
|
785 specific radius is:
|
|
|
786
|
|
|
787 NR<n>-<AtomType>-ATC<n>
|
|
|
788
|
|
|
789 NR: Neighborhood radius
|
|
|
790 AtomType: Assigned atom type
|
|
|
791 ATC: Atom type count
|
|
|
792
|
|
|
793 The atom neighborhood identifier for a non-hydrogen central atom corresponding to all specified radii
|
|
|
794 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:
|
|
|
795
|
|
|
796 NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...
|
|
|
797
|
|
|
798 The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
|
|
|
799 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.
|
|
|
800
|
|
|
801 Example of I<SD> file containing atom neighborhood fingerprints string data:
|
|
|
802
|
|
|
803 ... ...
|
|
|
804 ... ...
|
|
|
805 $$$$
|
|
|
806 ... ...
|
|
|
807 ... ...
|
|
|
808 ... ...
|
|
|
809 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
810 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
811 ... ...
|
|
|
812 2 3 1 0 0 0 0
|
|
|
813 ... ...
|
|
|
814 M END
|
|
|
815 > <CmpdID>
|
|
|
816 Cmpd1
|
|
|
817
|
|
|
818 > <AtomNeighborhoodsFingerprints>
|
|
|
819 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu
|
|
|
820 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-ATC1
|
|
|
821 :NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X1.B
|
|
|
822 O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
|
|
|
823 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C...
|
|
|
824
|
|
|
825 $$$$
|
|
|
826 ... ...
|
|
|
827 ... ...
|
|
|
828
|
|
|
829 Example of I<FP> file containing atom neighborhood fingerprints string data:
|
|
|
830
|
|
|
831 #
|
|
|
832 # Package = MayaChemTools 7.4
|
|
|
833 # Release Date = Oct 21, 2010
|
|
|
834 #
|
|
|
835 # TimeStamp = Fri Mar 11 14:15:27 2011
|
|
|
836 #
|
|
|
837 # FingerprintsStringType = FingerprintsVector
|
|
|
838 #
|
|
|
839 # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu...
|
|
|
840 # VectorStringFormat = ValuesString
|
|
|
841 # VectorValuesType = AlphaNumericalValues
|
|
|
842 #
|
|
|
843 Cmpd1 41;NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-A...
|
|
|
844 Cmpd2 23;NR0-C.X1.BO1.H3-ATC1:NR1-C.X2.BO2.H2-ATC1:NR2-C.X3.BO3.H1-A...
|
|
|
845 ... ...
|
|
|
846 ... ..
|
|
|
847
|
|
|
848 Example of CSV I<Text> file containing atom neighborhood fingerprints string data:
|
|
|
849
|
|
|
850 "CompoundID","AtomNeighborhoodsFingerprints"
|
|
|
851 "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes
|
|
|
852 :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.B
|
|
|
853 O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
|
|
|
854 NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3
|
|
|
855 .BO4-ATC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1..."
|
|
|
856 ... ...
|
|
|
857 ... ...
|
|
|
858
|
|
|
859 The current release of MayaChemTools generates the following types of atom neighborhoods
|
|
|
860 fingerprints vector strings:
|
|
|
861
|
|
|
862 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
|
|
|
863 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
|
|
|
864 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
|
|
|
865 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
|
|
|
866 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
|
|
|
867 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
|
|
|
868
|
|
|
869 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
|
|
|
870 adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
|
|
|
871 NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
|
|
|
872 _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
|
|
|
873 C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
|
|
|
874 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...
|
|
|
875
|
|
|
876 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
|
|
|
877 ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
|
|
|
878 NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
|
|
|
879 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
|
|
|
880 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
|
|
|
881 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...
|
|
|
882
|
|
|
883 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
|
|
|
884 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
|
|
|
885 ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
|
|
|
886 C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
|
|
|
887 R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
|
|
|
888 TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...
|
|
|
889
|
|
|
890 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
|
|
|
891 ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
|
|
|
892 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
|
|
|
893 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
|
|
|
894 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
|
|
|
895 C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...
|
|
|
896
|
|
|
897 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
|
|
|
898 us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
|
|
|
899 CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
|
|
|
900 NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
|
|
|
901 ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
|
|
|
902 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...
|
|
|
903
|
|
|
904 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
|
|
|
905 us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
|
|
|
906 -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
|
|
|
907 O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
|
|
|
908 ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
|
|
|
909 C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...
|
|
|
910
|
|
|
911 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
|
|
|
912 s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
|
|
|
913 -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
|
|
|
914 e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
|
|
|
915 ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
|
|
|
916 TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...
|
|
|
917
|
|
|
918 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
|
|
|
919 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
|
|
|
920 _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
|
|
|
921 C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
|
|
|
922 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
|
|
|
923 -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...
|
|
|
924
|
|
|
925 =head1 OPTIONS
|
|
|
926
|
|
|
927 =over 4
|
|
|
928
|
|
|
929 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
|
|
|
930
|
|
|
931 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
932 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
933 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
934 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
|
|
|
935
|
|
|
936 The supported aromaticity model names along with model specific control parameters
|
|
|
937 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
|
|
|
938 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
|
|
|
939 this file during class instantiation and makes it available to method B<DetectAromaticity>
|
|
|
940 for detecting aromaticity corresponding to a specific model.
|
|
|
941
|
|
|
942 =item B<-a, --AtomIdentifierType> I<AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes>
|
|
|
943
|
|
|
944 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
|
|
|
945 atoms during calculation of atom neighborhoods fingerprints. Possible values in the current
|
|
|
946 release are: I<AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
947 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
|
|
|
948 TPSAAtomTypes, UFFAtomTypes>. Default value: I<AtomicInvariantsAtomTypes>.
|
|
|
949
|
|
|
950 =item B<--AtomicInvariantsToUse> I<"AtomicInvariant,AtomicInvariant...">
|
|
|
951
|
|
|
952 This value is used during I<AtomicInvariantsAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
953 option. It's a list of comma separated valid atomic invariant atom types.
|
|
|
954
|
|
|
955 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB,
|
|
|
956 H, Ar, RA, FC, MN, SM>. Default value: I<AS,X,BO,H,FC>.
|
|
|
957
|
|
|
958 The atomic invariants abbreviations correspond to:
|
|
|
959
|
|
|
960 AS = Atom symbol corresponding to element symbol
|
|
|
961
|
|
|
962 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
963 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
964 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
965 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
966 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
967 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
968 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
969 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
970 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
971 FC<+n/-n> = Formal charge assigned to atom
|
|
|
972 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
973 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
974 3 (triplet)
|
|
|
975
|
|
|
976 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
977
|
|
|
978 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
979
|
|
|
980 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
981 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
982
|
|
|
983 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
984 are also allowed:
|
|
|
985
|
|
|
986 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
987 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
988 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
989 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
990 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
991 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
992 H : NumOfImplicitAndExplicitHydrogens
|
|
|
993 Ar : Aromatic
|
|
|
994 RA : RingAtom
|
|
|
995 FC : FormalCharge
|
|
|
996 MN : MassNumber
|
|
|
997 SM : SpinMultiplicity
|
|
|
998
|
|
|
999 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
|
|
|
1000 atom types.
|
|
|
1001
|
|
|
1002 =item B<--FunctionalClassesToUse> I<"FunctionalClass1,FunctionalClass2...">
|
|
|
1003
|
|
|
1004 This value is used during I<FunctionalClassAtomTypes> value of B<a, --AtomIdentifierType>
|
|
|
1005 option. It's a list of comma separated valid functional classes.
|
|
|
1006
|
|
|
1007 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1008 Default value [ Ref 24 ]: I<HBD,HBA,PI,NI,Ar,Hal>.
|
|
|
1009
|
|
|
1010 The functional class abbreviations correspond to:
|
|
|
1011
|
|
|
1012 HBD: HydrogenBondDonor
|
|
|
1013 HBA: HydrogenBondAcceptor
|
|
|
1014 PI : PositivelyIonizable
|
|
|
1015 NI : NegativelyIonizable
|
|
|
1016 Ar : Aromatic
|
|
|
1017 Hal : Halogen
|
|
|
1018 H : Hydrophobic
|
|
|
1019 RA : RingAtom
|
|
|
1020 CA : ChainAtom
|
|
|
1021
|
|
|
1022 Functional class atom type specification for an atom corresponds to:
|
|
|
1023
|
|
|
1024 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
1025
|
|
|
1026 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1027 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1028
|
|
|
1029 HydrogenBondDonor: NH, NH2, OH
|
|
|
1030 HydrogenBondAcceptor: N[!H], O
|
|
|
1031 PositivelyIonizable: +, NH2
|
|
|
1032 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1033
|
|
|
1034 =item B<--CompoundID> I<DataFieldName or LabelPrefixString>
|
|
|
1035
|
|
|
1036 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
|
|
|
1037
|
|
|
1038 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
|
|
|
1039 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
|
|
1040 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
|
|
|
1041 look like Cmpd<Number>.
|
|
|
1042
|
|
|
1043 Examples for I<DataField> value of B<--CompoundIDMode>:
|
|
|
1044
|
|
|
1045 MolID
|
|
|
1046 ExtReg
|
|
|
1047
|
|
|
1048 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
|
|
|
1049
|
|
|
1050 Compound
|
|
|
1051
|
|
|
1052 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
1053 instead of default value of Cmpd<Number>.
|
|
|
1054
|
|
|
1055
|
|
|
1056 =item B<--CompoundIDLabel> I<text>
|
|
|
1057
|
|
|
1058 Specify compound ID column label for FP or CSV/TSV text file(s) used during I<CompoundID> value
|
|
|
1059 of B<--DataFieldsMode> option. Default: I<CompoundID>.
|
|
|
1060
|
|
|
1061 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
1062
|
|
|
1063 Specify how to generate compound IDs and write to FP or CSV/TSV text file(s) along with generated
|
|
|
1064 fingerprints for I<FP | text | all> values of B<--output> option: use a I<SDFile(s)> datafield value;
|
|
|
1065 use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix; use combination
|
|
|
1066 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
|
|
|
1067
|
|
|
1068 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
1069 Default: I<LabelPrefix>.
|
|
|
1070
|
|
|
1071 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
|
|
|
1072 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
1073 values are replaced with sequential compound IDs.
|
|
|
1074
|
|
|
1075 This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
|
|
|
1076
|
|
|
1077 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,...">
|
|
|
1078
|
|
|
1079 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
1080 with generated fingerprints for I<text | all> values of B<--output> option.
|
|
|
1081
|
|
|
1082 This is only used for I<Specify> value of B<--DataFieldsMode> option.
|
|
|
1083
|
|
|
1084 Examples:
|
|
|
1085
|
|
|
1086 Extreg
|
|
|
1087 MolID,CompoundName
|
|
|
1088
|
|
|
1089 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
|
|
|
1090
|
|
|
1091 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
|
|
|
1092 with generated fingerprints for I<text | all> values of B<--output> option: transfer all SD
|
|
|
1093 data field; transfer SD data files common to all compounds; extract specified data fields;
|
|
|
1094 generate a compound ID using molname line, a compound prefix, or a combination of both.
|
|
|
1095 Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
|
|
|
1096
|
|
|
1097 =item B<-f, --Filter> I<Yes | No>
|
|
|
1098
|
|
|
1099 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
|
|
|
1100 Default value: I<Yes>.
|
|
|
1101
|
|
|
1102 By default, compound data is checked before calculating fingerprints and compounds containing
|
|
|
1103 atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
1104
|
|
|
1105 =item B<--FingerprintsLabel> I<text>
|
|
|
1106
|
|
|
1107 SD data label or text file column label to use for fingerprints string in output SD or
|
|
|
1108 CSV/TSV text file(s) specified by B<--output>. Default value: I<AtomNeighborhoodsFingerprints>.
|
|
|
1109
|
|
|
1110 =item B<-h, --help>
|
|
|
1111
|
|
|
1112 Print this help message.
|
|
|
1113
|
|
|
1114 =item B<-k, --KeepLargestComponent> I<Yes | No>
|
|
|
1115
|
|
|
1116 Generate fingerprints for only the largest component in molecule. Possible values:
|
|
|
1117 I<Yes or No>. Default value: I<Yes>.
|
|
|
1118
|
|
|
1119 For molecules containing multiple connected components, fingerprints can be generated
|
|
|
1120 in two different ways: use all connected components or just the largest connected
|
|
|
1121 component. By default, all atoms except for the largest connected component are
|
|
|
1122 deleted before generation of fingerprints.
|
|
|
1123
|
|
|
1124 =item B<--MinNeighborhoodRadius> I<number>
|
|
|
1125
|
|
|
1126 Minimum atom neighborhood radius for generating atom neighborhoods. Default value: I<0>.
|
|
|
1127 Valid values: positive integers and less than B<--MaxNeighborhoodRadius>. Neighborhood
|
|
|
1128 radius of zero corresponds to list of non-hydrogen atoms.
|
|
|
1129
|
|
|
1130 =item B<--MaxNeighborhoodRadius> I<number>
|
|
|
1131
|
|
|
1132 Maximum atom neighborhood radius for generating atom neighborhoods. Default value: I<2>.
|
|
|
1133 Valid values: positive integers and greater than B<--MineighborhoodRadius>.
|
|
|
1134
|
|
|
1135 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
1136
|
|
|
1137 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
|
|
|
1138 Default value: I<comma>.
|
|
|
1139
|
|
|
1140 =item B<--output> I<SD | FP | text | all>
|
|
|
1141
|
|
|
1142 Type of output files to generate. Possible values: I<SD, FP, text, or all>. Default value: I<text>.
|
|
|
1143
|
|
|
1144 =item B<-o, --overwrite>
|
|
|
1145
|
|
|
1146 Overwrite existing files.
|
|
|
1147
|
|
|
1148 =item B<-q, --quote> I<Yes | No>
|
|
|
1149
|
|
|
1150 Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
1151 I<Yes or No>. Default value: I<Yes>.
|
|
|
1152
|
|
|
1153 =item B<-r, --root> I<RootName>
|
|
|
1154
|
|
|
1155 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
1156 <SDFileName><AtomNeighborhoodsFP>.<Ext>. The file type determines <Ext>
|
|
|
1157 value. The sdf, fpf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab
|
|
|
1158 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
1159
|
|
|
1160 =item B<-w, --WorkingDir> I<DirName>
|
|
|
1161
|
|
|
1162 Location of working directory. Default: current directory.
|
|
|
1163
|
|
|
1164 =back
|
|
|
1165
|
|
|
1166 =head1 EXAMPLES
|
|
|
1167
|
|
|
1168 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1169 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
1170 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1171
|
|
|
1172 % AtomNeighborhoodsFingerprints.pl -r SampleANFP -o Sample.sdf
|
|
|
1173
|
|
|
1174 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1175 2 using DREIDING atom types in vector string format and create a SampleANFP.csv
|
|
|
1176 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1177
|
|
|
1178 % AtomNeighborhoodsFingerprints.pl -a DREIDINGAtomTypes -r SampleANFP
|
|
|
1179 -o Sample.sdf
|
|
|
1180
|
|
|
1181 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1182 2 using EStateAtomTypes types in vector string format and create a SampleANFP.csv
|
|
|
1183 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1184
|
|
|
1185 % AtomNeighborhoodsFingerprints.pl -a EStateAtomTypes -r SampleANFP
|
|
|
1186 -o Sample.sdf
|
|
|
1187
|
|
|
1188 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1189 2 using SYBYL atom types in vector string format and create a SampleANFP.csv
|
|
|
1190 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1191
|
|
|
1192 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
1193 -o Sample.sdf
|
|
|
1194
|
|
|
1195 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1196 2 using FunctionalClass atom types in vector string format and create a SampleANFP.csv
|
|
|
1197 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1198
|
|
|
1199 % AtomNeighborhoodsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
1200 -r SampleANFP -o Sample.sdf
|
|
|
1201
|
|
|
1202 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1203 2 using MMFF94 atom types in vector string format and create a SampleANFP.csv
|
|
|
1204 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1205
|
|
|
1206 % AtomNeighborhoodsFingerprints.pl -a MMFF94AtomTypes -r SampleANFP
|
|
|
1207 -o Sample.sdf
|
|
|
1208
|
|
|
1209 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1210 2 using SLogP atom types in vector string format and create a SampleANFP.csv
|
|
|
1211 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1212
|
|
|
1213 % AtomNeighborhoodsFingerprints.pl -a SLogPAtomTypes -r SampleANFP
|
|
|
1214 -o Sample.sdf
|
|
|
1215
|
|
|
1216 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1217 2 using SYBYL atom types in vector string format and create a SampleANFP.csv
|
|
|
1218 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1219
|
|
|
1220 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
1221 -o Sample.sdf
|
|
|
1222
|
|
|
1223 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1224 2 using TPSA atom types in vector string format and create a SampleANFP.csv
|
|
|
1225 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1226
|
|
|
1227 % AtomNeighborhoodsFingerprints.pl -a TPSAAtomTypes -r SampleANFP
|
|
|
1228 -o Sample.sdf
|
|
|
1229
|
|
|
1230 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1231 2 using UFF atom types in vector string format and create a SampleANFP.csv
|
|
|
1232 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1233
|
|
|
1234 % AtomNeighborhoodsFingerprints.pl -a UFFAtomTypes -r SampleANFP
|
|
|
1235 -o Sample.sdf
|
|
|
1236
|
|
|
1237 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1238 2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
|
|
|
1239 SampleANFP.fpf and SampleANFP.csv files containing sequential compound IDs in CSV file along
|
|
|
1240 with fingerprints vector strings data, type:
|
|
|
1241
|
|
|
1242 % AtomNeighborhoodsFingerprints.pl --output all -r SampleANFP
|
|
|
1243 -o Sample.sdf
|
|
|
1244
|
|
|
1245 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 1 to
|
|
|
1246 3 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
1247 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1248
|
|
|
1249 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1250 --MinNeighborhoodRadius 1 --MaxNeighborhoodRadius 3 -r SampleANFP
|
|
|
1251 -o Sample.sdf
|
|
|
1252
|
|
|
1253 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1254 2 using only AS,X atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
1255 file containing sequential compound IDs along with fingerprints vector strings data, type:
|
|
|
1256
|
|
|
1257 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1258 --AtomicInvariantsToUse "AS,X" --MinNeighborhoodRadius 0
|
|
|
1259 --MaxNeighborhoodRadius 3 -r SampleANFP -o Sample.sdf
|
|
|
1260
|
|
|
1261 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1262 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
1263 file containing compound ID from molecule name line along with fingerprints vector strings data, type:
|
|
|
1264
|
|
|
1265 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1266 --DataFieldsMode CompoundID --CompoundIDMode MolName
|
|
|
1267 -r SampleANFP -o Sample.sdf
|
|
|
1268
|
|
|
1269 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1270 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
1271 file containing compound IDs using specified data field along with fingerprints vector strings
|
|
|
1272 data, type:
|
|
|
1273
|
|
|
1274 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1275 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
|
|
|
1276 Mol_ID -r SampleANFP -o Sample.sdf
|
|
|
1277
|
|
|
1278 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1279 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
1280 file containing compound ID using combination of molecule name line and an explicit compound
|
|
|
1281 prefix along with fingerprints vector strings data, type:
|
|
|
1282
|
|
|
1283 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1284 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
|
|
|
1285 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleANFP -o Sample.sdf
|
|
|
1286
|
|
|
1287 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1288 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
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|
|
1289 file containing specific data fields columns along with fingerprints vector strings
|
|
|
1290 data, type:
|
|
|
1291
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|
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1292 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
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1293 --DataFieldsMode Specify --DataFields Mol_ID -r SampleANFP
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|
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1294 -o Sample.sdf
|
|
|
1295
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|
|
1296 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1297 2 using atomic invariants atom types in vector string format and create a SampleANFP.csv
|
|
|
1298 file containing common data fields columns along with fingerprints vector strings
|
|
|
1299 data, type:
|
|
|
1300
|
|
|
1301 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1302 --DataFieldsMode Common -r SampleANFP -o Sample.sdf
|
|
|
1303
|
|
|
1304 To generate atom neighborhoods fingerprints corresponding to atom neighborhood radii from 0 to
|
|
|
1305 2 using atomic invariants atom types in vector string format and create SampleANFP.sdf,
|
|
|
1306 SampleANFP.fpf and SampleANFP.csv files containing all data fields columns in CSV file along with
|
|
|
1307 fingerprints data, type:
|
|
|
1308
|
|
|
1309 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
1310 --DataFieldsMode All --output all -r SampleANFP
|
|
|
1311 -o Sample.sdf
|
|
|
1312
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|
|
1313 =head1 AUTHOR
|
|
|
1314
|
|
|
1315 Manish Sud <msud@san.rr.com>
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|
|
1316
|
|
|
1317 =head1 SEE ALSO
|
|
|
1318
|
|
|
1319 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, SimilaritySearchingFingerprints.pl,
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|
|
1320 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
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|
|
1321 TopologicalAtomPairsFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
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|
|
1322 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
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|
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1323
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|
|
1324 =head1 COPYRIGHT
|
|
|
1325
|
|
|
1326 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1327
|
|
|
1328 This file is part of MayaChemTools.
|
|
|
1329
|
|
|
1330 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1331 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1332 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1333 any later version.
|
|
|
1334
|
|
|
1335 =cut
|
