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1 #!/usr/bin/perl -w
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2 #
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3 # $RCSfile: CalculatePhysicochemicalProperties.pl,v $
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4 # $Date: 2015/02/28 20:46:19 $
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5 # $Revision: 1.20 $
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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 "$FindBin::Bin/../lib";
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31 use Getopt::Long;
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32 use File::Basename;
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33 use Text::ParseWords;
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34 use Benchmark;
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35 use FileUtil;
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36 use TextUtil;
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37 use SDFileUtil;
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38 use MoleculeFileIO;
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39 use Molecule;
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40 use AtomTypes::AtomicInvariantsAtomTypes;
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41 use AtomTypes::FunctionalClassAtomTypes;
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42 use MolecularDescriptors::MolecularDescriptorsGenerator;
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43
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44 my($ScriptName, %Options, $StartTime, $EndTime, $TotalTime);
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45
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46 # Autoflush STDOUT
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47 $| = 1;
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48
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49 # Starting message...
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50 $ScriptName = basename($0);
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51 print "\n$ScriptName: Starting...\n\n";
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52 $StartTime = new Benchmark;
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53
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54 # Get the options and setup script...
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55 SetupScriptUsage();
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56 if ($Options{help} || @ARGV < 1) {
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57 die GetUsageFromPod("$FindBin::Bin/$ScriptName");
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58 }
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59
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60 my(@SDFilesList);
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61 @SDFilesList = ExpandFileNames(\@ARGV, "sdf sd");
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62
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63 # Process options...
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64 print "Processing options...\n";
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65 my(%OptionsInfo);
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66 ProcessOptions();
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67
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68 # Setup information about input files...
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69 print "Checking input SD file(s)...\n";
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70 my(%SDFilesInfo);
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71 RetrieveSDFilesInfo();
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72
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73 # Process input files..
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74 my($FileIndex);
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75 if (@SDFilesList > 1) {
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76 print "\nProcessing SD files...\n";
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77 }
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78 for $FileIndex (0 .. $#SDFilesList) {
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79 if ($SDFilesInfo{FileOkay}[$FileIndex]) {
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80 print "\nProcessing file $SDFilesList[$FileIndex]...\n";
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81 CalculatePhysicochemicalProperties($FileIndex);
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82 }
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83 }
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84 print "\n$ScriptName:Done...\n\n";
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85
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86 $EndTime = new Benchmark;
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87 $TotalTime = timediff ($EndTime, $StartTime);
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88 print "Total time: ", timestr($TotalTime), "\n";
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89
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90 ###############################################################################
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91
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92 # Calculate physicochemical properties for a SD file...
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93 #
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94 sub CalculatePhysicochemicalProperties {
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95 my($FileIndex) = @_;
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96 my($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount, $SDFile, $MoleculeFileIO, $Molecule, $MolecularDescriptorsGenerator, $PhysicochemicalPropertiesDataRef, $NewSDFileRef, $NewTextFileRef);
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97
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98 $SDFile = $SDFilesList[$FileIndex];
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99
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100 # Setup output files...
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101 $NewSDFileRef = ''; $NewTextFileRef = '';
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102 ($NewSDFileRef, $NewTextFileRef) = SetupAndOpenOutputFiles($FileIndex);
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103
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104 # Setup molecular descriptor generator to calculate property values for specifed
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105 # property names...
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106 $MolecularDescriptorsGenerator = SetupMolecularDescriptorsGenerator();
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107
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108 ($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount) = ('0') x 4;
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109
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110 $MoleculeFileIO = new MoleculeFileIO('Name' => $SDFile);
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111 $MoleculeFileIO->Open();
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112
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113 COMPOUND: while ($Molecule = $MoleculeFileIO->ReadMolecule()) {
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114 $CmpdCount++;
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115
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116 # Filter compound data before calculating physiochemical properties...
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117 if ($OptionsInfo{Filter}) {
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118 if (CheckAndFilterCompound($CmpdCount, $Molecule)) {
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119 $IgnoredCmpdCount++;
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120 next COMPOUND;
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121 }
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122 }
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123
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124 # Calculate properties...
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125 $PhysicochemicalPropertiesDataRef = CalculateMoleculeProperties($MolecularDescriptorsGenerator, $Molecule);
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126
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127 if (!defined($PhysicochemicalPropertiesDataRef)) {
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128 $IgnoredCmpdCount++;
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129 ProcessIgnoredCompound('PropertiesCalculationFailed', $CmpdCount, $Molecule);
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130 next COMPOUND;
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131 }
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132
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133 # Calculate any rule violations...
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134 if ($OptionsInfo{RuleOf5Violations} && $PhysicochemicalPropertiesDataRef->{RuleOf5Violations}) {
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135 $RuleOf5ViolationsCount++;
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136 }
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137
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138 if ($OptionsInfo{RuleOf3Violations} && $PhysicochemicalPropertiesDataRef->{RuleOf3Violations}) {
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139 $RuleOf3ViolationsCount++;
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140 }
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141
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142 # Write out calculate properties...
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143 WriteDataToOutputFiles($FileIndex, $CmpdCount, $Molecule, $PhysicochemicalPropertiesDataRef, $NewSDFileRef, $NewTextFileRef);
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144 }
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145 $MoleculeFileIO->Close();
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146
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147 if ($OptionsInfo{SDOutput} && $NewSDFileRef) {
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148 close $NewSDFileRef;
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149 }
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150 if ($OptionsInfo{TextOutput} && $NewTextFileRef) {
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151 close $NewTextFileRef;
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152 }
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153
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154 WriteCalculationSummaryStatistics($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount);
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155 }
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156
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157 # Process compound being ignored due to problems in physicochemical properties calculation...
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158 #
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159 sub ProcessIgnoredCompound {
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160 my($Mode, $CmpdCount, $Molecule) = @_;
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161 my($CmpdID, $DataFieldLabelAndValuesRef);
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162
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163 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
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164 $CmpdID = SetupCmpdIDForTextFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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165
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166 MODE: {
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167 if ($Mode =~ /^ContainsNonElementalData$/i) {
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168 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains atom data corresponding to non-elemental atom symbol(s)...\n\n";
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169 next MODE;
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170 }
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171
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172 if ($Mode =~ /^ContainsNoElementalData$/i) {
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173 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Compound contains no atom data...\n\n";
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174 next MODE;
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175 }
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176
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177 if ($Mode =~ /^PropertiesCalculationFailed$/i) {
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178 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n";
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179 next MODE;
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180 }
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181 warn "\nWarning: Ignoring compound record number $CmpdCount with ID $CmpdID: Physicochemical properties calculation didn't succeed...\n\n";
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182 }
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183 }
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184
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185 # Check and filter compounds....
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186 #
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187 sub CheckAndFilterCompound {
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188 my($CmpdCount, $Molecule) = @_;
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189 my($ElementCount, $NonElementCount);
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190
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191 ($ElementCount, $NonElementCount) = $Molecule->GetNumOfElementsAndNonElements();
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192
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193 if ($NonElementCount) {
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194 ProcessIgnoredCompound('ContainsNonElementalData', $CmpdCount, $Molecule);
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195 return 1;
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196 }
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197
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198 if (!$ElementCount) {
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199 ProcessIgnoredCompound('ContainsNoElementalData', $CmpdCount, $Molecule);
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200 return 1;
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201 }
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202
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203 return 0;
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204 }
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205
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206 # Write out compounds physicochemical properties calculation summary statistics...
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207 #
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208 sub WriteCalculationSummaryStatistics {
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209 my($CmpdCount, $IgnoredCmpdCount, $RuleOf5ViolationsCount, $RuleOf3ViolationsCount) = @_;
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210 my($ProcessedCmpdCount);
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211
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212 $ProcessedCmpdCount = $CmpdCount - $IgnoredCmpdCount;
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213
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214 print "\nNumber of compounds: $CmpdCount\n";
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215 print "Number of compounds processed successfully during physicochemical properties calculation: $ProcessedCmpdCount\n";
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216 print "Number of compounds ignored during physicochemical properties calculation: $IgnoredCmpdCount\n";
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217
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218 if ($OptionsInfo{RuleOf5Violations}) {
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219 print "Number of compounds with one or more RuleOf5 violations: $RuleOf5ViolationsCount\n";
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220 }
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221
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222 if ($OptionsInfo{RuleOf3Violations}) {
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223 print "Number of compounds with one or more RuleOf3 violations: $RuleOf3ViolationsCount\n";
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224 }
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225
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226 }
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227
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228 # Open output files...
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229 #
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230 sub SetupAndOpenOutputFiles {
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231 my($FileIndex) = @_;
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232 my($NewSDFile, $NewTextFile, $NewSDFileRef, $NewTextFileRef);
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233
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234 $NewSDFileRef = '';
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235 $NewTextFileRef = '';
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236
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237 if ($OptionsInfo{SDOutput}) {
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238 $NewSDFile = $SDFilesInfo{SDOutFileNames}[$FileIndex];
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239 print "Generating SD file $NewSDFile...\n";
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240 open NEWSDFILE, ">$NewSDFile" or die "Error: Couldn't open $NewSDFile: $! \n";
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241 $NewSDFileRef = \*NEWSDFILE;
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242 }
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243 if ($OptionsInfo{TextOutput}) {
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244 $NewTextFile = $SDFilesInfo{TextOutFileNames}[$FileIndex];
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245 print "Generating text file $NewTextFile...\n";
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246 open NEWTEXTFILE, ">$NewTextFile" or die "Error: Couldn't open $NewTextFile: $! \n";
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247 WriteTextFileCoulmnLabels($FileIndex, \*NEWTEXTFILE);
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248 $NewTextFileRef = \*NEWTEXTFILE;
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249 }
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250 return ($NewSDFileRef, $NewTextFileRef);
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251 }
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252
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253 # Write calculated physicochemical properties and other data to appropriate output files...
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254 #
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255 sub WriteDataToOutputFiles {
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256 my($FileIndex, $CmpdCount, $Molecule, $PhysicochemicalPropertiesDataRef, $NewSDFileRef, $NewTextFileRef) = @_;
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257 my($PropertyName, $PropertyValue);
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258
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259 if ($OptionsInfo{SDOutput}) {
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260 # Retrieve input compound string used to create molecule and write it out
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261 # without last line containing a delimiter...
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262 my($CmpdString);
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263 $CmpdString = $Molecule->GetInputMoleculeString();
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264 $CmpdString =~ s/\$\$\$\$$//;
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265 print $NewSDFileRef "$CmpdString";
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266
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267 # Write out calculated physicochemical properties data...
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268 for $PropertyName (@{$OptionsInfo{SpecifiedPropertyNames}}) {
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269 $PropertyValue = $PhysicochemicalPropertiesDataRef->{$PropertyName};
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270 print $NewSDFileRef "> <$PropertyName>\n$PropertyValue\n\n";
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271 }
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272
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273 # Write out RuleOf5 violations for molecule....
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274 if ($OptionsInfo{RuleOf5Violations}) {
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275 $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf5Violations};
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276 print $NewSDFileRef "> <RuleOf5Violations>\n$PropertyValue\n\n";
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277 }
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278
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279 # Write out RuleOf3 violations for molecule....
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280 if ($OptionsInfo{RuleOf3Violations}) {
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281 $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf3Violations};
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282 print $NewSDFileRef "> <RuleOf3Violations>\n$PropertyValue\n\n";
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283 }
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284
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285 # Write out delimiter...
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286 print $NewSDFileRef "\$\$\$\$\n";
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287 }
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288
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289 if ($OptionsInfo{TextOutput}) {
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290 my($Line, $DataFieldLabelAndValuesRef, $DataFieldLabel, $DataFieldValue, @LineWords,);
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291
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292 $DataFieldLabelAndValuesRef = $Molecule->GetDataFieldLabelAndValues();
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293 @LineWords = ();
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294 if ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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295 push @LineWords, SetupCmpdIDForTextFiles($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef);
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296 }
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297 elsif ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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298 @LineWords = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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299 }
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300 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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301 @LineWords = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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302 }
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303 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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304 @LineWords = map { exists $DataFieldLabelAndValuesRef->{$_} ? $DataFieldLabelAndValuesRef->{$_} : ''} @{$OptionsInfo{SpecifiedDataFields}};
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305 }
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306
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307 # Append calculated physicochemical properties data...
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308 for $PropertyName (@{$OptionsInfo{SpecifiedPropertyNames}}) {
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309 $PropertyValue = $PhysicochemicalPropertiesDataRef->{$PropertyName};
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310 push @LineWords, $PropertyValue;
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311 }
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312
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313 # Write out RuleOf5 violations for molecule....
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314 if ($OptionsInfo{RuleOf5Violations}) {
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315 $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf5Violations};
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316 push @LineWords, $PropertyValue;
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317 }
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318
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319 # Write out RuleOf3 violations for molecule....
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320 if ($OptionsInfo{RuleOf3Violations}) {
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321 $PropertyValue = $PhysicochemicalPropertiesDataRef->{RuleOf3Violations};
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322 push @LineWords, $PropertyValue;
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323 }
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324
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325 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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326 print $NewTextFileRef "$Line\n";
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327 }
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328 }
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329
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330 # Write out approriate column labels to text file...
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331 sub WriteTextFileCoulmnLabels {
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332 my($FileIndex, $NewTextFileRef) = @_;
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333 my($Line, @LineWords);
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334
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335 @LineWords = ();
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336 if ($OptionsInfo{DataFieldsMode} =~ /^All$/i) {
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337 push @LineWords, @{$SDFilesInfo{AllDataFieldsRef}[$FileIndex]};
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338 }
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339 elsif ($OptionsInfo{DataFieldsMode} =~ /^Common$/i) {
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340 push @LineWords, @{$SDFilesInfo{CommonDataFieldsRef}[$FileIndex]};
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341 }
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342 elsif ($OptionsInfo{DataFieldsMode} =~ /^Specify$/i) {
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343 push @LineWords, @{$OptionsInfo{SpecifiedDataFields}};
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344 }
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345 elsif ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) {
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346 push @LineWords, $OptionsInfo{CompoundIDLabel};
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347 }
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348 my($SpecifiedPropertyName);
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349
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350 # Append physicochemical properties column labels...
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351 push @LineWords, @{$OptionsInfo{SpecifiedPropertyNames}};
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352
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353 # Write out RuleOf5 violations label...
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354 if ($OptionsInfo{RuleOf5Violations}) {
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355 push @LineWords, 'RuleOf5Violations';
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356 }
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357
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358 # Write out RuleOf3 violations label...
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359 if ($OptionsInfo{RuleOf3Violations}) {
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360 push @LineWords, 'RuleOf3Violations';
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361 }
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362
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363 $Line = JoinWords(\@LineWords, $OptionsInfo{OutDelim}, $OptionsInfo{OutQuote});
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364 print $NewTextFileRef "$Line\n";
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365 }
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366
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367 # Generate compound ID for text files..
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368 #
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369 sub SetupCmpdIDForTextFiles {
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370 my($CmpdCount, $Molecule, $DataFieldLabelAndValuesRef) = @_;
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371 my($CmpdID);
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372
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373 $CmpdID = '';
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374 if ($OptionsInfo{CompoundIDMode} =~ /^MolNameOrLabelPrefix$/i) {
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375 my($MolName);
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376 $MolName = $Molecule->GetName();
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377 $CmpdID = $MolName ? $MolName : "$OptionsInfo{CompoundID}${CmpdCount}";
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378 }
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379 elsif ($OptionsInfo{CompoundIDMode} =~ /^LabelPrefix$/i) {
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380 $CmpdID = "$OptionsInfo{CompoundID}${CmpdCount}";
|
|
|
381 }
|
|
|
382 elsif ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i) {
|
|
|
383 my($SpecifiedDataField);
|
|
|
384 $SpecifiedDataField = $OptionsInfo{CompoundID};
|
|
|
385 $CmpdID = exists $DataFieldLabelAndValuesRef->{$SpecifiedDataField} ? $DataFieldLabelAndValuesRef->{$SpecifiedDataField} : '';
|
|
|
386 }
|
|
|
387 elsif ($OptionsInfo{CompoundIDMode} =~ /^MolName$/i) {
|
|
|
388 $CmpdID = $Molecule->GetName();
|
|
|
389 }
|
|
|
390 return $CmpdID;
|
|
|
391 }
|
|
|
392
|
|
|
393 # Calculate physicochemical properties for molecule...
|
|
|
394 #
|
|
|
395 sub CalculateMoleculeProperties {
|
|
|
396 my($MolecularDescriptorsGenerator, $Molecule) = @_;
|
|
|
397 my($PropertyName, $PropertyValue, $MolecularDescriptorsObject, %CalculatedPhysicochemicalProperties);
|
|
|
398
|
|
|
399 %CalculatedPhysicochemicalProperties = ();
|
|
|
400
|
|
|
401 if ($OptionsInfo{KeepLargestComponent}) {
|
|
|
402 $Molecule->KeepLargestComponent();
|
|
|
403 }
|
|
|
404
|
|
|
405 if (!$Molecule->DetectRings()) {
|
|
|
406 return undef;
|
|
|
407 }
|
|
|
408 $Molecule->SetAromaticityModel($OptionsInfo{AromaticityModel});
|
|
|
409 $Molecule->DetectAromaticity();
|
|
|
410
|
|
|
411 if ($OptionsInfo{AddHydrogens}) {
|
|
|
412 $Molecule->AddHydrogens();
|
|
|
413 }
|
|
|
414
|
|
|
415 # Calculate physicochemical properties...
|
|
|
416 $MolecularDescriptorsGenerator->SetMolecule($Molecule);
|
|
|
417 $MolecularDescriptorsGenerator->GenerateDescriptors();
|
|
|
418
|
|
|
419 if (!$MolecularDescriptorsGenerator->IsDescriptorsGenerationSuccessful()) {
|
|
|
420 return undef;
|
|
|
421 }
|
|
|
422
|
|
|
423 %CalculatedPhysicochemicalProperties = $MolecularDescriptorsGenerator->GetDescriptorNamesAndValues();
|
|
|
424
|
|
|
425 # Count RuleOf3 violations...
|
|
|
426 if ($OptionsInfo{RuleOf3Violations}) {
|
|
|
427 CalculateRuleViolationsCount('RuleOf3Violations', \%CalculatedPhysicochemicalProperties);
|
|
|
428 }
|
|
|
429
|
|
|
430 # Count RuleOf5 violations...
|
|
|
431 if ($OptionsInfo{RuleOf5Violations}) {
|
|
|
432 CalculateRuleViolationsCount('RuleOf5Violations', \%CalculatedPhysicochemicalProperties);
|
|
|
433 }
|
|
|
434
|
|
|
435 return \%CalculatedPhysicochemicalProperties;
|
|
|
436 }
|
|
|
437
|
|
|
438 # Setup molecular descriptor generator to calculate property values for specifed
|
|
|
439 # property names...
|
|
|
440 #
|
|
|
441 sub SetupMolecularDescriptorsGenerator {
|
|
|
442 my($PropertyName, $MolecularDescriptorsGenerator);
|
|
|
443
|
|
|
444 $MolecularDescriptorsGenerator = new MolecularDescriptors::MolecularDescriptorsGenerator('Mode' => 'Specify', 'DescriptorNames' => \@{$OptionsInfo{SpecifiedPropertyNames}});
|
|
|
445
|
|
|
446 # Setup molecular desciptor calculation parameters...
|
|
|
447 if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('MolecularWeight')}) || exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('ExactMass')}) ) {
|
|
|
448 $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'WeightAndMassDescriptors', %{$OptionsInfo{PrecisionParametersMap}});
|
|
|
449 }
|
|
|
450
|
|
|
451 if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('RotatableBonds')})) {
|
|
|
452 $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'RotatableBondsDescriptors', %{$OptionsInfo{RotatableBondsParametersMap}});
|
|
|
453 }
|
|
|
454
|
|
|
455 if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('HydrogenBondDonors')}) || exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('HydrogenBondAcceptors')}) ) {
|
|
|
456 $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'HydrogenBondsDescriptors', 'HydrogenBondsType' => $OptionsInfo{HydrogenBonds});
|
|
|
457 }
|
|
|
458
|
|
|
459 if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('TPSA')})) {
|
|
|
460 $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'TPSADescriptors', %{$OptionsInfo{TPSAParametersMap}});
|
|
|
461 }
|
|
|
462
|
|
|
463 if (exists($OptionsInfo{SpecifiedPropertyNamesMap}{lc('MolecularComplexity')})) {
|
|
|
464 $MolecularDescriptorsGenerator->SetDescriptorClassParameters('DescriptorClassName' => 'MolecularComplexityDescriptors', %{$OptionsInfo{MolecularComplexityParametersMap}});
|
|
|
465 }
|
|
|
466
|
|
|
467 return $MolecularDescriptorsGenerator;
|
|
|
468 }
|
|
|
469
|
|
|
470 # Calculate RuleOf3 or RuleOf5 violations count...
|
|
|
471 #
|
|
|
472 sub CalculateRuleViolationsCount {
|
|
|
473 my($RuleViolationsType, $CalculatedPropertiesMapRef) = @_;
|
|
|
474 my($RuleViolationsCount, $PropertyName);
|
|
|
475
|
|
|
476 $RuleViolationsCount = 0;
|
|
|
477
|
|
|
478 RULEVIOLATIONSTYPE: {
|
|
|
479 if ($RuleViolationsType =~ /^RuleOf3Violations$/i) {
|
|
|
480 for $PropertyName (@{$OptionsInfo{RuleOf3PropertyNames}}) {
|
|
|
481 if ($CalculatedPropertiesMapRef->{$PropertyName} > $OptionsInfo{RuleOf3MaxPropertyValuesMap}{$PropertyName}) {
|
|
|
482 $RuleViolationsCount++;
|
|
|
483 }
|
|
|
484 }
|
|
|
485 last RULEVIOLATIONSTYPE;
|
|
|
486 }
|
|
|
487
|
|
|
488 if ($RuleViolationsType =~ /^RuleOf5Violations$/i) {
|
|
|
489 for $PropertyName (@{$OptionsInfo{RuleOf5PropertyNames}}) {
|
|
|
490 if ($CalculatedPropertiesMapRef->{$PropertyName} > $OptionsInfo{RuleOf5MaxPropertyValuesMap}{$PropertyName}) {
|
|
|
491 $RuleViolationsCount++;
|
|
|
492 }
|
|
|
493 }
|
|
|
494 last RULEVIOLATIONSTYPE;
|
|
|
495 }
|
|
|
496
|
|
|
497 die "Warning: Unknown rule violation type: $RuleViolationsType...";
|
|
|
498 }
|
|
|
499
|
|
|
500 # Set rule violation count...
|
|
|
501 $CalculatedPropertiesMapRef->{$RuleViolationsType} = $RuleViolationsCount;
|
|
|
502
|
|
|
503 }
|
|
|
504
|
|
|
505 # Retrieve information about SD files...
|
|
|
506 #
|
|
|
507 sub RetrieveSDFilesInfo {
|
|
|
508 my($SDFile, $Index, $FileDir, $FileExt, $FileName, $OutFileRoot, $TextOutFileExt, $SDOutFileExt, $NewSDFileName, $NewTextFileName, $CheckDataField, $CollectDataFields, $AllDataFieldsRef, $CommonDataFieldsRef);
|
|
|
509
|
|
|
510 %SDFilesInfo = ();
|
|
|
511 @{$SDFilesInfo{FileOkay}} = ();
|
|
|
512 @{$SDFilesInfo{OutFileRoot}} = ();
|
|
|
513 @{$SDFilesInfo{SDOutFileNames}} = ();
|
|
|
514 @{$SDFilesInfo{TextOutFileNames}} = ();
|
|
|
515 @{$SDFilesInfo{AllDataFieldsRef}} = ();
|
|
|
516 @{$SDFilesInfo{CommonDataFieldsRef}} = ();
|
|
|
517
|
|
|
518 $CheckDataField = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^CompoundID$/i) && ($OptionsInfo{CompoundIDMode} =~ /^DataField$/i)) ? 1 : 0;
|
|
|
519 $CollectDataFields = ($OptionsInfo{TextOutput} && ($OptionsInfo{DataFieldsMode} =~ /^(All|Common)$/i)) ? 1 : 0;
|
|
|
520
|
|
|
521 FILELIST: for $Index (0 .. $#SDFilesList) {
|
|
|
522 $SDFile = $SDFilesList[$Index];
|
|
|
523
|
|
|
524 $SDFilesInfo{FileOkay}[$Index] = 0;
|
|
|
525 $SDFilesInfo{OutFileRoot}[$Index] = '';
|
|
|
526 $SDFilesInfo{SDOutFileNames}[$Index] = '';
|
|
|
527 $SDFilesInfo{TextOutFileNames}[$Index] = '';
|
|
|
528
|
|
|
529 $SDFile = $SDFilesList[$Index];
|
|
|
530 if (!(-e $SDFile)) {
|
|
|
531 warn "Warning: Ignoring file $SDFile: It doesn't exist\n";
|
|
|
532 next FILELIST;
|
|
|
533 }
|
|
|
534 if (!CheckFileType($SDFile, "sd sdf")) {
|
|
|
535 warn "Warning: Ignoring file $SDFile: It's not a SD file\n";
|
|
|
536 next FILELIST;
|
|
|
537 }
|
|
|
538
|
|
|
539 if ($CheckDataField) {
|
|
|
540 # Make sure data field exists in SD file..
|
|
|
541 my($CmpdString, $SpecifiedDataField, @CmpdLines, %DataFieldValues);
|
|
|
542
|
|
|
543 @CmpdLines = ();
|
|
|
544 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
545 $CmpdString = ReadCmpdString(\*SDFILE);
|
|
|
546 close SDFILE;
|
|
|
547 @CmpdLines = split "\n", $CmpdString;
|
|
|
548 %DataFieldValues = GetCmpdDataHeaderLabelsAndValues(\@CmpdLines);
|
|
|
549 $SpecifiedDataField = $OptionsInfo{CompoundID};
|
|
|
550 if (!exists $DataFieldValues{$SpecifiedDataField}) {
|
|
|
551 warn "Warning: Ignoring file $SDFile: Data field value, $SpecifiedDataField, using \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\" doesn't exist\n";
|
|
|
552 next FILELIST;
|
|
|
553 }
|
|
|
554 }
|
|
|
555
|
|
|
556 $AllDataFieldsRef = '';
|
|
|
557 $CommonDataFieldsRef = '';
|
|
|
558 if ($CollectDataFields) {
|
|
|
559 my($CmpdCount);
|
|
|
560 open SDFILE, "$SDFile" or die "Error: Couldn't open $SDFile: $! \n";
|
|
|
561 ($CmpdCount, $AllDataFieldsRef, $CommonDataFieldsRef) = GetAllAndCommonCmpdDataHeaderLabels(\*SDFILE);
|
|
|
562 close SDFILE;
|
|
|
563 }
|
|
|
564
|
|
|
565 # Setup output file names...
|
|
|
566 $FileDir = ""; $FileName = ""; $FileExt = "";
|
|
|
567 ($FileDir, $FileName, $FileExt) = ParseFileName($SDFile);
|
|
|
568
|
|
|
569 $TextOutFileExt = "csv";
|
|
|
570 if ($Options{outdelim} =~ /^tab$/i) {
|
|
|
571 $TextOutFileExt = "tsv";
|
|
|
572 }
|
|
|
573 $SDOutFileExt = $FileExt;
|
|
|
574
|
|
|
575 if ($OptionsInfo{OutFileRoot} && (@SDFilesList == 1)) {
|
|
|
576 my ($RootFileDir, $RootFileName, $RootFileExt) = ParseFileName($OptionsInfo{OutFileRoot});
|
|
|
577 if ($RootFileName && $RootFileExt) {
|
|
|
578 $FileName = $RootFileName;
|
|
|
579 }
|
|
|
580 else {
|
|
|
581 $FileName = $OptionsInfo{OutFileRoot};
|
|
|
582 }
|
|
|
583 $OutFileRoot = $FileName;
|
|
|
584 }
|
|
|
585 else {
|
|
|
586 $OutFileRoot = "${FileName}PhysicochemicalProperties";
|
|
|
587 }
|
|
|
588
|
|
|
589 $NewSDFileName = "${OutFileRoot}.${SDOutFileExt}";
|
|
|
590 $NewTextFileName = "${OutFileRoot}.${TextOutFileExt}";
|
|
|
591
|
|
|
592 if ($OptionsInfo{SDOutput}) {
|
|
|
593 if ($SDFile =~ /$NewSDFileName/i) {
|
|
|
594 warn "Warning: Ignoring input file $SDFile: Same output, $NewSDFileName, and input file names.\n";
|
|
|
595 print "Specify a different name using \"-r --root\" option or use default name.\n";
|
|
|
596 next FILELIST;
|
|
|
597 }
|
|
|
598 }
|
|
|
599
|
|
|
600 if (!$OptionsInfo{OverwriteFiles}) {
|
|
|
601 # Check SD and text outout files...
|
|
|
602 if ($OptionsInfo{SDOutput}) {
|
|
|
603 if (-e $NewSDFileName) {
|
|
|
604 warn "Warning: Ignoring file $SDFile: The file $NewSDFileName already exists\n";
|
|
|
605 next FILELIST;
|
|
|
606 }
|
|
|
607 }
|
|
|
608 if ($OptionsInfo{TextOutput}) {
|
|
|
609 if (-e $NewTextFileName) {
|
|
|
610 warn "Warning: Ignoring file $SDFile: The file $NewTextFileName already exists\n";
|
|
|
611 next FILELIST;
|
|
|
612 }
|
|
|
613 }
|
|
|
614 }
|
|
|
615
|
|
|
616 $SDFilesInfo{FileOkay}[$Index] = 1;
|
|
|
617
|
|
|
618 $SDFilesInfo{OutFileRoot}[$Index] = $OutFileRoot;
|
|
|
619 $SDFilesInfo{SDOutFileNames}[$Index] = $NewSDFileName;
|
|
|
620 $SDFilesInfo{TextOutFileNames}[$Index] = $NewTextFileName;
|
|
|
621
|
|
|
622 $SDFilesInfo{AllDataFieldsRef}[$Index] = $AllDataFieldsRef;
|
|
|
623 $SDFilesInfo{CommonDataFieldsRef}[$Index] = $CommonDataFieldsRef;
|
|
|
624 }
|
|
|
625 }
|
|
|
626
|
|
|
627 # Process option values...
|
|
|
628 sub ProcessOptions {
|
|
|
629 %OptionsInfo = ();
|
|
|
630
|
|
|
631 $OptionsInfo{AromaticityModel} = $Options{aromaticitymodel};
|
|
|
632
|
|
|
633 # Process property name related options...
|
|
|
634 ProcessPropertyNamesOption();
|
|
|
635
|
|
|
636 # Setup RuleOf3 and RuleOf5 violation calculations...
|
|
|
637 $OptionsInfo{RuleOf3Violations} = ($Options{ruleof3violations} =~ /^Yes$/i) ? 1 : 0;
|
|
|
638 $OptionsInfo{RuleOf5Violations} = ($Options{ruleof5violations} =~ /^Yes$/i) ? 1 : 0;
|
|
|
639
|
|
|
640 $OptionsInfo{CompoundIDMode} = $Options{compoundidmode};
|
|
|
641 $OptionsInfo{CompoundIDLabel} = $Options{compoundidlabel};
|
|
|
642 $OptionsInfo{DataFieldsMode} = $Options{datafieldsmode};
|
|
|
643
|
|
|
644 my(@SpecifiedDataFields);
|
|
|
645 @SpecifiedDataFields = ();
|
|
|
646
|
|
|
647 @{$OptionsInfo{SpecifiedDataFields}} = ();
|
|
|
648 $OptionsInfo{CompoundID} = '';
|
|
|
649
|
|
|
650 if ($Options{datafieldsmode} =~ /^CompoundID$/i) {
|
|
|
651 if ($Options{compoundidmode} =~ /^DataField$/i) {
|
|
|
652 if (!$Options{compoundid}) {
|
|
|
653 die "Error: You must specify a value for \"--CompoundID\" option in \"DataField\" \"--CompoundIDMode\". \n";
|
|
|
654 }
|
|
|
655 $OptionsInfo{CompoundID} = $Options{compoundid};
|
|
|
656 }
|
|
|
657 elsif ($Options{compoundidmode} =~ /^(LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
658 $OptionsInfo{CompoundID} = $Options{compoundid} ? $Options{compoundid} : 'Cmpd';
|
|
|
659 }
|
|
|
660 }
|
|
|
661 elsif ($Options{datafieldsmode} =~ /^Specify$/i) {
|
|
|
662 if (!$Options{datafields}) {
|
|
|
663 die "Error: You must specify a value for \"--DataFields\" option in \"Specify\" \"-d, --DataFieldsMode\". \n";
|
|
|
664 }
|
|
|
665 @SpecifiedDataFields = split /\,/, $Options{datafields};
|
|
|
666 push @{$OptionsInfo{SpecifiedDataFields}}, @SpecifiedDataFields;
|
|
|
667 }
|
|
|
668
|
|
|
669 # Types of hydrogen bonds...
|
|
|
670 $OptionsInfo{HydrogenBonds} = $Options{hydrogenbonds};
|
|
|
671
|
|
|
672 # Process precision value parameters...
|
|
|
673 ProcessPrecisionOption();
|
|
|
674
|
|
|
675 # Process rotatable bonds parameters...
|
|
|
676 ProcessRotatableBondsOption();
|
|
|
677
|
|
|
678 # Process TPSA parameters...
|
|
|
679 ProcessTPSAOption();
|
|
|
680
|
|
|
681 # Process molecular complexity parameters...
|
|
|
682 ProcessMolecularComplexityOption();
|
|
|
683
|
|
|
684 $OptionsInfo{Filter} = ($Options{filter} =~ /^Yes$/i) ? 1 : 0;
|
|
|
685
|
|
|
686 $OptionsInfo{KeepLargestComponent} = ($Options{keeplargestcomponent} =~ /^Yes$/i) ? 1 : 0;
|
|
|
687
|
|
|
688 $OptionsInfo{Output} = $Options{output};
|
|
|
689 $OptionsInfo{SDOutput} = ($Options{output} =~ /^(SD|Both)$/i) ? 1 : 0;
|
|
|
690 $OptionsInfo{TextOutput} = ($Options{output} =~ /^(Text|Both)$/i) ? 1 : 0;
|
|
|
691
|
|
|
692 $OptionsInfo{OutDelim} = ($Options{outdelim} =~ /tab/i ) ? "\t" : (($Options{outdelim} =~ /semicolon/i) ? "\;" : "\,");
|
|
|
693 $OptionsInfo{OutQuote} = ($Options{quote} =~ /^Yes$/i) ? 1 : 0;
|
|
|
694
|
|
|
695 $OptionsInfo{OverwriteFiles} = $Options{overwrite} ? 1 : 0;
|
|
|
696 $OptionsInfo{OutFileRoot} = $Options{root} ? $Options{root} : 0;
|
|
|
697 }
|
|
|
698
|
|
|
699 # Process property name related options...
|
|
|
700 #
|
|
|
701 sub ProcessPropertyNamesOption {
|
|
|
702
|
|
|
703 # Setup supported physicochemical properties...
|
|
|
704 my($SupportedProperty);
|
|
|
705
|
|
|
706 @{$OptionsInfo{SupportedPropertyNames}} = ();
|
|
|
707 %{$OptionsInfo{SupportedPropertyNamesMap}} = ();
|
|
|
708
|
|
|
709 @{$OptionsInfo{RuleOf5PropertyNames}} = ();
|
|
|
710 %{$OptionsInfo{RuleOf5MaxPropertyValuesMap}} = ();
|
|
|
711
|
|
|
712 @{$OptionsInfo{RuleOf3PropertyNames}} = ();
|
|
|
713 %{$OptionsInfo{RuleOf3MaxPropertyValuesMap}} = ();
|
|
|
714
|
|
|
715 @{$OptionsInfo{DefaultPropertyNames}} = ();
|
|
|
716
|
|
|
717 @{$OptionsInfo{SupportedPropertyNames}} = qw(MolecularWeight ExactMass HeavyAtoms Rings AromaticRings MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP SMR TPSA Fsp3Carbons Sp3Carbons MolecularComplexity);
|
|
|
718
|
|
|
719 @{$OptionsInfo{RuleOf5PropertyNames}} = qw(MolecularWeight HydrogenBondDonors HydrogenBondAcceptors SLogP);
|
|
|
720 %{$OptionsInfo{RuleOf5MaxPropertyValuesMap}} = ('MolecularWeight' => 500, 'HydrogenBondDonors' => 5, 'HydrogenBondAcceptors' => 10, 'SLogP' => 5);
|
|
|
721
|
|
|
722 @{$OptionsInfo{RuleOf3PropertyNames}} = qw(MolecularWeight RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA);
|
|
|
723 %{$OptionsInfo{RuleOf3MaxPropertyValuesMap}} = ('MolecularWeight' => 300, 'RotatableBonds' => 3, 'HydrogenBondDonors' => 3, 'HydrogenBondAcceptors' => 3, 'SLogP' => 3, 'TPSA' => 60);
|
|
|
724
|
|
|
725 @{$OptionsInfo{DefaultPropertyNames}} = qw(MolecularWeight HeavyAtoms MolecularVolume RotatableBonds HydrogenBondDonors HydrogenBondAcceptors SLogP TPSA);
|
|
|
726
|
|
|
727 for $SupportedProperty (@{$OptionsInfo{SupportedPropertyNames}}) {
|
|
|
728 $OptionsInfo{SupportedPropertyNamesMap}{lc($SupportedProperty)} = $SupportedProperty;
|
|
|
729 }
|
|
|
730
|
|
|
731 # Process specified properties....
|
|
|
732 my($SpecifiedPropertyName, @SpecifiedPropertyNames, %SpecifiedPropertyNamesMap);
|
|
|
733
|
|
|
734 @SpecifiedPropertyNames = ();
|
|
|
735 %SpecifiedPropertyNamesMap = ();
|
|
|
736
|
|
|
737 @{$OptionsInfo{SpecifiedPropertyNames}} = ();
|
|
|
738 %{$OptionsInfo{SpecifiedPropertyNamesMap}} = ();
|
|
|
739
|
|
|
740 if ($Options{mode} =~ /^All$/i) {
|
|
|
741 @SpecifiedPropertyNames = @{$OptionsInfo{SupportedPropertyNames}};
|
|
|
742 }
|
|
|
743 elsif ($Options{mode} =~ /^RuleOf5$/i) {
|
|
|
744 @SpecifiedPropertyNames = @{$OptionsInfo{RuleOf5PropertyNames}};
|
|
|
745 }
|
|
|
746 elsif ($Options{mode} =~ /^RuleOf3$/i) {
|
|
|
747 @SpecifiedPropertyNames = @{$OptionsInfo{RuleOf3PropertyNames}};
|
|
|
748 }
|
|
|
749 elsif (IsEmpty($Options{mode})) {
|
|
|
750 @SpecifiedPropertyNames = @{$OptionsInfo{DefaultPropertyNames}};
|
|
|
751 }
|
|
|
752 else {
|
|
|
753 # Comma delimited lisr of specified property names...
|
|
|
754 my($Mode, $PropertyName, @PropertyNames, @UnsupportedPropertyNames);
|
|
|
755
|
|
|
756 $Mode = $Options{mode};
|
|
|
757 $Mode =~ s/ //g;
|
|
|
758
|
|
|
759 @PropertyNames = split ",", $Mode;
|
|
|
760 @UnsupportedPropertyNames = ();
|
|
|
761
|
|
|
762 for $PropertyName (@PropertyNames) {
|
|
|
763 if (exists($OptionsInfo{SupportedPropertyNamesMap}{lc($PropertyName)})) {
|
|
|
764 push @SpecifiedPropertyNames, $PropertyName;
|
|
|
765 }
|
|
|
766 else {
|
|
|
767 push @UnsupportedPropertyNames, $PropertyName;
|
|
|
768 }
|
|
|
769 }
|
|
|
770 if (@UnsupportedPropertyNames) {
|
|
|
771 if (@UnsupportedPropertyNames > 1) {
|
|
|
772 warn "Error: The physicochemical property names specified - ", JoinWords(\@UnsupportedPropertyNames, ", ", 0)," - for option \"-m --mode\" are not valid.\n";
|
|
|
773 }
|
|
|
774 else {
|
|
|
775 warn "Error: The physicochemical property name specified, @UnsupportedPropertyNames , for option \"-m --mode\" is not valid.\n";
|
|
|
776 }
|
|
|
777 die "Allowed values:", JoinWords(\@{$OptionsInfo{SupportedPropertyNames}}, ", ", 0), "\n";
|
|
|
778 }
|
|
|
779 if (!@SpecifiedPropertyNames) {
|
|
|
780 die "Error: No valid physicochemical property names specified for option \"-m --mode\".\n";
|
|
|
781 }
|
|
|
782 }
|
|
|
783
|
|
|
784 # Set up specified property names map...
|
|
|
785 PROPERTY: for $SpecifiedPropertyName (@SpecifiedPropertyNames) {
|
|
|
786 if (exists $SpecifiedPropertyNamesMap{lc($SpecifiedPropertyName)}) {
|
|
|
787 warn "Warning: The physicochemical property name, $SpecifiedPropertyName, is specified multiple times as value of option \"-m --mode\" .\n";
|
|
|
788 next PROPERTY;
|
|
|
789 }
|
|
|
790 # Canonical specified property name...
|
|
|
791 $SpecifiedPropertyNamesMap{lc($SpecifiedPropertyName)} = $OptionsInfo{SupportedPropertyNamesMap}{lc($SpecifiedPropertyName)};
|
|
|
792 }
|
|
|
793
|
|
|
794 # Make sure for calculation of RuleOf3Violations, all appropriate property names are specified...
|
|
|
795 if ($Options{ruleof3violations} =~ /^Yes$/i && $Options{mode} =~ /^RuleOf5$/i) {
|
|
|
796 die "Error: The value specified, $Options{ruleof3violations}, for \"--RuleOf3Violations\" option in \"RuleOf5\" \"-m --Mode\" is not valid. You must specify RuleOf3 value for \"-m --Mode\" to calculate RuleOf3 violations.\n";
|
|
|
797 }
|
|
|
798
|
|
|
799 if ($Options{ruleof3violations} =~ /^Yes$/i) {
|
|
|
800 my($RuleOf3PropertyName, @MissingRuleOf3Names);
|
|
|
801
|
|
|
802 @MissingRuleOf3Names = ();
|
|
|
803 PROPERTY: for $RuleOf3PropertyName (@{$OptionsInfo{RuleOf3PropertyNames}}) {
|
|
|
804 if (exists $SpecifiedPropertyNamesMap{lc($RuleOf3PropertyName)}) {
|
|
|
805 next PROPERTY;
|
|
|
806 }
|
|
|
807 push @MissingRuleOf3Names, $RuleOf3PropertyName;
|
|
|
808
|
|
|
809 # Add property name to specified properties names list and map...
|
|
|
810 push @SpecifiedPropertyNames, $RuleOf3PropertyName;
|
|
|
811 $SpecifiedPropertyNamesMap{lc($RuleOf3PropertyName)} = $OptionsInfo{SupportedPropertyNamesMap}{lc($RuleOf3PropertyName)};
|
|
|
812 }
|
|
|
813 if (@MissingRuleOf3Names) {
|
|
|
814 warn "Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf3Violations and have been added to the list of property names: @MissingRuleOf3Names\n";
|
|
|
815 }
|
|
|
816 }
|
|
|
817
|
|
|
818 # Make sure for calculation of RuleOf5Violations, all appropriate property names are specified...
|
|
|
819 if ($Options{ruleof5violations} =~ /^Yes$/i && $Options{mode} =~ /^RuleOf3$/i) {
|
|
|
820 die "Error: The value specified, $Options{ruleof5violations}, for \"--RuleOf5Violations\" option in \"RuleOf3\" \"-m --Mode\" is not valid. You must specify RuleOf5 value for \"-m --Mode\" to calculate RuleOf5 violations.\n";
|
|
|
821 }
|
|
|
822
|
|
|
823 if ($Options{ruleof5violations} =~ /^Yes$/i) {
|
|
|
824 my($RuleOf5PropertyName, @MissingRuleOf5Names);
|
|
|
825
|
|
|
826 @MissingRuleOf5Names = ();
|
|
|
827 PROPERTY: for $RuleOf5PropertyName (@{$OptionsInfo{RuleOf5PropertyNames}}) {
|
|
|
828 if (exists $SpecifiedPropertyNamesMap{lc($RuleOf5PropertyName)}) {
|
|
|
829 next PROPERTY;
|
|
|
830 }
|
|
|
831 push @MissingRuleOf5Names, $RuleOf5PropertyName;
|
|
|
832
|
|
|
833 # Add property name to specified properties names list and map...
|
|
|
834 push @SpecifiedPropertyNames, $RuleOf5PropertyName;
|
|
|
835 $SpecifiedPropertyNamesMap{lc($RuleOf5PropertyName)} = $OptionsInfo{SupportedPropertyNamesMap}{lc($RuleOf5PropertyName)};
|
|
|
836 }
|
|
|
837 if (@MissingRuleOf5Names) {
|
|
|
838 warn "Warning: The following physicochemical property names not specified in \"-m --Mode\" option are required for calculating RuleOf5Violations and have been added to the list of property names: @MissingRuleOf5Names\n";
|
|
|
839 }
|
|
|
840 }
|
|
|
841 $OptionsInfo{Mode} = $Options{mode};
|
|
|
842
|
|
|
843 # Setup canonical specified property names corresponding to supported names in mixed case...
|
|
|
844 my(@SpecifiedCanonicalPropertyNames);
|
|
|
845
|
|
|
846 @SpecifiedCanonicalPropertyNames = ();
|
|
|
847 for $SpecifiedPropertyName (@SpecifiedPropertyNames) {
|
|
|
848 push @SpecifiedCanonicalPropertyNames, $SpecifiedPropertyNamesMap{lc($SpecifiedPropertyName)};
|
|
|
849 }
|
|
|
850 @{$OptionsInfo{SpecifiedPropertyNames}} = @SpecifiedCanonicalPropertyNames;
|
|
|
851 %{$OptionsInfo{SpecifiedPropertyNamesMap}} = %SpecifiedPropertyNamesMap;
|
|
|
852
|
|
|
853 # Based on specified property names, figure out whether hydrogens need to be added before
|
|
|
854 # calculation of properties...
|
|
|
855 #
|
|
|
856 $OptionsInfo{AddHydrogens} = 0;
|
|
|
857 if (exists($SpecifiedPropertyNamesMap{lc('MolecularVolume')}) || exists($SpecifiedPropertyNamesMap{lc('SLogP')}) || exists($SpecifiedPropertyNamesMap{lc('SMR')})) {
|
|
|
858 $OptionsInfo{AddHydrogens} = 1;
|
|
|
859 }
|
|
|
860 }
|
|
|
861
|
|
|
862 # Process precision option...
|
|
|
863 #
|
|
|
864 sub ProcessPrecisionOption {
|
|
|
865 my($ParameterName, $ParameterValue, %PrecisionParametersMap, %PrecisionParameterNamesMap);
|
|
|
866
|
|
|
867 %{$OptionsInfo{PrecisionParametersMap}} = ();
|
|
|
868
|
|
|
869 %PrecisionParametersMap = ('WeightPrecision' => 2, 'MassPrecision' => 4);
|
|
|
870 %PrecisionParameterNamesMap = ('molecularweight' => 'WeightPrecision', 'exactmass' => 'MassPrecision');
|
|
|
871
|
|
|
872 if ($Options{precision}) {
|
|
|
873 # Process specified values...
|
|
|
874 my($Index, $SpecifiedPrecision, @SpecifiedPrecisionValuePairs);
|
|
|
875
|
|
|
876 $SpecifiedPrecision = $Options{precision};
|
|
|
877 $SpecifiedPrecision =~ s/ //g;
|
|
|
878 @SpecifiedPrecisionValuePairs = split ",", $SpecifiedPrecision;
|
|
|
879 if (@SpecifiedPrecisionValuePairs % 2) {
|
|
|
880 die "Error: Invalid number of values specified using \"--Precision\" option: It must contain even number of values.\n";
|
|
|
881 }
|
|
|
882 for ($Index = 0; (($Index + 1) < @SpecifiedPrecisionValuePairs); $Index += 2 ) {
|
|
|
883 $ParameterName = $SpecifiedPrecisionValuePairs[$Index];
|
|
|
884 $ParameterValue = $SpecifiedPrecisionValuePairs[$Index + 1];
|
|
|
885 if (!exists $PrecisionParameterNamesMap{lc($ParameterName)}) {
|
|
|
886 die "Error: The precision parameter name specified, $ParameterName, for option \"--Precision\" is not valid.\n";
|
|
|
887 }
|
|
|
888 if (!IsPositiveInteger($ParameterValue)) {
|
|
|
889 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--Precision\" is not valid. Allowed values: positive integer. \n";
|
|
|
890 }
|
|
|
891 $ParameterName = $PrecisionParameterNamesMap{lc($ParameterName)};
|
|
|
892 $PrecisionParametersMap{$ParameterName} = $ParameterValue;
|
|
|
893 }
|
|
|
894 }
|
|
|
895 $OptionsInfo{Precision} = $Options{precision};
|
|
|
896 %{$OptionsInfo{PrecisionParametersMap}} = %PrecisionParametersMap;
|
|
|
897 }
|
|
|
898
|
|
|
899 # Process rotatable bonds option...
|
|
|
900 sub ProcessRotatableBondsOption {
|
|
|
901 my($ParameterName, $ParameterValue, %RotatableBondsParametersMap, %RotatableBondsParameterNamesMap);
|
|
|
902
|
|
|
903 %{$OptionsInfo{RotatableBondsParametersMap}} = ();
|
|
|
904 %RotatableBondsParametersMap = ('IgnoreTerminalBonds' => 1, 'IgnoreBondsToTripleBonds' => 1, 'IgnoreAmideBonds' => 1, 'IgnoreThioamideBonds' => 1, 'IgnoreSulfonamideBonds' => 1);
|
|
|
905
|
|
|
906 for $ParameterName (keys %RotatableBondsParametersMap) {
|
|
|
907 $RotatableBondsParameterNamesMap{lc($ParameterName)} = $ParameterName;
|
|
|
908 }
|
|
|
909
|
|
|
910 if ($Options{rotatablebonds}) {
|
|
|
911 # Process specified values...
|
|
|
912 my($Index, $SpecifiedRotatableBonds, @SpecifiedRotatableBondsValuePairs);
|
|
|
913
|
|
|
914 $SpecifiedRotatableBonds = $Options{rotatablebonds};
|
|
|
915 $SpecifiedRotatableBonds =~ s/ //g;
|
|
|
916 @SpecifiedRotatableBondsValuePairs = split ",", $SpecifiedRotatableBonds;
|
|
|
917 if (@SpecifiedRotatableBondsValuePairs % 2) {
|
|
|
918 die "Error: Invalid number of values specified using \"--RotatableBonds\" option: It must contain even number of values.\n";
|
|
|
919 }
|
|
|
920 for ($Index = 0; (($Index + 1) < @SpecifiedRotatableBondsValuePairs); $Index += 2 ) {
|
|
|
921 $ParameterName = $SpecifiedRotatableBondsValuePairs[$Index];
|
|
|
922 $ParameterValue = $SpecifiedRotatableBondsValuePairs[$Index + 1];
|
|
|
923 if (!exists $RotatableBondsParameterNamesMap{lc($ParameterName)}) {
|
|
|
924 die "Error: The rotatable bonds parameter name specified, $ParameterName, for option \"--RotatableBonds\" is not valid.\n";
|
|
|
925 }
|
|
|
926 if ($ParameterValue !~ /^(Yes|No)$/i) {
|
|
|
927 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--RotatableBonds\" is not valid. Allowed values: Yes or No. \n";
|
|
|
928 }
|
|
|
929 $ParameterName = $RotatableBondsParameterNamesMap{lc($ParameterName)};
|
|
|
930 $ParameterValue = ($ParameterValue =~ /^Yes$/i) ? 1 : 0;
|
|
|
931 $RotatableBondsParametersMap{$ParameterName} = $ParameterValue;
|
|
|
932 }
|
|
|
933 }
|
|
|
934 $OptionsInfo{RotatableBonds} = $Options{rotatablebonds};
|
|
|
935 %{$OptionsInfo{RotatableBondsParametersMap}} = %RotatableBondsParametersMap;
|
|
|
936 }
|
|
|
937
|
|
|
938 # Process TPSA option...
|
|
|
939 #
|
|
|
940 sub ProcessTPSAOption {
|
|
|
941 my($ParameterName, $ParameterValue, %TPSAParametersMap, %TPSAParameterNamesMap);
|
|
|
942
|
|
|
943 %{$OptionsInfo{TPSAParametersMap}} = ();
|
|
|
944
|
|
|
945 %TPSAParametersMap = ('IgnorePhosphorus' => 1, 'IgnoreSulfur' => 1);
|
|
|
946 for $ParameterName (keys %TPSAParametersMap) {
|
|
|
947 $TPSAParameterNamesMap{lc($ParameterName)} = $ParameterName;
|
|
|
948 }
|
|
|
949
|
|
|
950 if ($Options{tpsa}) {
|
|
|
951 # Process specified values...
|
|
|
952 my($Index, $SpecifiedTPSA, @SpecifiedTPSAValuePairs);
|
|
|
953
|
|
|
954 $SpecifiedTPSA = $Options{tpsa};
|
|
|
955 $SpecifiedTPSA =~ s/ //g;
|
|
|
956 @SpecifiedTPSAValuePairs = split ",", $SpecifiedTPSA;
|
|
|
957 if (@SpecifiedTPSAValuePairs % 2) {
|
|
|
958 die "Error: Invalid number of values specified using \"--TPSA\" option: It must contain even number of values.\n";
|
|
|
959 }
|
|
|
960 for ($Index = 0; (($Index + 1) < @SpecifiedTPSAValuePairs); $Index += 2 ) {
|
|
|
961 $ParameterName = $SpecifiedTPSAValuePairs[$Index];
|
|
|
962 $ParameterValue = $SpecifiedTPSAValuePairs[$Index + 1];
|
|
|
963 if (!exists $TPSAParameterNamesMap{lc($ParameterName)}) {
|
|
|
964 die "Error: The TPSA parameter name specified, $ParameterName, for option \"--TPSA\" is not valid.\n";
|
|
|
965 }
|
|
|
966 if ($ParameterValue !~ /^(Yes|No)$/i) {
|
|
|
967 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--TPSA\" is not valid. Allowed values: Yes or No. \n";
|
|
|
968 }
|
|
|
969 $ParameterName = $TPSAParameterNamesMap{lc($ParameterName)};
|
|
|
970 $ParameterValue = ($ParameterValue =~ /^Yes$/i) ? 1 : 0;
|
|
|
971 $TPSAParametersMap{$ParameterName} = $ParameterValue;
|
|
|
972 }
|
|
|
973 }
|
|
|
974 $OptionsInfo{TPSA} = $Options{tpsa};
|
|
|
975 %{$OptionsInfo{TPSAParametersMap}} = %TPSAParametersMap;
|
|
|
976 }
|
|
|
977
|
|
|
978 # Process molecular complexity parameters...
|
|
|
979 #
|
|
|
980 sub ProcessMolecularComplexityOption {
|
|
|
981 my($MolecularComplexityType, $ParameterName, $ParameterValue, @ParameterNames, @ParameterValues, @AtomIdentifierTypeParameters, %ComplexityParametersMap, %ComplexityParameterNamesMap);
|
|
|
982
|
|
|
983 %{$OptionsInfo{MolecularComplexityParametersMap}} = ();
|
|
|
984
|
|
|
985 %ComplexityParametersMap = ('MolecularComplexityType' => '', 'AtomIdentifierType' => '',
|
|
|
986 'AtomicInvariantsToUse' => '', 'FunctionalClassesToUse' => '',
|
|
|
987 'MACCSKeysSize' => '166', 'NeighborhoodRadius' => '2',
|
|
|
988 'MinPathLength' => '1', 'MaxPathLength' => '8', 'UseBondSymbols' => '1',
|
|
|
989 'MinDistance' => '1', 'MaxDistance' => '10', 'UseTriangleInequality' => '',
|
|
|
990 'DistanceBinSize' => '2', 'NormalizationMethodology' => 'None');
|
|
|
991
|
|
|
992 %ComplexityParameterNamesMap = ();
|
|
|
993 for $ParameterName (keys %ComplexityParametersMap) {
|
|
|
994 $ComplexityParameterNamesMap{lc($ParameterName)} = $ParameterName;
|
|
|
995 }
|
|
|
996
|
|
|
997 if ($Options{molecularcomplexity}) {
|
|
|
998 # Process specified values...
|
|
|
999 my($Index, $SpecifiedComplexity, @SpecifiedComplexityValuePairs);
|
|
|
1000
|
|
|
1001 $SpecifiedComplexity = $Options{molecularcomplexity};
|
|
|
1002
|
|
|
1003 @SpecifiedComplexityValuePairs = split ",", $SpecifiedComplexity;
|
|
|
1004 if (@SpecifiedComplexityValuePairs % 2) {
|
|
|
1005 die "Error: Invalid number of values specified using \"--MolecularComplexity\" option: It must contain even number of values.\n";
|
|
|
1006 }
|
|
|
1007
|
|
|
1008 for ($Index = 0; (($Index + 1) < @SpecifiedComplexityValuePairs); $Index += 2 ) {
|
|
|
1009 $ParameterName = $SpecifiedComplexityValuePairs[$Index];
|
|
|
1010 $ParameterValue = $SpecifiedComplexityValuePairs[$Index + 1];
|
|
|
1011
|
|
|
1012 $ParameterName = RemoveLeadingAndTrailingWhiteSpaces($ParameterName);
|
|
|
1013 $ParameterValue = RemoveLeadingAndTrailingWhiteSpaces($ParameterValue);
|
|
|
1014
|
|
|
1015 if (!exists $ComplexityParameterNamesMap{lc($ParameterName)}) {
|
|
|
1016 die "Error: The molecular complexity parameter name specified, $ParameterName, for option \"--MolecularComplexity\" is not valid.\n";
|
|
|
1017 }
|
|
|
1018 $ParameterName = $ComplexityParameterNamesMap{lc($ParameterName)};
|
|
|
1019
|
|
|
1020 if ($ParameterName =~ /^AtomicInvariantsToUse$/i) {
|
|
|
1021 my($AtomSymbolFound);
|
|
|
1022
|
|
|
1023 $AtomSymbolFound = 0;
|
|
|
1024 @ParameterValues = split(' ', $ParameterValue);
|
|
|
1025 for $ParameterValue (@ParameterValues) {
|
|
|
1026 if (!AtomTypes::AtomicInvariantsAtomTypes::IsAtomicInvariantAvailable($ParameterValue)) {
|
|
|
1027 die "Error: The atomic invariant specified, $ParameterValue, for AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid.\n";
|
|
|
1028 }
|
|
|
1029 if ($ParameterValue =~ /^(AS|AtomSymbol)$/i) {
|
|
|
1030 $AtomSymbolFound = 1;
|
|
|
1031 }
|
|
|
1032 }
|
|
|
1033 if (!$AtomSymbolFound) {
|
|
|
1034 die "Error: The atomic invariants specified using AtomicInvariantsToUse in option \"--MolecularComplexity\" is not valid: AtomicInvariant atom symbol, AS or AtomSymbol, must be specified.\n";
|
|
|
1035 }
|
|
|
1036 $ParameterValue = JoinWords(\@ParameterValues, ",", 0);
|
|
|
1037 }
|
|
|
1038 elsif ($ParameterName =~ /^FunctionalClassesToUse$/i) {
|
|
|
1039 @ParameterValues = split(' ', $ParameterValue);
|
|
|
1040 for $ParameterValue (@ParameterValues) {
|
|
|
1041 if (!AtomTypes::FunctionalClassAtomTypes::IsFunctionalClassAvailable($ParameterValue)) {
|
|
|
1042 die "Error: The functional class specified, $ParameterValue, for FunctionalClassesToUse in option \"--MolecularComplexity\" is not valid.\n";
|
|
|
1043 }
|
|
|
1044 }
|
|
|
1045 $ParameterValue = JoinWords(\@ParameterValues, ",", 0);
|
|
|
1046 }
|
|
|
1047 else {
|
|
|
1048 if ($ParameterValue =~ / /) {
|
|
|
1049 $ParameterValue =~ s/ //g;
|
|
|
1050 }
|
|
|
1051 if ($ParameterValue =~ /^(Yes|No)$/i) {
|
|
|
1052 $ParameterValue = ($ParameterValue =~ /^Yes$/i) ? 1 : 0;
|
|
|
1053 }
|
|
|
1054 }
|
|
|
1055
|
|
|
1056 if ($ParameterName =~ /^MolecularComplexityType$/i) {
|
|
|
1057 if ($ParameterValue !~ /^(AtomTypesFingerprints|ExtendedConnectivityFingerprints|MACCSKeys|PathLengthFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints|TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i) {
|
|
|
1058 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: AtomTypesFingerprints, ExtendedConnectivityFingerprints, MACCSKeys, PathLengthFingerprints, TopologicalAtomPairsFingerprints, TopologicalAtomTripletsFingerprints, TopologicalAtomTorsionsFingerprints, TopologicalPharmacophoreAtomPairsFingerprints, or TopologicalPharmacophoreAtomTripletsFingerprints..\n";
|
|
|
1059 }
|
|
|
1060 }
|
|
|
1061 elsif ($ParameterName =~ /^AtomIdentifierType$/i) {
|
|
|
1062 if ($ParameterValue !~ /^(AtomicInvariantsAtomTypes|FunctionalClassAtomTypes|DREIDINGAtomTypes|EStateAtomTypes|MMFF94AtomTypes|SLogPAtomTypes|SYBYLAtomTypes|TPSAAtomTypes|UFFAtomTypes)$/i) {
|
|
|
1063 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Supported atom identifier types in current release of MayaChemTools: AtomicInvariantsAtomTypes, FunctionalClassAtomTypes, DREIDINGAtomTypes, EStateAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes and UFFAtomTypes.\n";
|
|
|
1064 }
|
|
|
1065 }
|
|
|
1066 elsif ($ParameterName =~ /^(MACCSKeysSize|MinPathLength|MaxPathLength|MinDistance|MaxDistance|DistanceBinSize)$/i) {
|
|
|
1067 if (!IsPositiveInteger($ParameterValue)) {
|
|
|
1068 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: positive integer. \n";
|
|
|
1069 }
|
|
|
1070 }
|
|
|
1071 elsif ($ParameterName =~ /^NeighborhoodRadius$/i) {
|
|
|
1072 if (!(IsInteger($ParameterValue) && $ParameterValue >=0)) {
|
|
|
1073 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: 0 or positive integer. \n";
|
|
|
1074 }
|
|
|
1075 }
|
|
|
1076 elsif ($ParameterName =~ /^NormalizationMethodology$/i) {
|
|
|
1077 if ($ParameterValue !~ /^(None|ByHeavyAtomsCount|ByPossibleKeysCount)$/i) {
|
|
|
1078 die "Error: The parameter value specified, $ParameterValue, for parameter name, $ParameterName in option \"--MolecularComplexity\" is not valid. Allowed values: None, ByHeavyAtomsCount, or ByPossibleKeysCount\n";
|
|
|
1079 }
|
|
|
1080 }
|
|
|
1081 $ComplexityParametersMap{$ParameterName} = $ParameterValue;
|
|
|
1082 }
|
|
|
1083
|
|
|
1084 if ($ComplexityParametersMap{MACCSKeysSize} !~ /^(166|322)$/i) {
|
|
|
1085 die "Error: The parameter value specified, $ComplexityParametersMap{MACCSKeysSize}, for parameter name, MACCSKeysSize in option \"--MolecularComplexity\" is not valid. Allowed values: 166 or 322\n";
|
|
|
1086 }
|
|
|
1087 if ($ComplexityParametersMap{MinPathLength} > $ComplexityParametersMap{MaxPathLength}) {
|
|
|
1088 die "Error: The parameter value specified for MinPathLength, $ComplexityParametersMap{MinPathLength}, must be <= MaxPathLength, $ComplexityParametersMap{MaxPathLength} ...\n";
|
|
|
1089 }
|
|
|
1090 if ($ComplexityParametersMap{MinDistance} > $ComplexityParametersMap{MaxDistance}) {
|
|
|
1091 die "Error: The parameter value specified for MinDistance, $ComplexityParametersMap{MinDistance}, must be <= MaxDistance, $ComplexityParametersMap{MaxDistance} ...\n";
|
|
|
1092 }
|
|
|
1093 }
|
|
|
1094
|
|
|
1095 # Set default parameter values...
|
|
|
1096
|
|
|
1097 if (IsEmpty($ComplexityParametersMap{MolecularComplexityType})) {
|
|
|
1098 $ComplexityParametersMap{MolecularComplexityType} = 'MACCSKeys';
|
|
|
1099 }
|
|
|
1100 $MolecularComplexityType = $ComplexityParametersMap{MolecularComplexityType};
|
|
|
1101
|
|
|
1102
|
|
|
1103 if (IsEmpty($ComplexityParametersMap{AtomIdentifierType})) {
|
|
|
1104 $ComplexityParametersMap{AtomIdentifierType} = ($MolecularComplexityType =~ /^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i) ? "FunctionalClassAtomTypes" : "AtomicInvariantsAtomTypes";
|
|
|
1105 }
|
|
|
1106
|
|
|
1107 if (IsEmpty($ComplexityParametersMap{AtomicInvariantsToUse})) {
|
|
|
1108 my($AtomicInvariantsToUse);
|
|
|
1109
|
|
|
1110 if ($MolecularComplexityType =~ /^(AtomTypesFingerprints|TopologicalAtomPairsFingerprints|TopologicalAtomTripletsFingerprints|TopologicalAtomTorsionsFingerprints)$/i) {
|
|
|
1111 $AtomicInvariantsToUse = "AS,X,BO,H,FC";
|
|
|
1112 }
|
|
|
1113 elsif ($MolecularComplexityType =~ /^ExtendedConnectivityFingerprints$/i) {
|
|
|
1114 $AtomicInvariantsToUse = "AS,X,BO,H,FC,MN";
|
|
|
1115 }
|
|
|
1116 else {
|
|
|
1117 $AtomicInvariantsToUse = "AS";
|
|
|
1118 }
|
|
|
1119 $ComplexityParametersMap{AtomicInvariantsToUse} = $AtomicInvariantsToUse;
|
|
|
1120 }
|
|
|
1121
|
|
|
1122 if (IsEmpty($ComplexityParametersMap{FunctionalClassesToUse})) {
|
|
|
1123 my($FunctionalClassesToUse);
|
|
|
1124
|
|
|
1125 if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomPairsFingerprints$/i) {
|
|
|
1126 $FunctionalClassesToUse = "HBD,HBA,PI,NI,H";
|
|
|
1127 }
|
|
|
1128 elsif ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomTripletsFingerprints$/i) {
|
|
|
1129 $FunctionalClassesToUse = "HBD,HBA,PI,NI,H,Ar";
|
|
|
1130 }
|
|
|
1131 else {
|
|
|
1132 $FunctionalClassesToUse = "HBD,HBA,PI,NI,H,Ar,Hal";
|
|
|
1133 }
|
|
|
1134 $ComplexityParametersMap{FunctionalClassesToUse} = $FunctionalClassesToUse;
|
|
|
1135 }
|
|
|
1136
|
|
|
1137 my(@AtomicInvariantsToUse);
|
|
|
1138 @AtomicInvariantsToUse = split ',', $ComplexityParametersMap{AtomicInvariantsToUse};
|
|
|
1139 $ComplexityParametersMap{AtomicInvariantsToUse} = \@AtomicInvariantsToUse;
|
|
|
1140
|
|
|
1141 my(@FunctionalClassesToUse);
|
|
|
1142 @FunctionalClassesToUse = split ',', $ComplexityParametersMap{FunctionalClassesToUse};
|
|
|
1143 $ComplexityParametersMap{FunctionalClassesToUse} = \@FunctionalClassesToUse;
|
|
|
1144
|
|
|
1145 if (IsEmpty($ComplexityParametersMap{UseTriangleInequality})) {
|
|
|
1146 $ComplexityParametersMap{UseTriangleInequality} = 0;
|
|
|
1147 if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomTripletsFingerprints$/i) {
|
|
|
1148 $ComplexityParametersMap{UseTriangleInequality} = 1;
|
|
|
1149 }
|
|
|
1150 }
|
|
|
1151
|
|
|
1152 if ($MolecularComplexityType =~ /^(TopologicalPharmacophoreAtomPairsFingerprints|TopologicalPharmacophoreAtomTripletsFingerprints)$/i) {
|
|
|
1153 if ($ComplexityParametersMap{AtomIdentifierType} !~ /^FunctionalClassAtomTypes$/i) {
|
|
|
1154 die "Error: The parameter value specified for AtomIdentifierType, $ComplexityParametersMap{AtomIdentifierType}, in option \"--MolecularComplexity\" is not valid for MolecularComplexityType, $MolecularComplexityType: Allowed value: FunctionalClassAtomTypes...\n";
|
|
|
1155 }
|
|
|
1156 }
|
|
|
1157
|
|
|
1158 # Set up approprate paremeter names for specified molecular complexity...
|
|
|
1159
|
|
|
1160 @ParameterNames = ();
|
|
|
1161 push @ParameterNames, 'MolecularComplexityType';
|
|
|
1162
|
|
|
1163 @AtomIdentifierTypeParameters = ();
|
|
|
1164 push @AtomIdentifierTypeParameters, 'AtomIdentifierType';
|
|
|
1165 if ($ComplexityParametersMap{AtomIdentifierType} =~ /^AtomicInvariantsAtomTypes$/i) {
|
|
|
1166 push @AtomIdentifierTypeParameters, 'AtomicInvariantsToUse';
|
|
|
1167 }
|
|
|
1168 elsif ($ComplexityParametersMap{AtomIdentifierType} =~ /^FunctionalClassAtomTypes$/i) {
|
|
|
1169 push @AtomIdentifierTypeParameters, 'FunctionalClassesToUse';
|
|
|
1170 }
|
|
|
1171
|
|
|
1172 COMPLEXITYTYPE: {
|
|
|
1173 if ($MolecularComplexityType =~ /^AtomTypesFingerprints$/i) {
|
|
|
1174 push @ParameterNames, @AtomIdentifierTypeParameters;
|
|
|
1175 last COMPLEXITYTYPE;
|
|
|
1176 }
|
|
|
1177 if ($MolecularComplexityType =~ /^ExtendedConnectivityFingerprints$/i) {
|
|
|
1178 push @ParameterNames, @AtomIdentifierTypeParameters;
|
|
|
1179 push @ParameterNames, ('NeighborhoodRadius', 'NormalizationMethodology');
|
|
|
1180 last COMPLEXITYTYPE;
|
|
|
1181 }
|
|
|
1182 if ($MolecularComplexityType =~ /^MACCSKeys$/i) {
|
|
|
1183 push @ParameterNames, 'MACCSKeysSize';
|
|
|
1184 last COMPLEXITYTYPE;
|
|
|
1185 }
|
|
|
1186 if ($MolecularComplexityType =~ /^PathLengthFingerprints$/i) {
|
|
|
1187 push @ParameterNames, @AtomIdentifierTypeParameters;
|
|
|
1188 push @ParameterNames, ('MinPathLength', 'MaxPathLength', 'UseBondSymbols');
|
|
|
1189 last COMPLEXITYTYPE;
|
|
|
1190 }
|
|
|
1191 if ($MolecularComplexityType =~ /^TopologicalAtomPairsFingerprints$/i) {
|
|
|
1192 push @ParameterNames, @AtomIdentifierTypeParameters;
|
|
|
1193 push @ParameterNames, ('MinDistance', 'MaxDistance');
|
|
|
1194 last COMPLEXITYTYPE;
|
|
|
1195 }
|
|
|
1196 if ($MolecularComplexityType =~ /^TopologicalAtomTripletsFingerprints$/i) {
|
|
|
1197 push @ParameterNames, @AtomIdentifierTypeParameters;
|
|
|
1198 push @ParameterNames, ('MinDistance', 'MaxDistance', 'UseTriangleInequality');
|
|
|
1199 last COMPLEXITYTYPE;
|
|
|
1200 }
|
|
|
1201 if ($MolecularComplexityType =~ /^TopologicalAtomTorsionsFingerprints$/i) {
|
|
|
1202 push @ParameterNames, @AtomIdentifierTypeParameters;
|
|
|
1203 last COMPLEXITYTYPE;
|
|
|
1204 }
|
|
|
1205 if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomPairsFingerprints$/i) {
|
|
|
1206 push @ParameterNames, ('AtomIdentifierType', 'FunctionalClassesToUse', 'MinDistance', 'MaxDistance', 'NormalizationMethodology');
|
|
|
1207 last COMPLEXITYTYPE;
|
|
|
1208 }
|
|
|
1209 if ($MolecularComplexityType =~ /^TopologicalPharmacophoreAtomTripletsFingerprints$/i) {
|
|
|
1210 push @ParameterNames, ('AtomIdentifierType', 'FunctionalClassesToUse', 'MinDistance', 'MaxDistance', 'UseTriangleInequality', 'NormalizationMethodology', 'DistanceBinSize');
|
|
|
1211 last COMPLEXITYTYPE;
|
|
|
1212 }
|
|
|
1213 die "Error: The parameter value specified, $ParameterValue, for parameter name MolecularComplexityType using \"--MolecularComplexity\" is not valid.\n";
|
|
|
1214 }
|
|
|
1215
|
|
|
1216 $OptionsInfo{MolecularComplexity} = $Options{molecularcomplexity};
|
|
|
1217
|
|
|
1218 %{$OptionsInfo{MolecularComplexityParametersMap}} = ();
|
|
|
1219 for $ParameterName (@ParameterNames) {
|
|
|
1220 $ParameterValue = $ComplexityParametersMap{$ParameterName};
|
|
|
1221 $OptionsInfo{MolecularComplexityParametersMap}{$ParameterName} = $ParameterValue;
|
|
|
1222 }
|
|
|
1223 }
|
|
|
1224
|
|
|
1225 # Setup script usage and retrieve command line arguments specified using various options...
|
|
|
1226 sub SetupScriptUsage {
|
|
|
1227
|
|
|
1228 # Retrieve all the options...
|
|
|
1229 %Options = ();
|
|
|
1230
|
|
|
1231 $Options{aromaticitymodel} = 'MayaChemToolsAromaticityModel';
|
|
|
1232
|
|
|
1233 $Options{compoundidmode} = 'LabelPrefix';
|
|
|
1234 $Options{compoundidlabel} = 'CompoundID';
|
|
|
1235 $Options{datafieldsmode} = 'CompoundID';
|
|
|
1236
|
|
|
1237 $Options{filter} = 'Yes';
|
|
|
1238
|
|
|
1239 $Options{hydrogenbonds} = 'HBondsType2';
|
|
|
1240
|
|
|
1241 $Options{keeplargestcomponent} = 'Yes';
|
|
|
1242
|
|
|
1243 # Default mode values are set later...
|
|
|
1244 $Options{mode} = '';
|
|
|
1245
|
|
|
1246 # Default moelcular complexity values are set later...
|
|
|
1247 $Options{molecularcomplexity} = '';
|
|
|
1248
|
|
|
1249 # Default precision values are set later...
|
|
|
1250 $Options{precision} = '';
|
|
|
1251
|
|
|
1252 $Options{output} = 'text';
|
|
|
1253 $Options{outdelim} = 'comma';
|
|
|
1254 $Options{quote} = 'yes';
|
|
|
1255
|
|
|
1256 # Default rotatable bond parameter values are set later...
|
|
|
1257 $Options{rotatablebonds} = '';
|
|
|
1258
|
|
|
1259 $Options{ruleof3violations} = 'No';
|
|
|
1260 $Options{ruleof5violations} = 'No';
|
|
|
1261
|
|
|
1262 # Default TPSA paramater values are set later...
|
|
|
1263 $Options{tpsa} = '';
|
|
|
1264
|
|
|
1265 if (!GetOptions(\%Options, "aromaticitymodel=s", "compoundid=s", "compoundidlabel=s", "compoundidmode=s", "datafields=s", "datafieldsmode|d=s", "filter|f=s", "help|h", "hydrogenbonds=s", "keeplargestcomponent|k=s", "mode|m=s", "molecularcomplexity=s", "outdelim=s", "output=s", "overwrite|o", "precision=s", "rotatablebonds=s", "ruleof3violations=s", "ruleof5violations=s", "quote|q=s", "root|r=s", "tpsa=s", "workingdir|w=s")) {
|
|
|
1266 die "\nTo get a list of valid options and their values, use \"$ScriptName -h\" or\n\"perl -S $ScriptName -h\" command and try again...\n";
|
|
|
1267 }
|
|
|
1268 if ($Options{workingdir}) {
|
|
|
1269 if (! -d $Options{workingdir}) {
|
|
|
1270 die "Error: The value specified, $Options{workingdir}, for option \"-w --workingdir\" is not a directory name.\n";
|
|
|
1271 }
|
|
|
1272 chdir $Options{workingdir} or die "Error: Couldn't chdir $Options{workingdir}: $! \n";
|
|
|
1273 }
|
|
|
1274 if (!Molecule::IsSupportedAromaticityModel($Options{aromaticitymodel})) {
|
|
|
1275 my(@SupportedModels) = Molecule::GetSupportedAromaticityModels();
|
|
|
1276 die "Error: The value specified, $Options{aromaticitymodel}, for option \"--AromaticityModel\" is not valid. Supported aromaticity models in current release of MayaChemTools: @SupportedModels\n";
|
|
|
1277 }
|
|
|
1278 if ($Options{compoundidmode} !~ /^(DataField|MolName|LabelPrefix|MolNameOrLabelPrefix)$/i) {
|
|
|
1279 die "Error: The value specified, $Options{compoundidmode}, for option \"--CompoundIDMode\" is not valid. Allowed values: DataField, MolName, LabelPrefix or MolNameOrLabelPrefix\n";
|
|
|
1280 }
|
|
|
1281 if ($Options{datafieldsmode} !~ /^(All|Common|Specify|CompoundID)$/i) {
|
|
|
1282 die "Error: The value specified, $Options{datafieldsmode}, for option \"-d, --DataFieldsMode\" is not valid. Allowed values: All, Common, Specify or CompoundID\n";
|
|
|
1283 }
|
|
|
1284 if ($Options{filter} !~ /^(Yes|No)$/i) {
|
|
|
1285 die "Error: The value specified, $Options{filter}, for option \"-f, --Filter\" is not valid. Allowed values: Yes or No\n";
|
|
|
1286 }
|
|
|
1287 if ($Options{hydrogenbonds} !~ /^(HBondsType1|HydrogenBondsType1|HBondsType2|HydrogenBondsType2)$/i) {
|
|
|
1288 die "Error: The value specified, $Options{hydrogenbonds}, for option \"--HydrogenBonds\" is not valid. Allowed values: HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2\n";
|
|
|
1289 }
|
|
|
1290 if ($Options{keeplargestcomponent} !~ /^(Yes|No)$/i) {
|
|
|
1291 die "Error: The value specified, $Options{keeplargestcomponent}, for option \"-k, --KeepLargestComponent\" is not valid. Allowed values: Yes or No\n";
|
|
|
1292 }
|
|
|
1293 if ($Options{output} !~ /^(SD|text|both)$/i) {
|
|
|
1294 die "Error: The value specified, $Options{output}, for option \"--output\" is not valid. Allowed values: SD, text, or both\n";
|
|
|
1295 }
|
|
|
1296 if ($Options{outdelim} !~ /^(comma|semicolon|tab)$/i) {
|
|
|
1297 die "Error: The value specified, $Options{outdelim}, for option \"--outdelim\" is not valid. Allowed values: comma, tab, or semicolon\n";
|
|
|
1298 }
|
|
|
1299 if ($Options{quote} !~ /^(Yes|No)$/i) {
|
|
|
1300 die "Error: The value specified, $Options{quote}, for option \"-q --quote\" is not valid. Allowed values: Yes or No\n";
|
|
|
1301 }
|
|
|
1302 if ($Options{ruleof3violations} !~ /^(Yes|No)$/i) {
|
|
|
1303 die "Error: The value specified, $Options{ruleof3violations}, for option \"--RuleOf3Violations\" is not valid. Allowed values: Yes or No\n";
|
|
|
1304 }
|
|
|
1305 if ($Options{ruleof5violations} !~ /^(Yes|No)$/i) {
|
|
|
1306 die "Error: The value specified, $Options{ruleof5violations}, for option \"--RuleOf5Violations\" is not valid. Allowed values: Yes or No\n";
|
|
|
1307 }
|
|
|
1308 }
|
|
|
1309
|
|
|
1310 __END__
|
|
|
1311
|
|
|
1312 =head1 NAME
|
|
|
1313
|
|
|
1314 CalculatePhysicochemicalProperties.pl - Calculate physicochemical properties for SD files
|
|
|
1315
|
|
|
1316 =head1 SYNOPSIS
|
|
|
1317
|
|
|
1318 CalculatePhysicochemicalProperties.pl SDFile(s)...
|
|
|
1319
|
|
|
1320 PhysicochemicalProperties.pl [B<--AromaticityModel> I<AromaticityModelType>]
|
|
|
1321 [B<--CompoundID> DataFieldName or LabelPrefixString]
|
|
|
1322 [B<--CompoundIDLabel> text] [B<--CompoundIDMode>] [B<--DataFields> "FieldLabel1, FieldLabel2,..."]
|
|
|
1323 [B<-d, --DataFieldsMode> All | Common | Specify | CompoundID] [B<-f, --Filter> Yes | No] [B<-h, --help>]
|
|
|
1324 [B<--HydrogenBonds> HBondsType1 | HBondsType2] [B<-k, --KeepLargestComponent> Yes | No]
|
|
|
1325 [B<-m, --mode> All | RuleOf5 | RuleOf3 | "name1, [name2,...]"]
|
|
|
1326 [B<--MolecularComplexity> I<Name,Value, [Name,Value,...]>]
|
|
|
1327 [B<--OutDelim> comma | tab | semicolon] [B<--output> SD | text | both] [B<-o, --overwrite>]
|
|
|
1328 [B<--Precision> Name,Number,[Name,Number,..]] [B<--RotatableBonds> Name,Value, [Name,Value,...]]
|
|
|
1329 [B<--RuleOf3Violations> Yes | No] [B<--RuleOf5Violations> Yes | No]
|
|
|
1330 [B<-q, --quote> Yes | No] [B<-r, --root> RootName]
|
|
|
1331 [B<-w, --WorkingDir> dirname] SDFile(s)...
|
|
|
1332
|
|
|
1333 =head1 DESCRIPTION
|
|
|
1334
|
|
|
1335 Calculate physicochemical properties for I<SDFile(s)> and create appropriate SD or CSV/TSV
|
|
|
1336 text file(s) containing calculated properties.
|
|
|
1337
|
|
|
1338 The current release of MayaChemTools supports the calculation of these physicochemical
|
|
|
1339 properties:
|
|
|
1340
|
|
|
1341 MolecularWeight, ExactMass, HeavyAtoms, Rings, AromaticRings,
|
|
|
1342 van der Waals MolecularVolume [ Ref 93 ], RotatableBonds,
|
|
|
1343 HydrogenBondDonors, HydrogenBondAcceptors, LogP and
|
|
|
1344 Molar Refractivity (SLogP and SMR) [ Ref 89 ], Topological Polar
|
|
|
1345 Surface Area (TPSA) [ Ref 90 ], Fraction of SP3 carbons (Fsp3Carbons)
|
|
|
1346 and SP3 carbons (Sp3Carbons) [ Ref 115-116, Ref 119 ],
|
|
|
1347 MolecularComplexity [ Ref 117-119 ]
|
|
|
1348
|
|
|
1349 Multiple SDFile names are separated by spaces. The valid file extensions are I<.sdf>
|
|
|
1350 and I<.sd>. All other file names are ignored. All the SD files in a current directory
|
|
|
1351 can be specified either by I<*.sdf> or the current directory name.
|
|
|
1352
|
|
|
1353 The calculation of molecular complexity using I<MolecularComplexityType> parameter
|
|
|
1354 corresponds to the number of bits-set or unique keys [ Ref 117-119 ] in molecular fingerprints.
|
|
|
1355 Default value for I<MolecularComplexityType>: I<MACCSKeys> of size 166. The calculation
|
|
|
1356 of MACCSKeys is relatively expensive and can take rather substantial amount of time.
|
|
|
1357
|
|
|
1358 =head1 OPTIONS
|
|
|
1359
|
|
|
1360 =over 4
|
|
|
1361
|
|
|
1362 =item B<--AromaticityModel> I<MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel>
|
|
|
1363
|
|
|
1364 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
|
|
|
1365 release are: I<MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
1366 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
|
|
|
1367 or MayaChemToolsAromaticityModel>. Default value: I<MayaChemToolsAromaticityModel>.
|
|
|
1368
|
|
|
1369 The supported aromaticity model names along with model specific control parameters
|
|
|
1370 are defined in B<AromaticityModelsData.csv>, which is distributed with the current release
|
|
|
1371 and is available under B<lib/data> directory. B<Molecule.pm> module retrieves data from
|
|
|
1372 this file during class instantiation and makes it available to method B<DetectAromaticity>
|
|
|
1373 for detecting aromaticity corresponding to a specific model.
|
|
|
1374
|
|
|
1375 =item B<--CompoundID> I<DataFieldName or LabelPrefixString>
|
|
|
1376
|
|
|
1377 This value is B<--CompoundIDMode> specific and indicates how compound ID is generated.
|
|
|
1378
|
|
|
1379 For I<DataField> value of B<--CompoundIDMode> option, it corresponds to datafield label name
|
|
|
1380 whose value is used as compound ID; otherwise, it's a prefix string used for generating compound
|
|
|
1381 IDs like LabelPrefixString<Number>. Default value, I<Cmpd>, generates compound IDs which
|
|
|
1382 look like Cmpd<Number>.
|
|
|
1383
|
|
|
1384 Examples for I<DataField> value of B<--CompoundIDMode>:
|
|
|
1385
|
|
|
1386 MolID
|
|
|
1387 ExtReg
|
|
|
1388
|
|
|
1389 Examples for I<LabelPrefix> or I<MolNameOrLabelPrefix> value of B<--CompoundIDMode>:
|
|
|
1390
|
|
|
1391 Compound
|
|
|
1392
|
|
|
1393 The value specified above generates compound IDs which correspond to Compound<Number>
|
|
|
1394 instead of default value of Cmpd<Number>.
|
|
|
1395
|
|
|
1396 =item B<--CompoundIDLabel> I<text>
|
|
|
1397
|
|
|
1398 Specify compound ID column label for CSV/TSV text file(s) used during I<CompoundID> value
|
|
|
1399 of B<--DataFieldsMode> option. Default value: I<CompoundID>.
|
|
|
1400
|
|
|
1401 =item B<--CompoundIDMode> I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>
|
|
|
1402
|
|
|
1403 Specify how to generate compound IDs and write to CSV/TSV text file(s) along with calculated
|
|
|
1404 physicochemical properties for I<text | both> values of B<--output> option: use a I<SDFile(s)>
|
|
|
1405 datafield value; use molname line from I<SDFile(s)>; generate a sequential ID with specific prefix;
|
|
|
1406 use combination of both MolName and LabelPrefix with usage of LabelPrefix values for empty
|
|
|
1407 molname lines.
|
|
|
1408
|
|
|
1409 Possible values: I<DataField | MolName | LabelPrefix | MolNameOrLabelPrefix>.
|
|
|
1410 Default value: I<LabelPrefix>.
|
|
|
1411
|
|
|
1412 For I<MolNameAndLabelPrefix> value of B<--CompoundIDMode>, molname line in I<SDFile(s)> takes
|
|
|
1413 precedence over sequential compound IDs generated using I<LabelPrefix> and only empty molname
|
|
|
1414 values are replaced with sequential compound IDs.
|
|
|
1415
|
|
|
1416 This is only used for I<CompoundID> value of B<--DataFieldsMode> option.
|
|
|
1417
|
|
|
1418 =item B<--DataFields> I<"FieldLabel1,FieldLabel2,...">
|
|
|
1419
|
|
|
1420 Comma delimited list of I<SDFiles(s)> data fields to extract and write to CSV/TSV text file(s) along
|
|
|
1421 with calculated physicochemical properties for I<text | both> values of B<--output> option.
|
|
|
1422
|
|
|
1423 This is only used for I<Specify> value of B<--DataFieldsMode> option.
|
|
|
1424
|
|
|
1425 Examples:
|
|
|
1426
|
|
|
1427 Extreg
|
|
|
1428 MolID,CompoundName
|
|
|
1429
|
|
|
1430 =item B<-d, --DataFieldsMode> I<All | Common | Specify | CompoundID>
|
|
|
1431
|
|
|
1432 Specify how data fields in I<SDFile(s)> are transferred to output CSV/TSV text file(s) along
|
|
|
1433 with calculated physicochemical properties for I<text | both> values of B<--output> option:
|
|
|
1434 transfer all SD data field; transfer SD data files common to all compounds; extract specified
|
|
|
1435 data fields; generate a compound ID using molname line, a compound prefix, or a combination
|
|
|
1436 of both. Possible values: I<All | Common | specify | CompoundID>. Default value: I<CompoundID>.
|
|
|
1437
|
|
|
1438 =item B<-f, --Filter> I<Yes | No>
|
|
|
1439
|
|
|
1440 Specify whether to check and filter compound data in SDFile(s). Possible values: I<Yes or No>.
|
|
|
1441 Default value: I<Yes>.
|
|
|
1442
|
|
|
1443 By default, compound data is checked before calculating physiochemical properties and compounds
|
|
|
1444 containing atom data corresponding to non-element symbols or no atom data are ignored.
|
|
|
1445
|
|
|
1446 =item B<-h, --help>
|
|
|
1447
|
|
|
1448 Print this help message.
|
|
|
1449
|
|
|
1450 =item B<--HydrogenBonds> I<HBondsType1 | HBondsType2>
|
|
|
1451
|
|
|
1452 Parameters to control calculation of hydrogen bond donors and acceptors. Possible values:
|
|
|
1453 I<HBondsType1, HydrogenBondsType1, HBondsType2, HydrogenBondsType2>. Default value:
|
|
|
1454 I<HBondsType2> which corresponds to B<RuleOf5> definition for number of hydrogen bond
|
|
|
1455 donors and acceptors.
|
|
|
1456
|
|
|
1457 The current release of MayaChemTools supports identification of two types of hydrogen bond
|
|
|
1458 donor and acceptor atoms with these names:
|
|
|
1459
|
|
|
1460 HBondsType1 or HydrogenBondsType1
|
|
|
1461 HBondsType2 or HydrogenBondsType2
|
|
|
1462
|
|
|
1463 The names of these hydrogen bond types are rather arbitrary. However, their definitions have
|
|
|
1464 specific meaning and are as follows:
|
|
|
1465
|
|
|
1466 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:
|
|
|
1467
|
|
|
1468 Donor: NH, NH2, OH - Any N and O with available H
|
|
|
1469 Acceptor: N[!H], O - Any N without available H and any O
|
|
|
1470
|
|
|
1471 HydrogenBondsType2 [ Ref 91 ]:
|
|
|
1472
|
|
|
1473 Donor: NH, NH2, OH - N and O with available H
|
|
|
1474 Acceptor: N, O - And N and O
|
|
|
1475
|
|
|
1476 =item B<-k, --KeepLargestComponent> I<Yes | No>
|
|
|
1477
|
|
|
1478 Calculate physicochemical properties for only the largest component in molecule. Possible values:
|
|
|
1479 I<Yes or No>. Default value: I<Yes>.
|
|
|
1480
|
|
|
1481 For molecules containing multiple connected components, physicochemical properties can be
|
|
|
1482 calculated in two different ways: use all connected components or just the largest connected
|
|
|
1483 component. By default, all atoms except for the largest connected component are
|
|
|
1484 deleted before calculation of physicochemical properties.
|
|
|
1485
|
|
|
1486 =item B<-m, --mode> I<All | RuleOf5 | RuleOf3 | "name1, [name2,...]">
|
|
|
1487
|
|
|
1488 Specify physicochemical properties to calculate for SDFile(s): calculate all available physical
|
|
|
1489 chemical properties; calculate properties corresponding to Rule of 5; or use a comma delimited
|
|
|
1490 list of supported physicochemical properties. Possible values: I<All | RuleOf5 | RuleOf3 |
|
|
|
1491 "name1, [name2,...]">.
|
|
|
1492
|
|
|
1493 Default value: I<MolecularWeight, HeavyAtoms, MolecularVolume, RotatableBonds, HydrogenBondDonors,
|
|
|
1494 HydrogenBondAcceptors, SLogP, TPSA>. These properties are calculated by default.
|
|
|
1495
|
|
|
1496 I<RuleOf5> [ Ref 91 ] includes these properties: I<MolecularWeight, HydrogenBondDonors, HydrogenBondAcceptors,
|
|
|
1497 SLogP>. I<RuleOf5> states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and
|
|
|
1498 logP <= 5.
|
|
|
1499
|
|
|
1500 I<RuleOf3> [ Ref 92 ] includes these properties: I<MolecularWeight, RotatableBonds, HydrogenBondDonors,
|
|
|
1501 HydrogenBondAcceptors, SLogP, TPSA>. I<RuleOf3> states: MolecularWeight <= 300, RotatableBonds <= 3,
|
|
|
1502 HydrogenBondDonors <= 3, HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.
|
|
|
1503
|
|
|
1504 I<All> calculates all supported physicochemical properties: I<MolecularWeight, ExactMass,
|
|
|
1505 HeavyAtoms, Rings, AromaticRings, MolecularVolume, RotatableBonds, HydrogenBondDonors,
|
|
|
1506 HydrogenBondAcceptors, SLogP, SMR, TPSA, Fsp3Carbons, Sp3Carbons, MolecularComplexity>.
|
|
|
1507
|
|
|
1508 =item B<--MolecularComplexity> I<Name,Value, [Name,Value,...]>
|
|
|
1509
|
|
|
1510 Parameters to control calculation of molecular complexity: it's a comma delimited list of parameter
|
|
|
1511 name and value pairs.
|
|
|
1512
|
|
|
1513 Possible parameter names: I<MolecularComplexityType, AtomIdentifierType,
|
|
|
1514 AtomicInvariantsToUse, FunctionalClassesToUse, MACCSKeysSize, NeighborhoodRadius,
|
|
|
1515 MinPathLength, MaxPathLength, UseBondSymbols, MinDistance, MaxDistance,
|
|
|
1516 UseTriangleInequality, DistanceBinSize, NormalizationMethodology>.
|
|
|
1517
|
|
|
1518 The valid paramater valuse for each parameter name are described in the following sections.
|
|
|
1519
|
|
|
1520 The current release of MayaChemTools supports calculation of molecular complexity using
|
|
|
1521 I<MolecularComplexityType> parameter corresponding to the number of bits-set or unique
|
|
|
1522 keys [ Ref 117-119 ] in molecular fingerprints. The valid values for I<MolecularComplexityType>
|
|
|
1523 are:
|
|
|
1524
|
|
|
1525 AtomTypesFingerprints
|
|
|
1526 ExtendedConnectivityFingerprints
|
|
|
1527 MACCSKeys
|
|
|
1528 PathLengthFingerprints
|
|
|
1529 TopologicalAtomPairsFingerprints
|
|
|
1530 TopologicalAtomTripletsFingerprints
|
|
|
1531 TopologicalAtomTorsionsFingerprints
|
|
|
1532 TopologicalPharmacophoreAtomPairsFingerprints
|
|
|
1533 TopologicalPharmacophoreAtomTripletsFingerprints
|
|
|
1534
|
|
|
1535 Default value for I<MolecularComplexityType>: I<MACCSKeys>.
|
|
|
1536
|
|
|
1537 I<AtomIdentifierType> parameter name correspods to atom types used during generation of
|
|
|
1538 fingerprints. The valid values for I<AtomIdentifierType> are: I<AtomicInvariantsAtomTypes,
|
|
|
1539 DREIDINGAtomTypes, EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
|
|
|
1540 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes>. I<AtomicInvariantsAtomTypes>
|
|
|
1541 is not supported for during the following values of I<MolecularComplexityType>: I<MACCSKeys,
|
|
|
1542 TopologicalPharmacophoreAtomPairsFingerprints, TopologicalPharmacophoreAtomTripletsFingerprints>.
|
|
|
1543 I<FunctionalClassAtomTypes> is the only valid value for I<AtomIdentifierType> for topological
|
|
|
1544 pharmacophore fingerprints.
|
|
|
1545
|
|
|
1546 Default value for I<AtomIdentifierType>: I<AtomicInvariantsAtomTypes>
|
|
|
1547 for all except topological pharmacophore fingerprints where it is I<FunctionalClassAtomTypes>.
|
|
|
1548
|
|
|
1549 I<AtomicInvariantsToUse> parameter name and values are used during I<AtomicInvariantsAtomTypes>
|
|
|
1550 value of parameter I<AtomIdentifierType>. It's a list of space separated valid atomic invariant atom types.
|
|
|
1551
|
|
|
1552 Possible values for atomic invariants are: I<AS, X, BO, LBO, SB, DB, TB, H, Ar, RA, FC, MN, SM>.
|
|
|
1553 Default value for I<AtomicInvariantsToUse> parameter are set differently for different fingerprints
|
|
|
1554 using I<MolecularComplexityType> parameter as shown below:
|
|
|
1555
|
|
|
1556 MolecularComplexityType AtomicInvariantsToUse
|
|
|
1557
|
|
|
1558 AtomTypesFingerprints AS X BO H FC
|
|
|
1559 TopologicalAtomPairsFingerprints AS X BO H FC
|
|
|
1560 TopologicalAtomTripletsFingerprints AS X BO H FC
|
|
|
1561 TopologicalAtomTorsionsFingerprints AS X BO H FC
|
|
|
1562
|
|
|
1563 ExtendedConnectivityFingerprints AS X BO H FC MN
|
|
|
1564 PathLengthFingerprints AS
|
|
|
1565
|
|
|
1566
|
|
|
1567 The atomic invariants abbreviations correspond to:
|
|
|
1568
|
|
|
1569 AS = Atom symbol corresponding to element symbol
|
|
|
1570
|
|
|
1571 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
1572 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
1573 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
1574 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1575 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1576 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
1577 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
1578 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
1579 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
1580 FC<+n/-n> = Formal charge assigned to atom
|
|
|
1581 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
1582 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
1583 3 (triplet)
|
|
|
1584
|
|
|
1585 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
|
|
|
1586
|
|
|
1587 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
1588
|
|
|
1589 Except for AS which is a required atomic invariant in atom types, all other atomic invariants are
|
|
|
1590 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
|
|
|
1591
|
|
|
1592 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
|
|
|
1593 are also allowed:
|
|
|
1594
|
|
|
1595 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
1596 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
1597 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
1598 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
1599 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
1600 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
1601 H : NumOfImplicitAndExplicitHydrogens
|
|
|
1602 Ar : Aromatic
|
|
|
1603 RA : RingAtom
|
|
|
1604 FC : FormalCharge
|
|
|
1605 MN : MassNumber
|
|
|
1606 SM : SpinMultiplicity
|
|
|
1607
|
|
|
1608 I<AtomTypes::AtomicInvariantsAtomTypes> module is used to assign atomic invariant
|
|
|
1609 atom types.
|
|
|
1610
|
|
|
1611 I<FunctionalClassesToUse> parameter name and values are used during I<FunctionalClassAtomTypes>
|
|
|
1612 value of parameter I<AtomIdentifierType>. It's a list of space separated valid atomic invariant atom types.
|
|
|
1613
|
|
|
1614 Possible values for atom functional classes are: I<Ar, CA, H, HBA, HBD, Hal, NI, PI, RA>.
|
|
|
1615
|
|
|
1616 Default value for I<FunctionalClassesToUse> parameter is set to:
|
|
|
1617
|
|
|
1618 HBD HBA PI NI Ar Hal
|
|
|
1619
|
|
|
1620 for all fingerprints except for the following two I<MolecularComplexityType> fingerints:
|
|
|
1621
|
|
|
1622 MolecularComplexityType FunctionalClassesToUse
|
|
|
1623
|
|
|
1624 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
|
|
|
1625 TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar
|
|
|
1626
|
|
|
1627 The functional class abbreviations correspond to:
|
|
|
1628
|
|
|
1629 HBD: HydrogenBondDonor
|
|
|
1630 HBA: HydrogenBondAcceptor
|
|
|
1631 PI : PositivelyIonizable
|
|
|
1632 NI : NegativelyIonizable
|
|
|
1633 Ar : Aromatic
|
|
|
1634 Hal : Halogen
|
|
|
1635 H : Hydrophobic
|
|
|
1636 RA : RingAtom
|
|
|
1637 CA : ChainAtom
|
|
|
1638
|
|
|
1639 Functional class atom type specification for an atom corresponds to:
|
|
|
1640
|
|
|
1641 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
1642
|
|
|
1643 I<AtomTypes::FunctionalClassAtomTypes> module is used to assign functional class atom
|
|
|
1644 types. It uses following definitions [ Ref 60-61, Ref 65-66 ]:
|
|
|
1645
|
|
|
1646 HydrogenBondDonor: NH, NH2, OH
|
|
|
1647 HydrogenBondAcceptor: N[!H], O
|
|
|
1648 PositivelyIonizable: +, NH2
|
|
|
1649 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
1650
|
|
|
1651 I<MACCSKeysSize> parameter name is only used during I<MACCSKeys> value of
|
|
|
1652 I<MolecularComplexityType> and corresponds to the size of MACCS key set. Possible
|
|
|
1653 values: I<166 or 322>. Default value: I<166>.
|
|
|
1654
|
|
|
1655 I<NeighborhoodRadius> parameter name is only used during I<ExtendedConnectivityFingerprints>
|
|
|
1656 value of I<MolecularComplexityType> and corresponds to atomic neighborhoods radius for
|
|
|
1657 generating extended connectivity fingerprints. Possible values: positive integer. Default value:
|
|
|
1658 I<2>.
|
|
|
1659
|
|
|
1660 I<MinPathLength> and I<MaxPathLength> parameters are only used during I<PathLengthFingerprints>
|
|
|
1661 value of I<MolecularComplexityType> and correspond to minimum and maximum path lengths to use
|
|
|
1662 for generating path length fingerprints. Possible values: positive integers. Default value: I<MinPathLength - 1>;
|
|
|
1663 I<MaxPathLength - 8>.
|
|
|
1664
|
|
|
1665 I<UseBondSymbols> parameter is only used during I<PathLengthFingerprints> value of
|
|
|
1666 I<MolecularComplexityType> and indicates whether bond symbols are included in atom path
|
|
|
1667 strings used to generate path length fingerprints. Possible value: I<Yes or No>. Default value:
|
|
|
1668 I<Yes>.
|
|
|
1669
|
|
|
1670 I<MinDistance> and I<MaxDistance> parameters are only used during I<TopologicalAtomPairsFingerprints>
|
|
|
1671 and I<TopologicalAtomTripletsFingerprints> values of I<MolecularComplexityType> and correspond to
|
|
|
1672 minimum and maximum bond distance between atom pairs during topological pharmacophore fingerprints.
|
|
|
1673 Possible values: positive integers. Default value: I<MinDistance - 1>; I<MaxDistance - 10>.
|
|
|
1674
|
|
|
1675 I<UseTriangleInequality> parameter is used during these values for I<MolecularComplexityType>:
|
|
|
1676 I<TopologicalAtomTripletsFingerprints> and I<TopologicalPharmacophoreAtomTripletsFingerprints>.
|
|
|
1677 Possible values: I<Yes or No>. It determines wheter to apply triangle inequality to distance triplets.
|
|
|
1678 Default value: I<TopologicalAtomTripletsFingerprints - No>;
|
|
|
1679 I<TopologicalPharmacophoreAtomTripletsFingerprints - Yes>.
|
|
|
1680
|
|
|
1681 I<DistanceBinSize> parameter is used during I<TopologicalPharmacophoreAtomTripletsFingerprints>
|
|
|
1682 value of I<MolecularComplexityType> and correspons to distance bin size used for binning
|
|
|
1683 distances during generation of topological pharmacophore atom triplets fingerprints. Possible
|
|
|
1684 value: positive integer. Default value: I<2>.
|
|
|
1685
|
|
|
1686 I<NormalizationMethodology> is only used for these values for I<MolecularComplexityType>:
|
|
|
1687 I<ExtendedConnectivityFingerprints>, I<TopologicalPharmacophoreAtomPairsFingerprints>
|
|
|
1688 and I<TopologicalPharmacophoreAtomTripletsFingerprints>. It corresponds to normalization
|
|
|
1689 methodology to use for scaling the number of bits-set or unique keys during generation of
|
|
|
1690 fingerprints. Possible values during I<ExtendedConnectivityFingerprints>: I<None or
|
|
|
1691 ByHeavyAtomsCount>; Default value: I<None>. Possible values during topological
|
|
|
1692 pharmacophore atom pairs and tripletes fingerprints: I<None or ByPossibleKeysCount>;
|
|
|
1693 Default value: I<None>. I<ByPossibleKeysCount> corresponds to total number of
|
|
|
1694 possible topological pharmacophore atom pairs or triplets in a molecule.
|
|
|
1695
|
|
|
1696 Examples of I<MolecularComplexity> name and value parameters:
|
|
|
1697
|
|
|
1698 MolecularComplexityType,AtomTypesFingerprints,AtomIdentifierType,
|
|
|
1699 AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS X BO H FC
|
|
|
1700
|
|
|
1701 MolecularComplexityType,ExtendedConnectivityFingerprints,
|
|
|
1702 AtomIdentifierType,AtomicInvariantsAtomTypes,
|
|
|
1703 AtomicInvariantsToUse,AS X BO H FC MN,NeighborhoodRadius,2,
|
|
|
1704 NormalizationMethodology,None
|
|
|
1705
|
|
|
1706 MolecularComplexityType,MACCSKeys,MACCSKeysSize,166
|
|
|
1707
|
|
|
1708 MolecularComplexityType,PathLengthFingerprints,AtomIdentifierType,
|
|
|
1709 AtomicInvariantsAtomTypes,AtomicInvariantsToUse,AS,MinPathLength,
|
|
|
1710 1,MaxPathLength,8,UseBondSymbols,Yes
|
|
|
1711
|
|
|
1712 MolecularComplexityType,TopologicalAtomPairsFingerprints,
|
|
|
1713 AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
|
|
|
1714 AS X BO H FC,MinDistance,1,MaxDistance,10
|
|
|
1715
|
|
|
1716 MolecularComplexityType,TopologicalAtomTripletsFingerprints,
|
|
|
1717 AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
|
|
|
1718 AS X BO H FC,MinDistance,1,MaxDistance,10,UseTriangleInequality,No
|
|
|
1719
|
|
|
1720 MolecularComplexityType,TopologicalAtomTorsionsFingerprints,
|
|
|
1721 AtomIdentifierType,AtomicInvariantsAtomTypes,AtomicInvariantsToUse,
|
|
|
1722 AS X BO H FC
|
|
|
1723
|
|
|
1724 MolecularComplexityType,TopologicalPharmacophoreAtomPairsFingerprints,
|
|
|
1725 AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
|
|
|
1726 HBD HBA PI NI H,MinDistance,1,MaxDistance,10,NormalizationMethodology,
|
|
|
1727 None
|
|
|
1728
|
|
|
1729 MolecularComplexityType,TopologicalPharmacophoreAtomTripletsFingerprints,
|
|
|
1730 AtomIdentifierType,FunctionalClassAtomTypes,FunctionalClassesToUse,
|
|
|
1731 HBD HBA PI NI H Ar,MinDistance,1,MaxDistance,10,NormalizationMethodology,
|
|
|
1732 None,UseTriangleInequality,Yes,NormalizationMethodology,None,
|
|
|
1733 DistanceBinSize,2
|
|
|
1734
|
|
|
1735 =item B<--OutDelim> I<comma | tab | semicolon>
|
|
|
1736
|
|
|
1737 Delimiter for output CSV/TSV text file(s). Possible values: I<comma, tab, or semicolon>
|
|
|
1738 Default value: I<comma>.
|
|
|
1739
|
|
|
1740 =item B<--output> I<SD | text | both>
|
|
|
1741
|
|
|
1742 Type of output files to generate. Possible values: I<SD, text, or both>. Default value: I<text>.
|
|
|
1743
|
|
|
1744 =item B<-o, --overwrite>
|
|
|
1745
|
|
|
1746 Overwrite existing files.
|
|
|
1747
|
|
|
1748 =item B<--Precision> I<Name,Number,[Name,Number,..]>
|
|
|
1749
|
|
|
1750 Precision of calculated property values in the output file: it's a comma delimited list of
|
|
|
1751 property name and precision value pairs. Possible property names: I<MolecularWeight,
|
|
|
1752 ExactMass>. Possible values: positive intergers. Default value: I<MolecularWeight,2,
|
|
|
1753 ExactMass,4>.
|
|
|
1754
|
|
|
1755 Examples:
|
|
|
1756
|
|
|
1757 ExactMass,3
|
|
|
1758 MolecularWeight,1,ExactMass,2
|
|
|
1759
|
|
|
1760 =item B<-q, --quote> I<Yes | No>
|
|
|
1761
|
|
|
1762 Put quote around column values in output CSV/TSV text file(s). Possible values:
|
|
|
1763 I<Yes or No>. Default value: I<Yes>.
|
|
|
1764
|
|
|
1765 =item B<-r, --root> I<RootName>
|
|
|
1766
|
|
|
1767 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
|
|
|
1768 <SDFileName><PhysicochemicalProperties>.<Ext>. The file type determines <Ext> value.
|
|
|
1769 The sdf, csv, and tsv <Ext> values are used for SD, comma/semicolon, and tab
|
|
|
1770 delimited text files, respectively.This option is ignored for multiple input files.
|
|
|
1771
|
|
|
1772 =item B<--RotatableBonds> I<Name,Value, [Name,Value,...]>
|
|
|
1773
|
|
|
1774 Parameters to control calculation of rotatable bonds [ Ref 92 ]: it's a comma delimited list of parameter
|
|
|
1775 name and value pairs. Possible parameter names: I<IgnoreTerminalBonds, IgnoreBondsToTripleBonds,
|
|
|
1776 IgnoreAmideBonds, IgnoreThioamideBonds, IgnoreSulfonamideBonds>. Possible parameter values:
|
|
|
1777 I<Yes or No>. By default, value of all parameters is set to I<Yes>.
|
|
|
1778
|
|
|
1779 =item B<--RuleOf3Violations> I<Yes | No>
|
|
|
1780
|
|
|
1781 Specify whether to calculate B<RuleOf3Violations> for SDFile(s). Possible values: I<Yes or No>.
|
|
|
1782 Default value: I<No>.
|
|
|
1783
|
|
|
1784 For I<Yes> value of B<RuleOf3Violations>, in addition to calculating total number of B<RuleOf3> violations,
|
|
|
1785 individual violations for compounds are also written to output files.
|
|
|
1786
|
|
|
1787 B<RuleOf3> [ Ref 92 ] states: MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
|
|
|
1788 HydrogenBondAcceptors <= 3, logP <= 3, and TPSA <= 60.
|
|
|
1789
|
|
|
1790 =item B<--RuleOf5Violations> I<Yes | No>
|
|
|
1791
|
|
|
1792 Specify whether to calculate B<RuleOf5Violations> for SDFile(s). Possible values: I<Yes or No>.
|
|
|
1793 Default value: I<No>.
|
|
|
1794
|
|
|
1795 For I<Yes> value of B<RuleOf5Violations>, in addition to calculating total number of B<RuleOf5> violations,
|
|
|
1796 individual violations for compounds are also written to output files.
|
|
|
1797
|
|
|
1798 B<RuleOf5> [ Ref 91 ] states: MolecularWeight <= 500, HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10,
|
|
|
1799 and logP <= 5.
|
|
|
1800
|
|
|
1801 =item B<--TPSA> I<Name,Value, [Name,Value,...]>
|
|
|
1802
|
|
|
1803 Parameters to control calculation of TPSA: it's a comma delimited list of parameter name and value
|
|
|
1804 pairs. Possible parameter names: I<IgnorePhosphorus, IgnoreSulfur>. Possible parameter values:
|
|
|
1805 I<Yes or No>. By default, value of all parameters is set to I<Yes>.
|
|
|
1806
|
|
|
1807 By default, TPSA atom contributions from Phosphorus and Sulfur atoms are not included during
|
|
|
1808 TPSA calculations. [ Ref 91 ]
|
|
|
1809
|
|
|
1810 =item B<-w, --WorkingDir> I<DirName>
|
|
|
1811
|
|
|
1812 Location of working directory. Default value: current directory.
|
|
|
1813
|
|
|
1814 =back
|
|
|
1815
|
|
|
1816 =head1 EXAMPLES
|
|
|
1817
|
|
|
1818 To calculate default set of physicochemical properties - MolecularWeight, HeavyAtoms,
|
|
|
1819 MolecularVolume, RotatableBonds, HydrogenBondDonor, HydrogenBondAcceptors, SLogP,
|
|
|
1820 TPSA - and generate a SamplePhysicochemicalProperties.csv file containing sequential
|
|
|
1821 compound IDs along with properties data, type:
|
|
|
1822
|
|
|
1823 % CalculatePhysicochemicalProperties.pl -o Sample.sdf
|
|
|
1824
|
|
|
1825 To calculate all available physicochemical properties and generate both SampleAllProperties.csv
|
|
|
1826 and SampleAllProperties.sdf files containing sequential compound IDs in CSV file along with
|
|
|
1827 properties data, type:
|
|
|
1828
|
|
|
1829 % CalculatePhysicochemicalProperties.pl -m All --output both
|
|
|
1830 -r SampleAllProperties -o Sample.sdf
|
|
|
1831
|
|
|
1832 To calculate RuleOf5 physicochemical properties and generate a SampleRuleOf5Properties.csv file
|
|
|
1833 containing sequential compound IDs along with properties data, type:
|
|
|
1834
|
|
|
1835 % CalculatePhysicochemicalProperties.pl -m RuleOf5
|
|
|
1836 -r SampleRuleOf5Properties -o Sample.sdf
|
|
|
1837
|
|
|
1838 To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate
|
|
|
1839 a SampleRuleOf5Properties.csv file containing sequential compound IDs along with properties data, type:
|
|
|
1840
|
|
|
1841 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
|
|
|
1842 -r SampleRuleOf5Properties -o Sample.sdf
|
|
|
1843
|
|
|
1844 To calculate RuleOf3 physicochemical properties and generate a SampleRuleOf3Properties.csv file
|
|
|
1845 containing sequential compound IDs along with properties data, type:
|
|
|
1846
|
|
|
1847 % CalculatePhysicochemicalProperties.pl -m RuleOf3
|
|
|
1848 -r SampleRuleOf3Properties -o Sample.sdf
|
|
|
1849
|
|
|
1850 To calculate RuleOf3 physicochemical properties along with counting RuleOf3 violations and generate
|
|
|
1851 a SampleRuleOf3Properties.csv file containing sequential compound IDs along with properties data, type:
|
|
|
1852
|
|
|
1853 % CalculatePhysicochemicalProperties.pl -m RuleOf3 --RuleOf3Violations Yes
|
|
|
1854 -r SampleRuleOf3Properties -o Sample.sdf
|
|
|
1855
|
|
|
1856 To calculate a specific set of physicochemical properties and generate a SampleProperties.csv file
|
|
|
1857 containing sequential compound IDs along with properties data, type:
|
|
|
1858
|
|
|
1859 % CalculatePhysicochemicalProperties.pl -m "Rings,AromaticRings"
|
|
|
1860 -r SampleProperties -o Sample.sdf
|
|
|
1861
|
|
|
1862 To calculate HydrogenBondDonors and HydrogenBondAcceptors using HydrogenBondsType1 definition
|
|
|
1863 and generate a SampleProperties.csv file containing sequential compound IDs along with properties
|
|
|
1864 data, type:
|
|
|
1865
|
|
|
1866 % CalculatePhysicochemicalProperties.pl -m "HydrogenBondDonors,HydrogenBondAcceptors"
|
|
|
1867 --HydrogenBonds HBondsType1 -r SampleProperties -o Sample.sdf
|
|
|
1868
|
|
|
1869 To calculate TPSA using sulfur and phosphorus atoms along with nitrogen and oxygen atoms and
|
|
|
1870 generate a SampleProperties.csv file containing sequential compound IDs along with properties
|
|
|
1871 data, type:
|
|
|
1872
|
|
|
1873 % CalculatePhysicochemicalProperties.pl -m "TPSA" --TPSA "IgnorePhosphorus,No,
|
|
|
1874 IgnoreSulfur,No" -r SampleProperties -o Sample.sdf
|
|
|
1875
|
|
|
1876 To calculate MolecularComplexity using extendend connectivity fingerprints corresponding
|
|
|
1877 to atom neighborhood radius of 2 with atomic invariant atom types without any scaling and
|
|
|
1878 generate a SampleProperties.csv file containing sequential compound IDs along with properties
|
|
|
1879 data, type:
|
|
|
1880
|
|
|
1881 % CalculatePhysicochemicalProperties.pl -m MolecularComplexity --MolecularComplexity
|
|
|
1882 "MolecularComplexityType,ExtendedConnectivityFingerprints,NeighborhoodRadius,2,
|
|
|
1883 AtomIdentifierType, AtomicInvariantsAtomTypes,
|
|
|
1884 AtomicInvariantsToUse,AS X BO H FC MN,NormalizationMethodology,None"
|
|
|
1885 -r SampleProperties -o Sample.sdf
|
|
|
1886
|
|
|
1887 To calculate RuleOf5 physicochemical properties along with counting RuleOf5 violations and generate
|
|
|
1888 a SampleRuleOf5Properties.csv file containing compound IDs from molecule name line along with
|
|
|
1889 properties data, type:
|
|
|
1890
|
|
|
1891 % CalculatePhysicochemicalProperties.pl -m RuleOf5 --RuleOf5Violations Yes
|
|
|
1892 --DataFieldsMode CompoundID --CompoundIDMode MolName
|
|
|
1893 -r SampleRuleOf5Properties -o Sample.sdf
|
|
|
1894
|
|
|
1895 To calculate all available physicochemical properties and generate a SampleAllProperties.csv
|
|
|
1896 file containing compound ID using specified data field along with along with properties data,
|
|
|
1897 type:
|
|
|
1898
|
|
|
1899 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
1900 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID Mol_ID
|
|
|
1901 -r SampleAllProperties -o Sample.sdf
|
|
|
1902
|
|
|
1903 To calculate all available physicochemical properties and generate a SampleAllProperties.csv
|
|
|
1904 file containing compound ID using combination of molecule name line and an explicit compound
|
|
|
1905 prefix along with properties data, type:
|
|
|
1906
|
|
|
1907 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
1908 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
|
|
|
1909 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleAllProperties
|
|
|
1910 -o Sample.sdf
|
|
|
1911
|
|
|
1912 To calculate all available physicochemical properties and generate a SampleAllProperties.csv
|
|
|
1913 file containing specific data fields columns along with with properties data, type:
|
|
|
1914
|
|
|
1915 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
1916 --DataFieldsMode Specify --DataFields Mol_ID -r SampleAllProperties
|
|
|
1917 -o Sample.sdf
|
|
|
1918
|
|
|
1919 To calculate all available physicochemical properties and generate a SampleAllProperties.csv
|
|
|
1920 file containing common data fields columns along with with properties data, type:
|
|
|
1921
|
|
|
1922 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
1923 --DataFieldsMode Common -r SampleAllProperties -o Sample.sdf
|
|
|
1924
|
|
|
1925 To calculate all available physicochemical properties and generate both SampleAllProperties.csv
|
|
|
1926 and CSV files containing all data fields columns in CSV files along with with properties data, type:
|
|
|
1927
|
|
|
1928 % CalculatePhysicochemicalProperties.pl -m All
|
|
|
1929 --DataFieldsMode All --output both -r SampleAllProperties
|
|
|
1930 -o Sample.sdf
|
|
|
1931
|
|
|
1932 =head1 AUTHOR
|
|
|
1933
|
|
|
1934 Manish Sud <msud@san.rr.com>
|
|
|
1935
|
|
|
1936 =head1 SEE ALSO
|
|
|
1937
|
|
|
1938 ExtractFromSDtFiles.pl, ExtractFromTextFiles.pl, InfoSDFiles.pl, InfoTextFiles.pl
|
|
|
1939
|
|
|
1940 =head1 COPYRIGHT
|
|
|
1941
|
|
|
1942 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
1943
|
|
|
1944 This file is part of MayaChemTools.
|
|
|
1945
|
|
|
1946 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
1947 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
1948 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
1949 any later version.
|
|
|
1950
|
|
|
1951 =cut
|
