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1 package Molecule;
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2 #
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3 # $RCSfile: Molecule.pm,v $
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4 # $Date: 2015/02/28 20:47:18 $
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5 # $Revision: 1.59 $
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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 Carp;
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31 use Exporter;
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32 use Storable ();
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33 use Scalar::Util ();
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34 use ObjectProperty;
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35 use MathUtil;
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36 use PeriodicTable;
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37 use Text::ParseWords;
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38 use TextUtil;
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39 use FileUtil;
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40 use Graph;
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41 use Atom;
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42 use Bond;
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43 use MolecularFormula;
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44
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45 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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46
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47 @ISA = qw(Graph ObjectProperty Exporter);
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48 @EXPORT = qw(IsMolecule);
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49 @EXPORT_OK = qw(FormatElementalCompositionInformation GetSupportedAromaticityModels IsSupportedAromaticityModel);
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50
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51 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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52
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53 # Setup class variables...
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54 my($ClassName, $ObjectID, %AromaticityModelsDataMap, %CanonicalAromaticityModelNamesMap);
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55 _InitializeClass();
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56
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57 # Overload Perl functions...
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58 use overload '""' => 'StringifyMolecule';
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59
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60 # Class constructor...
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61 sub new {
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62 my($Class, %NamesAndValues) = @_;
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63
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64 # Initialize object...
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65 my $This = $Class->SUPER::new();
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66 bless $This, ref($Class) || $Class;
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67 $This->_InitializeMolecule();
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68
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69 if (keys %NamesAndValues) { $This->_InitializeMoleculeProperties(%NamesAndValues); }
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70
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71 return $This;
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72 }
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73
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74 # Initialize object data...
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75 sub _InitializeMolecule {
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76 my($This) = @_;
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77 my($ObjectID) = _GetNewObjectID();
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78
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79 # All other property names and values along with all Set/Get<PropertyName> methods
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80 # are implemented on-demand using ObjectProperty class.
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81 $This->{ID} = $ObjectID;
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82 $This->{Name} = "Molecule ${ObjectID}";
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83 }
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84
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85 # Initialize molecule properties...
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86 sub _InitializeMoleculeProperties {
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87 my($This, %NamesAndValues) = @_;
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88
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89 my($Name, $Value, $MethodName);
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90 while (($Name, $Value) = each %NamesAndValues) {
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91 $MethodName = "Set${Name}";
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92 $This->$MethodName($Value);
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93 }
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94 }
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95
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96 # Initialize class ...
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97 sub _InitializeClass {
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98 #Class name...
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99 $ClassName = __PACKAGE__;
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100
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101 # ID to keep track of objects...
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102 $ObjectID = 0;
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103
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104 # Load molecule class data...
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105 _LoadMoleculeClassData();
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106 }
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107
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108 # Setup an explicit SetID method to block setting of ID by AUTOLOAD function...
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109 sub SetID {
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110 my($This, $Value) = @_;
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111
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112 carp "Warning: ${ClassName}->SetID: Object ID can't be changed: it's used for internal tracking...";
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113
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114 return $This;
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115 }
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116
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117 # Add an atom...
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118 sub AddAtom {
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119 my($This, $Atom) = @_;
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120
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121 if (!defined $Atom) {
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122 carp "Warning: ${ClassName}->AddAtom: No atom added: Atom must be specified...";
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123 return undef;
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124 }
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125 if ($This->HasAtom($Atom)) {
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126 carp "Warning: ${ClassName}->AddAtom: No atom added: Atom already exists...";
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127 return undef;
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128 }
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129 return $This->_AddAtom($Atom);
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130 }
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131
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132 # Add an atom...
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133 sub _AddAtom {
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134 my($This, $Atom) = @_;
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135
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136 # Assign atom to this molecule...
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137 $Atom->_SetMolecule($This);
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138
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139 # Add it to the graph as a vertex...
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140 my($AtomID);
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141 $AtomID = $Atom->GetID();
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142 $This->AddVertex($AtomID);
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143 $This->SetVertexProperty('Atom', $Atom, $AtomID);
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144
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145 return $This;
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146 }
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147
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148 # Add atoms...
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149 sub AddAtoms {
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150 my($This, @Atoms) = @_;
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151
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152 if (!@Atoms) {
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153 carp "Warning: ${ClassName}->AddAtoms: No atoms added: Atoms list must be specified...";
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154 return undef;
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155 }
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156 my($Atom);
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157 for $Atom (@Atoms) {
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158 $This->AddAtom($Atom);
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159 }
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160 return $This;
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161 }
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162
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163 # Create an atom and add it to molecule...
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164 sub NewAtom {
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165 my($This, %NamesAndValues) = @_;
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166 my($Atom);
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167
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168 $Atom = new Atom(%NamesAndValues);
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169 $This->AddAtom($Atom);
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170
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171 return $Atom;
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172 }
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173
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174 # Delete an atom...
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175 sub DeleteAtom {
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176 my($This, $Atom) = @_;
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177
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178 if (!defined $Atom) {
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179 carp "Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom must be specified...";
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180 return undef;
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181 }
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182 # Does the atom exist in molecule?
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183 if (!$This->HasAtom($Atom)) {
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184 carp "Warning: ${ClassName}->DeleteAtom: No atom deleted: Atom doesn't exist...";
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185 return undef;
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186 }
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187 return $This->_DeleteAtom($Atom);
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188 }
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189
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190 # Delete atom...
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191 sub _DeleteAtom {
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192 my($This, $Atom) = @_;
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193
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194 my($AtomID);
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195 $AtomID = $Atom->GetID();
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196 $This->DeleteVertex($AtomID);
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197
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198 return $This;
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199 }
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200
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201 # Delete atoms...
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202 sub DeleteAtoms {
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203 my($This, @Atoms) = @_;
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204
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205 if (!@Atoms) {
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206 carp "Warning: ${ClassName}->DeleteAtoms: No atoms added: Atoms list must be specified...";
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207 return undef;
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208 }
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209 my($Atom);
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210 for $Atom (@Atoms) {
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211 $This->DeleteAtom($Atom);
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212 }
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213
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214 return $This;
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215 }
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216
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217 # Is this atom present?
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218 sub HasAtom {
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219 my($This, $Atom) = @_;
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220
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221 if (!defined $Atom) {
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222 return 0;
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223 }
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224 if (!$Atom->HasProperty('Molecule')) {
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225 # It's not in molecule...
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226 return 0;
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227 }
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228 my($AtomID);
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229 $AtomID = $Atom->GetID();
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230 if (!$This->HasVertex($AtomID)) {
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231 # It's not in molecule...
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232 return 0;
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233 }
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234 my($Molecule);
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235 $Molecule = $Atom->GetProperty('Molecule');
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236
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237 return ($This->HasVertex($AtomID) && $This->GetID() == $Molecule->GetID()) ? 1 : 0;
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238 }
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239
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240 # Return an array of atoms. In scalar context, it returns number of atoms. Additionally,
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241 # atoms array can be filtered by any user specifiable Atom class method...
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242 #
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243 sub GetAtoms {
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244 my($This, $AtomCheckMethodName, $NegateMethodResult) = @_;
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245 my(@Atoms, @AtomIDs);
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246
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247 @Atoms = (); @AtomIDs = ();
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248
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249 @AtomIDs = $This->GetVertices();
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250 if (!@AtomIDs) {
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251 return wantarray ? @Atoms : scalar @Atoms;
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252 }
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253
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254 @Atoms = $This->GetVerticesProperty('Atom', @AtomIDs);
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255
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256 if (!defined $AtomCheckMethodName) {
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257 return wantarray ? @Atoms : scalar @Atoms;
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258 }
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259 $NegateMethodResult = (defined($NegateMethodResult) && $NegateMethodResult) ? 1 : 0;
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260
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261 # Filter out atoms...
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262 my($Atom, $KeepAtom, @FilteredAtoms);
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263 @FilteredAtoms = ();
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264 for $Atom (@Atoms) {
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265 $KeepAtom = $NegateMethodResult ? (!$Atom->$AtomCheckMethodName()) : $Atom->$AtomCheckMethodName();
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266 if ($KeepAtom) {
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267 push @FilteredAtoms, $Atom;
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268 }
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269 }
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270 return wantarray ? @FilteredAtoms : scalar @FilteredAtoms;
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271 }
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272
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273 # Return an array of bonds. In scalar context, it returns number of bonds...
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274 sub GetBonds {
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275 my($This) = @_;
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276 my(@Bonds, @EdgesAtomsIDs);
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277
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278 @Bonds = (); @EdgesAtomsIDs = ();
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279
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280 @EdgesAtomsIDs = $This->GetEdges();
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281 if (@EdgesAtomsIDs) {
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282 @Bonds = $This->GetEdgesProperty('Bond', @EdgesAtomsIDs);
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283 }
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284 return wantarray ? @Bonds : scalar @Bonds;
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285 }
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286
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287 # Get number of atoms in molecule...
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288 sub GetNumOfAtoms {
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289 my($This) = @_;
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290 my($NumOfAtoms);
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291
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292 $NumOfAtoms = $This->GetAtoms();
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293
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294 return $NumOfAtoms;
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295 }
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296
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297 # Get number of bonds in molecule...
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298 sub GetNumOfBonds {
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299 my($This) = @_;
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300 my($NumOfBonds);
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301
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302 $NumOfBonds = $This->GetBonds();
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303
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304 return $NumOfBonds;
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305 }
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306
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307 # Get number of heavy atoms in molecule...
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308 sub GetNumOfHeavyAtoms {
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309 my($This) = @_;
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310
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311 return $This->GetNumOfNonHydrogenAtoms();
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312 }
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313
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314 # Get number of non-hydrogen atoms in molecule...
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315 sub GetNumOfNonHydrogenAtoms {
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316 my($This) = @_;
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317 my($NumOfNonHydrogenAtoms, $Atom, @Atoms);
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318
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319 @Atoms = $This->GetAtoms();
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320 $NumOfNonHydrogenAtoms = 0;
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321 for $Atom (@Atoms) {
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322 if (!$Atom->IsHydrogen()) {
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323 $NumOfNonHydrogenAtoms++;
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324 }
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325 }
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326 return $NumOfNonHydrogenAtoms;
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327 }
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328
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329 # Get number of hydrogen atoms in molecule...
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330 sub GetNumOfHydrogenAtoms {
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331 my($This) = @_;
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332 my($NumOfHydrogenAtoms, $Atom, @Atoms);
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333
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334 @Atoms = $This->GetAtoms();
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335 $NumOfHydrogenAtoms = 0;
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336 for $Atom (@Atoms) {
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337 if ($Atom->IsHydrogen()) {
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338 $NumOfHydrogenAtoms++;
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339 }
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340 }
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341 return $NumOfHydrogenAtoms;
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342 }
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343
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344 # Get number of missing hydrogen atoms in molecule...
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345 sub GetNumOfMissingHydrogenAtoms {
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346 my($This) = @_;
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347 my($NumOfMissingHydrogenAtoms, $Atom, @Atoms);
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348
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349 @Atoms = $This->GetAtoms();
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350 $NumOfMissingHydrogenAtoms = 0;
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351 for $Atom (@Atoms) {
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352 if (!$Atom->IsHydrogen()) {
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353 $NumOfMissingHydrogenAtoms += $Atom->GetNumOfMissingHydrogens();
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354 }
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355 }
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356 return $NumOfMissingHydrogenAtoms;
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357 }
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358
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359 # Add bond...
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360 sub AddBond {
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361 my($This, $Bond) = @_;
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362 my($Atom1, $Atom2);
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363
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364 ($Atom1, $Atom2) = $Bond->GetAtoms();
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365 if (!(defined($Atom1) && defined($Atom2))) {
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366 carp "Warning: ${ClassName}->AddBond: No bond added: Both atoms must be specified...";
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367 return undef;
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368 }
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369 if (!($This->HasAtom($Atom1) && $This->HasAtom($Atom2))) {
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370 carp "Warning: ${ClassName}->AddBond: No bond added: Both atoms must be present...";
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371 return undef;
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372 }
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373 if ($This->HasBond($Bond)) {
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374 carp "Warning: ${ClassName}->AddBond: No bond added: Bond already exists...";
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375 return undef;
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376 }
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377 return $This->_AddBond($Bond);
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378 }
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379
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380 # Add bond...
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381 sub _AddBond {
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382 my($This, $Bond) = @_;
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383
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384 # Assign bond to this molecule...
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385 $Bond->_SetMolecule($This);
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386
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387 # Add it to the graph as an edge...
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388 my($Atom1, $Atom2, $AtomID1, $AtomID2);
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389 ($Atom1, $Atom2) = $Bond->GetAtoms();
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390 $AtomID1 = $Atom1->GetID(); $AtomID2 = $Atom2->GetID();
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391 $This->AddEdge($AtomID1, $AtomID2);
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392 $This->SetEdgeProperty('Bond', $Bond, $AtomID1, $AtomID2);
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393
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394 return $This;
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395 }
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396
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397 # Add Bonds...
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398 sub AddBonds {
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399 my($This, @Bonds) = @_;
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400
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401 if (!@Bonds) {
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402 carp "Warning: ${ClassName}->AddBonds: No bonds added: Bonds list must be specified...";
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403 return undef;
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404 }
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405 my($Bond);
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406 for $Bond (@Bonds) {
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407 $This->AddBond($Bond);
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408 }
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409 return $This;
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410 }
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411
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412 # Create a bond and add it to molecule...
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413 sub NewBond {
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414 my($This, %NamesAndValues) = @_;
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415 my($Bond);
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416
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417 $Bond = new Bond(%NamesAndValues);
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418 $This->AddBond($Bond);
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419
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420 return $Bond;
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421 }
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422
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423 # Delete a bond...
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424 sub DeleteBond {
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425 my($This, $Bond) = @_;
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426
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427 if (!defined $Bond) {
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428 carp "Warning: ${ClassName}->DeleteBond: No bond deleted: Bond must be specified...";
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429 return undef;
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430 }
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|
431 # Does the bond exist in molecule?
|
|
|
432 if (!$This->HasBond($Bond)) {
|
|
|
433 carp "Warning: ${ClassName}->DeleteBond: No bond deleted: Bond doesn't exist...";
|
|
|
434 return undef;
|
|
|
435 }
|
|
|
436 return $This->_DeleteBond($Bond);
|
|
|
437 }
|
|
|
438
|
|
|
439 # Delete bond...
|
|
|
440 sub _DeleteBond {
|
|
|
441 my($This, $Bond) = @_;
|
|
|
442
|
|
|
443 my($Atom1, $Atom2, $AtomID1, $AtomID2);
|
|
|
444 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
445 $AtomID1 = $Atom1->GetID(); $AtomID2 = $Atom2->GetID();
|
|
|
446 $This->DeleteEdge($AtomID1, $AtomID2);
|
|
|
447
|
|
|
448 return $This;
|
|
|
449 }
|
|
|
450
|
|
|
451 # Delete bonds...
|
|
|
452 sub DeleteBonds {
|
|
|
453 my($This, @Bonds) = @_;
|
|
|
454
|
|
|
455 if (!@Bonds) {
|
|
|
456 carp "Warning: ${ClassName}->DeleteBonds: No bonds added: Bonds list must be specified...";
|
|
|
457 return undef;
|
|
|
458 }
|
|
|
459 my($Bond);
|
|
|
460 for $Bond (@Bonds) {
|
|
|
461 $This->DeleteBond($Bond);
|
|
|
462 }
|
|
|
463
|
|
|
464 return $This;
|
|
|
465 }
|
|
|
466
|
|
|
467 # Has bond...
|
|
|
468 sub HasBond {
|
|
|
469 my($This, $Bond) = @_;
|
|
|
470 my($Atom1, $Atom2);
|
|
|
471
|
|
|
472 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
473 if (!($This->HasAtom($Atom1) && $This->HasAtom($Atom2))) {
|
|
|
474 return 0;
|
|
|
475 }
|
|
|
476 if (!$Bond->HasProperty('Molecule')) {
|
|
|
477 # It's not in molecule...
|
|
|
478 return 0;
|
|
|
479 }
|
|
|
480 my($AtomID1, $AtomID2, $Molecule);
|
|
|
481 $AtomID1 = $Atom1->GetID(); $AtomID2 = $Atom2->GetID();
|
|
|
482 $Molecule = $Bond->GetMolecule();
|
|
|
483
|
|
|
484 return ($This->HasEdge($AtomID1, $AtomID2) && $This->GetID() == $Molecule->GetID()) ? 1 : 0;
|
|
|
485 }
|
|
|
486
|
|
|
487 # Get atom neighbors...
|
|
|
488 sub _GetAtomNeighbors {
|
|
|
489 my($This, $Atom) = @_;
|
|
|
490
|
|
|
491 my($AtomID, @Atoms, @AtomIDs);
|
|
|
492
|
|
|
493 @Atoms = (); @AtomIDs = ();
|
|
|
494 $AtomID = $Atom->GetID();
|
|
|
495 @AtomIDs = $This->GetNeighbors($AtomID);
|
|
|
496 if (@AtomIDs) {
|
|
|
497 @Atoms = $This->GetVerticesProperty('Atom', @AtomIDs);
|
|
|
498 }
|
|
|
499 return wantarray ? @Atoms : scalar @Atoms;
|
|
|
500 }
|
|
|
501
|
|
|
502 # Get atom bonds...
|
|
|
503 sub _GetAtomBonds {
|
|
|
504 my($This, $Atom) = @_;
|
|
|
505 my($AtomID, @AtomIDs, @Bonds);
|
|
|
506
|
|
|
507 @Bonds = (); @AtomIDs = ();
|
|
|
508 $AtomID = $Atom->GetID();
|
|
|
509 @AtomIDs = $This->GetEdges($AtomID);
|
|
|
510 if (@AtomIDs) {
|
|
|
511 @Bonds = $This->GetEdgesProperty('Bond', @AtomIDs);
|
|
|
512 }
|
|
|
513 return wantarray ? @Bonds : scalar @Bonds;
|
|
|
514 }
|
|
|
515
|
|
|
516 # Get bond to specified atom...
|
|
|
517 sub _GetBondToAtom {
|
|
|
518 my($This, $Atom1, $Atom2) = @_;
|
|
|
519 my($AtomID1, $AtomID2);
|
|
|
520
|
|
|
521 $AtomID1 = $Atom1->GetID();
|
|
|
522 $AtomID2 = $Atom2->GetID();
|
|
|
523
|
|
|
524 return $This->GetEdgeProperty('Bond', $AtomID1, $AtomID2);
|
|
|
525 }
|
|
|
526
|
|
|
527 # Are two specified atoms bonded?
|
|
|
528 sub _IsBondedToAtom {
|
|
|
529 my($This, $Atom1, $Atom2) = @_;
|
|
|
530 my($AtomID1, $AtomID2);
|
|
|
531
|
|
|
532 $AtomID1 = $Atom1->GetID();
|
|
|
533 $AtomID2 = $Atom2->GetID();
|
|
|
534
|
|
|
535 return $This->HasEdgeProperty('Bond', $AtomID1, $AtomID2);
|
|
|
536 }
|
|
|
537
|
|
|
538 # Add hydrogens to each atoms in molecule and return total number of hydrogens added...
|
|
|
539 sub AddHydrogens {
|
|
|
540 my($This) = @_;
|
|
|
541
|
|
|
542 return $This->_AddHydrogens();
|
|
|
543 }
|
|
|
544
|
|
|
545 # Add hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens added...
|
|
|
546 sub AddPolarHydrogens {
|
|
|
547 my($This) = @_;
|
|
|
548 my($PolarHydrogensOnly) = 1;
|
|
|
549
|
|
|
550 return $This->_AddHydrogens($PolarHydrogensOnly);
|
|
|
551 }
|
|
|
552
|
|
|
553 # Add all the hydrogens or hydrogens for polar atoms only...
|
|
|
554 #
|
|
|
555 # Note:
|
|
|
556 # . The current release of MayaChemTools doesn't assign any hydrogen positions.
|
|
|
557 #
|
|
|
558 sub _AddHydrogens {
|
|
|
559 my($This, $PolarHydrogensOnly) = @_;
|
|
|
560 my($Atom, $NumOfHydrogensAdded, $HydrogenPositionsWarning, @Atoms);
|
|
|
561
|
|
|
562 if (! defined $PolarHydrogensOnly) {
|
|
|
563 $PolarHydrogensOnly = 0;
|
|
|
564 }
|
|
|
565
|
|
|
566 $NumOfHydrogensAdded = 0;
|
|
|
567 @Atoms = $This->GetAtoms();
|
|
|
568 $HydrogenPositionsWarning = 0;
|
|
|
569
|
|
|
570 ATOM: for $Atom (@Atoms) {
|
|
|
571 if ($PolarHydrogensOnly) {
|
|
|
572 if (!$Atom->IsPolarAtom()) {
|
|
|
573 next ATOM;
|
|
|
574 }
|
|
|
575 }
|
|
|
576 $NumOfHydrogensAdded += $Atom->AddHydrogens($HydrogenPositionsWarning);
|
|
|
577 }
|
|
|
578 return $NumOfHydrogensAdded;
|
|
|
579 }
|
|
|
580
|
|
|
581 # Delete all hydrogens atoms in molecule and return total number of hydrogens removed...
|
|
|
582 sub DeleteHydrogens {
|
|
|
583 my($This) = @_;
|
|
|
584
|
|
|
585 return $This->_DeleteHydrogens();
|
|
|
586 }
|
|
|
587
|
|
|
588 # Delete hydrogens to polar atoms (N, O, P, S) in molecule and return total number of hydrogens removed...
|
|
|
589 sub DeletePolarHydrogens {
|
|
|
590 my($This) = @_;
|
|
|
591 my($PolarHydrogensOnly) = 1;
|
|
|
592
|
|
|
593 return $This->_DeleteHydrogens($PolarHydrogensOnly);
|
|
|
594 }
|
|
|
595
|
|
|
596 # Delete all hydrogens atoms in molecule and return total number of hydrogens removed...
|
|
|
597 sub _DeleteHydrogens {
|
|
|
598 my($This, $PolarHydrogensOnly) = @_;
|
|
|
599 my($Atom, $NumOfHydrogensRemoved, @Atoms);
|
|
|
600
|
|
|
601 if (! defined $PolarHydrogensOnly) {
|
|
|
602 $PolarHydrogensOnly = 0;
|
|
|
603 }
|
|
|
604
|
|
|
605 $NumOfHydrogensRemoved = 0;
|
|
|
606 @Atoms = $This->GetAtoms();
|
|
|
607
|
|
|
608 ATOM: for $Atom (@Atoms) {
|
|
|
609 if ($PolarHydrogensOnly) {
|
|
|
610 if (!$Atom->IsPolarHydrogen()) {
|
|
|
611 next ATOM;
|
|
|
612 }
|
|
|
613 }
|
|
|
614 elsif (!$Atom->IsHydrogen()) {
|
|
|
615 next ATOM;
|
|
|
616 }
|
|
|
617 $This->_DeleteAtom($Atom);
|
|
|
618 $NumOfHydrogensRemoved++;
|
|
|
619 }
|
|
|
620 return $NumOfHydrogensRemoved;
|
|
|
621 }
|
|
|
622
|
|
|
623 # Get molecular weight by summing up atomic weights of all the atoms...
|
|
|
624 sub GetMolecularWeight {
|
|
|
625 my($This, $IncludeMissingHydrogens) = @_;
|
|
|
626 my($MolecularWeight, $AtomicWeight, @Atoms, $Atom);
|
|
|
627
|
|
|
628 $IncludeMissingHydrogens = defined($IncludeMissingHydrogens) ? $IncludeMissingHydrogens : 1;
|
|
|
629
|
|
|
630 $MolecularWeight = 0;
|
|
|
631 @Atoms = $This->GetAtoms();
|
|
|
632 for $Atom (@Atoms) {
|
|
|
633 $AtomicWeight = $Atom->GetAtomicWeight();
|
|
|
634 if (defined $AtomicWeight) {
|
|
|
635 $MolecularWeight += $AtomicWeight;
|
|
|
636 }
|
|
|
637 }
|
|
|
638
|
|
|
639 if (!$IncludeMissingHydrogens) {
|
|
|
640 return $MolecularWeight;
|
|
|
641 }
|
|
|
642
|
|
|
643 # Account for missing hydrogen atoms...
|
|
|
644 my($NumOfMissingHydrogenAtoms);
|
|
|
645
|
|
|
646 $NumOfMissingHydrogenAtoms = $This->GetNumOfMissingHydrogenAtoms();
|
|
|
647 if ($NumOfMissingHydrogenAtoms) {
|
|
|
648 $MolecularWeight += $NumOfMissingHydrogenAtoms * PeriodicTable::GetElementAtomicWeight('H');
|
|
|
649 }
|
|
|
650
|
|
|
651 return $MolecularWeight;
|
|
|
652 }
|
|
|
653
|
|
|
654 # Get exact mass by summing up exact masses of all the atoms...
|
|
|
655 sub GetExactMass {
|
|
|
656 my($This, $IncludeMissingHydrogens) = @_;
|
|
|
657 my($ExactMass, $AtomicMass, @Atoms, $Atom);
|
|
|
658
|
|
|
659 $IncludeMissingHydrogens = defined($IncludeMissingHydrogens) ? $IncludeMissingHydrogens : 1;
|
|
|
660
|
|
|
661 $ExactMass = 0;
|
|
|
662 @Atoms = $This->GetAtoms();
|
|
|
663 for $Atom (@Atoms) {
|
|
|
664 $AtomicMass = $Atom->GetExactMass();
|
|
|
665 if (defined $AtomicMass) {
|
|
|
666 $ExactMass += $AtomicMass;
|
|
|
667 }
|
|
|
668 }
|
|
|
669
|
|
|
670 if (!$IncludeMissingHydrogens) {
|
|
|
671 return $ExactMass;
|
|
|
672 }
|
|
|
673
|
|
|
674 # Account for missing hydrogen atoms...
|
|
|
675 my($NumOfMissingHydrogenAtoms);
|
|
|
676
|
|
|
677 $NumOfMissingHydrogenAtoms = $This->GetNumOfMissingHydrogenAtoms();
|
|
|
678 if ($NumOfMissingHydrogenAtoms) {
|
|
|
679 $ExactMass += $NumOfMissingHydrogenAtoms * PeriodicTable::GetElementMostAbundantNaturalIsotopeMass('H');
|
|
|
680 }
|
|
|
681
|
|
|
682 return $ExactMass;
|
|
|
683 }
|
|
|
684
|
|
|
685 # Get net formal charge on the molecule using one of the following two methods:
|
|
|
686 # . Using explicitly set FormalCharge property
|
|
|
687 # . Adding up formal charge on each atom in the molecule
|
|
|
688 #
|
|
|
689 # Caveats:
|
|
|
690 # . FormalCharge is different from Charge property of the molecule which corresponds to
|
|
|
691 # sum of partial atomic charges explicitly set for each atom using a specific methodology.
|
|
|
692 #
|
|
|
693 sub GetFormalCharge {
|
|
|
694 my($This) = @_;
|
|
|
695
|
|
|
696 # Is FormalCharge property explicitly set?
|
|
|
697 if ($This->HasProperty('FormalCharge')) {
|
|
|
698 return $This->GetProperty('FormalCharge');
|
|
|
699 }
|
|
|
700 my($FormalCharge, $AtomicFormalCharge, @Atoms, $Atom);
|
|
|
701
|
|
|
702 $FormalCharge = 0;
|
|
|
703 @Atoms = $This->GetAtoms();
|
|
|
704 for $Atom (@Atoms) {
|
|
|
705 $AtomicFormalCharge = $Atom->GetFormalCharge();
|
|
|
706 if (defined $AtomicFormalCharge) {
|
|
|
707 $FormalCharge += $AtomicFormalCharge;
|
|
|
708 }
|
|
|
709 }
|
|
|
710 return $FormalCharge;
|
|
|
711 }
|
|
|
712
|
|
|
713 # Get net charge on the molecule using one of the following two methods:
|
|
|
714 # . Using explicitly set Charge property
|
|
|
715 # . Adding up charge on each atom in the molecule
|
|
|
716 #
|
|
|
717 # Caveats:
|
|
|
718 # . FormalCharge is different from Charge property of the molecule which corresponds to
|
|
|
719 # sum of partial atomic charges explicitly set for each atom using a specific methodology.
|
|
|
720 #
|
|
|
721 sub GetCharge {
|
|
|
722 my($This) = @_;
|
|
|
723
|
|
|
724 # Is Charge property explicitly set?
|
|
|
725 if ($This->HasProperty('Charge')) {
|
|
|
726 return $This->GetProperty('Charge');
|
|
|
727 }
|
|
|
728 my($Charge, $AtomicCharge, @Atoms, $Atom);
|
|
|
729
|
|
|
730 $Charge = 0;
|
|
|
731 @Atoms = $This->GetAtoms();
|
|
|
732 for $Atom (@Atoms) {
|
|
|
733 $AtomicCharge = $Atom->GetCharge();
|
|
|
734 if (defined $AtomicCharge) {
|
|
|
735 $Charge += $AtomicCharge;
|
|
|
736 }
|
|
|
737 }
|
|
|
738 return $Charge;
|
|
|
739 }
|
|
|
740
|
|
|
741 # Get total SpinMultiplicity for the molecule using one of the following two methods:
|
|
|
742 # . Using explicitly set SpinMultiplicity property
|
|
|
743 # . Adding up SpinMultiplicity on each atom in the molecule
|
|
|
744 #
|
|
|
745 #
|
|
|
746 sub GetSpinMultiplicity {
|
|
|
747 my($This) = @_;
|
|
|
748
|
|
|
749 # Is SpinMultiplicity property explicitly set?
|
|
|
750 if ($This->HasProperty('SpinMultiplicity')) {
|
|
|
751 return $This->GetProperty('SpinMultiplicity');
|
|
|
752 }
|
|
|
753 my($AtomicSpinMultiplicity, $SpinMultiplicity, @Atoms, $Atom);
|
|
|
754
|
|
|
755 $SpinMultiplicity = 0;
|
|
|
756 @Atoms = $This->GetAtoms();
|
|
|
757 for $Atom (@Atoms) {
|
|
|
758 $AtomicSpinMultiplicity = $Atom->GetSpinMultiplicity();
|
|
|
759 if (defined $AtomicSpinMultiplicity) {
|
|
|
760 $SpinMultiplicity += $AtomicSpinMultiplicity;
|
|
|
761 }
|
|
|
762 }
|
|
|
763 return $SpinMultiplicity;
|
|
|
764 }
|
|
|
765
|
|
|
766 # Get total FreeRadicalElectrons for the molecule using one of the following two methods:
|
|
|
767 # . Using explicitly set FreeRadicalElectrons property
|
|
|
768 # . Adding up FreeRadicalElectrons on each atom in the molecule
|
|
|
769 #
|
|
|
770 #
|
|
|
771 sub GetFreeRadicalElectrons {
|
|
|
772 my($This) = @_;
|
|
|
773
|
|
|
774 # Is FreeRadicalElectrons property explicitly set?
|
|
|
775 if ($This->HasProperty('FreeRadicalElectrons')) {
|
|
|
776 return $This->GetProperty('FreeRadicalElectrons');
|
|
|
777 }
|
|
|
778 my($AtomicFreeRadicalElectrons, $FreeRadicalElectrons, @Atoms, $Atom);
|
|
|
779
|
|
|
780 $FreeRadicalElectrons = 0;
|
|
|
781 @Atoms = $This->GetAtoms();
|
|
|
782 for $Atom (@Atoms) {
|
|
|
783 $AtomicFreeRadicalElectrons = $Atom->GetFreeRadicalElectrons();
|
|
|
784 if (defined $AtomicFreeRadicalElectrons) {
|
|
|
785 $FreeRadicalElectrons += $AtomicFreeRadicalElectrons;
|
|
|
786 }
|
|
|
787 }
|
|
|
788 return $FreeRadicalElectrons;
|
|
|
789 }
|
|
|
790
|
|
|
791 # Set valence model...
|
|
|
792 #
|
|
|
793 sub SetValenceModel {
|
|
|
794 my($This, $ValenceModel) = @_;
|
|
|
795
|
|
|
796 if ($ValenceModel !~ /^(MDLValenceModel|DaylightValenceModel|InternalValenceModel|MayaChemToolsValenceModel)$/i) {
|
|
|
797 carp "Warning: ${ClassName}->SetValenceModel: The current release of MayaChemTools doesn't support the specified valence model $ValenceModel. Supported valence models: MDLValenceModel, DaylightValenceModel, InternalValenceModel or MayaChemToolsValenceModel. Using internal valence model...";
|
|
|
798 $ValenceModel = 'InternalValenceModel';
|
|
|
799 }
|
|
|
800
|
|
|
801 $This->SetProperty('ValenceModel', $ValenceModel);
|
|
|
802
|
|
|
803 return $This;
|
|
|
804 }
|
|
|
805
|
|
|
806 # Get valence model...
|
|
|
807 #
|
|
|
808 sub GetValenceModel {
|
|
|
809 my($This) = @_;
|
|
|
810
|
|
|
811 # Is ValenceModel property explicitly set?
|
|
|
812 if ($This->HasProperty('ValenceModel')) {
|
|
|
813 return $This->GetProperty('ValenceModel');
|
|
|
814 }
|
|
|
815
|
|
|
816 # Used internal valence model as default model...
|
|
|
817 return 'InternalValenceModel';
|
|
|
818 }
|
|
|
819
|
|
|
820 # Get molecular formula by collecting information about all atoms in the molecule and
|
|
|
821 # composing the formula using Hills ordering system:
|
|
|
822 # . C shows up first and H follows assuming C is present
|
|
|
823 # . All other standard elements are sorted alphanumerically
|
|
|
824 # . All other non-stanard atom symbols are also sorted alphanumerically and follow standard elements
|
|
|
825 #
|
|
|
826 # Caveats:
|
|
|
827 # . By default, missing hydrogens and nonelements are also included
|
|
|
828 # . Elements for disconnected fragments are combined into the same formula
|
|
|
829 #
|
|
|
830 # Handle formula generation for disconnected structures. e.g: molecule generated by
|
|
|
831 # [Na+].[O-]c1ccccc1
|
|
|
832 #
|
|
|
833 sub GetMolecularFormula {
|
|
|
834 my($This, $IncludeMissingHydrogens, $IncludeNonElements) = @_;
|
|
|
835 my($MolecularFormula, $AtomSymbol, $ElementsCountRef, $NonElementsCountRef);
|
|
|
836
|
|
|
837 $IncludeMissingHydrogens = defined($IncludeMissingHydrogens) ? $IncludeMissingHydrogens : 1;
|
|
|
838 $IncludeNonElements = defined($IncludeNonElements) ? $IncludeNonElements : 1;
|
|
|
839
|
|
|
840 # Get elements count and setup molecular formula...
|
|
|
841 ($ElementsCountRef, $NonElementsCountRef) = $This->GetElementsAndNonElements($IncludeMissingHydrogens);
|
|
|
842 $MolecularFormula = '';
|
|
|
843
|
|
|
844 # Count C and H first...
|
|
|
845 if (exists $ElementsCountRef->{C} ) {
|
|
|
846 $MolecularFormula .= 'C' . ($ElementsCountRef->{C} > 1 ? $ElementsCountRef->{C} : '');
|
|
|
847 delete $ElementsCountRef->{C};
|
|
|
848
|
|
|
849 if (exists $ElementsCountRef->{H} ) {
|
|
|
850 $MolecularFormula .= 'H' . ($ElementsCountRef->{H} > 1 ? $ElementsCountRef->{H} : '');
|
|
|
851 delete $ElementsCountRef->{H};
|
|
|
852 }
|
|
|
853 }
|
|
|
854
|
|
|
855 # Sort elements...
|
|
|
856 for $AtomSymbol (sort {$a cmp $b} keys %{$ElementsCountRef}) {
|
|
|
857 $MolecularFormula .= $AtomSymbol . ($ElementsCountRef->{$AtomSymbol} > 1 ? $ElementsCountRef->{$AtomSymbol} : '');
|
|
|
858 }
|
|
|
859
|
|
|
860 # Sort non-elements...
|
|
|
861 if ($IncludeNonElements) {
|
|
|
862 for $AtomSymbol (sort {$a cmp $b} keys %{$NonElementsCountRef}) {
|
|
|
863 $MolecularFormula .= $AtomSymbol . ($NonElementsCountRef->{$AtomSymbol} > 1 ? $NonElementsCountRef->{$AtomSymbol} : '');
|
|
|
864 }
|
|
|
865 }
|
|
|
866
|
|
|
867 # Check formal charge...
|
|
|
868 my($FormalCharge);
|
|
|
869 $FormalCharge = $This->GetFormalCharge();
|
|
|
870 if ($FormalCharge) {
|
|
|
871 # Setup formal charge string...
|
|
|
872 my($FormalChargeString);
|
|
|
873 if ($FormalCharge == 1 ) {
|
|
|
874 $FormalChargeString = "+";
|
|
|
875 }
|
|
|
876 elsif ($FormalCharge == -1 ) {
|
|
|
877 $FormalChargeString = "-";
|
|
|
878 }
|
|
|
879 else {
|
|
|
880 $FormalChargeString = ($FormalCharge > 0) ? ("+" . abs($FormalCharge)) : ("-" . abs($FormalCharge));
|
|
|
881 }
|
|
|
882 $MolecularFormula = "${MolecularFormula}${FormalChargeString}";
|
|
|
883 }
|
|
|
884
|
|
|
885 return $MolecularFormula;
|
|
|
886 }
|
|
|
887
|
|
|
888 # Count elements and non-elements in molecule and return references to hashes
|
|
|
889 # containing count of elements and non-elements respectively. By default, missing
|
|
|
890 # hydrogens are not added to the element hash.
|
|
|
891 #
|
|
|
892 #
|
|
|
893 sub GetElementsAndNonElements {
|
|
|
894 my($This, $IncludeMissingHydrogens) = @_;
|
|
|
895 my($Atom, $AtomicNumber, $AtomSymbol, $NumOfMissingHydrogens, @Atoms, %ElementsCount, %NonElementsCount);
|
|
|
896
|
|
|
897 $IncludeMissingHydrogens = defined($IncludeMissingHydrogens) ? $IncludeMissingHydrogens : 0;
|
|
|
898
|
|
|
899 %ElementsCount = (); %NonElementsCount = ();
|
|
|
900 $NumOfMissingHydrogens = 0;
|
|
|
901
|
|
|
902 # Count elements and non elements...
|
|
|
903 @Atoms = $This->GetAtoms();
|
|
|
904 for $Atom (@Atoms) {
|
|
|
905 $AtomicNumber = $Atom->GetAtomicNumber();
|
|
|
906 $AtomSymbol = $Atom->GetAtomSymbol();
|
|
|
907 if ($AtomicNumber) {
|
|
|
908 if (exists $ElementsCount{$AtomSymbol}) {
|
|
|
909 $ElementsCount{$AtomSymbol} += 1;
|
|
|
910 }
|
|
|
911 else {
|
|
|
912 $ElementsCount{$AtomSymbol} = 1;
|
|
|
913 }
|
|
|
914 if ($IncludeMissingHydrogens) {
|
|
|
915 $NumOfMissingHydrogens += $Atom->GetNumOfMissingHydrogens();
|
|
|
916 }
|
|
|
917 }
|
|
|
918 else {
|
|
|
919 if (exists $NonElementsCount{$AtomSymbol}) {
|
|
|
920 $NonElementsCount{$AtomSymbol} += 1;
|
|
|
921 }
|
|
|
922 else {
|
|
|
923 $NonElementsCount{$AtomSymbol} = 1;
|
|
|
924 }
|
|
|
925 }
|
|
|
926 }
|
|
|
927 if ($IncludeMissingHydrogens && $NumOfMissingHydrogens) {
|
|
|
928 $AtomSymbol = 'H';
|
|
|
929 if (exists $ElementsCount{$AtomSymbol}) {
|
|
|
930 $ElementsCount{$AtomSymbol} += $NumOfMissingHydrogens;
|
|
|
931 }
|
|
|
932 else {
|
|
|
933 $ElementsCount{$AtomSymbol} = $NumOfMissingHydrogens;
|
|
|
934 }
|
|
|
935 }
|
|
|
936
|
|
|
937 return (\%ElementsCount, \%NonElementsCount);
|
|
|
938 }
|
|
|
939
|
|
|
940 # Get number of element and non-elements in molecule. By default, missing
|
|
|
941 # hydrogens are not added to element count.
|
|
|
942 #
|
|
|
943 sub GetNumOfElementsAndNonElements {
|
|
|
944 my($This, $IncludeMissingHydrogens) = @_;
|
|
|
945 my($ElementCount, $NonElementCount, $Atom);
|
|
|
946
|
|
|
947 $IncludeMissingHydrogens = defined($IncludeMissingHydrogens) ? $IncludeMissingHydrogens : 0;
|
|
|
948
|
|
|
949 ($ElementCount, $NonElementCount) = (0, 0);
|
|
|
950
|
|
|
951 ATOM: for $Atom ($This->GetAtoms()) {
|
|
|
952 if (!$Atom->GetAtomicNumber()) {
|
|
|
953 $NonElementCount++;
|
|
|
954 next ATOM;
|
|
|
955 }
|
|
|
956 # Process element...
|
|
|
957 $ElementCount++;
|
|
|
958 if ($IncludeMissingHydrogens) {
|
|
|
959 if (!$Atom->IsHydrogen()) {
|
|
|
960 $ElementCount += $Atom->GetNumOfMissingHydrogens();
|
|
|
961 }
|
|
|
962 }
|
|
|
963 }
|
|
|
964
|
|
|
965 return ($ElementCount, $NonElementCount);
|
|
|
966 }
|
|
|
967
|
|
|
968 # Calculate elemental composition and return reference to arrays
|
|
|
969 # containing elements and their percent composition.
|
|
|
970 #
|
|
|
971 # Caveats:
|
|
|
972 # . By default, missing hydrogens are included
|
|
|
973 # . Non elemnents are ignored
|
|
|
974 # . Mass number are ignored
|
|
|
975 #
|
|
|
976 sub GetElementalComposition {
|
|
|
977 my($This, $IncludeMissingHydrogens) = @_;
|
|
|
978 my($MolecularFormula, $IncludeNonElements, $ElementsCountRef, $NonElementsCountRef, $ElementsRef, $ElementsCompositionRef);
|
|
|
979
|
|
|
980 $IncludeMissingHydrogens = defined($IncludeMissingHydrogens) ? $IncludeMissingHydrogens : 1;
|
|
|
981
|
|
|
982 $IncludeNonElements = 0;
|
|
|
983 ($ElementsCountRef, $NonElementsCountRef) = $This->GetElementsAndNonElements($IncludeMissingHydrogens);
|
|
|
984
|
|
|
985 $MolecularFormula = $This->GetMolecularFormula($IncludeMissingHydrogens, $IncludeNonElements);
|
|
|
986
|
|
|
987 ($ElementsRef, $ElementsCompositionRef) = MolecularFormula::CalculateElementalComposition($MolecularFormula);
|
|
|
988
|
|
|
989 return ($ElementsRef, $ElementsCompositionRef);
|
|
|
990 }
|
|
|
991
|
|
|
992 # Using refernece to element and its composition arrays, format composition information
|
|
|
993 # as: Element: Composition;...
|
|
|
994 #
|
|
|
995 sub FormatElementalCompositionInformation {
|
|
|
996 my($FirstParameter, $SecondParameter, $ThirdParameter, $FourthParameter) = @_;
|
|
|
997 my($This, $ElementsRef, $ElementCompositionRef, $Precision);
|
|
|
998
|
|
|
999 if (_IsMolecule($FirstParameter)) {
|
|
|
1000 ($This, $ElementsRef, $ElementCompositionRef, $Precision) = ($FirstParameter, $SecondParameter, $ThirdParameter, $FourthParameter);
|
|
|
1001 }
|
|
|
1002 else {
|
|
|
1003 ($ElementsRef, $ElementCompositionRef, $Precision) = ($FirstParameter, $SecondParameter, $ThirdParameter);
|
|
|
1004 }
|
|
|
1005 my($FormattedInfo) = '';
|
|
|
1006
|
|
|
1007 if (!(defined($ElementsRef) && @{$ElementsRef})) {
|
|
|
1008 carp "Warning: ${ClassName}->FormatElementalCompositionInformation: Elements list is not defined or empty...";
|
|
|
1009 return undef;
|
|
|
1010 }
|
|
|
1011 if (!(defined($ElementCompositionRef) && @{$ElementCompositionRef})) {
|
|
|
1012 carp "Warning: ${ClassName}->FormatElementalCompositionInformation: Elements composition list is not defined or empty...";
|
|
|
1013 return undef;
|
|
|
1014 }
|
|
|
1015
|
|
|
1016 if (!defined $Precision) {
|
|
|
1017 $Precision = 2;
|
|
|
1018 }
|
|
|
1019
|
|
|
1020 $FormattedInfo = MolecularFormula::FormatCompositionInfomation($ElementsRef, $ElementCompositionRef, $Precision);
|
|
|
1021
|
|
|
1022 return $FormattedInfo;
|
|
|
1023 }
|
|
|
1024
|
|
|
1025 # Copy molecule and its associated data using Storable::dclone and update:
|
|
|
1026 #
|
|
|
1027 # o Atom references corresponding atoms and bonds objects
|
|
|
1028 # o Bond object references
|
|
|
1029 #
|
|
|
1030 # Object IDs for Atoms and Bonds don't get changed. So there is no need to clear
|
|
|
1031 # up any exisiting ring data attached to molecule via graph as vertex IDs.
|
|
|
1032 #
|
|
|
1033 sub Copy {
|
|
|
1034 my($This) = @_;
|
|
|
1035 my($NewMolecule, $Atom, $NewAtom, $AtomID, @Atoms, @AtomIDs, %AtomsIDsToNewAtoms);
|
|
|
1036
|
|
|
1037 $NewMolecule = Storable::dclone($This);
|
|
|
1038
|
|
|
1039 # Update atom references stored as vertex property...
|
|
|
1040
|
|
|
1041 @Atoms = (); @AtomIDs = ();
|
|
|
1042 %AtomsIDsToNewAtoms = ();
|
|
|
1043
|
|
|
1044 @AtomIDs = $This->GetVertices();
|
|
|
1045 if (@AtomIDs) {
|
|
|
1046 @Atoms = $This->GetVerticesProperty('Atom', @AtomIDs);
|
|
|
1047 }
|
|
|
1048
|
|
|
1049 for $Atom (@Atoms) {
|
|
|
1050 $AtomID = $Atom->GetID();
|
|
|
1051
|
|
|
1052 # Setup a reference to copied atom object...
|
|
|
1053 $NewAtom = $Atom->Copy();
|
|
|
1054 $AtomsIDsToNewAtoms{$AtomID} = $NewAtom;
|
|
|
1055
|
|
|
1056 # Update atom reference to new atom object...
|
|
|
1057 $NewMolecule->UpdateVertexProperty('Atom', $NewAtom, $AtomID);
|
|
|
1058 }
|
|
|
1059
|
|
|
1060 # Update bond object and bond atom references stored as edge property...
|
|
|
1061 my($Index, $AtomID1, $AtomID2, $Bond, $NewBond, $NewAtom1, $NewAtom2, @EdgesAtomsIDs);
|
|
|
1062 @EdgesAtomsIDs = ();
|
|
|
1063 @EdgesAtomsIDs = $This->GetEdges();
|
|
|
1064 for ($Index = 0; $Index < $#EdgesAtomsIDs; $Index += 2) {
|
|
|
1065 $AtomID1 = $EdgesAtomsIDs[$Index]; $AtomID2 = $EdgesAtomsIDs[$Index + 1];
|
|
|
1066
|
|
|
1067 # Get reference to bond object...
|
|
|
1068 $Bond = $This->GetEdgeProperty('Bond', $AtomID1, $AtomID2);
|
|
|
1069
|
|
|
1070 # Make a new bond object and update its atom references...
|
|
|
1071 $NewBond = $Bond->Copy();
|
|
|
1072 $NewAtom1 = $AtomsIDsToNewAtoms{$AtomID1};
|
|
|
1073 $NewAtom2 = $AtomsIDsToNewAtoms{$AtomID2};
|
|
|
1074 $NewBond->SetAtoms($NewAtom1, $NewAtom2);
|
|
|
1075
|
|
|
1076 # Update bond object reference in the new molecule...
|
|
|
1077 $NewMolecule->UpdateEdgeProperty('Bond', $NewBond, $AtomID1, $AtomID2);
|
|
|
1078 }
|
|
|
1079
|
|
|
1080 return $NewMolecule;
|
|
|
1081 }
|
|
|
1082
|
|
|
1083 # Get number of connected components...
|
|
|
1084 #
|
|
|
1085 sub GetNumOfConnectedComponents {
|
|
|
1086 my($This) = @_;
|
|
|
1087 my($NumOfComponents);
|
|
|
1088
|
|
|
1089 $NumOfComponents = $This->GetConnectedComponentsVertices();
|
|
|
1090
|
|
|
1091 return $NumOfComponents;
|
|
|
1092 }
|
|
|
1093
|
|
|
1094 # Return a reference to an array containing molecules corresponding
|
|
|
1095 # to connected components sorted in decreasing order of component size...
|
|
|
1096 #
|
|
|
1097 sub GetConnectedComponents {
|
|
|
1098 my($This) = @_;
|
|
|
1099 my($Index, @ComponentMolecules, @ConnectedComponents);
|
|
|
1100
|
|
|
1101 @ConnectedComponents = ();
|
|
|
1102 @ConnectedComponents = $This->GetConnectedComponentsVertices();
|
|
|
1103 @ComponentMolecules = ();
|
|
|
1104
|
|
|
1105 for $Index (0 .. $#ConnectedComponents) {
|
|
|
1106 push @ComponentMolecules, $This->_GetConnectedComponent(\@ConnectedComponents, $Index);
|
|
|
1107 }
|
|
|
1108 return @ComponentMolecules;
|
|
|
1109 }
|
|
|
1110
|
|
|
1111 # Return a reference to largest connected component as a molecule object...
|
|
|
1112 #
|
|
|
1113 sub GetLargestConnectedComponent {
|
|
|
1114 my($This) = @_;
|
|
|
1115 my($LargestComponentIndex, @ConnectedComponents);
|
|
|
1116
|
|
|
1117 $LargestComponentIndex = 0;
|
|
|
1118 @ConnectedComponents = ();
|
|
|
1119 @ConnectedComponents = $This->GetConnectedComponentsVertices();
|
|
|
1120
|
|
|
1121 return $This->_GetConnectedComponent(\@ConnectedComponents, $LargestComponentIndex);
|
|
|
1122 }
|
|
|
1123
|
|
|
1124 # Return connected component as a molecule...
|
|
|
1125 #
|
|
|
1126 sub _GetConnectedComponent {
|
|
|
1127 my($This, $ConnectedComponentsRef, $ComponentIndex) = @_;
|
|
|
1128 my($ComponentMolecule);
|
|
|
1129
|
|
|
1130 # Copy existing molecule...
|
|
|
1131 $ComponentMolecule = $This->Copy();
|
|
|
1132
|
|
|
1133 # Delete all atoms besides the ones in specified component...
|
|
|
1134 $ComponentMolecule->_DeleteConnectedComponents($ConnectedComponentsRef, $ComponentIndex);
|
|
|
1135
|
|
|
1136 # Clear any deteced rings...
|
|
|
1137 if ($ComponentMolecule->HasRings()) {
|
|
|
1138 $ComponentMolecule->ClearRings();
|
|
|
1139 }
|
|
|
1140 return $ComponentMolecule;
|
|
|
1141 }
|
|
|
1142
|
|
|
1143 # Delete atoms corresponding to all connected components except the one specified...
|
|
|
1144 #
|
|
|
1145 sub _DeleteConnectedComponents {
|
|
|
1146 my($This, $ConnectedComponentsRef, $KeepComponentIndex) = @_;
|
|
|
1147 my($Index, $AtomID);
|
|
|
1148
|
|
|
1149 INDEX: for $Index (0 .. $#{$ConnectedComponentsRef}) {
|
|
|
1150 if ($Index == $KeepComponentIndex) {
|
|
|
1151 next INDEX;
|
|
|
1152 }
|
|
|
1153 for $AtomID (@{$ConnectedComponentsRef->[$Index]}) {
|
|
|
1154 $This->DeleteVertex($AtomID);
|
|
|
1155 }
|
|
|
1156 }
|
|
|
1157 return $This;
|
|
|
1158 }
|
|
|
1159
|
|
|
1160 # Return an array containing references to atom arrays corresponding to atoms of
|
|
|
1161 # connected components sorted in order of their decreasing size...
|
|
|
1162 #
|
|
|
1163 sub GetConnectedComponentsAtoms {
|
|
|
1164 my($This) = @_;
|
|
|
1165 my($Index, @ComponentsAtoms, @ConnectedComponents);
|
|
|
1166
|
|
|
1167 @ConnectedComponents = ();
|
|
|
1168 @ConnectedComponents = $This->GetConnectedComponentsVertices();
|
|
|
1169
|
|
|
1170 @ComponentsAtoms = ();
|
|
|
1171 for $Index (0 .. $#ConnectedComponents) {
|
|
|
1172 my(@ComponentAtoms);
|
|
|
1173
|
|
|
1174 @ComponentAtoms = ();
|
|
|
1175 @ComponentAtoms = $This->_GetConnectedComponentAtoms(\@ConnectedComponents, $Index);
|
|
|
1176 push @ComponentsAtoms, \@ComponentAtoms;
|
|
|
1177 }
|
|
|
1178 return @ComponentsAtoms;
|
|
|
1179 }
|
|
|
1180
|
|
|
1181 # Return an array containing atoms correspondig to largest connected component...
|
|
|
1182 #
|
|
|
1183 sub GetLargestConnectedComponentAtoms {
|
|
|
1184 my($This) = @_;
|
|
|
1185 my($LargestComponentIndex, @ConnectedComponents);
|
|
|
1186
|
|
|
1187 $LargestComponentIndex = 0;
|
|
|
1188 @ConnectedComponents = ();
|
|
|
1189 @ConnectedComponents = $This->GetConnectedComponentsVertices();
|
|
|
1190
|
|
|
1191 return $This->_GetConnectedComponentAtoms(\@ConnectedComponents, $LargestComponentIndex);
|
|
|
1192 }
|
|
|
1193
|
|
|
1194 # Return an array containing atoms corresponding to specified connected component...
|
|
|
1195 #
|
|
|
1196 sub _GetConnectedComponentAtoms {
|
|
|
1197 my($This, $ConnectedComponentsRef, $ComponentIndex) = @_;
|
|
|
1198 my($AtomID, @AtomIDs, @ComponentAtoms);
|
|
|
1199
|
|
|
1200 @ComponentAtoms = ();
|
|
|
1201 @AtomIDs = ();
|
|
|
1202
|
|
|
1203 for $AtomID (@{$ConnectedComponentsRef->[$ComponentIndex]}) {
|
|
|
1204 push @AtomIDs, $AtomID;
|
|
|
1205 }
|
|
|
1206 @ComponentAtoms = $This->_GetAtomsFromAtomIDs(@AtomIDs);
|
|
|
1207
|
|
|
1208 return @ComponentAtoms;
|
|
|
1209 }
|
|
|
1210
|
|
|
1211 # Except for the largest connected component, delete atoms corresponding to all other
|
|
|
1212 # connected components...
|
|
|
1213 #
|
|
|
1214 sub KeepLargestComponent {
|
|
|
1215 my($This) = @_;
|
|
|
1216 my($LargestComponentIndex, @ConnectedComponents);
|
|
|
1217
|
|
|
1218 @ConnectedComponents = ();
|
|
|
1219 @ConnectedComponents = $This->GetConnectedComponentsVertices();
|
|
|
1220 if (@ConnectedComponents == 1) {
|
|
|
1221 return $This;
|
|
|
1222 }
|
|
|
1223 $LargestComponentIndex = 0;
|
|
|
1224 $This->_DeleteConnectedComponents(\@ConnectedComponents, $LargestComponentIndex);
|
|
|
1225
|
|
|
1226 # Clear any deteced rings...
|
|
|
1227 if ($This->HasRings()) {
|
|
|
1228 $This->ClearRings();
|
|
|
1229 }
|
|
|
1230
|
|
|
1231 return $This;
|
|
|
1232 }
|
|
|
1233
|
|
|
1234 # Get an array of topologically sorted atoms starting from a specified atom or
|
|
|
1235 # an arbitrary atom in the molecule...
|
|
|
1236 #
|
|
|
1237 sub GetTopologicallySortedAtoms {
|
|
|
1238 my($This, $StartAtom) = @_;
|
|
|
1239 my(@SortedAtoms);
|
|
|
1240
|
|
|
1241 @SortedAtoms = ();
|
|
|
1242 if (defined($StartAtom) && !$This->HasAtom($StartAtom)) {
|
|
|
1243 carp "Warning: ${ClassName}->_GetTopologicallySortedAtoms: No atoms retrieved: Start atom doesn't exist...";
|
|
|
1244 return @SortedAtoms;
|
|
|
1245 }
|
|
|
1246 my($StartAtomID, @AtomIDs);
|
|
|
1247
|
|
|
1248 @AtomIDs = ();
|
|
|
1249 $StartAtomID = defined($StartAtom) ? $StartAtom->GetID() : undef;
|
|
|
1250
|
|
|
1251 @AtomIDs = $This->GetTopologicallySortedVertices($StartAtomID);
|
|
|
1252 @SortedAtoms = $This->_GetAtomsFromAtomIDs(@AtomIDs);
|
|
|
1253
|
|
|
1254 return @SortedAtoms;
|
|
|
1255 }
|
|
|
1256
|
|
|
1257 # Detect rings in molecule...
|
|
|
1258 #
|
|
|
1259 sub DetectRings {
|
|
|
1260 my($This) = @_;
|
|
|
1261
|
|
|
1262 # Use graph method to detect all cycles and associate 'em to graph as graph
|
|
|
1263 # and vertex properties...
|
|
|
1264 return $This->DetectCycles();
|
|
|
1265 }
|
|
|
1266
|
|
|
1267 # Clear rings in molecule...
|
|
|
1268 #
|
|
|
1269 sub ClearRings {
|
|
|
1270 my($This) = @_;
|
|
|
1271
|
|
|
1272 # Use graph method to clear all cycles...
|
|
|
1273 $This->ClearCycles();
|
|
|
1274
|
|
|
1275 return $This;
|
|
|
1276 }
|
|
|
1277
|
|
|
1278 # Setup rings type paths to use during all ring related methods. Possible values:
|
|
|
1279 # Independent or All. Default is to use Independent rings.
|
|
|
1280 #
|
|
|
1281 sub SetActiveRings {
|
|
|
1282 my($This, $RingsType) = @_;
|
|
|
1283
|
|
|
1284 if (!defined $This->SetActiveCyclicPaths($RingsType)) {
|
|
|
1285 return undef;
|
|
|
1286 }
|
|
|
1287 return $This;
|
|
|
1288 }
|
|
|
1289
|
|
|
1290 # Is it a supported aromaticity model?
|
|
|
1291 #
|
|
|
1292 sub IsSupportedAromaticityModel {
|
|
|
1293 my($FirstParameter, $SecondParameter) = @_;
|
|
|
1294 my($This, $AromaticityModel);
|
|
|
1295
|
|
|
1296 if (_IsMolecule($FirstParameter)) {
|
|
|
1297 ($This, $AromaticityModel) = ($FirstParameter, $SecondParameter);
|
|
|
1298 }
|
|
|
1299 else {
|
|
|
1300 ($This, $AromaticityModel) = (undef, $FirstParameter);
|
|
|
1301 }
|
|
|
1302
|
|
|
1303 return exists $CanonicalAromaticityModelNamesMap{lc($AromaticityModel)} ? 1 : 0;
|
|
|
1304 }
|
|
|
1305
|
|
|
1306 # Get a list of supported aromaticity model names...
|
|
|
1307 #
|
|
|
1308 sub GetSupportedAromaticityModels {
|
|
|
1309 return (sort values %CanonicalAromaticityModelNamesMap);
|
|
|
1310 }
|
|
|
1311
|
|
|
1312 # Set aromaticity model...
|
|
|
1313 #
|
|
|
1314 sub SetAromaticityModel {
|
|
|
1315 my($This, $AromaticityModel) = @_;
|
|
|
1316
|
|
|
1317 if (!$This->IsSupportedAromaticityModel($AromaticityModel)) {
|
|
|
1318 my(@SupportedModels) = $This->GetSupportedAromaticityModels();
|
|
|
1319
|
|
|
1320 carp "Warning: ${ClassName}->SetAromaticityModel: The current release of MayaChemTools doesn't support the specified aromaticity model $AromaticityModel. Supported aromaticity models defined in AromaticityModelsData.csv file are: @SupportedModels . Using MayaChemToolsAromaticityModel...";
|
|
|
1321 $AromaticityModel = 'MayaChemToolsAromaticityModel';
|
|
|
1322 }
|
|
|
1323
|
|
|
1324 $This->SetProperty('AromaticityModel', $AromaticityModel);
|
|
|
1325
|
|
|
1326 return $This;
|
|
|
1327 }
|
|
|
1328
|
|
|
1329 # Get aromaticity model...
|
|
|
1330 #
|
|
|
1331 sub GetAromaticityModel {
|
|
|
1332 my($This) = @_;
|
|
|
1333
|
|
|
1334 # Is ValenceModel property explicitly set?
|
|
|
1335 if ($This->HasProperty('AromaticityModel')) {
|
|
|
1336 return $This->GetProperty('AromaticityModel');
|
|
|
1337 }
|
|
|
1338
|
|
|
1339 # Used internal aromaticity model as default model...
|
|
|
1340 return 'MayaChemToolsAromaticityModel';
|
|
|
1341 }
|
|
|
1342
|
|
|
1343 # Identify aromatic rings and ring systems in a molecule and set aromaticity for
|
|
|
1344 # corresponding atoms and bonds.
|
|
|
1345 #
|
|
|
1346 # What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you
|
|
|
1347 # say? Agree. The implementation of aromaticity varies widely across different
|
|
|
1348 # packages [ Ref 125 ]; additionally, the implementation details are not always
|
|
|
1349 # completely available, and it's not possible to figure out the exact implementation
|
|
|
1350 # of aromaticity across various packages. Using the publicly available information,
|
|
|
1351 # however, one can try to reproduce the available results to the extent possible,
|
|
|
1352 # along with parameterizing all the control parameters used to implement different
|
|
|
1353 # aromaticity models, and that's exactly what the current release of MayaChemTools
|
|
|
1354 # does.
|
|
|
1355 #
|
|
|
1356 # The implementation of aromaticity corresponding to various aromaticity models in
|
|
|
1357 # MayaChemTools package is driven by an external CSV file AromaticityModelsData.csv,
|
|
|
1358 # which is distributed with the package and is available in lib/data directory. The CSV
|
|
|
1359 # files contains names of supported aromaticity models, along with various control
|
|
|
1360 # parameters and their values. This file is loaded and processed during instantiation
|
|
|
1361 # of Molecule class and data corresponding to specific aromaticity model are used
|
|
|
1362 # to detect aromaticity for that model. Any new aromaticity model added to the
|
|
|
1363 # aromaticity data file, using different combinations of values for existing control
|
|
|
1364 # parameters would work without any changes to the code; the addition of any new
|
|
|
1365 # control parameters, however, requires its implementation in the code used to
|
|
|
1366 # calculate number of pi electrons available towards delocalization in a ring or ring
|
|
|
1367 # systems.
|
|
|
1368 #
|
|
|
1369 # The current release of MayaChemTools package supports these aromaticity
|
|
|
1370 # models: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
1371 # ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
|
|
|
1372 # DaylightAromaticityModel, MayaChemToolsAromaticityModel.
|
|
|
1373 #
|
|
|
1374 # The current list of control parameters available to detect aromaticity corresponding
|
|
|
1375 # to different aromaticity models are: AllowHeteroRingAtoms, HeteroRingAtomsList,
|
|
|
1376 # AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds,
|
|
|
1377 # AllowElectronegativeRingAtomExocyclicDoubleBonds, AllowRingAtomFormalCharge,
|
|
|
1378 # AllowHeteroRingAtomFormalCharge, MinimumRingSize. The values for these control
|
|
|
1379 # parameters are specified in AromaticityModelsData.csv file.
|
|
|
1380 #
|
|
|
1381 # Although definition of aromaticity differs across various aromaticity models, a ring
|
|
|
1382 # or a ring system containing 4n + 2 pi electrons (Huckel's rule) corresponding to
|
|
|
1383 # alternate single and double bonds, in general, is considered aromatic.
|
|
|
1384 #
|
|
|
1385 # The available valence free electrons on heterocyclic ring atoms, involved in two single
|
|
|
1386 # ring bonds, are also allowed to participate in pi electron delocalizaiton for most of
|
|
|
1387 # the supported aromaticity models.
|
|
|
1388 #
|
|
|
1389 # The presence of exocyclic terminal double bond on ring atoms involved in pi electron
|
|
|
1390 # delocalization is only allowed for some of the aromaticity models. Additionally, the type
|
|
|
1391 # atoms involved in exocyclic terminal double bonds may result in making a ring or ring
|
|
|
1392 # system non-aromatic.
|
|
|
1393 #
|
|
|
1394 sub DetectAromaticity {
|
|
|
1395 my($This) = @_;
|
|
|
1396
|
|
|
1397 # Delete aromaticity property for atoms and bonds...
|
|
|
1398 $This->DeleteAromaticity();
|
|
|
1399
|
|
|
1400 # Any ring out there...
|
|
|
1401 if (!$This->HasRings()) {
|
|
|
1402 return $This;
|
|
|
1403 }
|
|
|
1404
|
|
|
1405 if ($This->HasFusedRings()) {
|
|
|
1406 $This->_DetectAromaticityUsingFusedRingSets();
|
|
|
1407 }
|
|
|
1408 else {
|
|
|
1409 $This->_DetectAromaticityUsingIndividualRings();
|
|
|
1410 }
|
|
|
1411 return $This;
|
|
|
1412 }
|
|
|
1413
|
|
|
1414 # Go over all rings and set aromaticity property for corresponding ring atoms
|
|
|
1415 # and bonds involved in aromatic rings...
|
|
|
1416 #
|
|
|
1417 sub _DetectAromaticityUsingIndividualRings {
|
|
|
1418 my($This) = @_;
|
|
|
1419
|
|
|
1420 return $This->_DetectRingsAromaticity($This->GetRings());
|
|
|
1421 }
|
|
|
1422
|
|
|
1423 # For each fused ring set, detect aromaticity by treating all of its ring as one aromatic
|
|
|
1424 # system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in
|
|
|
1425 # fused set are treated individually for aromaticity detection. Additionally, non-fused
|
|
|
1426 # rings are handled on their own during aromaticity detection.
|
|
|
1427 #
|
|
|
1428 # Note:
|
|
|
1429 # . pi electrons in common bonds involved in fused ring sets are only counted once.
|
|
|
1430 #
|
|
|
1431 #
|
|
|
1432 sub _DetectAromaticityUsingFusedRingSets {
|
|
|
1433 my($This) = @_;
|
|
|
1434 my($Index, $RingAtomsRef, $FusedRingSetRef, $FusedRingSetsRef, $NonFusedRingsRef, @FusedRingSetIsAromatic);
|
|
|
1435
|
|
|
1436 ($FusedRingSetsRef, $NonFusedRingsRef) = $This->GetFusedAndNonFusedRings();
|
|
|
1437
|
|
|
1438 @FusedRingSetIsAromatic = ();
|
|
|
1439 RINGSET: for $Index (0 .. $#{$FusedRingSetsRef}) {
|
|
|
1440 $FusedRingSetRef = $FusedRingSetsRef->[$Index];
|
|
|
1441 $FusedRingSetIsAromatic[$Index] = 0;
|
|
|
1442
|
|
|
1443 my($NumOfPiElectronsInRingSet, $NumOfPiElectronsInRing, $Bond, $BondID, %FusedRingSetsBondsMap, %FusedRingSetsBondsVisitedMap, %FusedRingBondsMap);
|
|
|
1444
|
|
|
1445 $NumOfPiElectronsInRingSet = 0;
|
|
|
1446
|
|
|
1447 %FusedRingSetsBondsMap = ();
|
|
|
1448 %FusedRingSetsBondsVisitedMap = ();
|
|
|
1449 %FusedRingBondsMap = ();
|
|
|
1450
|
|
|
1451 # Setup a bond ID map for all bonds in fused ring set and another one
|
|
|
1452 # for bonds involved in more than one ring...
|
|
|
1453 #
|
|
|
1454 for $RingAtomsRef (@{$FusedRingSetRef}) {
|
|
|
1455 for $Bond ($This->GetRingBonds(@{$RingAtomsRef})) {
|
|
|
1456 $BondID = $Bond->GetID();
|
|
|
1457 $FusedRingSetsBondsMap{$BondID} = $BondID;
|
|
|
1458
|
|
|
1459 if ($Bond->GetNumOfRings() == 2) {
|
|
|
1460 $FusedRingBondsMap{$BondID} = $BondID;
|
|
|
1461 }
|
|
|
1462 }
|
|
|
1463 }
|
|
|
1464
|
|
|
1465 for $RingAtomsRef (@{$FusedRingSetRef}) {
|
|
|
1466 my(@RingBonds);
|
|
|
1467
|
|
|
1468 @RingBonds = ();
|
|
|
1469 @RingBonds = $This->GetRingBonds(@{$RingAtomsRef});
|
|
|
1470 $NumOfPiElectronsInRing = $This->_GetNumOfPiElectronsAvailableForDelocalization($RingAtomsRef, \@RingBonds, \%FusedRingSetsBondsMap, \%FusedRingSetsBondsVisitedMap, \%FusedRingBondsMap);
|
|
|
1471
|
|
|
1472 if (!$NumOfPiElectronsInRing) {
|
|
|
1473 next RINGSET;
|
|
|
1474 }
|
|
|
1475 $NumOfPiElectronsInRingSet += $NumOfPiElectronsInRing;
|
|
|
1476 }
|
|
|
1477 if ($This->_DoPiElectronSatifyHuckelsRule($NumOfPiElectronsInRingSet)) {
|
|
|
1478 $FusedRingSetIsAromatic[$Index] = 1;
|
|
|
1479 }
|
|
|
1480 }
|
|
|
1481
|
|
|
1482 # Set atom and bond aromatic flags for ring sets whose pi electrons satisfy Huckel's rule; otherwise,
|
|
|
1483 # treat rings in a ring set as individual rings for detecting aromaticity...
|
|
|
1484 for $Index (0 .. $#{$FusedRingSetsRef}) {
|
|
|
1485 $FusedRingSetRef = $FusedRingSetsRef->[$Index];
|
|
|
1486 if ($FusedRingSetIsAromatic[$Index]) {
|
|
|
1487 $This->_SetRingsAromaticity(@{$FusedRingSetRef});
|
|
|
1488 }
|
|
|
1489 else {
|
|
|
1490 $This->_DetectRingsAromaticity(@{$FusedRingSetRef});
|
|
|
1491 }
|
|
|
1492 }
|
|
|
1493
|
|
|
1494 $This->_DetectRingsAromaticity(@{$NonFusedRingsRef});
|
|
|
1495
|
|
|
1496 return $This;
|
|
|
1497 }
|
|
|
1498
|
|
|
1499 # Detect and set aromaticity for rings...
|
|
|
1500 #
|
|
|
1501 sub _DetectRingsAromaticity {
|
|
|
1502 my($This, @Rings) = @_;
|
|
|
1503 my($RingAtom, $RingBond, $RingAtomsRef);
|
|
|
1504
|
|
|
1505 RING: for $RingAtomsRef (@Rings) {
|
|
|
1506 if (!$This->_CheckRingAromaticity(@{$RingAtomsRef})) {
|
|
|
1507 next RING;
|
|
|
1508 }
|
|
|
1509 $This->_SetRingAromaticity(@{$RingAtomsRef});
|
|
|
1510 }
|
|
|
1511 return $This;
|
|
|
1512 }
|
|
|
1513
|
|
|
1514 # Set aromatic property for all all atoms and bonds involved in all specified rings..
|
|
|
1515 #
|
|
|
1516 sub _SetRingsAromaticity {
|
|
|
1517 my($This, @Rings) = @_;
|
|
|
1518 my($RingAtomsRef );
|
|
|
1519
|
|
|
1520 for $RingAtomsRef (@Rings) {
|
|
|
1521 $This->_SetRingAromaticity(@{$RingAtomsRef});
|
|
|
1522 }
|
|
|
1523 return $This;
|
|
|
1524 }
|
|
|
1525
|
|
|
1526 # Set aromatic property for all all atoms and bonds involved in ring..
|
|
|
1527 #
|
|
|
1528 sub _SetRingAromaticity {
|
|
|
1529 my($This, @RingAtoms) = @_;
|
|
|
1530 my($RingAtom, $RingBond);
|
|
|
1531
|
|
|
1532 for $RingAtom (@RingAtoms) {
|
|
|
1533 $RingAtom->SetAromatic(1);
|
|
|
1534 }
|
|
|
1535 for $RingBond ($This->GetRingBonds(@RingAtoms)) {
|
|
|
1536 $RingBond->SetAromatic(1);
|
|
|
1537 }
|
|
|
1538 return $This;
|
|
|
1539 }
|
|
|
1540
|
|
|
1541
|
|
|
1542 # For a ring to be an aromatic ring, all of its atoms must have aromatic property
|
|
|
1543 # set.
|
|
|
1544 #
|
|
|
1545 sub IsRingAromatic {
|
|
|
1546 my($This, @RingAtoms) = @_;
|
|
|
1547 my($RingAtom);
|
|
|
1548
|
|
|
1549 for $RingAtom (@RingAtoms) {
|
|
|
1550 if (!$RingAtom->IsAromatic()) {
|
|
|
1551 return 0;
|
|
|
1552 }
|
|
|
1553 }
|
|
|
1554 return 1;
|
|
|
1555 }
|
|
|
1556
|
|
|
1557 # Delete aromatic property for all atoms and bonds...
|
|
|
1558 #
|
|
|
1559 sub DeleteAromaticity {
|
|
|
1560 my($This) = @_;
|
|
|
1561
|
|
|
1562 return $This->_DeleteAtomsAndBondsAromaticity();
|
|
|
1563 }
|
|
|
1564
|
|
|
1565 # Check ring aromaticity...
|
|
|
1566 #
|
|
|
1567 sub _CheckRingAromaticity {
|
|
|
1568 my($This, @RingAtoms) = @_;
|
|
|
1569 my($NumOfPiElectrons, $BondID, @RingBonds);
|
|
|
1570
|
|
|
1571 @RingBonds = ();
|
|
|
1572 @RingBonds = $This->GetRingBonds(@RingAtoms);
|
|
|
1573
|
|
|
1574 $NumOfPiElectrons = $This->_GetNumOfPiElectronsAvailableForDelocalization(\@RingAtoms, \@RingBonds);
|
|
|
1575
|
|
|
1576 return $This->_DoPiElectronSatifyHuckelsRule($NumOfPiElectrons);
|
|
|
1577 }
|
|
|
1578
|
|
|
1579 # Get number of pi electrons available for delocalizaiton in a ring or ring system...
|
|
|
1580 #
|
|
|
1581 sub _GetNumOfPiElectronsAvailableForDelocalization {
|
|
|
1582 my($This, $RingAtomsRef, $RingBondsRef, $FusedRingSetsBondsMapRef, $FusedRingSetsBondsVisitedMapRef, $FusedRingBondsMapRef) = @_;
|
|
|
1583 my($AromaticityModelName, $AromaticityModelDataRef, $ExocyclicDoubleBondsDataMapRef, $NumOfConjugatedDoubleBonds, $NumOfExplicitAromaticBonds, $NumOfRingAtomElectronPairs, $NumOfRingBondsProcessed, $NumOfPiElectrons, $Index, $RingBond, $RingAtom, $RingAtomSymbol, $BondOrder, $RingAtomID, $RingBondID, $PreviousIndex, $PreviousRingBond, $ExcludeFreeRadicalElectrons, %ElectronPairContributionProcessedMap);
|
|
|
1584
|
|
|
1585 $AromaticityModelName = $CanonicalAromaticityModelNamesMap{lc($This->GetAromaticityModel())};
|
|
|
1586 $AromaticityModelDataRef = \%{$AromaticityModelsDataMap{$AromaticityModelName}};
|
|
|
1587
|
|
|
1588 # Perform an intial check for potential atomatic ring atoms..
|
|
|
1589 if (!$This->_CheckRingAtomsForPotentialAromaticity($RingAtomsRef, $RingBondsRef, $AromaticityModelDataRef)) {
|
|
|
1590 return 0;
|
|
|
1591 }
|
|
|
1592
|
|
|
1593 $ExocyclicDoubleBondsDataMapRef = undef;
|
|
|
1594 $ExcludeFreeRadicalElectrons = 1;
|
|
|
1595
|
|
|
1596 %ElectronPairContributionProcessedMap = ();
|
|
|
1597
|
|
|
1598 ($NumOfPiElectrons, $NumOfRingBondsProcessed, $NumOfConjugatedDoubleBonds, $NumOfExplicitAromaticBonds, $NumOfRingAtomElectronPairs) = ('0') x 5;
|
|
|
1599
|
|
|
1600 # Go over ring atoms and bonds to check their participation in aromaticity and count
|
|
|
1601 # pi electrons available for delocalization corresponding to various aromaticity models...
|
|
|
1602 #
|
|
|
1603 RINGBOND: for $Index (0 .. $#{$RingBondsRef}) {
|
|
|
1604 $RingBond = $RingBondsRef->[$Index];
|
|
|
1605 $RingAtom = $RingAtomsRef->[$Index];
|
|
|
1606 $BondOrder = $RingBond->GetBondOrder();
|
|
|
1607
|
|
|
1608 # Is this ring bond part of a fused ring system which has been already processed?
|
|
|
1609 if (defined($FusedRingSetsBondsVisitedMapRef) && $RingBond->GetNumOfRings() == 2) {
|
|
|
1610 $RingBondID = $RingBond->GetID();
|
|
|
1611 if (exists $FusedRingSetsBondsVisitedMapRef->{$RingBondID}) {
|
|
|
1612 next RINGBOND;
|
|
|
1613 }
|
|
|
1614 $FusedRingSetsBondsVisitedMapRef->{$RingBondID} = $RingBondID;
|
|
|
1615 }
|
|
|
1616 $NumOfRingBondsProcessed++;
|
|
|
1617
|
|
|
1618 # For first ring, previous ring bond corrresponds to last ring bond...
|
|
|
1619 $PreviousIndex = $Index ? ($Index -1) : $#{$RingBondsRef};
|
|
|
1620 $PreviousRingBond = $RingBondsRef->[$PreviousIndex];
|
|
|
1621
|
|
|
1622 # Check for presence of alternate single/double bond configuration, and pesence of
|
|
|
1623 # hetero atoms with two single ring bonds along with any exocyclic double bonds...
|
|
|
1624 #
|
|
|
1625 BONDORDER: {
|
|
|
1626 # Is current ring double bond in an alternate single/double bond configuration?
|
|
|
1627 if ($BondOrder == 2) {
|
|
|
1628 if ($PreviousRingBond->GetBondOrder() != 1) {
|
|
|
1629 return 0;
|
|
|
1630 }
|
|
|
1631 $NumOfConjugatedDoubleBonds += 1;
|
|
|
1632 last BONDORDER;
|
|
|
1633 }
|
|
|
1634
|
|
|
1635 # Is current ring bond order correspond to an explicit aromatic bond?
|
|
|
1636 if ($BondOrder == 1.5) {
|
|
|
1637 if ($PreviousRingBond->GetBondOrder() != 1.5) {
|
|
|
1638 return 0;
|
|
|
1639 }
|
|
|
1640 $NumOfExplicitAromaticBonds += 1;
|
|
|
1641 last BONDORDER;
|
|
|
1642 }
|
|
|
1643
|
|
|
1644 # Check for potential hetero atoms involved in two single ring bonds along
|
|
|
1645 # with any terminal exocyclic bonds...
|
|
|
1646 if ($BondOrder == 1) {
|
|
|
1647 if ($PreviousRingBond->GetBondOrder() != 1) {
|
|
|
1648 # Part of a conjugated system...
|
|
|
1649 last BONDORDER;
|
|
|
1650 }
|
|
|
1651
|
|
|
1652 # Identify any exocylic bonds on rings atoms...
|
|
|
1653 if (!defined $ExocyclicDoubleBondsDataMapRef) {
|
|
|
1654 $ExocyclicDoubleBondsDataMapRef = $This->_IdentifyRingAtomsInvolvedInExocyclicDoubleBonds($RingAtomsRef, $RingBondsRef, $FusedRingSetsBondsMapRef);
|
|
|
1655 }
|
|
|
1656
|
|
|
1657 # Is current ring atom part of an allowed exocyclic terminal bond?
|
|
|
1658 if (!$This->_CheckPotentialAromaticRingAtomForExocylicDoubleBonds($RingAtom, $AromaticityModelDataRef, $ExocyclicDoubleBondsDataMapRef)) {
|
|
|
1659 return 0;
|
|
|
1660 }
|
|
|
1661
|
|
|
1662 # Is it allowed to have any formal charge?
|
|
|
1663 if (!$This->_CheckPotentialAromaticRingAtomForFormalCharge($RingAtom, $AromaticityModelDataRef)) {
|
|
|
1664 return 0;
|
|
|
1665 }
|
|
|
1666
|
|
|
1667 # It it an allowed hetero ring atom or a carbon atom?
|
|
|
1668 if (!$This->_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms($RingAtom, $AromaticityModelDataRef)) {
|
|
|
1669 return 0;
|
|
|
1670 }
|
|
|
1671
|
|
|
1672 $RingAtomID = $RingAtom->GetID();
|
|
|
1673 $ElectronPairContributionProcessedMap{$RingAtomID} = $RingAtomID;
|
|
|
1674
|
|
|
1675 # Is it able to donate a pair for electrons towards pi electron delocalization?
|
|
|
1676 if ($RingAtom->GetValenceFreeElectrons($ExcludeFreeRadicalElectrons) >= 2) {
|
|
|
1677 # Possibilites:
|
|
|
1678 # . Hetero atom with or without formal charge and an available electron pair
|
|
|
1679 # . Carbon atom with -ve formal charge and with an available electron pair
|
|
|
1680 #
|
|
|
1681 $NumOfRingAtomElectronPairs += 1;
|
|
|
1682 }
|
|
|
1683 else {
|
|
|
1684 # Is ring atom involved in two single bonds without any electron pair allowed?
|
|
|
1685 if (!$This->_AllowRingAtomInTwoSingleBondsWithoutElectronPair($RingAtom, $RingBond, $PreviousRingBond, $ExocyclicDoubleBondsDataMapRef, $FusedRingBondsMapRef)) {
|
|
|
1686 return 0;
|
|
|
1687 }
|
|
|
1688 }
|
|
|
1689 last BONDORDER;
|
|
|
1690 }
|
|
|
1691
|
|
|
1692 # Any other type of ring atom/bond is not allowed to contribute towards pi electron count
|
|
|
1693 # and caused loss of aromaticity...
|
|
|
1694 return 0;
|
|
|
1695 }
|
|
|
1696 }
|
|
|
1697
|
|
|
1698 # Check for any electron pair contributions towards pi electron delocalization due to
|
|
|
1699 # -ve formal charge on ring atoms which haven't been already processed and part of
|
|
|
1700 # conjugated single/double bond system...
|
|
|
1701 #
|
|
|
1702 $NumOfRingAtomElectronPairs += $This->_GetElectronPairsContributionFromConjugatedRingAtoms($RingAtomsRef, $RingBondsRef, $ExcludeFreeRadicalElectrons, $AromaticityModelDataRef, \%ElectronPairContributionProcessedMap);
|
|
|
1703
|
|
|
1704 # Setup pi electron count available for delocalization...
|
|
|
1705 COUNT: {
|
|
|
1706 if ($NumOfExplicitAromaticBonds == $NumOfRingBondsProcessed) {
|
|
|
1707 # Each aromatic bond contribute one electron towards pi electron delocalization...
|
|
|
1708 $NumOfPiElectrons = $NumOfExplicitAromaticBonds;
|
|
|
1709 last COUNT;
|
|
|
1710 }
|
|
|
1711
|
|
|
1712 # Each conjugated double bond contribute two electrons towards pi electron delocalization...
|
|
|
1713 $NumOfPiElectrons = 2*$NumOfConjugatedDoubleBonds + 2*$NumOfRingAtomElectronPairs;
|
|
|
1714 }
|
|
|
1715
|
|
|
1716 return $NumOfPiElectrons;
|
|
|
1717 }
|
|
|
1718
|
|
|
1719 # Check ring atoms for their potential participation in aromatic systems..
|
|
|
1720 #
|
|
|
1721 sub _CheckRingAtomsForPotentialAromaticity {
|
|
|
1722 my($This, $RingAtomsRef, $RingBondsRef, $AromaticityModelDataRef) = @_;
|
|
|
1723 my($Index, $RingBond, $RingAtom);
|
|
|
1724
|
|
|
1725 # Check availability of ring atoms and bonds...
|
|
|
1726 if (!(defined($RingAtomsRef) && @{$RingBondsRef})) {
|
|
|
1727 return 0;
|
|
|
1728 }
|
|
|
1729
|
|
|
1730 # Is there any minimum ring size limit?
|
|
|
1731 if ($AromaticityModelDataRef->{MinimumRingSize}) {
|
|
|
1732 if (@{$RingAtomsRef} < $AromaticityModelDataRef->{MinimumRingSize}) {
|
|
|
1733 return 0;
|
|
|
1734 }
|
|
|
1735 }
|
|
|
1736
|
|
|
1737 # Make sure ring bond order is not greater than 2 and ring atom is not connected to more
|
|
|
1738 # than 3 other atoms to eliminate any non sp2 carbon atoms and still allow for hetero atoms
|
|
|
1739 # to contrbute towards electron delocalization...
|
|
|
1740 #
|
|
|
1741 for $Index (0 .. $#{$RingBondsRef}) {
|
|
|
1742 $RingBond = $RingBondsRef->[$Index];
|
|
|
1743 $RingAtom = $RingAtomsRef->[$Index];
|
|
|
1744
|
|
|
1745 if (($RingBond->GetBondOrder() > 2) || ($RingAtom->GetNumOfBonds() + $RingAtom->GetNumOfMissingHydrogens()) > 3) {
|
|
|
1746 return 0;
|
|
|
1747 }
|
|
|
1748 }
|
|
|
1749
|
|
|
1750 return 1;
|
|
|
1751 }
|
|
|
1752
|
|
|
1753 # Identify any exocylic double bonds on ring atoms...
|
|
|
1754 #
|
|
|
1755 sub _IdentifyRingAtomsInvolvedInExocyclicDoubleBonds {
|
|
|
1756 my($This, $RingAtomsRef, $RingBondsRef, $FusedRingSetsBondsMapRef) = @_;
|
|
|
1757 my($Index, $RingAtom, $RingBond, $RingAtomID, $Bond, $BondID, $BondedAtom, $RingBondsMapRef, %RingBondsMap, %ExocyclicDoubleBondsDataMap);
|
|
|
1758
|
|
|
1759 # Setup a ring bond map to process exocyclic bonds...
|
|
|
1760 $RingBondsMapRef = undef;
|
|
|
1761 %RingBondsMap = ();
|
|
|
1762
|
|
|
1763 if (defined $FusedRingSetsBondsMapRef) {
|
|
|
1764 $RingBondsMapRef = $FusedRingSetsBondsMapRef;
|
|
|
1765 }
|
|
|
1766 else {
|
|
|
1767 for $BondID (map { $_->GetID() } @{$RingBondsRef}) {
|
|
|
1768 $RingBondsMap{$BondID} = $BondID;
|
|
|
1769 }
|
|
|
1770 $RingBondsMapRef = \%RingBondsMap;
|
|
|
1771 }
|
|
|
1772
|
|
|
1773 # Intialize exocyclic terminal double bond data...
|
|
|
1774 %ExocyclicDoubleBondsDataMap = ();
|
|
|
1775 %{$ExocyclicDoubleBondsDataMap{RingAtomID}} = ();
|
|
|
1776
|
|
|
1777 for $Index (0 .. $#{$RingBondsRef}) {
|
|
|
1778 $RingBond = $RingBondsRef->[$Index];
|
|
|
1779 $RingAtom = $RingAtomsRef->[$Index];
|
|
|
1780
|
|
|
1781 $RingAtomID = $RingAtom->GetID();
|
|
|
1782
|
|
|
1783 BOND: for $Bond ($RingAtom->GetBonds()) {
|
|
|
1784 if ($Bond->GetBondOrder != 2) {
|
|
|
1785 next BOND;
|
|
|
1786 }
|
|
|
1787
|
|
|
1788 # Is it part of ring or ring system under consideration?
|
|
|
1789 if (exists $RingBondsMapRef->{$Bond->GetID()}) {
|
|
|
1790 next BOND;
|
|
|
1791 }
|
|
|
1792
|
|
|
1793 # Is bonded atom in a ring or a non-terminal atom?
|
|
|
1794 $BondedAtom = $Bond->GetBondedAtom($RingAtom);
|
|
|
1795 if ($BondedAtom->IsInRing() || !$BondedAtom->IsTerminal() ) {
|
|
|
1796 next BOND;
|
|
|
1797 }
|
|
|
1798
|
|
|
1799 # Track exocyclic terminal double bond information...
|
|
|
1800 if (!exists $ExocyclicDoubleBondsDataMap{RingAtomID}{$RingAtomID}) {
|
|
|
1801 @{$ExocyclicDoubleBondsDataMap{RingAtomID}{$RingAtomID}} = ();
|
|
|
1802 }
|
|
|
1803 push @{$ExocyclicDoubleBondsDataMap{RingAtomID}{$RingAtomID}}, $BondedAtom;
|
|
|
1804 }
|
|
|
1805 }
|
|
|
1806
|
|
|
1807 return \%ExocyclicDoubleBondsDataMap;
|
|
|
1808 }
|
|
|
1809
|
|
|
1810 # Check to see whether ring atoms are allowed to participate in exocyclic terminal double
|
|
|
1811 # bonds...
|
|
|
1812 #
|
|
|
1813 sub _CheckPotentialAromaticRingAtomForExocylicDoubleBonds {
|
|
|
1814 my($This, $RingAtom, $AromaticityModelDataRef, $ExocyclicDoubleBondsDataMapRef) = @_;
|
|
|
1815 my($RingAtomID, $ExocyclicTerminalAtom, $RingAtomElectronegativity, $TerminalAtomElectronagativity);
|
|
|
1816
|
|
|
1817 $RingAtomID = $RingAtom->GetID();
|
|
|
1818
|
|
|
1819 # Is it part of an exocyclic terminal double bond?
|
|
|
1820 if (!exists $ExocyclicDoubleBondsDataMapRef->{RingAtomID}{$RingAtomID}) {
|
|
|
1821 return 1;
|
|
|
1822 }
|
|
|
1823
|
|
|
1824 # Are exocyclic terminal double bonds allowed?
|
|
|
1825 if (!$AromaticityModelDataRef->{AllowExocyclicDoubleBonds}) {
|
|
|
1826 return 0;
|
|
|
1827 }
|
|
|
1828
|
|
|
1829 # Are there multiple exocyclic double bonds?
|
|
|
1830 if (@{$ExocyclicDoubleBondsDataMapRef->{RingAtomID}{$RingAtomID}} > 1) {
|
|
|
1831 return 0;
|
|
|
1832 }
|
|
|
1833 ($ExocyclicTerminalAtom) = @{$ExocyclicDoubleBondsDataMapRef->{RingAtomID}{$RingAtomID}};
|
|
|
1834
|
|
|
1835 # Are homo nuclear exocyclic terminal double bonds allowed?
|
|
|
1836 if (!$AromaticityModelDataRef->{AllowHomoNuclearExocyclicDoubleBonds}) {
|
|
|
1837 if ($RingAtom->GetAtomicNumber() == $ExocyclicTerminalAtom->GetAtomicNumber()) {
|
|
|
1838 return 0;
|
|
|
1839 }
|
|
|
1840 }
|
|
|
1841
|
|
|
1842 # Are ring atoms with higher electronegativity allowed in exocyclic double bonds?
|
|
|
1843 if (!$AromaticityModelDataRef->{AllowElectronegativeRingAtomExocyclicDoubleBonds}) {
|
|
|
1844 $RingAtomElectronegativity = PeriodicTable::GetElementPaulingElectronegativity($RingAtom->GetAtomicNumber());
|
|
|
1845 $TerminalAtomElectronagativity = PeriodicTable::GetElementPaulingElectronegativity($ExocyclicTerminalAtom->GetAtomicNumber());
|
|
|
1846
|
|
|
1847 if ($RingAtomElectronegativity && $TerminalAtomElectronagativity) {
|
|
|
1848 if ($RingAtomElectronegativity > $TerminalAtomElectronagativity) {
|
|
|
1849 return 0;
|
|
|
1850 }
|
|
|
1851 }
|
|
|
1852 }
|
|
|
1853
|
|
|
1854 return 1;
|
|
|
1855 }
|
|
|
1856
|
|
|
1857 #
|
|
|
1858 # Check for any formal charge participation into electron delocalization...
|
|
|
1859 #
|
|
|
1860 sub _CheckPotentialAromaticRingAtomForFormalCharge {
|
|
|
1861 my($This, $RingAtom, $AromaticityModelDataRef) = @_;
|
|
|
1862 my($FormalCharge);
|
|
|
1863
|
|
|
1864 # Does atom has any formal charge?
|
|
|
1865 $FormalCharge = $RingAtom->GetFormalCharge();
|
|
|
1866 if (!$FormalCharge) {
|
|
|
1867 return 1;
|
|
|
1868 }
|
|
|
1869
|
|
|
1870 # Are ring atoms with formal charge allowed to participate in electron delocalization?
|
|
|
1871 if (!$AromaticityModelDataRef->{AllowRingAtomFormalCharge}) {
|
|
|
1872 return 0;
|
|
|
1873 }
|
|
|
1874
|
|
|
1875 # Are hetero ring atoms with formal charge allowed to participate in electron delocalization?
|
|
|
1876 if (!$RingAtom->IsCarbon()) {
|
|
|
1877 if (!$AromaticityModelDataRef->{AllowHeteroRingAtomFormalCharge}) {
|
|
|
1878 return 0;
|
|
|
1879 }
|
|
|
1880 }
|
|
|
1881
|
|
|
1882 return 1;
|
|
|
1883 }
|
|
|
1884
|
|
|
1885 #
|
|
|
1886 # Check ring atoms for allowed hetero atoms...
|
|
|
1887 #
|
|
|
1888 sub _CheckPotentialAromaticRingAtomForAllowedHeteroAtoms {
|
|
|
1889 my($This, $RingAtom, $AromaticityModelDataRef) = @_;
|
|
|
1890 my($RingAtomSymbol);
|
|
|
1891
|
|
|
1892 # Is it a Carbon atom?
|
|
|
1893 if ($RingAtom->IsCarbon()) {
|
|
|
1894 return 1;
|
|
|
1895 }
|
|
|
1896
|
|
|
1897 # Are heteroatoms allowed?
|
|
|
1898 if (!$AromaticityModelDataRef->{AllowHeteroRingAtoms}) {
|
|
|
1899 return 0;
|
|
|
1900 }
|
|
|
1901
|
|
|
1902 # Is it an allowed hetero atom?
|
|
|
1903 $RingAtomSymbol = $RingAtom->GetAtomSymbol();
|
|
|
1904 if (!exists $AromaticityModelDataRef->{HeteroRingAtomsListMapRef}->{$RingAtomSymbol}) {
|
|
|
1905 return 0;
|
|
|
1906 }
|
|
|
1907
|
|
|
1908 return 1;
|
|
|
1909 }
|
|
|
1910
|
|
|
1911 # Check for any electron pair contributions toward pi electron delocalization due to
|
|
|
1912 # -ve formal charge on ring atoms which haven't been already processed and part of
|
|
|
1913 # conjugated single/double bond system...
|
|
|
1914 #
|
|
|
1915 sub _GetElectronPairsContributionFromConjugatedRingAtoms {
|
|
|
1916 my($This, $RingAtomsRef, $RingBondsRef, $ExcludeFreeRadicalElectrons, $AromaticityModelDataRef, $ElectronPairContributionProcessedMapRef) = @_;
|
|
|
1917 my($Index, $RingBond, $RingAtom, $NumOfRingAtomElectronPairs, $RingAtomID);
|
|
|
1918
|
|
|
1919 # Is formal charge allowed on ring atoms?
|
|
|
1920 if (!$AromaticityModelDataRef->{AllowRingAtomFormalCharge}) {
|
|
|
1921 return 0;
|
|
|
1922 }
|
|
|
1923
|
|
|
1924 $NumOfRingAtomElectronPairs = 0;
|
|
|
1925
|
|
|
1926 # Process ring atoms...
|
|
|
1927 RINGBOND: for $Index (0 .. $#{$RingBondsRef}) {
|
|
|
1928 $RingBond = $RingBondsRef->[$Index];
|
|
|
1929 $RingAtom = $RingAtomsRef->[$Index];
|
|
|
1930 $RingAtomID = $RingAtom->GetID();
|
|
|
1931
|
|
|
1932 # Is is already processed?
|
|
|
1933 if (exists $ElectronPairContributionProcessedMapRef->{$RingAtomID}) {
|
|
|
1934 next RINGBOND;
|
|
|
1935 }
|
|
|
1936 $ElectronPairContributionProcessedMapRef->{$RingAtomID} = $RingAtomID;
|
|
|
1937
|
|
|
1938 # Is it allowed to have any formal charge?
|
|
|
1939 if (!$This->_CheckPotentialAromaticRingAtomForFormalCharge($RingAtom, $AromaticityModelDataRef)) {
|
|
|
1940 next RINGBOND;
|
|
|
1941 }
|
|
|
1942
|
|
|
1943 # It it an allowed hetero ring atom or a carbon atom?
|
|
|
1944 if (!$This->_CheckPotentialAromaticRingAtomForAllowedHeteroAtoms($RingAtom, $AromaticityModelDataRef)) {
|
|
|
1945 next RINGBOND;
|
|
|
1946 }
|
|
|
1947
|
|
|
1948 # It is an atom with -ve formal charge?
|
|
|
1949 if ($RingAtom->GetFormalCharge() >= 0) {
|
|
|
1950 next RINGBOND;
|
|
|
1951 }
|
|
|
1952
|
|
|
1953 # Is it able to donate a pair for electrons towards pi electron delocalization?
|
|
|
1954 if ($RingAtom->GetValenceFreeElectrons($ExcludeFreeRadicalElectrons) < 2) {
|
|
|
1955 next RINGBOND;
|
|
|
1956 }
|
|
|
1957 $NumOfRingAtomElectronPairs += 1;
|
|
|
1958 }
|
|
|
1959
|
|
|
1960 return $NumOfRingAtomElectronPairs;
|
|
|
1961 }
|
|
|
1962
|
|
|
1963 # Check for ring atoms involved in two single ring bonds without any available electron
|
|
|
1964 # pair which are allowed to participate in aromatic system, after all other checks
|
|
|
1965 # corresponding to specified aromaticity models have already been performed...
|
|
|
1966 #
|
|
|
1967 sub _AllowRingAtomInTwoSingleBondsWithoutElectronPair {
|
|
|
1968 my($This, $RingAtom, $RingBond, $PreviousRingBond, $ExocyclicDoubleBondsDataMapRef, $FusedRingBondsMapRef) = @_;
|
|
|
1969
|
|
|
1970 ALLOWRINGATOM: {
|
|
|
1971 if (exists $ExocyclicDoubleBondsDataMapRef->{RingAtomID}{$RingAtom->GetID()}) {
|
|
|
1972 # Ring atom in an exocylic terminal double bond without any available electron pair...
|
|
|
1973 last ALLOWRINGATOM;
|
|
|
1974 }
|
|
|
1975
|
|
|
1976 if ($RingAtom->GetFormalCharge() > 0) {
|
|
|
1977 # Ring atom with positive formal charge without any available electron pair...
|
|
|
1978 last ALLOWRINGATOM;
|
|
|
1979 }
|
|
|
1980
|
|
|
1981 if (defined $FusedRingBondsMapRef && (exists $FusedRingBondsMapRef->{$RingBond->GetID()} || exists $FusedRingBondsMapRef->{$PreviousRingBond->GetID()})) {
|
|
|
1982 # Ring atom involved in fused ring bond, which might end up being part of a conjugated
|
|
|
1983 # system in another fused ring...
|
|
|
1984 last ALLOWRINGATOM;
|
|
|
1985 }
|
|
|
1986
|
|
|
1987 # Ring atom in any other environment is not allowed...
|
|
|
1988 return 0;
|
|
|
1989 }
|
|
|
1990
|
|
|
1991 return 1;
|
|
|
1992 }
|
|
|
1993
|
|
|
1994 # Do pi electrons satify huckel's rule: Number of pi electrons correspond to 4n + 2 where
|
|
|
1995 # n is a positive integer...
|
|
|
1996 #
|
|
|
1997 sub _DoPiElectronSatifyHuckelsRule {
|
|
|
1998 my($This, $NumOfPiElectrons) = @_;
|
|
|
1999
|
|
|
2000 $NumOfPiElectrons = $NumOfPiElectrons - 2;
|
|
|
2001
|
|
|
2002 return ($NumOfPiElectrons > 0) ? (($NumOfPiElectrons % 4) ? 0 : 1) : 0;
|
|
|
2003 }
|
|
|
2004
|
|
|
2005 # Delete aromatic property for all atoms and bonds...
|
|
|
2006 #
|
|
|
2007 sub _DeleteAtomsAndBondsAromaticity {
|
|
|
2008 my($This) = @_;
|
|
|
2009 my($Atom, $Bond);
|
|
|
2010
|
|
|
2011 for $Atom ($This->GetAtoms()) {
|
|
|
2012 $Atom->DeleteAromatic();
|
|
|
2013 }
|
|
|
2014 for $Bond ($This->GetBonds()) {
|
|
|
2015 $Bond->DeleteAromatic();
|
|
|
2016 }
|
|
|
2017 return $This;
|
|
|
2018 }
|
|
|
2019
|
|
|
2020 # Kekulize marked ring and non-ring aromatic atoms in a molecule...
|
|
|
2021 #
|
|
|
2022 sub KekulizeAromaticAtoms {
|
|
|
2023 my($This) = @_;
|
|
|
2024
|
|
|
2025 if (!$This->_KekulizeAromaticAtomsInRings()) {
|
|
|
2026 return 0;
|
|
|
2027 }
|
|
|
2028
|
|
|
2029 if (!$This->_KekulizeAromaticAtomsNotInRings()) {
|
|
|
2030 return 0;
|
|
|
2031 }
|
|
|
2032
|
|
|
2033 return 1;
|
|
|
2034 }
|
|
|
2035
|
|
|
2036 # Kekulize marked aromatic atoms in rings and fused ring sets...
|
|
|
2037 #
|
|
|
2038 sub _KekulizeAromaticAtomsInRings {
|
|
|
2039 my($This) = @_;
|
|
|
2040
|
|
|
2041 if (!$This->HasRings()) {
|
|
|
2042 # Nothing to do...
|
|
|
2043 return 1;
|
|
|
2044 }
|
|
|
2045
|
|
|
2046 if (!$This->HasAromaticAtomsInRings()) {
|
|
|
2047 # Nothing to do...
|
|
|
2048 return 1;
|
|
|
2049 }
|
|
|
2050
|
|
|
2051 # Identify fully aromatic fused and individual rings along with any partially aromatic ring components
|
|
|
2052 # using marked aromatic atoms in a molecule and kekulize them as individual stes...
|
|
|
2053 #
|
|
|
2054 my($AromaticFusedRingSetsRef, $AromaticRingsRef, $PartiallyAromaticRingComponentsRef) = (undef) x 3;
|
|
|
2055 if ($This->HasFusedRings()) {
|
|
|
2056 ($AromaticFusedRingSetsRef, $AromaticRingsRef, $PartiallyAromaticRingComponentsRef) = $This->_GetFusedAndNonFusedRingsContainingAromaticAtoms();
|
|
|
2057 }
|
|
|
2058 else {
|
|
|
2059 ($AromaticRingsRef, $PartiallyAromaticRingComponentsRef) = $This->_GetIndividualRingsContainingAromaticAtoms();
|
|
|
2060 }
|
|
|
2061
|
|
|
2062 return $This->_KekulizeCompleteAndPartialAromaticRings($AromaticFusedRingSetsRef, $AromaticRingsRef, $PartiallyAromaticRingComponentsRef);
|
|
|
2063 }
|
|
|
2064
|
|
|
2065 # Identify fully aromatic fused and individual rings along with any partially aromatic ring components
|
|
|
2066 # using marked aromatic atoms in a molecule...
|
|
|
2067 #
|
|
|
2068 sub _GetFusedAndNonFusedRingsContainingAromaticAtoms {
|
|
|
2069 my($This) = @_;
|
|
|
2070 my($Index, $SetAtomsCount, $SetAromaticAtomsCount, $FusedRingSetRef, $FusedRingSetsRef, $NonFusedRingsRef, $IndividualRingsRef, $RingAtomsRef, $RingAtomsCount, $AromaticAtomsCount, $RingAtom, $NonFusedFullyAromaticRingsRef, $NonFusedPartiallyAromaticRingComponentsRef, $PartiallyAromaticRingComponentsRef, @FullyAromaticFusedRingSets, @PotentialFullyAromaticRings, @FullyAromaticRings, @PotentialPartiallyAromaticRings, @PartiallyAromaticRingComponents);
|
|
|
2071
|
|
|
2072 @FullyAromaticFusedRingSets = ();
|
|
|
2073
|
|
|
2074 @PotentialFullyAromaticRings = ();
|
|
|
2075 @FullyAromaticRings = ();
|
|
|
2076
|
|
|
2077 @PotentialPartiallyAromaticRings = ();
|
|
|
2078 @PartiallyAromaticRingComponents = ();
|
|
|
2079
|
|
|
2080 ($FusedRingSetsRef, $NonFusedRingsRef) = $This->GetFusedAndNonFusedRings();
|
|
|
2081
|
|
|
2082 # Go over fused ring sets...
|
|
|
2083 RINGSET: for $Index (0 .. $#{$FusedRingSetsRef}) {
|
|
|
2084 $FusedRingSetRef = $FusedRingSetsRef->[$Index];
|
|
|
2085
|
|
|
2086 $SetAtomsCount = 0;
|
|
|
2087 $SetAromaticAtomsCount = 0;
|
|
|
2088
|
|
|
2089 for $RingAtomsRef (@{$FusedRingSetRef}) {
|
|
|
2090 $SetAtomsCount += scalar @{$RingAtomsRef};
|
|
|
2091
|
|
|
2092 for $RingAtom (@{$RingAtomsRef}) {
|
|
|
2093 if ($RingAtom->IsAromatic()) {
|
|
|
2094 $SetAromaticAtomsCount += 1;
|
|
|
2095 }
|
|
|
2096 }
|
|
|
2097 }
|
|
|
2098
|
|
|
2099 if (!($SetAtomsCount && $SetAromaticAtomsCount)) {
|
|
|
2100 next RINGSET;
|
|
|
2101 }
|
|
|
2102
|
|
|
2103 if ($SetAromaticAtomsCount == $SetAtomsCount) {
|
|
|
2104 push @FullyAromaticFusedRingSets, $FusedRingSetRef;
|
|
|
2105 }
|
|
|
2106 else {
|
|
|
2107 # Identify any individual rings in partial aromatic fused ring sets which might be
|
|
|
2108 # fully or partially aromatic...
|
|
|
2109 #
|
|
|
2110 RING: for $RingAtomsRef (@{$FusedRingSetRef}) {
|
|
|
2111 $RingAtomsCount = scalar @{$RingAtomsRef};
|
|
|
2112 $AromaticAtomsCount = 0;
|
|
|
2113
|
|
|
2114 RINGATOM: for $RingAtom (@{$RingAtomsRef}) {
|
|
|
2115 if (!$RingAtom->IsAromatic()) {
|
|
|
2116 next RINGATOM;
|
|
|
2117 }
|
|
|
2118 $AromaticAtomsCount += 1;
|
|
|
2119 }
|
|
|
2120
|
|
|
2121 if (!($RingAtomsCount && $AromaticAtomsCount)) {
|
|
|
2122 next RING;
|
|
|
2123 }
|
|
|
2124
|
|
|
2125 if ($RingAtomsCount == $AromaticAtomsCount) {
|
|
|
2126 push @PotentialFullyAromaticRings, $RingAtomsRef;
|
|
|
2127 }
|
|
|
2128 else {
|
|
|
2129 # Track partially aromatic rings in an different list before removing them for
|
|
|
2130 # any overlap with other rings and then add to fully aromatic rings...
|
|
|
2131 push @PotentialPartiallyAromaticRings, $RingAtomsRef;
|
|
|
2132 }
|
|
|
2133 }
|
|
|
2134 }
|
|
|
2135 }
|
|
|
2136
|
|
|
2137 if (@PotentialFullyAromaticRings > 1) {
|
|
|
2138 # Get any fully aromatic fused ring subsets from potentially fully aromatic rings...
|
|
|
2139 my($FullyAromaticFusedRingSetsRefs, $FullyAromaticNonFusedRingsRef);
|
|
|
2140 ($FullyAromaticFusedRingSetsRefs, $FullyAromaticNonFusedRingsRef) = $This->_GetFullyAromaticFusedAndNonFusedRingsInFusedSubset(\@PotentialFullyAromaticRings);
|
|
|
2141
|
|
|
2142 if (@{$FullyAromaticFusedRingSetsRefs}) {
|
|
|
2143 push @FullyAromaticFusedRingSets, @{$FullyAromaticFusedRingSetsRefs};
|
|
|
2144 }
|
|
|
2145 if (@{$FullyAromaticNonFusedRingsRef}) {
|
|
|
2146 push @FullyAromaticRings, @{$FullyAromaticNonFusedRingsRef};
|
|
|
2147 }
|
|
|
2148 }
|
|
|
2149 else {
|
|
|
2150 push @FullyAromaticRings, @PotentialFullyAromaticRings;
|
|
|
2151 }
|
|
|
2152
|
|
|
2153 # Go over partial aromatic ring components...
|
|
|
2154 if (@PotentialPartiallyAromaticRings) {
|
|
|
2155 $PartiallyAromaticRingComponentsRef = $This->_GetPartiallyAromaticRingComponents(\@PotentialPartiallyAromaticRings, \@PotentialFullyAromaticRings);
|
|
|
2156 if (@{$PartiallyAromaticRingComponentsRef}) {
|
|
|
2157 push @PartiallyAromaticRingComponents, @{$PartiallyAromaticRingComponentsRef};
|
|
|
2158 }
|
|
|
2159 }
|
|
|
2160
|
|
|
2161 # Go over non-fused rings...
|
|
|
2162 if (@{$NonFusedRingsRef}) {
|
|
|
2163 ($NonFusedFullyAromaticRingsRef, $NonFusedPartiallyAromaticRingComponentsRef) = $This->_GetRingsContainingAromaticAtoms(@{$NonFusedRingsRef});
|
|
|
2164
|
|
|
2165 if (@{$NonFusedFullyAromaticRingsRef}) {
|
|
|
2166 push @FullyAromaticRings, @{$NonFusedFullyAromaticRingsRef};
|
|
|
2167 }
|
|
|
2168 if (@{$NonFusedPartiallyAromaticRingComponentsRef}) {
|
|
|
2169 push @PartiallyAromaticRingComponents, @{$NonFusedPartiallyAromaticRingComponentsRef};
|
|
|
2170 }
|
|
|
2171 }
|
|
|
2172
|
|
|
2173 return (\@FullyAromaticFusedRingSets, \@FullyAromaticRings, \@PartiallyAromaticRingComponents);
|
|
|
2174 }
|
|
|
2175
|
|
|
2176 # Identify fully aromatic fused sets and non-fused rings in potentially fully aromatic
|
|
|
2177 # rings in fused ring sets...
|
|
|
2178 #
|
|
|
2179 # Fully aromatic rings in fused ring sets might contain fully aromatic fused subsets. These
|
|
|
2180 # fused subets need to be tracked and treated as fused sets.
|
|
|
2181 #
|
|
|
2182 # Note:
|
|
|
2183 # . Fused ring sets share at least one common bond, which could be used to identify
|
|
|
2184 # any multiple fully aromatic fused rings sets; absence of a shared ring bond implies
|
|
|
2185 # there are no fused ring sets.
|
|
|
2186 #
|
|
|
2187 #
|
|
|
2188 sub _GetFullyAromaticFusedAndNonFusedRingsInFusedSubset {
|
|
|
2189 my($This, $PotentialFullyAromaticFusedRingsRef) = @_;
|
|
|
2190 my($RingIndex, $RingIndex1, $RingIndex2, $RingAtom, $RingAtomID, $RingIsFuesd, $RingIndicesGraph, $FusedRingSetIndicesRef, @RingIndices, @FusedRingPairIndices, @FusedRingSetIndicesRefs, @FullyAromaticFusedRingSets, @FullyAromaticRings, %RingIndexToAtomIDMap, %FullyAromaticFusedRingIndexMap);
|
|
|
2191
|
|
|
2192 @FullyAromaticFusedRingSets = ();
|
|
|
2193 @FullyAromaticRings = ();
|
|
|
2194
|
|
|
2195 # Setup a ring index map for ring atoms...
|
|
|
2196 #
|
|
|
2197 %RingIndexToAtomIDMap = ();
|
|
|
2198 for $RingIndex (0 .. $#{$PotentialFullyAromaticFusedRingsRef}) {
|
|
|
2199 %{$RingIndexToAtomIDMap{$RingIndex}} = ();
|
|
|
2200 for $RingAtom (@{$PotentialFullyAromaticFusedRingsRef->[$RingIndex]}) {
|
|
|
2201 $RingAtomID = $RingAtom->GetID();
|
|
|
2202 $RingIndexToAtomIDMap{$RingIndex}{$RingAtomID} = $RingAtomID;
|
|
|
2203 }
|
|
|
2204 }
|
|
|
2205
|
|
|
2206 # Identify fused ring pairs...
|
|
|
2207 #
|
|
|
2208 @RingIndices = ();
|
|
|
2209 @FusedRingPairIndices = ();
|
|
|
2210
|
|
|
2211 for $RingIndex1 (0 .. $#{$PotentialFullyAromaticFusedRingsRef}) {
|
|
|
2212 push @RingIndices, $RingIndex1;
|
|
|
2213 for $RingIndex2 (($RingIndex1 + 1) .. $#{$PotentialFullyAromaticFusedRingsRef}) {
|
|
|
2214 $RingIsFuesd = 0;
|
|
|
2215 RINGATOM: for $RingAtom (@{$PotentialFullyAromaticFusedRingsRef->[$RingIndex2]}) {
|
|
|
2216 $RingAtomID = $RingAtom->GetID();
|
|
|
2217 if (exists $RingIndexToAtomIDMap{$RingIndex1}{$RingAtomID}) {
|
|
|
2218 $RingIsFuesd = 1;
|
|
|
2219 last RINGATOM;
|
|
|
2220 }
|
|
|
2221 }
|
|
|
2222 if ($RingIsFuesd) {
|
|
|
2223 push @FusedRingPairIndices, ($RingIndex1, $RingIndex2);
|
|
|
2224 }
|
|
|
2225 }
|
|
|
2226 }
|
|
|
2227
|
|
|
2228 if (!@FusedRingPairIndices) {
|
|
|
2229 # No fused ring subset out there...
|
|
|
2230 push @FullyAromaticRings, @{$PotentialFullyAromaticFusedRingsRef};
|
|
|
2231
|
|
|
2232 return (\@FullyAromaticFusedRingSets, \@FullyAromaticRings);
|
|
|
2233 }
|
|
|
2234
|
|
|
2235 # Identify fused ring sets...
|
|
|
2236 #
|
|
|
2237 $RingIndicesGraph = new Graph(@RingIndices);
|
|
|
2238 $RingIndicesGraph->AddEdges(@FusedRingPairIndices);
|
|
|
2239 @FusedRingSetIndicesRefs = $RingIndicesGraph->GetConnectedComponentsVertices();
|
|
|
2240
|
|
|
2241 # Collect fully aromatic fused ring sets...
|
|
|
2242 #
|
|
|
2243 %FullyAromaticFusedRingIndexMap = ();
|
|
|
2244 for $FusedRingSetIndicesRef (@FusedRingSetIndicesRefs) {
|
|
|
2245 my(@FullyAromaticFusedRingSet) = ();
|
|
|
2246 for $RingIndex (@{$FusedRingSetIndicesRef}) {
|
|
|
2247 $FullyAromaticFusedRingIndexMap{$RingIndex} = $RingIndex;
|
|
|
2248 push @FullyAromaticFusedRingSet, $PotentialFullyAromaticFusedRingsRef->[$RingIndex];
|
|
|
2249 }
|
|
|
2250 if (@FullyAromaticFusedRingSet) {
|
|
|
2251 # Sort rings by size with in the fused ring set...
|
|
|
2252 @FullyAromaticFusedRingSet = sort { scalar @$a <=> scalar @$b } @FullyAromaticFusedRingSet;
|
|
|
2253 push @FullyAromaticFusedRingSets, \@FullyAromaticFusedRingSet;
|
|
|
2254 }
|
|
|
2255 }
|
|
|
2256
|
|
|
2257 # Collect fully aromatic non-fused rings...
|
|
|
2258 #
|
|
|
2259 RINGINDEX: for $RingIndex (0 .. $#{$PotentialFullyAromaticFusedRingsRef}) {
|
|
|
2260 if (exists $FullyAromaticFusedRingIndexMap{$RingIndex}) {
|
|
|
2261 next RINGINDEX;
|
|
|
2262 }
|
|
|
2263 push @FullyAromaticRings, $PotentialFullyAromaticFusedRingsRef->[$RingIndex];
|
|
|
2264 }
|
|
|
2265
|
|
|
2266 return (\@FullyAromaticFusedRingSets, \@FullyAromaticRings);
|
|
|
2267 }
|
|
|
2268
|
|
|
2269 # Identify individual non-fused rings containing aromatic atoms...
|
|
|
2270 #
|
|
|
2271 sub _GetIndividualRingsContainingAromaticAtoms {
|
|
|
2272 my($This) = @_;
|
|
|
2273
|
|
|
2274 return $This->_GetRingsContainingAromaticAtoms($This->GetRings());
|
|
|
2275 }
|
|
|
2276
|
|
|
2277 # Identify individual non-fused rings containing aromatic atoms...
|
|
|
2278 #
|
|
|
2279 sub _GetRingsContainingAromaticAtoms {
|
|
|
2280 my($This, @Rings) = @_;
|
|
|
2281 my($RingAtom, $RingAtomsRef, $RingAtomsCount, $AromaticAtomsCount, $PartiallyAromaticRingComponentsRef, @FullyAromaticRings, @PartiallyAromaticRings);
|
|
|
2282
|
|
|
2283 @FullyAromaticRings = ();
|
|
|
2284 @PartiallyAromaticRings = ();
|
|
|
2285
|
|
|
2286 RING: for $RingAtomsRef (@Rings) {
|
|
|
2287 $RingAtomsCount = scalar @{$RingAtomsRef};
|
|
|
2288 $AromaticAtomsCount = 0;
|
|
|
2289
|
|
|
2290 for $RingAtom (@{$RingAtomsRef}) {
|
|
|
2291 if ($RingAtom->IsAromatic()) {
|
|
|
2292 $AromaticAtomsCount += 1;
|
|
|
2293 }
|
|
|
2294 }
|
|
|
2295
|
|
|
2296 if (!($AromaticAtomsCount && $RingAtomsCount)) {
|
|
|
2297 next RING;
|
|
|
2298 }
|
|
|
2299
|
|
|
2300 if ($AromaticAtomsCount == $RingAtomsCount) {
|
|
|
2301 push @FullyAromaticRings, $RingAtomsRef;
|
|
|
2302 }
|
|
|
2303 else {
|
|
|
2304 push @PartiallyAromaticRings, $RingAtomsRef;
|
|
|
2305 }
|
|
|
2306 }
|
|
|
2307
|
|
|
2308 $PartiallyAromaticRingComponentsRef = $This->_GetPartiallyAromaticRingComponents(\@PartiallyAromaticRings);
|
|
|
2309
|
|
|
2310 return (\@FullyAromaticRings, $PartiallyAromaticRingComponentsRef);
|
|
|
2311 }
|
|
|
2312
|
|
|
2313 # Get connected aromatic components with in partially aromatic rings...
|
|
|
2314 #
|
|
|
2315 sub _GetPartiallyAromaticRingComponents {
|
|
|
2316 my($This, $PotentialPartiallyAromaticRingsRef, $FullyAromaticRingsRef) = @_;
|
|
|
2317 my($RingAtomsRef, $RingAtom, $RingAtomID, $Index, @PartiallyAromaticRingComponents, %FullyAromaticRingAtomsMap);
|
|
|
2318
|
|
|
2319 @PartiallyAromaticRingComponents = ();
|
|
|
2320
|
|
|
2321 # Setup a map for atoms involve in fully aromatic rings to remove remove partial rings
|
|
|
2322 # containing only those atoms which are already part of some other fully aromatic ring
|
|
|
2323 # in fused ring scenarios or some other partially aromatic ring...
|
|
|
2324 #
|
|
|
2325 %FullyAromaticRingAtomsMap = ();
|
|
|
2326 if (defined $FullyAromaticRingsRef) {
|
|
|
2327 for $RingAtomsRef (@{$FullyAromaticRingsRef}) {
|
|
|
2328 for $RingAtom (@{$RingAtomsRef}) {
|
|
|
2329 $RingAtomID = $RingAtom->GetID();
|
|
|
2330 $FullyAromaticRingAtomsMap{$RingAtomID} = $RingAtomID;
|
|
|
2331 }
|
|
|
2332 }
|
|
|
2333 }
|
|
|
2334
|
|
|
2335 # . Identify any connected components with in each partially aromatic ring.
|
|
|
2336 # . Use ring atom indices to figure out connnected components in rings: All ring atoms
|
|
|
2337 # in a connected component have sequential indices and a difference by more than
|
|
|
2338 # 1 indicates a new component in the list.
|
|
|
2339 #
|
|
|
2340 RING: for $RingAtomsRef (@{$PotentialPartiallyAromaticRingsRef}) {
|
|
|
2341 my(@AromaticRingAtoms, @AromaticRingAtomsIndices);
|
|
|
2342
|
|
|
2343 @AromaticRingAtoms = ();
|
|
|
2344 @AromaticRingAtomsIndices = ();
|
|
|
2345
|
|
|
2346 RINGATOM: for $Index (0 .. $#{$RingAtomsRef}) {
|
|
|
2347 $RingAtom = $RingAtomsRef->[$Index];
|
|
|
2348 $RingAtomID = $RingAtom->GetID();
|
|
|
2349
|
|
|
2350 if (defined $FullyAromaticRingsRef && exists $FullyAromaticRingAtomsMap{$RingAtomID}) {
|
|
|
2351 next RINGATOM;
|
|
|
2352 }
|
|
|
2353 if (!$RingAtom->IsAromatic()) {
|
|
|
2354 next RINGATOM;
|
|
|
2355 }
|
|
|
2356 push @AromaticRingAtoms, $RingAtom;
|
|
|
2357 push @AromaticRingAtomsIndices, $Index;
|
|
|
2358
|
|
|
2359 }
|
|
|
2360 if (!@AromaticRingAtoms) {
|
|
|
2361 next RING;
|
|
|
2362 }
|
|
|
2363
|
|
|
2364 # Start off with a new connected component...
|
|
|
2365 #
|
|
|
2366 my($ComponentNum);
|
|
|
2367 $ComponentNum = scalar @PartiallyAromaticRingComponents;
|
|
|
2368 @{$PartiallyAromaticRingComponents[$ComponentNum]} = ();
|
|
|
2369
|
|
|
2370 $Index = 0;
|
|
|
2371 push @{$PartiallyAromaticRingComponents[$ComponentNum]}, $AromaticRingAtoms[$Index];
|
|
|
2372
|
|
|
2373 for $Index (1 .. $#AromaticRingAtoms) {
|
|
|
2374 if (($AromaticRingAtomsIndices[$Index] - $AromaticRingAtomsIndices[$Index -1]) > 1) {
|
|
|
2375 # New connected component...
|
|
|
2376 $ComponentNum += 1;
|
|
|
2377 @{$PartiallyAromaticRingComponents[$ComponentNum]} = ();
|
|
|
2378 }
|
|
|
2379 push @{$PartiallyAromaticRingComponents[$ComponentNum]}, $AromaticRingAtoms[$Index];
|
|
|
2380 }
|
|
|
2381 }
|
|
|
2382
|
|
|
2383 return (\@PartiallyAromaticRingComponents);
|
|
|
2384 }
|
|
|
2385
|
|
|
2386 # Kekulize fully aromatic fused and individual rings along with any partially aromatic ring
|
|
|
2387 # components...
|
|
|
2388 #
|
|
|
2389 sub _KekulizeCompleteAndPartialAromaticRings {
|
|
|
2390 my($This, $AromaticFusedRingSetsRef, $AromaticRingsRef, $PartiallyAromaticRingComponentsRef) = @_;
|
|
|
2391 my($Status, $ConnectedPathsAtomsSetsRef, $ConnectedPathsBondsSetsRef, $ConnectdPathsSetsTypesRef, $PathSetIndex, $PathAtom, $AtomID, $BondID, $PathBondsRef, $DeleteAtomsAromaticity, $DeleteBondsAromaticity, %PathAtomsProcessingStatusMap, %PathBondsProcessingStatusMap);
|
|
|
2392
|
|
|
2393 ($ConnectedPathsAtomsSetsRef, $ConnectedPathsBondsSetsRef, $ConnectdPathsSetsTypesRef) = $This->_SetupCompleteAndPartialAromaticRingsForKekulizaiton($AromaticFusedRingSetsRef, $AromaticRingsRef, $PartiallyAromaticRingComponentsRef);
|
|
|
2394
|
|
|
2395 if (!@{$ConnectedPathsAtomsSetsRef}) {
|
|
|
2396 # Nothing to do...
|
|
|
2397 return 1;
|
|
|
2398 }
|
|
|
2399
|
|
|
2400 # Delete any aromaticity property set for non-ring bonds connected any two ring
|
|
|
2401 # aromatic atoms...
|
|
|
2402 #
|
|
|
2403 $This->_ProcessNonRingAromaticBondsBetweenAromaticRingAtoms();
|
|
|
2404
|
|
|
2405 %PathAtomsProcessingStatusMap = ();
|
|
|
2406 %PathBondsProcessingStatusMap = ();
|
|
|
2407
|
|
|
2408 $Status = 1;
|
|
|
2409
|
|
|
2410 PATHSET: for $PathSetIndex (0 .. $#{$ConnectedPathsAtomsSetsRef}) {
|
|
|
2411 my($AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathSetProcessingStatusRef);
|
|
|
2412
|
|
|
2413 ($AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathSetProcessingStatusRef) = (undef) x 3;
|
|
|
2414
|
|
|
2415 if ($ConnectdPathsSetsTypesRef->[$PathSetIndex] =~ /^FusedAromatic$/i) {
|
|
|
2416 # Fused set of connected paths...
|
|
|
2417 #
|
|
|
2418 my($FusedConnectedPathAtomsSetRef, $FusedConnectedPathBondsSetRef);
|
|
|
2419
|
|
|
2420 $FusedConnectedPathAtomsSetRef = $ConnectedPathsAtomsSetsRef->[$PathSetIndex];
|
|
|
2421 $FusedConnectedPathBondsSetRef = $ConnectedPathsBondsSetsRef->[$PathSetIndex];
|
|
|
2422
|
|
|
2423 # Prepare for kekulization...
|
|
|
2424 ($AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathSetProcessingStatusRef) = $This->_SetupConnectedPathSetsForKekulization($FusedConnectedPathAtomsSetRef, $FusedConnectedPathBondsSetRef);
|
|
|
2425
|
|
|
2426 # Perform kekulization starting with the first path set...
|
|
|
2427 $PathSetProcessingStatusRef->[0] = 'Processed';
|
|
|
2428 if (!$This->_KekulizeConnectedPathSets($FusedConnectedPathAtomsSetRef->[0], $FusedConnectedPathBondsSetRef->[0], $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $FusedConnectedPathAtomsSetRef, $FusedConnectedPathBondsSetRef, $PathSetProcessingStatusRef)) {
|
|
|
2429 # Kekulization failed for the current fused paths set...
|
|
|
2430 $Status = 0;
|
|
|
2431 }
|
|
|
2432 }
|
|
|
2433 else {
|
|
|
2434 # An individual connected path...
|
|
|
2435 #
|
|
|
2436 my(@ConnectedPathAtomsSet, @ConnectedPathBondsSet);
|
|
|
2437
|
|
|
2438 @ConnectedPathAtomsSet = ($ConnectedPathsAtomsSetsRef->[$PathSetIndex]);
|
|
|
2439 @ConnectedPathBondsSet = ($ConnectedPathsBondsSetsRef->[$PathSetIndex]);
|
|
|
2440
|
|
|
2441 # Prepare for kekulization...
|
|
|
2442 ($AtomProcessingStatusMapRef, $BondProcessingStatusMapRef) = $This->_SetupConnectedPathSetsForKekulization(\@ConnectedPathAtomsSet, \@ConnectedPathBondsSet);
|
|
|
2443
|
|
|
2444 # Perform kekulization...
|
|
|
2445 if (!$This->_KekulizeConnectedPathSets($ConnectedPathsAtomsSetsRef->[$PathSetIndex], $ConnectedPathsBondsSetsRef->[$PathSetIndex], $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef)) {
|
|
|
2446 # Kekulization failed for the current path...
|
|
|
2447 $Status = 0;
|
|
|
2448 }
|
|
|
2449 }
|
|
|
2450
|
|
|
2451 # Did kekulization succeed for the current path or path set?
|
|
|
2452 if (!$Status) {
|
|
|
2453 last PATHSET;
|
|
|
2454 }
|
|
|
2455
|
|
|
2456 # Track atom and bond processing state for final assignment after kekulization
|
|
|
2457 # is successfully completed for all the paths and fused path sets...
|
|
|
2458 #
|
|
|
2459 for $AtomID (keys %{$AtomProcessingStatusMapRef}) {
|
|
|
2460 $PathAtomsProcessingStatusMap{$AtomID} = $AtomProcessingStatusMapRef->{$AtomID};
|
|
|
2461 }
|
|
|
2462
|
|
|
2463 for $BondID (keys %{$BondProcessingStatusMapRef}) {
|
|
|
2464 $PathBondsProcessingStatusMap{$BondID} = $BondProcessingStatusMapRef->{$BondID};
|
|
|
2465 }
|
|
|
2466 }
|
|
|
2467
|
|
|
2468 if (!$Status) {
|
|
|
2469 carp "Warning: ${ClassName}->_KekulizeCompleteAndPartialAromaticRings: Couldn't perform kekulization for marked ring aromatic atoms...";
|
|
|
2470 return 0;
|
|
|
2471 }
|
|
|
2472
|
|
|
2473 # Use PathAtomsProcessingStatusMap and PathBondsProcessingStatusMap to set
|
|
|
2474 # single/double bonds in the molecule after successful kekulization along with modification of
|
|
|
2475 # any aromatic flags...
|
|
|
2476
|
|
|
2477 for $PathSetIndex (0 .. $#{$ConnectedPathsAtomsSetsRef}) {
|
|
|
2478 $DeleteAtomsAromaticity = 0; $DeleteBondsAromaticity = 0;
|
|
|
2479
|
|
|
2480 if ($ConnectdPathsSetsTypesRef->[$PathSetIndex] =~ /^FusedAromatic$/i) {
|
|
|
2481 for $PathBondsRef (@{$ConnectedPathsBondsSetsRef->[$PathSetIndex]}) {
|
|
|
2482 $This->_ProcessBondOrdersAssignedDuringSuccessfulKekulization($PathBondsRef, \%PathBondsProcessingStatusMap, $DeleteBondsAromaticity);
|
|
|
2483 }
|
|
|
2484 }
|
|
|
2485 else {
|
|
|
2486 if ($ConnectdPathsSetsTypesRef->[$PathSetIndex] =~ /^PartiallyAromatic$/i ) {
|
|
|
2487 $DeleteBondsAromaticity = 1; $DeleteAtomsAromaticity = 1;
|
|
|
2488 }
|
|
|
2489
|
|
|
2490 if ($DeleteAtomsAromaticity) {
|
|
|
2491 for $PathAtom (@{$ConnectedPathsAtomsSetsRef->[$PathSetIndex]}) {
|
|
|
2492 $PathAtom->DeleteAromatic();
|
|
|
2493 }
|
|
|
2494 }
|
|
|
2495
|
|
|
2496 $This->_ProcessBondOrdersAssignedDuringSuccessfulKekulization($ConnectedPathsBondsSetsRef->[$PathSetIndex], \%PathBondsProcessingStatusMap, $DeleteBondsAromaticity);
|
|
|
2497 }
|
|
|
2498 }
|
|
|
2499
|
|
|
2500 return 1;
|
|
|
2501 }
|
|
|
2502
|
|
|
2503 # Look for any aromatic bonds outside the rings between two ring aromatic atoms
|
|
|
2504 # and turn them into single non-aromatic bonds before kekulization; otherwise, kekulization
|
|
|
2505 # fails.
|
|
|
2506 #
|
|
|
2507 # Note:
|
|
|
2508 # . Two atoms marked as aromatic atoms in two different rings, such as two rings
|
|
|
2509 # connected through a single bond, are still aromatic, but the bond is outside
|
|
|
2510 # the ring and shouldn't be marked as aromatic. It should be set to single bond without
|
|
|
2511 # any aromatic property for kekulization to succeed.
|
|
|
2512 #
|
|
|
2513 # For example, the molecule generated by SMILES parser for biphenyl SMILES string
|
|
|
2514 # "c1ccccc1c2ccccc2" sets up an aromatic bond between the two phenyl rings, as
|
|
|
2515 # it's connected to two aromatic atoms.
|
|
|
2516 #
|
|
|
2517 sub _ProcessNonRingAromaticBondsBetweenAromaticRingAtoms {
|
|
|
2518 my($This) = @_;
|
|
|
2519 my($Bond, $Atom1, $Atom2);
|
|
|
2520
|
|
|
2521 BOND: for $Bond ($This->GetBonds()) {
|
|
|
2522 if (!($Bond->IsAromatic() && $Bond->IsNotInRing())) {
|
|
|
2523 next BOND;
|
|
|
2524 }
|
|
|
2525
|
|
|
2526 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
2527 if (!($Atom1->IsAromatic() && $Atom2->IsAromatic() && $Atom1->IsInRing() && $Atom2->IsInRing())) {
|
|
|
2528 next BOND;
|
|
|
2529 }
|
|
|
2530
|
|
|
2531 $Bond->SetBondOrder(1);
|
|
|
2532 $Bond->DeleteAromatic();
|
|
|
2533 }
|
|
|
2534
|
|
|
2535 return $This;
|
|
|
2536 }
|
|
|
2537
|
|
|
2538 # Setup completelty aromatic fused and individual rings along with partially aromatic ring
|
|
|
2539 # components as sets of connected paths...
|
|
|
2540 #
|
|
|
2541 sub _SetupCompleteAndPartialAromaticRingsForKekulizaiton {
|
|
|
2542 my($This, $AromaticFusedRingSetsRef, $AromaticRingsRef, $PartiallyAromaticRingComponentsRef) = @_;
|
|
|
2543 my(@ConnectedPathsSets, @ConnectedPathsBondsSets, @ConnectdPathsSetsTypes);
|
|
|
2544
|
|
|
2545 @ConnectedPathsSets = ();
|
|
|
2546 @ConnectedPathsBondsSets = ();
|
|
|
2547 @ConnectdPathsSetsTypes = ();
|
|
|
2548
|
|
|
2549 # Setup atoms and bonds for connected paths in fused aromatic ring sets...
|
|
|
2550 #
|
|
|
2551 if (defined $AromaticFusedRingSetsRef && @{$AromaticFusedRingSetsRef}) {
|
|
|
2552 my($RingSetIndex);
|
|
|
2553
|
|
|
2554 push @ConnectdPathsSetsTypes, ('FusedAromatic') x scalar @{$AromaticFusedRingSetsRef};
|
|
|
2555 push @ConnectedPathsSets, @{$AromaticFusedRingSetsRef};
|
|
|
2556
|
|
|
2557 for $RingSetIndex (0 .. $#{$AromaticFusedRingSetsRef}) {
|
|
|
2558 my(@AromaticFusedRingBondsSet);
|
|
|
2559
|
|
|
2560 # Get ring bonds for each ring set...
|
|
|
2561 #
|
|
|
2562 @AromaticFusedRingBondsSet = $This->GetRingBondsFromRings(@{$AromaticFusedRingSetsRef->[$RingSetIndex]});
|
|
|
2563 push @ConnectedPathsBondsSets, \@AromaticFusedRingBondsSet;
|
|
|
2564 }
|
|
|
2565 }
|
|
|
2566
|
|
|
2567 # Set up atoms and bonds for connected paths in aromatic rings...
|
|
|
2568 #
|
|
|
2569 if (defined $AromaticRingsRef && @{$AromaticRingsRef}) {
|
|
|
2570 my(@AromaticRingBondsSets);
|
|
|
2571
|
|
|
2572 push @ConnectdPathsSetsTypes, ('Aromatic') x scalar @{$AromaticRingsRef};
|
|
|
2573 push @ConnectedPathsSets, @{$AromaticRingsRef};
|
|
|
2574
|
|
|
2575 # Get ring bonds for each ring...
|
|
|
2576 @AromaticRingBondsSets = $This->GetRingBondsFromRings(@{$AromaticRingsRef});
|
|
|
2577 push @ConnectedPathsBondsSets, @AromaticRingBondsSets;
|
|
|
2578 }
|
|
|
2579
|
|
|
2580 # Set up atoms and bonds for connected paths in partially aromatic rings...
|
|
|
2581 #
|
|
|
2582 if (defined $PartiallyAromaticRingComponentsRef && @{$PartiallyAromaticRingComponentsRef}) {
|
|
|
2583 my($ComponentIndex);
|
|
|
2584
|
|
|
2585 push @ConnectedPathsSets, @{$PartiallyAromaticRingComponentsRef};
|
|
|
2586 push @ConnectdPathsSetsTypes, ('PartiallyAromatic') x scalar @{$PartiallyAromaticRingComponentsRef};
|
|
|
2587
|
|
|
2588 for $ComponentIndex (0 .. $#{$PartiallyAromaticRingComponentsRef}) {
|
|
|
2589 my(@ComponentBonds);
|
|
|
2590 @ComponentBonds = $This->_GetPathBonds($This->_GetAtomsIDsFromAtoms(@{$PartiallyAromaticRingComponentsRef->[$ComponentIndex]}));
|
|
|
2591 push @ConnectedPathsBondsSets, \@ComponentBonds;
|
|
|
2592 }
|
|
|
2593 }
|
|
|
2594
|
|
|
2595 return (\@ConnectedPathsSets, \@ConnectedPathsBondsSets, \@ConnectdPathsSetsTypes);
|
|
|
2596 }
|
|
|
2597
|
|
|
2598 # Process non-ring connected atoms which are marked aromatic and set connected
|
|
|
2599 # bonds as alternate single/double bonds...
|
|
|
2600 #
|
|
|
2601 # Notes:
|
|
|
2602 # . Atom and bond aromaticity is deleted during kekulization of non-ring atoms.
|
|
|
2603 #
|
|
|
2604 sub _KekulizeAromaticAtomsNotInRings {
|
|
|
2605 my($This) = @_;
|
|
|
2606 my($Status, $PathIndex, $PathAtom, $PathAtomID, $PathBondID, $ConnectedPathsAtomsRef, $ConnectedPathsBondsRef, $DeleteAtomsAromaticity, $DeleteBondsAromaticity, %PathAtomsProcessingStatusMap, %PathBondsProcessingStatusMap);
|
|
|
2607
|
|
|
2608 if (!$This->HasAromaticAtomsNotInRings()) {
|
|
|
2609 # Nothing to do...
|
|
|
2610 return 1;
|
|
|
2611 }
|
|
|
2612
|
|
|
2613 # Identify paths for connected components containing non-ring aromatic atoms...
|
|
|
2614 ($ConnectedPathsAtomsRef, $ConnectedPathsBondsRef) = $This->_GetConnectedComponentsPathsForNonRingAromaticAtoms();
|
|
|
2615
|
|
|
2616 if (!@{$ConnectedPathsAtomsRef}) {
|
|
|
2617 carp "Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms...";
|
|
|
2618 return 0;
|
|
|
2619 }
|
|
|
2620
|
|
|
2621 %PathAtomsProcessingStatusMap = ();
|
|
|
2622 %PathBondsProcessingStatusMap = ();
|
|
|
2623
|
|
|
2624 $Status = 1;
|
|
|
2625
|
|
|
2626 PATH: for $PathIndex (0 .. $#{$ConnectedPathsAtomsRef}) {
|
|
|
2627 my($AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, @ConnectedPathAtomsSet, @ConnectedPathBondsSet);
|
|
|
2628
|
|
|
2629 ($AtomProcessingStatusMapRef, $BondProcessingStatusMapRef) = (undef) x 2;
|
|
|
2630
|
|
|
2631 @ConnectedPathAtomsSet = ($ConnectedPathsAtomsRef->[$PathIndex]);
|
|
|
2632 @ConnectedPathBondsSet = ($ConnectedPathsBondsRef->[$PathIndex]);
|
|
|
2633
|
|
|
2634 # Prepare for kekulization...
|
|
|
2635 ($AtomProcessingStatusMapRef, $BondProcessingStatusMapRef) = $This->_SetupConnectedPathSetsForKekulization(\@ConnectedPathAtomsSet, \@ConnectedPathBondsSet);
|
|
|
2636
|
|
|
2637 # Perform kekulization...
|
|
|
2638 if (!$This->_KekulizeConnectedPathSets($ConnectedPathsAtomsRef->[$PathIndex], $ConnectedPathsBondsRef->[$PathIndex], $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef)) {
|
|
|
2639 # Kekulization failed for the current path...
|
|
|
2640 $Status = 0;
|
|
|
2641 last PATH;
|
|
|
2642 }
|
|
|
2643
|
|
|
2644 # Track atom and bond processing state for final assignment after kekulization
|
|
|
2645 # is successfully completed for all the paths and fused path sets...
|
|
|
2646 #
|
|
|
2647 for $PathAtomID (keys %{$AtomProcessingStatusMapRef}) {
|
|
|
2648 $PathAtomsProcessingStatusMap{$PathAtomID} = $AtomProcessingStatusMapRef->{$PathAtomID};
|
|
|
2649 }
|
|
|
2650
|
|
|
2651 for $PathBondID (keys %{$BondProcessingStatusMapRef}) {
|
|
|
2652 $PathBondsProcessingStatusMap{$PathBondID} = $BondProcessingStatusMapRef->{$PathBondID};
|
|
|
2653 }
|
|
|
2654 }
|
|
|
2655
|
|
|
2656 if (!$Status) {
|
|
|
2657 carp "Warning: ${ClassName}->_KekulizeAromaticAtomsNotInRings: Couldn't perform kekulization for marked non-ring aromatic atoms...";
|
|
|
2658 return 0;
|
|
|
2659 }
|
|
|
2660
|
|
|
2661 $DeleteAtomsAromaticity = 1; $DeleteBondsAromaticity = 1;
|
|
|
2662 for $PathIndex (0 .. $#{$ConnectedPathsAtomsRef}) {
|
|
|
2663 if ($DeleteAtomsAromaticity) {
|
|
|
2664 for $PathAtom (@{$ConnectedPathsAtomsRef->[$PathIndex]}) {
|
|
|
2665 $PathAtom->DeleteAromatic();
|
|
|
2666 }
|
|
|
2667 }
|
|
|
2668 $This->_ProcessBondOrdersAssignedDuringSuccessfulKekulization($ConnectedPathsBondsRef->[$PathIndex], \%PathBondsProcessingStatusMap, $DeleteBondsAromaticity);
|
|
|
2669 }
|
|
|
2670
|
|
|
2671 return 1;
|
|
|
2672 }
|
|
|
2673
|
|
|
2674 # Collect path atoms for connected components paths containing non-ring aromatic atoms...
|
|
|
2675 #
|
|
|
2676 sub _GetConnectedComponentsPathsForNonRingAromaticAtoms {
|
|
|
2677 my($This) = @_;
|
|
|
2678 my($ComponentRef, $AtomIDsRef, $AtomIDsMapRef, $ConnectedComponentsAtomIDsRef, $ConnectedComponentsAtomIDsMapRef, $ConnectedComponentsPathsAtomIDsRef, $ConnectedComponentsPathsAtomsRef, $ConnectedComponentsPathsBondsRef);
|
|
|
2679
|
|
|
2680 # Retrieve information for marked aromatic atoms not in the rings...
|
|
|
2681 ($AtomIDsRef, $AtomIDsMapRef) = $This->_GetNonRingAromaticAtomIDs();
|
|
|
2682
|
|
|
2683 # Identify connected components containing marked aromatic atoms not in the rings...
|
|
|
2684 ($ConnectedComponentsAtomIDsRef, $ConnectedComponentsAtomIDsMapRef) = $This->_GetConnectedComponentsForNonRingAromaticAtoms($AtomIDsRef);
|
|
|
2685
|
|
|
2686 # Identify paths for connected components containing non-ring aromatic atoms...
|
|
|
2687 ($ConnectedComponentsPathsAtomsRef, $ConnectedComponentsPathsBondsRef) = $This->_GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms($AtomIDsMapRef, $ConnectedComponentsAtomIDsRef, $ConnectedComponentsAtomIDsMapRef);
|
|
|
2688
|
|
|
2689 return ($ConnectedComponentsPathsAtomsRef, $ConnectedComponentsPathsBondsRef);
|
|
|
2690 }
|
|
|
2691
|
|
|
2692 # Collect information for marked aromatic atoms not in the rings...
|
|
|
2693 #
|
|
|
2694 sub _GetNonRingAromaticAtomIDs {
|
|
|
2695 my($This) = @_;
|
|
|
2696 my($Atom, $AtomID, @AtomIDs, %AtomIDsMap);
|
|
|
2697
|
|
|
2698 @AtomIDs = ();
|
|
|
2699 %AtomIDsMap = ();
|
|
|
2700
|
|
|
2701 ATOM: for $Atom ($This->GetAtoms()) {
|
|
|
2702 if (!$Atom->IsAromatic()) {
|
|
|
2703 next ATOM;
|
|
|
2704 }
|
|
|
2705 if ($Atom->IsInRing()) {
|
|
|
2706 next ATOM;
|
|
|
2707 }
|
|
|
2708 $AtomID = $Atom->GetID();
|
|
|
2709
|
|
|
2710 push @AtomIDs, $AtomID;
|
|
|
2711 $AtomIDsMap{$AtomID} = $Atom;
|
|
|
2712 }
|
|
|
2713
|
|
|
2714 return (\@AtomIDs, \%AtomIDsMap);
|
|
|
2715 }
|
|
|
2716
|
|
|
2717 # Retrieve connected non-ring atom components as a reference to an array of references
|
|
|
2718 # containing atom IDs of connecnted components...
|
|
|
2719 #
|
|
|
2720 sub _GetConnectedComponentsForNonRingAromaticAtoms {
|
|
|
2721 my($This, $AtomIDsRef) = @_;
|
|
|
2722 my($Index, $AtomID, $AtomIDsGraph, @BondedAtomPairIDs, @ComponentsAtomIDsRefs, @ComponentsAtomIDsMapRefs);
|
|
|
2723
|
|
|
2724 @ComponentsAtomIDsRefs = ();
|
|
|
2725 @ComponentsAtomIDsMapRefs = ();
|
|
|
2726
|
|
|
2727 # Get bonded atom pair IDs...
|
|
|
2728 @BondedAtomPairIDs = $This->_GetBondedAtomPairAtomIDsFromAtomIDs(@{$AtomIDsRef});
|
|
|
2729
|
|
|
2730 if (!@BondedAtomPairIDs) {
|
|
|
2731 return (\@ComponentsAtomIDsRefs, \@ComponentsAtomIDsMapRefs);
|
|
|
2732 }
|
|
|
2733
|
|
|
2734 $AtomIDsGraph = new Graph(@{$AtomIDsRef});
|
|
|
2735 $AtomIDsGraph->AddEdges(@BondedAtomPairIDs);
|
|
|
2736
|
|
|
2737 @ComponentsAtomIDsRefs = $AtomIDsGraph->GetConnectedComponentsVertices();
|
|
|
2738
|
|
|
2739 # Setup atom IDs map for each component...
|
|
|
2740 for $Index (0 .. $#ComponentsAtomIDsRefs) {
|
|
|
2741 %{$ComponentsAtomIDsMapRefs[$Index]} = ();
|
|
|
2742
|
|
|
2743 for $AtomID (@{$ComponentsAtomIDsRefs[$Index]}) {
|
|
|
2744 $ComponentsAtomIDsMapRefs[$Index]{$AtomID} = $AtomID;
|
|
|
2745 }
|
|
|
2746 }
|
|
|
2747
|
|
|
2748 return (\@ComponentsAtomIDsRefs, \@ComponentsAtomIDsMapRefs);
|
|
|
2749 }
|
|
|
2750
|
|
|
2751 # Get linear paths for connected components starting and ending at terminal aromatic atoms,
|
|
|
2752 # which are connected to only one other aromatic atom in the connected component..
|
|
|
2753 #
|
|
|
2754 sub _GetConnectedComponentsPathsAtomsAndBondsForNonRingAromaticAtoms {
|
|
|
2755 my($This, $AtomIDsMapRef, $ComponentsAtomIDsRef, $ComponentsAtomIDsMapRef) = @_;
|
|
|
2756 my($Index, $AtomID, $Atom, $AtomNbr, $AtomNbrID, $NumOfNonRingAromaticNbrs, $AtomIndex1, $AtomIndex2, $AtomID1, $AtomID2, $Atom1, $Atom2, $AtomIDsGraph, $StartTerminalAtomID, $EndTerminalAtomID, @Paths, @PathAtomIDs, @PathsAtoms, @PathsBonds, @TerminalAtomIDs, @AtomIDs, @BondedAtomPairIDs);
|
|
|
2757
|
|
|
2758 @PathsAtoms = ();
|
|
|
2759 @PathsBonds = ();
|
|
|
2760
|
|
|
2761 @TerminalAtomIDs = ();
|
|
|
2762
|
|
|
2763 $Index = 0;
|
|
|
2764 COMPONENT: for $Index (0 .. $#{$ComponentsAtomIDsRef}) {
|
|
|
2765 @{$TerminalAtomIDs[$Index]} = ();
|
|
|
2766
|
|
|
2767 # Identify terminal atoms for connected components...
|
|
|
2768 #
|
|
|
2769 # Notes:
|
|
|
2770 # . Terminal atoms are defined as atoms connected to only one marked
|
|
|
2771 # aromatic atom.
|
|
|
2772 # . Linear connected compoents contain only two terminal atoms.
|
|
|
2773 #
|
|
|
2774 ATOM: for $AtomID (@{$ComponentsAtomIDsRef->[$Index]}) {
|
|
|
2775 $Atom = $AtomIDsMapRef->{$AtomID};
|
|
|
2776 $NumOfNonRingAromaticNbrs = 0;
|
|
|
2777
|
|
|
2778 ATOMNBRID: for $AtomNbr ($Atom->GetNeighbors()) {
|
|
|
2779 $AtomNbrID = $AtomNbr->GetID();
|
|
|
2780
|
|
|
2781 # Is neighbor in the same connected components containing aromatic atoms?
|
|
|
2782 if (!exists $ComponentsAtomIDsMapRef->[$Index]{$AtomNbrID}) {
|
|
|
2783 next ATOMNBRID;
|
|
|
2784 }
|
|
|
2785 $NumOfNonRingAromaticNbrs++;
|
|
|
2786 }
|
|
|
2787
|
|
|
2788 # Is it a terminal atom?
|
|
|
2789 if ($NumOfNonRingAromaticNbrs != 1) {
|
|
|
2790 next ATOM;
|
|
|
2791 }
|
|
|
2792 push @{$TerminalAtomIDs[$Index]}, $AtomID;
|
|
|
2793 }
|
|
|
2794
|
|
|
2795 if (@{$TerminalAtomIDs[$Index]} != 2) {
|
|
|
2796 next COMPONENT;
|
|
|
2797 }
|
|
|
2798
|
|
|
2799 # Setup bonded atom pair IDs for connected component...
|
|
|
2800 #
|
|
|
2801 @AtomIDs = @{$ComponentsAtomIDsRef->[$Index]};
|
|
|
2802 @BondedAtomPairIDs = ();
|
|
|
2803
|
|
|
2804 for $AtomIndex1 ( 0 .. $#AtomIDs) {
|
|
|
2805 $AtomID1 = $AtomIDs[$AtomIndex1];
|
|
|
2806 $Atom1 = $AtomIDsMapRef->{$AtomID1};
|
|
|
2807
|
|
|
2808 for $AtomIndex2 ( ($AtomIndex1 + 1) .. $#AtomIDs) {
|
|
|
2809 $AtomID2 = $AtomIDs[$AtomIndex2];
|
|
|
2810 $Atom2 = $AtomIDsMapRef->{$AtomID2};
|
|
|
2811
|
|
|
2812 if ($Atom1->IsBondedToAtom($Atom2)) {
|
|
|
2813 push @BondedAtomPairIDs, ($AtomID1, $AtomID2);
|
|
|
2814 }
|
|
|
2815 }
|
|
|
2816 }
|
|
|
2817
|
|
|
2818 if (!@BondedAtomPairIDs) {
|
|
|
2819 next COMPONENT;
|
|
|
2820 }
|
|
|
2821
|
|
|
2822 # Get path for connected component...
|
|
|
2823 $AtomIDsGraph = new Graph(@AtomIDs);
|
|
|
2824 $AtomIDsGraph->AddEdges(@BondedAtomPairIDs);
|
|
|
2825
|
|
|
2826 ($StartTerminalAtomID, $EndTerminalAtomID) = sort { $a <=> $b } @{$TerminalAtomIDs[$Index]};
|
|
|
2827 @Paths = $AtomIDsGraph->GetPathsBetween($StartTerminalAtomID, $EndTerminalAtomID);
|
|
|
2828
|
|
|
2829 if (@Paths != 1) {
|
|
|
2830 next COMPONENT;
|
|
|
2831 }
|
|
|
2832
|
|
|
2833 @PathAtomIDs = $Paths[0]->GetVertices();
|
|
|
2834
|
|
|
2835 my(@PathAtoms);
|
|
|
2836 @PathAtoms = $This->_GetAtomsFromAtomIDs(@PathAtomIDs);
|
|
|
2837 push @PathsAtoms, \@PathAtoms;
|
|
|
2838
|
|
|
2839 my(@PathBonds);
|
|
|
2840 @PathBonds = $This->_GetPathBonds(@PathAtomIDs);
|
|
|
2841 push @PathsBonds, \@PathBonds;
|
|
|
2842
|
|
|
2843 }
|
|
|
2844
|
|
|
2845 return (\@PathsAtoms, \@PathsBonds);
|
|
|
2846 }
|
|
|
2847
|
|
|
2848 # Setup initial processing status of atoms and bonds involved in connected paths
|
|
|
2849 # before starting kekulization...
|
|
|
2850 #
|
|
|
2851 # Possible atom processing status: DoubleBondPossible, DoubleBondAssigned, DoubleBondNotPossible
|
|
|
2852 # Initial status: DoubleBondPossible or DoubleBondNotPossible
|
|
|
2853 #
|
|
|
2854 # Possible bond processing status: DoubleBondAssigned, SingleBondAssigned, NotProcessed
|
|
|
2855 #
|
|
|
2856 # Possible paths processing status: Processed, NotProcessed
|
|
|
2857 # Initial status: NotProcessed
|
|
|
2858 #
|
|
|
2859 sub _SetupConnectedPathSetsForKekulization {
|
|
|
2860 my($This, $PathAtomsSetsRef, $PathBondsSetsRef) = @_;
|
|
|
2861 my($PathIndex, $PathAtomsRef, $PathBondsRef, $Atom, $AtomID, $Bond, $BondID, %AtomProcessingStatusMap, %BondProcessingStatusMap, @PathsProcessingStatus, %InitialPathBondOrderMap);
|
|
|
2862
|
|
|
2863 # Possible path set status values: Processed, NotProcessed
|
|
|
2864 # Initial value: NotProcessed
|
|
|
2865 #
|
|
|
2866 @PathsProcessingStatus = ('NotProcessed') x scalar @{$PathAtomsSetsRef};
|
|
|
2867
|
|
|
2868 # Collect initial bond order of path bonds before setting bond orders to 1
|
|
|
2869 # and use it to set the bond order back to intial value after it has been processed for
|
|
|
2870 # availability of double bonds...
|
|
|
2871 #
|
|
|
2872 %InitialPathBondOrderMap = ();
|
|
|
2873 for $PathBondsRef (@{$PathBondsSetsRef}) {
|
|
|
2874 BOND: for $Bond (@{$PathBondsRef}) {
|
|
|
2875 $BondID = $Bond->GetID();
|
|
|
2876 if (exists $InitialPathBondOrderMap{$BondID}) {
|
|
|
2877 next BOND;
|
|
|
2878 }
|
|
|
2879 $InitialPathBondOrderMap{$BondID} = $Bond->GetBondOrder();
|
|
|
2880 $Bond->SetBondOrder(1);
|
|
|
2881 }
|
|
|
2882 }
|
|
|
2883
|
|
|
2884 %AtomProcessingStatusMap = ();
|
|
|
2885 %BondProcessingStatusMap = ();
|
|
|
2886
|
|
|
2887 for $PathIndex (0 .. $#{$PathAtomsSetsRef}) {
|
|
|
2888
|
|
|
2889 $PathAtomsRef = $PathAtomsSetsRef->[$PathIndex];
|
|
|
2890 ATOM: for $Atom (@{$PathAtomsRef}) {
|
|
|
2891 $AtomID = $Atom->GetID();
|
|
|
2892 if (exists $AtomProcessingStatusMap{$AtomID}) {
|
|
|
2893 next ATOM;
|
|
|
2894 }
|
|
|
2895 $AtomProcessingStatusMap{$AtomID} = ($Atom->GetNumOfBondsAvailableForNonHydrogenAtoms() >= 1) ? 'DoubleBondPossible' : 'DoubleBondNotPossible';
|
|
|
2896 }
|
|
|
2897
|
|
|
2898 $PathBondsRef = $PathBondsSetsRef->[$PathIndex];
|
|
|
2899 BOND: for $Bond (@{$PathBondsRef}) {
|
|
|
2900 $BondID = $Bond->GetID();
|
|
|
2901 if (exists $BondProcessingStatusMap{$BondID}) {
|
|
|
2902 next BOND;
|
|
|
2903 }
|
|
|
2904 $BondProcessingStatusMap{$BondID} = 'NotProcessed';
|
|
|
2905 }
|
|
|
2906 }
|
|
|
2907
|
|
|
2908 # Set bond orders back to initial bond orders...
|
|
|
2909 for $PathIndex (0 .. $#{$PathAtomsSetsRef}) {
|
|
|
2910 $PathBondsRef = $PathBondsSetsRef->[$PathIndex];
|
|
|
2911
|
|
|
2912 for $Bond (@{$PathBondsRef}) {
|
|
|
2913 $BondID = $Bond->GetID();
|
|
|
2914 if (exists $InitialPathBondOrderMap{$BondID}) {
|
|
|
2915 $Bond->SetBondOrder($InitialPathBondOrderMap{$BondID});
|
|
|
2916 }
|
|
|
2917 }
|
|
|
2918 }
|
|
|
2919
|
|
|
2920 return (\%AtomProcessingStatusMap, \%BondProcessingStatusMap, \@PathsProcessingStatus);
|
|
|
2921 }
|
|
|
2922
|
|
|
2923 # Kekulize connected path sets corresponding to fused rings, individual rings, or any other
|
|
|
2924 # connected path...
|
|
|
2925 #
|
|
|
2926 # Note:
|
|
|
2927 # . PathAtomsRef and PathBondsRef contain paths and bonds corresponding to path
|
|
|
2928 # under consideration for kekulization
|
|
|
2929 # . PathAtomsSetsRef and PathBondsSetsRef contain any other available paths fused
|
|
|
2930 # to the path being kekulized
|
|
|
2931 # . _KekulizeConnectedPathSets is invoked recursively to kekulize all available paths
|
|
|
2932 #
|
|
|
2933 sub _KekulizeConnectedPathSets {
|
|
|
2934 my($This, $PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef) = @_;
|
|
|
2935 my($PathBond);
|
|
|
2936
|
|
|
2937 # Get next available path bond...
|
|
|
2938 $PathBond = $This->_GetNextAvailablePathBondForKekulization($PathBondsRef, $BondProcessingStatusMapRef);
|
|
|
2939
|
|
|
2940 if ($PathBond) {
|
|
|
2941 return $This->_ProcessNextAvailablePathBondForKekulization($PathBond, $PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef);
|
|
|
2942 }
|
|
|
2943
|
|
|
2944 # Did kekulization succeed for the current path bonds?
|
|
|
2945 if (!$This->_DidKekulizationSucceedForPathBonds($PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef)) {
|
|
|
2946 return 0;
|
|
|
2947 }
|
|
|
2948
|
|
|
2949 # Is there any other path available for kekulization?
|
|
|
2950 ($PathAtomsRef, $PathBondsRef) = $This->_GetNextAvailablePathForKekulization($PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef);
|
|
|
2951
|
|
|
2952 if ($PathAtomsRef && $PathBondsRef) {
|
|
|
2953 # Recursively call itself to kekulize next path, which could either be a new path or part
|
|
|
2954 # of a fused paths corresponding to fused ring sets...
|
|
|
2955 #
|
|
|
2956 return $This->_KekulizeConnectedPathSets($PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef);
|
|
|
2957 }
|
|
|
2958
|
|
|
2959 return 1;
|
|
|
2960 }
|
|
|
2961
|
|
|
2962 # Get next available path bond in a list of path bonds...
|
|
|
2963 #
|
|
|
2964 sub _GetNextAvailablePathBondForKekulization {
|
|
|
2965 my($This, $PathBondsRef, $BondProcessingStatusMapRef) = @_;
|
|
|
2966 my($AvailablePathBond, $PathBond, $PathBondID);
|
|
|
2967
|
|
|
2968 $AvailablePathBond = undef;
|
|
|
2969
|
|
|
2970 BOND: for $PathBond (@{$PathBondsRef}) {
|
|
|
2971 $PathBondID = $PathBond->GetID();
|
|
|
2972 if (!exists $BondProcessingStatusMapRef->{$PathBondID}) {
|
|
|
2973 next BOND;
|
|
|
2974 }
|
|
|
2975 if ($BondProcessingStatusMapRef->{$PathBondID} =~ /^NotProcessed$/i) {
|
|
|
2976 $AvailablePathBond = $PathBond;
|
|
|
2977 last BOND;
|
|
|
2978 }
|
|
|
2979 }
|
|
|
2980
|
|
|
2981 return ($AvailablePathBond);
|
|
|
2982 }
|
|
|
2983
|
|
|
2984 # Process next available path bond for kekulizaiton...
|
|
|
2985 #
|
|
|
2986 sub _ProcessNextAvailablePathBondForKekulization {
|
|
|
2987 my($This, $PathBond, $PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef) = @_;
|
|
|
2988 my($PathBondID, $PathAtom1, $PathAtom2, $PathAtomID1, $PathAtomID2, %CurrentAtomProcessingStatusMap, %CurrentBondProcessingStatusMap);
|
|
|
2989
|
|
|
2990 $PathBondID = $PathBond->GetID();
|
|
|
2991
|
|
|
2992 ($PathAtom1, $PathAtom2) = $PathBond->GetAtoms();
|
|
|
2993 ($PathAtomID1, $PathAtomID2) = ($PathAtom1->GetID(), $PathAtom2->GetID());
|
|
|
2994
|
|
|
2995 %CurrentAtomProcessingStatusMap = %{$AtomProcessingStatusMapRef};
|
|
|
2996 %CurrentBondProcessingStatusMap = %{$BondProcessingStatusMapRef};
|
|
|
2997
|
|
|
2998 # Is it possible to assign a double bond to the current path bond?
|
|
|
2999 if ($AtomProcessingStatusMapRef->{$PathAtomID1} =~ /^DoubleBondPossible$/i && $AtomProcessingStatusMapRef->{$PathAtomID2} =~ /^DoubleBondPossible$/i ) {
|
|
|
3000 # Set current bond to double bond by appropriately marking atom and bond process status...
|
|
|
3001 $AtomProcessingStatusMapRef->{$PathAtomID1} = 'DoubleBondAssigned';
|
|
|
3002 $AtomProcessingStatusMapRef->{$PathAtomID2} = 'DoubleBondAssigned';
|
|
|
3003
|
|
|
3004 $BondProcessingStatusMapRef->{$PathBondID} = 'DoubleBondAssigned';
|
|
|
3005
|
|
|
3006 # Recursively call _KekulizeConnectedPathSets to kekulize next available bond...
|
|
|
3007 if ($This->_KekulizeConnectedPathSets($PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef)) {
|
|
|
3008 return 1;
|
|
|
3009 }
|
|
|
3010
|
|
|
3011 # Double bond at the current ring bond position didn't lead to successful kekulization...
|
|
|
3012 %{$AtomProcessingStatusMapRef} = %CurrentAtomProcessingStatusMap;
|
|
|
3013 %{$BondProcessingStatusMapRef} = %CurrentBondProcessingStatusMap;
|
|
|
3014 }
|
|
|
3015
|
|
|
3016 # Try single bond at the current ring bond position and recursively call _KekulizeConnectedPathSets to kekulize
|
|
|
3017 # rest of the ring bonds...
|
|
|
3018 #
|
|
|
3019 $BondProcessingStatusMapRef->{$PathBondID} = 'SingleBondAssigned';
|
|
|
3020
|
|
|
3021 if ($This->_KekulizeConnectedPathSets($PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef, $PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef)) {
|
|
|
3022 return 1;
|
|
|
3023 }
|
|
|
3024
|
|
|
3025 %{$AtomProcessingStatusMapRef} = %CurrentAtomProcessingStatusMap;
|
|
|
3026 %{$BondProcessingStatusMapRef} = %CurrentBondProcessingStatusMap;
|
|
|
3027
|
|
|
3028 # Kekulization didn't work out for path bonds...
|
|
|
3029
|
|
|
3030 return 0;
|
|
|
3031
|
|
|
3032 }
|
|
|
3033
|
|
|
3034 # Get next available path for kekulization from a set of fused ring paths...
|
|
|
3035 #
|
|
|
3036 sub _GetNextAvailablePathForKekulization {
|
|
|
3037 my($This, $PathAtomsSetsRef, $PathBondsSetsRef, $PathsProcessingStatusRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef) = @_;
|
|
|
3038 my($PathIndex, $AvailablePathIndex, $PathAtomsRef, $PathBondsRef, $PathBond, $PathBondID, $MaxNumOfPathBondsProcessed, $NumOfPathBondsProcessed);
|
|
|
3039
|
|
|
3040 ($PathAtomsRef, $PathBondsRef, $AvailablePathIndex) = (undef) x 3;
|
|
|
3041
|
|
|
3042 if (!(defined($PathAtomsSetsRef) && defined($PathBondsSetsRef) && defined($PathsProcessingStatusRef))) {
|
|
|
3043 return ($PathAtomsRef, $PathBondsRef);
|
|
|
3044 }
|
|
|
3045
|
|
|
3046 $MaxNumOfPathBondsProcessed = -999;
|
|
|
3047 $AvailablePathIndex = undef;
|
|
|
3048
|
|
|
3049 PATHINDEX: for $PathIndex (0 .. $#{$PathsProcessingStatusRef}) {
|
|
|
3050 if ($PathsProcessingStatusRef->[$PathIndex] =~ /^Processed$/i) {
|
|
|
3051 next PATHINDEX;
|
|
|
3052 }
|
|
|
3053
|
|
|
3054 # Count of already processed bonds in an unprocessed path bonds through
|
|
|
3055 # their participation in any fused bonds sets...
|
|
|
3056 #
|
|
|
3057 $NumOfPathBondsProcessed = 0;
|
|
|
3058 PATHBOND: for $PathBond (@{$PathBondsSetsRef->[$PathIndex]}) {
|
|
|
3059 $PathBondID = $PathBond->GetID();
|
|
|
3060 if ($BondProcessingStatusMapRef->{$PathBondID} =~ /^NotProcessed$/i) {
|
|
|
3061 next PATHBOND;
|
|
|
3062 }
|
|
|
3063 $NumOfPathBondsProcessed++;
|
|
|
3064 }
|
|
|
3065
|
|
|
3066 if ($NumOfPathBondsProcessed > $MaxNumOfPathBondsProcessed) {
|
|
|
3067 $AvailablePathIndex = $PathIndex;
|
|
|
3068 $MaxNumOfPathBondsProcessed = $NumOfPathBondsProcessed;
|
|
|
3069 }
|
|
|
3070
|
|
|
3071 }
|
|
|
3072
|
|
|
3073 # Is any path available?
|
|
|
3074 if (!$AvailablePathIndex) {
|
|
|
3075 return ($PathAtomsRef, $PathBondsRef);
|
|
|
3076 }
|
|
|
3077
|
|
|
3078 $PathsProcessingStatusRef->[$AvailablePathIndex] = 'Processed';
|
|
|
3079
|
|
|
3080 $PathAtomsRef = $PathAtomsSetsRef->[$AvailablePathIndex];
|
|
|
3081 $PathBondsRef = $PathBondsSetsRef->[$AvailablePathIndex];
|
|
|
3082
|
|
|
3083 return ($PathAtomsRef, $PathBondsRef);
|
|
|
3084 }
|
|
|
3085
|
|
|
3086 # Check for kekulization in a specific set of path bonds. For successful kekulization, all
|
|
|
3087 # all path atoms marked with DoubleBondPossible must be involved in a path double bond...
|
|
|
3088 #
|
|
|
3089 sub _DidKekulizationSucceedForPathBonds {
|
|
|
3090 my($This, $PathAtomsRef, $PathBondsRef, $AtomProcessingStatusMapRef, $BondProcessingStatusMapRef) = @_;
|
|
|
3091 my($PathAtom, $PathAtomID);
|
|
|
3092
|
|
|
3093 for $PathAtom (@{$PathAtomsRef}) {
|
|
|
3094 $PathAtomID = $PathAtom->GetID();
|
|
|
3095 if (exists $AtomProcessingStatusMapRef->{$PathAtomID} && $AtomProcessingStatusMapRef->{$PathAtomID} =~ /^DoubleBondPossible$/i) {
|
|
|
3096 return 0;
|
|
|
3097 }
|
|
|
3098 }
|
|
|
3099 return 1;
|
|
|
3100 }
|
|
|
3101
|
|
|
3102 # Assign bond orders to the bonds in a molecule which have been successfully
|
|
|
3103 # kekulized along with optional clearing of aromaticty property...
|
|
|
3104 #
|
|
|
3105 sub _ProcessBondOrdersAssignedDuringSuccessfulKekulization {
|
|
|
3106 my($This, $BondsRef, $BondsProcessingStatusMapRef, $DeleteBondsAromaticity) = @_;
|
|
|
3107 my($Bond, $BondID, $BondOrder);
|
|
|
3108
|
|
|
3109 $DeleteBondsAromaticity = defined $DeleteBondsAromaticity ? $DeleteBondsAromaticity : 0;
|
|
|
3110
|
|
|
3111 BOND: for $Bond (@{$BondsRef}) {
|
|
|
3112 $BondID = $Bond->GetID();
|
|
|
3113
|
|
|
3114 if (!exists $BondsProcessingStatusMapRef->{$BondID}) {
|
|
|
3115 carp "Warning: ${ClassName}->_ProcessBondOrdersAssignedDuringSuccessfulKekulization: Couldn't process bond with bond ID, $BondID: It's not available in the list of bonds processed for kekulization...";
|
|
|
3116 next BOND;
|
|
|
3117 }
|
|
|
3118
|
|
|
3119 $BondOrder = ($BondsProcessingStatusMapRef->{$BondID} =~ /^DoubleBondAssigned$/i) ? 2 : 1;
|
|
|
3120 $Bond->SetBondOrder($BondOrder);
|
|
|
3121
|
|
|
3122 if ($DeleteBondsAromaticity) {
|
|
|
3123 $Bond->DeleteAromatic();
|
|
|
3124 }
|
|
|
3125 }
|
|
|
3126 return $This;
|
|
|
3127 }
|
|
|
3128
|
|
|
3129 # Does molecule contains aromatic rings?
|
|
|
3130 #
|
|
|
3131 sub HasAromaticRings {
|
|
|
3132 my($This) = @_;
|
|
|
3133
|
|
|
3134 return $This->GetNumOfAromaticRings() ? 1 : 0;
|
|
|
3135 }
|
|
|
3136
|
|
|
3137 # Does molecule contains any aromatic atom in a ring?
|
|
|
3138 #
|
|
|
3139 sub HasAromaticAtomsInRings {
|
|
|
3140 my($This) = @_;
|
|
|
3141 my($Atom);
|
|
|
3142
|
|
|
3143 ATOM: for $Atom ($This->GetAtoms()) {
|
|
|
3144 if (!$Atom->IsAromatic()) {
|
|
|
3145 next ATOM;
|
|
|
3146 }
|
|
|
3147 if ($Atom->IsInRing()) {
|
|
|
3148 return 1;
|
|
|
3149 }
|
|
|
3150 }
|
|
|
3151 return 0;
|
|
|
3152 }
|
|
|
3153
|
|
|
3154 # Does molecule contains any aromatic atom not in a ring?
|
|
|
3155 #
|
|
|
3156 sub HasAromaticAtomsNotInRings {
|
|
|
3157 my($This) = @_;
|
|
|
3158 my($Atom);
|
|
|
3159
|
|
|
3160 ATOM: for $Atom ($This->GetAtoms()) {
|
|
|
3161 if (!$Atom->IsAromatic()) {
|
|
|
3162 next ATOM;
|
|
|
3163 }
|
|
|
3164 if ($Atom->IsNotInRing()) {
|
|
|
3165 return 1;
|
|
|
3166 }
|
|
|
3167 }
|
|
|
3168 return 0;
|
|
|
3169 }
|
|
|
3170
|
|
|
3171 # Does molecule contains rings?
|
|
|
3172 #
|
|
|
3173 sub HasRings {
|
|
|
3174 my($This) = @_;
|
|
|
3175
|
|
|
3176 return $This->IsCyclic();
|
|
|
3177 }
|
|
|
3178
|
|
|
3179 # Does molecule contains only one ring?
|
|
|
3180 #
|
|
|
3181 sub HasOnlyOneRing {
|
|
|
3182 my($This) = @_;
|
|
|
3183
|
|
|
3184 return $This->IsUnicyclic();
|
|
|
3185 }
|
|
|
3186
|
|
|
3187 # Does molecule contains any rings?
|
|
|
3188 #
|
|
|
3189 sub HasNoRings {
|
|
|
3190 my($This) = @_;
|
|
|
3191
|
|
|
3192 return $This->IsAcyclic();
|
|
|
3193 }
|
|
|
3194
|
|
|
3195 # Get size of smallest ring...
|
|
|
3196 #
|
|
|
3197 sub GetSizeOfSmallestRing {
|
|
|
3198 my($This) = @_;
|
|
|
3199
|
|
|
3200 return $This->GetSizeOfSmallestCycle();
|
|
|
3201 }
|
|
|
3202
|
|
|
3203 # Get size of largest ring...
|
|
|
3204 #
|
|
|
3205 sub GetSizeOfLargestRing {
|
|
|
3206 my($This) = @_;
|
|
|
3207
|
|
|
3208 return $This->GetSizeOfLargestCycle();
|
|
|
3209 }
|
|
|
3210
|
|
|
3211 # Get number of rings...
|
|
|
3212 #
|
|
|
3213 sub GetNumOfRings {
|
|
|
3214 my($This) = @_;
|
|
|
3215
|
|
|
3216 return $This->GetNumOfCycles();
|
|
|
3217 }
|
|
|
3218
|
|
|
3219 # Get number of aromatic rings...
|
|
|
3220 #
|
|
|
3221 sub GetNumOfAromaticRings {
|
|
|
3222 my($This) = @_;
|
|
|
3223 my($NumOfRings);
|
|
|
3224
|
|
|
3225 $NumOfRings = scalar $This->GetAromaticRings();
|
|
|
3226
|
|
|
3227 return $NumOfRings;
|
|
|
3228 }
|
|
|
3229
|
|
|
3230 # Get num of rings with odd size...
|
|
|
3231 #
|
|
|
3232 sub GetNumOfRingsWithOddSize {
|
|
|
3233 my($This) = @_;
|
|
|
3234
|
|
|
3235 return $This->GetNumOfCyclesWithOddSize();
|
|
|
3236 }
|
|
|
3237
|
|
|
3238 # Get num of rings with even size...
|
|
|
3239 #
|
|
|
3240 sub GetNumOfRingsWithEvenSize {
|
|
|
3241 my($This) = @_;
|
|
|
3242
|
|
|
3243 return $This->GetNumOfCyclesWithEvenSize();
|
|
|
3244 }
|
|
|
3245
|
|
|
3246 # Get num of rings with specified size...
|
|
|
3247 #
|
|
|
3248 sub GetNumOfRingsWithSize {
|
|
|
3249 my($This, $RingSize) = @_;
|
|
|
3250
|
|
|
3251 return $This->GetNumOfCyclesWithSize($RingSize);
|
|
|
3252 }
|
|
|
3253
|
|
|
3254 # Get num of rings with size less than a specified size...
|
|
|
3255 #
|
|
|
3256 sub GetNumOfRingsWithSizeLessThan {
|
|
|
3257 my($This, $RingSize) = @_;
|
|
|
3258
|
|
|
3259 return $This->GetNumOfCyclesWithSizeLessThan($RingSize);
|
|
|
3260 }
|
|
|
3261
|
|
|
3262 # Get num of rings with size greater than a specified size...
|
|
|
3263 #
|
|
|
3264 sub GetNumOfRingsWithSizeGreaterThan {
|
|
|
3265 my($This, $RingSize) = @_;
|
|
|
3266
|
|
|
3267 return $This->GetNumOfCyclesWithSizeGreaterThan($RingSize);
|
|
|
3268 }
|
|
|
3269
|
|
|
3270 # Get largest ring as an array containing ring atoms...
|
|
|
3271 #
|
|
|
3272 sub GetLargestRing {
|
|
|
3273 my($This) = @_;
|
|
|
3274
|
|
|
3275 return $This->_GetRing($This->GetLargestCycle());
|
|
|
3276 }
|
|
|
3277
|
|
|
3278 # Get smallest ring as an array containing ring atoms...
|
|
|
3279 #
|
|
|
3280 sub GetSmallestRing {
|
|
|
3281 my($This) = @_;
|
|
|
3282
|
|
|
3283 return $This->_GetRing($This->GetSmallestCycle());
|
|
|
3284 }
|
|
|
3285
|
|
|
3286 # Get rings as an array containing references to arrays with ring atoms...
|
|
|
3287 #
|
|
|
3288 sub GetRings {
|
|
|
3289 my($This) = @_;
|
|
|
3290
|
|
|
3291 return $This->_GetRings($This->GetCycles());
|
|
|
3292 }
|
|
|
3293
|
|
|
3294 # Get aromatic rings as an array containing references to arrays with ring atoms...
|
|
|
3295 #
|
|
|
3296 sub GetAromaticRings {
|
|
|
3297 my($This) = @_;
|
|
|
3298
|
|
|
3299 return $This->_GetAromaticRings($This->GetCycles());
|
|
|
3300 }
|
|
|
3301
|
|
|
3302 # Get odd size rings as an array containing references to arrays with ring atoms...
|
|
|
3303 #
|
|
|
3304 sub GetRingsWithOddSize {
|
|
|
3305 my($This) = @_;
|
|
|
3306
|
|
|
3307 return $This->_GetRings($This->GetCyclesWithOddSize());
|
|
|
3308 }
|
|
|
3309
|
|
|
3310 # Get even size rings as an array containing references to arrays with ring atoms...
|
|
|
3311 #
|
|
|
3312 sub GetRingsWithEvenSize {
|
|
|
3313 my($This) = @_;
|
|
|
3314
|
|
|
3315 return $This->_GetRings($This->GetCyclesWithEvenSize());
|
|
|
3316 }
|
|
|
3317
|
|
|
3318 # Get rings with a specific size as an array containing references to arrays with ring atoms...
|
|
|
3319 #
|
|
|
3320 sub GetRingsWithSize {
|
|
|
3321 my($This, $RingSize) = @_;
|
|
|
3322
|
|
|
3323 return $This->_GetRings($This->GetCyclesWithSize($RingSize));
|
|
|
3324 }
|
|
|
3325
|
|
|
3326 # Get rings with size less than a specific size as an array containing references to arrays with ring atoms...
|
|
|
3327 #
|
|
|
3328 sub GetRingsWithSizeLessThan {
|
|
|
3329 my($This, $RingSize) = @_;
|
|
|
3330
|
|
|
3331 return $This->_GetRings($This->GetCyclesWithSizeLessThan($RingSize));
|
|
|
3332 }
|
|
|
3333
|
|
|
3334 # Get rings with size greater than a specific size as an array containing references to arrays with ring atoms...
|
|
|
3335 #
|
|
|
3336 sub GetRingsWithSizeGreaterThan {
|
|
|
3337 my($This, $RingSize) = @_;
|
|
|
3338
|
|
|
3339 return $This->_GetRings($This->GetCyclesWithSizeGreaterThan($RingSize));
|
|
|
3340 }
|
|
|
3341
|
|
|
3342 # Generate an array of bond objects for an array of ring atoms and return an array
|
|
|
3343 # of bond objects...
|
|
|
3344 #
|
|
|
3345 sub GetRingBonds {
|
|
|
3346 my($This, @RingAtoms) = @_;
|
|
|
3347 my(@Bonds);
|
|
|
3348
|
|
|
3349 @Bonds = ();
|
|
|
3350 if (!@RingAtoms) {
|
|
|
3351 # Return an empty ring bonds list...
|
|
|
3352 return @Bonds;
|
|
|
3353 }
|
|
|
3354
|
|
|
3355 my(@RingAtomIDs);
|
|
|
3356
|
|
|
3357 @RingAtomIDs = ();
|
|
|
3358 @RingAtomIDs = $This->_GetAtomsIDsFromAtoms(@RingAtoms);
|
|
|
3359 if (!@RingAtomIDs) {
|
|
|
3360 carp "Warning: ${ClassName}->GetRingBonds: No ring bonds retrieved: Atom IDs couldn't be retrieved for specified atoms...";
|
|
|
3361 return @Bonds;
|
|
|
3362 }
|
|
|
3363
|
|
|
3364 # Add start atom to the end to make it a cyclic path for ring: It's taken out during conversion
|
|
|
3365 # of cyclic path to a ring...
|
|
|
3366 push @RingAtomIDs, $RingAtomIDs[0];
|
|
|
3367
|
|
|
3368 return $This->_GetPathBonds(@RingAtomIDs);
|
|
|
3369 }
|
|
|
3370
|
|
|
3371 # Generate an array containing references to arrays of ring bond objects for rings specified
|
|
|
3372 # in an array of references to ring atoms...
|
|
|
3373 #
|
|
|
3374 sub GetRingBondsFromRings {
|
|
|
3375 my($This, @RingAtomsSets) = @_;
|
|
|
3376 my($RingAtomsRef, @RingBondsSets);
|
|
|
3377
|
|
|
3378 @RingBondsSets = ();
|
|
|
3379 for $RingAtomsRef (@RingAtomsSets) {
|
|
|
3380 my(@RingBonds);
|
|
|
3381 @RingBonds = $This->GetRingBonds(@{$RingAtomsRef});
|
|
|
3382
|
|
|
3383 push @RingBondsSets, \@RingBonds;
|
|
|
3384 }
|
|
|
3385
|
|
|
3386 return @RingBondsSets;
|
|
|
3387 }
|
|
|
3388
|
|
|
3389 # Does molecule has any fused rings?
|
|
|
3390 #
|
|
|
3391 sub HasFusedRings {
|
|
|
3392 my($This) = @_;
|
|
|
3393
|
|
|
3394 return $This->HasFusedCycles();
|
|
|
3395 }
|
|
|
3396
|
|
|
3397 # Get references to array of fused ring sets and non-fused rings. Fused ring sets array reference
|
|
|
3398 # contains refernces to arrays of rings; Non-fused rings array reference contains references to
|
|
|
3399 # arrays of ring atoms...
|
|
|
3400 # rings.
|
|
|
3401 #
|
|
|
3402 sub GetFusedAndNonFusedRings {
|
|
|
3403 my($This) = @_;
|
|
|
3404 my($FusedCyclesSetsRef, $NonFusedCyclesRef, @FusedRingSets, @NonFusedRings);
|
|
|
3405
|
|
|
3406 @FusedRingSets = (); @NonFusedRings = ();
|
|
|
3407 ($FusedCyclesSetsRef, $NonFusedCyclesRef) = $This->GetFusedAndNonFusedCycles();
|
|
|
3408 if (!(defined($FusedCyclesSetsRef) && defined($NonFusedCyclesRef))) {
|
|
|
3409 return (\@FusedRingSets, \@NonFusedRings);
|
|
|
3410 }
|
|
|
3411 my($FusedCyclesSetRef);
|
|
|
3412
|
|
|
3413 for $FusedCyclesSetRef (@{$FusedCyclesSetsRef}) {
|
|
|
3414 my(@FusedRingSet);
|
|
|
3415 @FusedRingSet = ();
|
|
|
3416 @FusedRingSet = $This->_GetRings(@{$FusedCyclesSetRef});
|
|
|
3417 push @FusedRingSets, \@FusedRingSet;
|
|
|
3418 }
|
|
|
3419
|
|
|
3420 @NonFusedRings = $This->_GetRings(@{$NonFusedCyclesRef});
|
|
|
3421
|
|
|
3422 return (\@FusedRingSets, \@NonFusedRings);
|
|
|
3423 }
|
|
|
3424
|
|
|
3425 # Get rings as an array containing references to arrays with ring atoms...
|
|
|
3426 #
|
|
|
3427 sub _GetRings {
|
|
|
3428 my($This, @CyclicPaths) = @_;
|
|
|
3429 my($CyclicPath, @Rings);
|
|
|
3430
|
|
|
3431 @Rings = ();
|
|
|
3432 if (!@CyclicPaths) {
|
|
|
3433 return @Rings;
|
|
|
3434 }
|
|
|
3435 if (!@CyclicPaths) {
|
|
|
3436 # Return an empty ring list...
|
|
|
3437 return @Rings;
|
|
|
3438 }
|
|
|
3439
|
|
|
3440 for $CyclicPath (@CyclicPaths) {
|
|
|
3441 my(@RingAtoms);
|
|
|
3442 @RingAtoms = ();
|
|
|
3443 push @RingAtoms, $This->_GetRing($CyclicPath);
|
|
|
3444
|
|
|
3445 push @Rings, \@RingAtoms;
|
|
|
3446 }
|
|
|
3447 return @Rings;
|
|
|
3448 }
|
|
|
3449
|
|
|
3450 # Get aromatic rings as an array containing references to arrays with ring atoms...
|
|
|
3451 #
|
|
|
3452 sub _GetAromaticRings {
|
|
|
3453 my($This, @CyclicPaths) = @_;
|
|
|
3454 my($RingAtomsRef, @Rings, @AromaticRings);
|
|
|
3455
|
|
|
3456 @AromaticRings = ();
|
|
|
3457 @Rings = $This->_GetRings(@CyclicPaths);
|
|
|
3458
|
|
|
3459 if (!@Rings) {
|
|
|
3460 return @AromaticRings;
|
|
|
3461 }
|
|
|
3462 RING: for $RingAtomsRef (@Rings) {
|
|
|
3463 if (!$This->IsRingAromatic(@{$RingAtomsRef})) {
|
|
|
3464 next RING;
|
|
|
3465 }
|
|
|
3466 my(@RingAtoms);
|
|
|
3467 @RingAtoms = ();
|
|
|
3468 push @RingAtoms, @{$RingAtomsRef};
|
|
|
3469
|
|
|
3470 push @AromaticRings, \@RingAtoms;
|
|
|
3471 }
|
|
|
3472 return @AromaticRings;
|
|
|
3473 }
|
|
|
3474
|
|
|
3475 # Map atom IDs in cyclic path to atoms and return a reference to an array containing ring atoms...
|
|
|
3476 #
|
|
|
3477 # Note:
|
|
|
3478 # . Start and end vertex is same for cyclic paths. So end atom is removed before
|
|
|
3479 # returning atoms array as ring atoms...
|
|
|
3480 #
|
|
|
3481 sub _GetRing {
|
|
|
3482 my($This, $CyclicPath) = @_;
|
|
|
3483 my(@RingAtoms);
|
|
|
3484
|
|
|
3485 @RingAtoms = ();
|
|
|
3486 if (!defined $CyclicPath) {
|
|
|
3487 # Return an empty atoms list...
|
|
|
3488 return @RingAtoms;
|
|
|
3489 }
|
|
|
3490
|
|
|
3491 @RingAtoms = $This->_GetPathAtoms($CyclicPath);
|
|
|
3492 if (@RingAtoms) {
|
|
|
3493 pop @RingAtoms;
|
|
|
3494 }
|
|
|
3495 return @RingAtoms;
|
|
|
3496 }
|
|
|
3497
|
|
|
3498 # Map atom IDs to atoms and return a reference to an array containing these atoms...
|
|
|
3499 #
|
|
|
3500 sub _GetPathAtoms {
|
|
|
3501 my($This, $Path) = @_;
|
|
|
3502 my(@PathAtoms);
|
|
|
3503
|
|
|
3504 @PathAtoms = ();
|
|
|
3505 if (!defined $Path) {
|
|
|
3506 carp "Warning: ${ClassName}->_GetPathAtoms: No path atoms retrieved: Path must be defined...";
|
|
|
3507 return @PathAtoms;
|
|
|
3508 }
|
|
|
3509 my(@AtomIDs);
|
|
|
3510
|
|
|
3511 @AtomIDs = ();
|
|
|
3512 @AtomIDs = $Path->GetVertices();
|
|
|
3513
|
|
|
3514 @PathAtoms = $This->_GetAtomsFromAtomIDs(@AtomIDs);
|
|
|
3515
|
|
|
3516 return @PathAtoms;
|
|
|
3517 }
|
|
|
3518
|
|
|
3519 # Get bonds for a path specified by atom IDs...
|
|
|
3520 #
|
|
|
3521 sub _GetPathBonds {
|
|
|
3522 my($This, @AtomIDs) = @_;
|
|
|
3523 my($Index, $AtomID1, $AtomID2, @Bonds, @EdgesAtomIDs);
|
|
|
3524
|
|
|
3525 @Bonds = (); @EdgesAtomIDs = ();
|
|
|
3526
|
|
|
3527 if (!@AtomIDs || @AtomIDs == 1) {
|
|
|
3528 return @Bonds;
|
|
|
3529 }
|
|
|
3530
|
|
|
3531 # Setup edges...
|
|
|
3532 for $Index (0 .. ($#AtomIDs - 1) ) {
|
|
|
3533 $AtomID1 = $AtomIDs[$Index];
|
|
|
3534 $AtomID2 = $AtomIDs[$Index + 1];
|
|
|
3535 push @EdgesAtomIDs, ($AtomID1, $AtomID2);
|
|
|
3536 }
|
|
|
3537 @Bonds = $This->GetEdgesProperty('Bond', @EdgesAtomIDs);
|
|
|
3538
|
|
|
3539 return @Bonds;
|
|
|
3540 }
|
|
|
3541
|
|
|
3542 # Map atom ID to an atom...
|
|
|
3543 #
|
|
|
3544 sub _GetAtomFromAtomID {
|
|
|
3545 my($This, $AtomID) = @_;
|
|
|
3546
|
|
|
3547 return $This->GetVertexProperty('Atom', $AtomID);
|
|
|
3548 }
|
|
|
3549
|
|
|
3550 # Map atom IDs to atoms and return an array containing these atoms...
|
|
|
3551 #
|
|
|
3552 sub _GetAtomsFromAtomIDs {
|
|
|
3553 my($This, @AtomIDs) = @_;
|
|
|
3554
|
|
|
3555 return $This->GetVerticesProperty('Atom', @AtomIDs);
|
|
|
3556 }
|
|
|
3557
|
|
|
3558 # Map atoms to atom IDs and return an array containing these atoms...
|
|
|
3559 #
|
|
|
3560 sub _GetAtomsIDsFromAtoms {
|
|
|
3561 my($This, @Atoms) = @_;
|
|
|
3562
|
|
|
3563 return map { $_->GetID() } @Atoms;
|
|
|
3564 }
|
|
|
3565
|
|
|
3566 # Get bonded atom pair atom IDs for specified list of atom IDs...
|
|
|
3567 #
|
|
|
3568 sub _GetBondedAtomPairAtomIDsFromAtomIDs {
|
|
|
3569 my($This, @AtomIDs) = @_;
|
|
|
3570 my($AtomIndex1, $AtomID1, $Atom1, $AtomIndex2, $AtomID2, $Atom2, @Atoms, @BondedAtomPairIDs);
|
|
|
3571
|
|
|
3572 @BondedAtomPairIDs = ();
|
|
|
3573 @Atoms = $This->_GetAtomsFromAtomIDs(@AtomIDs);
|
|
|
3574
|
|
|
3575 for $AtomIndex1 ( 0 .. $#Atoms) {
|
|
|
3576 $Atom1 = $Atoms[$AtomIndex1];
|
|
|
3577 $AtomID1 = $Atom1->GetID();
|
|
|
3578
|
|
|
3579 ATOMINDEX2: for $AtomIndex2 ( ($AtomIndex1 + 1) .. $#Atoms) {
|
|
|
3580 $Atom2 = $Atoms[$AtomIndex2];
|
|
|
3581 if (!$Atom1->IsBondedToAtom($Atom2)) {
|
|
|
3582 next ATOMINDEX2;
|
|
|
3583 }
|
|
|
3584 $AtomID2 = $Atom2->GetID();
|
|
|
3585
|
|
|
3586 push @BondedAtomPairIDs, ($AtomID1, $AtomID2);
|
|
|
3587 }
|
|
|
3588 }
|
|
|
3589
|
|
|
3590 return @BondedAtomPairIDs;
|
|
|
3591 }
|
|
|
3592
|
|
|
3593 # Get bonded atom pair atoms for specified list of atoms...
|
|
|
3594 #
|
|
|
3595 sub _GetBondedAtomPairAtomsFromAtoms {
|
|
|
3596 my($This, @Atoms) = @_;
|
|
|
3597 my($AtomIndex1, $Atom1, $AtomIndex2, $Atom2, @BondedAtomPairAtoms);
|
|
|
3598
|
|
|
3599 @BondedAtomPairAtoms = ();
|
|
|
3600
|
|
|
3601 for $AtomIndex1 ( 0 .. $#Atoms) {
|
|
|
3602 $Atom1 = $Atoms[$AtomIndex1];
|
|
|
3603
|
|
|
3604 ATOMINDEX2: for $AtomIndex2 ( ($AtomIndex1 + 1) .. $#Atoms) {
|
|
|
3605 $Atom2 = $Atoms[$AtomIndex2];
|
|
|
3606 if ($Atom1->IsBondedToAtom($Atom2)) {
|
|
|
3607 next ATOMINDEX2;
|
|
|
3608 }
|
|
|
3609
|
|
|
3610 push @BondedAtomPairAtoms, ($Atom1, $Atom2);
|
|
|
3611 }
|
|
|
3612 }
|
|
|
3613
|
|
|
3614 return @BondedAtomPairAtoms;
|
|
|
3615 }
|
|
|
3616
|
|
|
3617 # Is atom in a ring?
|
|
|
3618 #
|
|
|
3619 sub _IsAtomInRing {
|
|
|
3620 my($This, $Atom) = @_;
|
|
|
3621
|
|
|
3622 return $This->IsCyclicVertex($Atom->GetID());
|
|
|
3623 }
|
|
|
3624
|
|
|
3625 # Is atom not in a ring?
|
|
|
3626 #
|
|
|
3627 sub _IsAtomNotInRing {
|
|
|
3628 my($This, $Atom) = @_;
|
|
|
3629
|
|
|
3630 return $This->IsAcyclicVertex($Atom->GetID());
|
|
|
3631 }
|
|
|
3632
|
|
|
3633 # Is atom only in one ring?
|
|
|
3634 #
|
|
|
3635 sub _IsAtomInOnlyOneRing {
|
|
|
3636 my($This, $Atom) = @_;
|
|
|
3637
|
|
|
3638 return $This->IsUnicyclicVertex($Atom->GetID());
|
|
|
3639 }
|
|
|
3640
|
|
|
3641 # Is atom in a ring of specified size?
|
|
|
3642 #
|
|
|
3643 sub _IsAtomInRingOfSize {
|
|
|
3644 my($This, $Atom, $RingSize) = @_;
|
|
|
3645
|
|
|
3646 return $This->GetNumOfVertexCyclesWithSize($Atom->GetID(), $RingSize) ? 1 : 0;
|
|
|
3647 }
|
|
|
3648
|
|
|
3649 # Get size of smallest ring containing specified atom...
|
|
|
3650 #
|
|
|
3651 sub _GetSizeOfSmallestAtomRing {
|
|
|
3652 my($This, $Atom) = @_;
|
|
|
3653
|
|
|
3654 return $This->GetSizeOfSmallestVertexCycle($Atom->GetID());
|
|
|
3655 }
|
|
|
3656
|
|
|
3657 # Get size of largest ring containing specified atom...
|
|
|
3658 #
|
|
|
3659 sub _GetSizeOfLargestAtomRing {
|
|
|
3660 my($This, $Atom) = @_;
|
|
|
3661
|
|
|
3662 return $This->GetSizeOfLargestVertexCycle($Atom->GetID());
|
|
|
3663 }
|
|
|
3664
|
|
|
3665 # Get number of rings containing specified atom...
|
|
|
3666 #
|
|
|
3667 sub _GetNumOfAtomRings {
|
|
|
3668 my($This, $Atom) = @_;
|
|
|
3669
|
|
|
3670 return $This->GetNumOfVertexCycles($Atom->GetID());
|
|
|
3671 }
|
|
|
3672
|
|
|
3673 # Get number of rings with odd size containing specified atom...
|
|
|
3674 #
|
|
|
3675 sub _GetNumOfAtomRingsWithOddSize {
|
|
|
3676 my($This, $Atom) = @_;
|
|
|
3677
|
|
|
3678 return $This->GetNumOfVertexCyclesWithOddSize($Atom->GetID());
|
|
|
3679 }
|
|
|
3680
|
|
|
3681 # Get number of rings with even size containing specified atom...
|
|
|
3682 #
|
|
|
3683 sub _GetNumOfAtomRingsWithEvenSize {
|
|
|
3684 my($This, $Atom) = @_;
|
|
|
3685
|
|
|
3686 return $This->GetNumOfVertexCyclesWithEvenSize($Atom->GetID());
|
|
|
3687 }
|
|
|
3688
|
|
|
3689 # Get number of rings with specified size containing specified atom...
|
|
|
3690 #
|
|
|
3691 sub _GetNumOfAtomRingsWithSize {
|
|
|
3692 my($This, $Atom, $RingSize) = @_;
|
|
|
3693
|
|
|
3694 return $This->GetNumOfVertexCyclesWithSize($Atom->GetID(), $RingSize);
|
|
|
3695 }
|
|
|
3696
|
|
|
3697 # Get number of rings with size less than specified containing specified atom...
|
|
|
3698 #
|
|
|
3699 sub _GetNumOfAtomRingsWithSizeLessThan {
|
|
|
3700 my($This, $Atom, $RingSize) = @_;
|
|
|
3701
|
|
|
3702 return $This->GetNumOfVertexCyclesWithSizeLessThan($Atom->GetID(), $RingSize);
|
|
|
3703 }
|
|
|
3704
|
|
|
3705 # Get number of rings with size greater than specified containing specified atom...
|
|
|
3706 #
|
|
|
3707 sub _GetNumOfAtomRingsWithSizeGreaterThan {
|
|
|
3708 my($This, $Atom, $RingSize) = @_;
|
|
|
3709
|
|
|
3710 return $This->GetNumOfVertexCyclesWithSizeGreaterThan($Atom->GetID(), $RingSize);
|
|
|
3711 }
|
|
|
3712
|
|
|
3713 # Get smallest ring as an array containing ring atoms...
|
|
|
3714 #
|
|
|
3715 sub _GetSmallestAtomRing {
|
|
|
3716 my($This, $Atom) = @_;
|
|
|
3717
|
|
|
3718 return $This->_GetRing($This->GetSmallestVertexCycle($Atom->GetID()));
|
|
|
3719 }
|
|
|
3720
|
|
|
3721 # Get odd size rings an array of references to arrays containing ring atoms...
|
|
|
3722 #
|
|
|
3723 sub _GetLargestAtomRing {
|
|
|
3724 my($This, $Atom) = @_;
|
|
|
3725
|
|
|
3726 return $This->_GetRing($This->GetLargestVertexCycle($Atom->GetID()));
|
|
|
3727 }
|
|
|
3728
|
|
|
3729 # Get all rings an array of references to arrays containing ring atoms...
|
|
|
3730 #
|
|
|
3731 sub _GetAtomRings {
|
|
|
3732 my($This, $Atom) = @_;
|
|
|
3733
|
|
|
3734 return $This->_GetRings($This->GetVertexCycles($Atom->GetID()));
|
|
|
3735 }
|
|
|
3736
|
|
|
3737 # Get odd size rings an array of references to arrays containing ring atoms...
|
|
|
3738 #
|
|
|
3739 sub _GetAtomRingsWithOddSize {
|
|
|
3740 my($This, $Atom) = @_;
|
|
|
3741
|
|
|
3742 return $This->_GetRings($This->GetVertexCyclesWithOddSize($Atom->GetID()));
|
|
|
3743 }
|
|
|
3744
|
|
|
3745 # Get even size rings an array of references to arrays containing ring atoms...
|
|
|
3746 #
|
|
|
3747 sub _GetAtomRingsWithEvenSize {
|
|
|
3748 my($This, $Atom) = @_;
|
|
|
3749
|
|
|
3750 return $This->_GetRings($This->GetVertexCyclesWithEvenSize($Atom->GetID()));
|
|
|
3751 }
|
|
|
3752
|
|
|
3753 # Get rings with specified size an array of references to arrays containing ring atoms...
|
|
|
3754 #
|
|
|
3755 sub _GetAtomRingsWithSize {
|
|
|
3756 my($This, $Atom, $RingSize) = @_;
|
|
|
3757
|
|
|
3758 return $This->_GetRings($This->GetVertexCyclesWithSize($Atom->GetID(), $RingSize));
|
|
|
3759 }
|
|
|
3760
|
|
|
3761 # Get rings with size less than specfied size as an array of references to arrays containing ring atoms...
|
|
|
3762 #
|
|
|
3763 sub _GetAtomRingsWithSizeLessThan {
|
|
|
3764 my($This, $Atom, $RingSize) = @_;
|
|
|
3765
|
|
|
3766 return $This->_GetRings($This->GetVertexCyclesWithSizeLessThan($Atom->GetID(), $RingSize));
|
|
|
3767 }
|
|
|
3768
|
|
|
3769 # Get rings with size less than specfied size as an array of references to arrays containing ring atoms...
|
|
|
3770 #
|
|
|
3771 sub _GetAtomRingsWithSizeGreaterThan {
|
|
|
3772 my($This, $Atom, $RingSize) = @_;
|
|
|
3773
|
|
|
3774 return $This->_GetRings($This->GetVertexCyclesWithSizeGreaterThan($Atom->GetID(), $RingSize));
|
|
|
3775 }
|
|
|
3776
|
|
|
3777 # Is bond in a ring?
|
|
|
3778 #
|
|
|
3779 sub _IsBondInRing {
|
|
|
3780 my($This, $Bond) = @_;
|
|
|
3781 my($Atom1, $Atom2);
|
|
|
3782
|
|
|
3783 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3784
|
|
|
3785 return $This->IsCyclicEdge($Atom1->GetID(), $Atom2->GetID());
|
|
|
3786 }
|
|
|
3787
|
|
|
3788 # Is bond not in a ring?
|
|
|
3789 #
|
|
|
3790 sub _IsBondNotInRing {
|
|
|
3791 my($This, $Bond) = @_;
|
|
|
3792 my($Atom1, $Atom2);
|
|
|
3793
|
|
|
3794 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3795
|
|
|
3796 return $This->IsAcyclicEdge($Atom1->GetID(), $Atom2->GetID());
|
|
|
3797 }
|
|
|
3798
|
|
|
3799 # Is bond only in one ring?
|
|
|
3800 #
|
|
|
3801 sub _IsBondInOnlyOneRing {
|
|
|
3802 my($This, $Bond) = @_;
|
|
|
3803 my($Atom1, $Atom2);
|
|
|
3804
|
|
|
3805 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3806
|
|
|
3807 return $This->IsUnicyclicEdge($Atom1->GetID(), $Atom2->GetID());
|
|
|
3808 }
|
|
|
3809
|
|
|
3810 # Is bond in a ring of specified size?
|
|
|
3811 #
|
|
|
3812 sub _IsBondInRingOfSize {
|
|
|
3813 my($This, $Bond, $RingSize) = @_;
|
|
|
3814 my($Atom1, $Atom2);
|
|
|
3815
|
|
|
3816 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3817
|
|
|
3818 return $This->GetNumOfEdgeCyclesWithSize($Atom1->GetID(), $Atom2->GetID(), $RingSize) ? 1 : 0;
|
|
|
3819 }
|
|
|
3820
|
|
|
3821 # Get size of smallest ring containing specified bond...
|
|
|
3822 #
|
|
|
3823 sub _GetSizeOfSmallestBondRing {
|
|
|
3824 my($This, $Bond) = @_;
|
|
|
3825 my($Atom1, $Atom2);
|
|
|
3826
|
|
|
3827 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3828
|
|
|
3829 return $This->GetSizeOfSmallestEdgeCycle($Atom1->GetID(), $Atom2->GetID());
|
|
|
3830 }
|
|
|
3831
|
|
|
3832 # Get size of largest ring containing specified bond...
|
|
|
3833 #
|
|
|
3834 sub _GetSizeOfLargestBondRing {
|
|
|
3835 my($This, $Bond) = @_;
|
|
|
3836 my($Atom1, $Atom2);
|
|
|
3837
|
|
|
3838 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3839
|
|
|
3840 return $This->GetSizeOfLargestEdgeCycle($Atom1->GetID(), $Atom2->GetID());
|
|
|
3841 }
|
|
|
3842
|
|
|
3843 # Get number of rings containing specified bond...
|
|
|
3844 #
|
|
|
3845 sub _GetNumOfBondRings {
|
|
|
3846 my($This, $Bond) = @_;
|
|
|
3847 my($Atom1, $Atom2);
|
|
|
3848
|
|
|
3849 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3850
|
|
|
3851 return $This->GetNumOfEdgeCycles($Atom1->GetID(), $Atom2->GetID());
|
|
|
3852 }
|
|
|
3853
|
|
|
3854 # Get number of rings with odd size containing specified bond...
|
|
|
3855 #
|
|
|
3856 sub _GetNumOfBondRingsWithOddSize {
|
|
|
3857 my($This, $Bond) = @_;
|
|
|
3858 my($Atom1, $Atom2);
|
|
|
3859
|
|
|
3860 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3861
|
|
|
3862 return $This->GetNumOfEdgeCyclesWithOddSize($Atom1->GetID(), $Atom2->GetID());
|
|
|
3863 }
|
|
|
3864
|
|
|
3865 # Get number of rings with even size containing specified bond...
|
|
|
3866 #
|
|
|
3867 sub _GetNumOfBondRingsWithEvenSize {
|
|
|
3868 my($This, $Bond) = @_;
|
|
|
3869 my($Atom1, $Atom2);
|
|
|
3870
|
|
|
3871 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3872
|
|
|
3873 return $This->GetNumOfEdgeCyclesWithEvenSize($Atom1->GetID(), $Atom2->GetID());
|
|
|
3874 }
|
|
|
3875
|
|
|
3876 # Get number of rings with specified size containing specified bond...
|
|
|
3877 #
|
|
|
3878 sub _GetNumOfBondRingsWithSize {
|
|
|
3879 my($This, $Bond, $RingSize) = @_;
|
|
|
3880 my($Atom1, $Atom2);
|
|
|
3881
|
|
|
3882 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3883
|
|
|
3884 return $This->GetNumOfEdgeCyclesWithSize($Atom1->GetID(), $Atom2->GetID(), $RingSize);
|
|
|
3885 }
|
|
|
3886
|
|
|
3887 # Get number of rings with size less than specified containing specified bond...
|
|
|
3888 #
|
|
|
3889 sub _GetNumOfBondRingsWithSizeLessThan {
|
|
|
3890 my($This, $Bond, $RingSize) = @_;
|
|
|
3891 my($Atom1, $Atom2);
|
|
|
3892
|
|
|
3893 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3894
|
|
|
3895 return $This->GetNumOfEdgeCyclesWithSizeLessThan($Atom1->GetID(), $Atom2->GetID(), $RingSize);
|
|
|
3896 }
|
|
|
3897
|
|
|
3898 # Get number of rings with size greater than specified containing specified bond...
|
|
|
3899 #
|
|
|
3900 sub _GetNumOfBondRingsWithSizeGreaterThan {
|
|
|
3901 my($This, $Bond, $RingSize) = @_;
|
|
|
3902 my($Atom1, $Atom2);
|
|
|
3903
|
|
|
3904 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3905
|
|
|
3906 return $This->GetNumOfEdgeCyclesWithSizeGreaterThan($Atom1->GetID(), $Atom2->GetID(), $RingSize);
|
|
|
3907 }
|
|
|
3908
|
|
|
3909 # Get smallest ring as an array containing ring atoms...
|
|
|
3910 #
|
|
|
3911 sub _GetSmallestBondRing {
|
|
|
3912 my($This, $Bond) = @_;
|
|
|
3913 my($Atom1, $Atom2);
|
|
|
3914
|
|
|
3915 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3916
|
|
|
3917 return $This->_GetRing($This->GetSmallestEdgeCycle($Atom1->GetID(), $Atom2->GetID()));
|
|
|
3918 }
|
|
|
3919
|
|
|
3920 # Get odd size rings an array of references to arrays containing ring atoms...
|
|
|
3921 #
|
|
|
3922 sub _GetLargestBondRing {
|
|
|
3923 my($This, $Bond) = @_;
|
|
|
3924 my($Atom1, $Atom2);
|
|
|
3925
|
|
|
3926 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3927
|
|
|
3928 return $This->_GetRing($This->GetLargestEdgeCycle($Atom1->GetID(), $Atom2->GetID()));
|
|
|
3929 }
|
|
|
3930
|
|
|
3931 # Get all rings an array of references to arrays containing ring atoms...
|
|
|
3932 #
|
|
|
3933 sub _GetBondRings {
|
|
|
3934 my($This, $Bond) = @_;
|
|
|
3935 my($Atom1, $Atom2);
|
|
|
3936
|
|
|
3937 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3938
|
|
|
3939 return $This->_GetRings($This->GetEdgeCycles($Atom1->GetID(), $Atom2->GetID()));
|
|
|
3940 }
|
|
|
3941
|
|
|
3942 # Get odd size rings an array of references to arrays containing ring atoms...
|
|
|
3943 #
|
|
|
3944 sub _GetBondRingsWithOddSize {
|
|
|
3945 my($This, $Bond) = @_;
|
|
|
3946 my($Atom1, $Atom2);
|
|
|
3947
|
|
|
3948 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3949
|
|
|
3950 return $This->_GetRings($This->GetEdgeCyclesWithOddSize($Atom1->GetID(), $Atom2->GetID()));
|
|
|
3951 }
|
|
|
3952
|
|
|
3953 # Get even size rings an array of references to arrays containing ring atoms...
|
|
|
3954 #
|
|
|
3955 sub _GetBondRingsWithEvenSize {
|
|
|
3956 my($This, $Bond) = @_;
|
|
|
3957 my($Atom1, $Atom2);
|
|
|
3958
|
|
|
3959 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3960
|
|
|
3961 return $This->_GetRings($This->GetEdgeCyclesWithEvenSize($Atom1->GetID(), $Atom2->GetID()));
|
|
|
3962 }
|
|
|
3963
|
|
|
3964 # Get rings with specified size an array of references to arrays containing ring atoms...
|
|
|
3965 #
|
|
|
3966 sub _GetBondRingsWithSize {
|
|
|
3967 my($This, $Bond, $RingSize) = @_;
|
|
|
3968 my($Atom1, $Atom2);
|
|
|
3969
|
|
|
3970 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3971
|
|
|
3972 return $This->_GetRings($This->GetEdgeCyclesWithSize($Atom1->GetID(), $Atom2->GetID(), $RingSize));
|
|
|
3973 }
|
|
|
3974
|
|
|
3975 # Get rings with size less than specfied size as an array of references to arrays containing ring atoms...
|
|
|
3976 #
|
|
|
3977 sub _GetBondRingsWithSizeLessThan {
|
|
|
3978 my($This, $Bond, $RingSize) = @_;
|
|
|
3979 my($Atom1, $Atom2);
|
|
|
3980
|
|
|
3981 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3982
|
|
|
3983 return $This->_GetRings($This->GetEdgeCyclesWithSizeLessThan($Atom1->GetID(), $Atom2->GetID(), $RingSize));
|
|
|
3984 }
|
|
|
3985
|
|
|
3986 # Get rings with size less than specfied size as an array of references to arrays containing ring atoms...
|
|
|
3987 #
|
|
|
3988 sub _GetBondRingsWithSizeGreaterThan {
|
|
|
3989 my($This, $Bond, $RingSize) = @_;
|
|
|
3990 my($Atom1, $Atom2);
|
|
|
3991
|
|
|
3992 ($Atom1, $Atom2) = $Bond->GetAtoms();
|
|
|
3993
|
|
|
3994 return $This->_GetRings($This->GetEdgeCyclesWithSizeGreaterThan($Atom1->GetID(), $Atom2->GetID(), $RingSize));
|
|
|
3995 }
|
|
|
3996
|
|
|
3997
|
|
|
3998 # Get atom paths starting from a specified atom as a reference to an array containing references
|
|
|
3999 # to arrays with path atoms.
|
|
|
4000 #
|
|
|
4001 # Path atoms atoms correspond to to all possible paths for specified atom in molecule with length
|
|
|
4002 # upto a specified length and sharing of bonds in paths traversed. By default, rings are
|
|
|
4003 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4004 #
|
|
|
4005 # Note:
|
|
|
4006 # . For molecule without any rings, this method returns the same set of atom paths
|
|
|
4007 # as GetAtomPathsStartingAtWithLengthUpto method.
|
|
|
4008 #
|
|
|
4009 sub GetAllAtomPathsStartingAtWithLengthUpto {
|
|
|
4010 my($This, $StartAtom, $Length, $AllowCycles) = @_;
|
|
|
4011
|
|
|
4012 return $This->_GetAtomPathsStartingAt('AllAtomPathsWithLengthUpto', $StartAtom, $Length, $AllowCycles);
|
|
|
4013 }
|
|
|
4014
|
|
|
4015 # Get atom paths starting from a specified atom as a reference to an array containing references
|
|
|
4016 # to arrays with path atoms.
|
|
|
4017 #
|
|
|
4018 # Path atoms atoms correspond to to all possible paths for specified atom in molecule with
|
|
|
4019 # specified length and sharing of bonds in paths traversed. By default, rings are
|
|
|
4020 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4021 #
|
|
|
4022 # Note:
|
|
|
4023 # . For molecule without any rings, this method returns the same set of atom paths
|
|
|
4024 # as GetAtomPathsStartingAtWithLengthUpto method.
|
|
|
4025 #
|
|
|
4026 sub GetAllAtomPathsStartingAtWithLength {
|
|
|
4027 my($This, $StartAtom, $Length, $AllowCycles) = @_;
|
|
|
4028
|
|
|
4029 return $This->_GetAtomPathsStartingAt('AllAtomPathsWithLength', $StartAtom, $Length, $AllowCycles);
|
|
|
4030 }
|
|
|
4031
|
|
|
4032 # Get atom paths starting from a specified atom as a reference to an array containing references
|
|
|
4033 # to arrays with path atoms.
|
|
|
4034 #
|
|
|
4035 # Path atoms atoms correspond to to all possible paths for specified atom in molecule with all
|
|
|
4036 # possible lengths and sharing of bonds in paths traversed. By default, rings are
|
|
|
4037 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4038 #
|
|
|
4039 # Note:
|
|
|
4040 # . For molecule without any rings, this method returns the same set of atom paths
|
|
|
4041 # as GetAtomPathsStartingAt method.
|
|
|
4042 #
|
|
|
4043 sub GetAllAtomPathsStartingAt {
|
|
|
4044 my($This, $StartAtom, $AllowCycles) = @_;
|
|
|
4045
|
|
|
4046 return $This->_GetAtomPathsStartingAt('AllAtomPathsWithAllLengths', $StartAtom, undef, $AllowCycles);
|
|
|
4047 }
|
|
|
4048
|
|
|
4049 # Get atom paths starting from a specified atom as a reference to an array containing references
|
|
|
4050 # to arrays with path atoms.
|
|
|
4051 #
|
|
|
4052 # Path atoms atoms correspond to to all possible paths for specified atom in molecule with length
|
|
|
4053 # upto a specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
4054 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4055 #
|
|
|
4056 sub GetAtomPathsStartingAtWithLengthUpto {
|
|
|
4057 my($This, $StartAtom, $Length, $AllowCycles) = @_;
|
|
|
4058
|
|
|
4059 return $This->_GetAtomPathsStartingAt('AtomPathsWithLengthUpto', $StartAtom, $Length, $AllowCycles);
|
|
|
4060 }
|
|
|
4061
|
|
|
4062 # Get atom paths starting from a specified atom as a reference to an array containing references
|
|
|
4063 # to arrays with path atoms.
|
|
|
4064 #
|
|
|
4065 # Path atoms atoms correspond to to all possible paths for specified atom in molecule with
|
|
|
4066 # specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
4067 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4068 #
|
|
|
4069 sub GetAtomPathsStartingAtWithLength {
|
|
|
4070 my($This, $StartAtom, $Length, $AllowCycles) = @_;
|
|
|
4071
|
|
|
4072 return $This->_GetAtomPathsStartingAt('AtomPathsWithLength', $StartAtom, $Length, $AllowCycles);
|
|
|
4073 }
|
|
|
4074
|
|
|
4075 # Get atom paths starting from a specified atom as a reference to an array containing references
|
|
|
4076 # to arrays with path atoms.
|
|
|
4077 #
|
|
|
4078 # Path atoms atoms correspond to to all possible paths for specified atom in molecule with all
|
|
|
4079 # possible lengths and no sharing of bonds in paths traversed. By default, rings are
|
|
|
4080 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4081 #
|
|
|
4082 #
|
|
|
4083 sub GetAtomPathsStartingAt {
|
|
|
4084 my($This, $StartAtom, $AllowCycles) = @_;
|
|
|
4085
|
|
|
4086 return $This->_GetAtomPathsStartingAt('AtomPathsWithAllLengths', $StartAtom, undef, $AllowCycles);
|
|
|
4087 }
|
|
|
4088
|
|
|
4089 # Get atom paths as an array containing references to arrays with path atoms...
|
|
|
4090 #
|
|
|
4091 sub _GetAtomPathsStartingAt {
|
|
|
4092 my($This, $Mode, $StartAtom, $Length, $AllowCycles) = @_;
|
|
|
4093 my(@AtomPaths);
|
|
|
4094
|
|
|
4095 @AtomPaths = ();
|
|
|
4096 if (!defined $StartAtom) {
|
|
|
4097 carp "Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom is not defined...";
|
|
|
4098 return @AtomPaths;
|
|
|
4099 }
|
|
|
4100 if (!$This->HasAtom($StartAtom)) {
|
|
|
4101 carp "Warning: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Start atom doesn't exist...";
|
|
|
4102 return @AtomPaths;
|
|
|
4103 }
|
|
|
4104 my($StartAtomID, @Paths);
|
|
|
4105
|
|
|
4106 $StartAtomID = $StartAtom->GetID();
|
|
|
4107 @Paths = ();
|
|
|
4108
|
|
|
4109 # Collect appropriate atom paths...
|
|
|
4110 MODE: {
|
|
|
4111 if ($Mode =~ /^AtomPathsWithLengthUpto$/i) { @Paths = $This->GetPathsStartingAtWithLengthUpto($StartAtomID, $Length, $AllowCycles); last MODE; }
|
|
|
4112 if ($Mode =~ /^AtomPathsWithLength$/i) { @Paths = $This->GetPathsStartingAtWithLength($StartAtomID, $Length, $AllowCycles); last MODE; }
|
|
|
4113 if ($Mode =~ /^AtomPathsWithAllLengths$/i) { @Paths = $This->GetPathsStartingAt($StartAtomID, $AllowCycles); last MODE; }
|
|
|
4114
|
|
|
4115 if ($Mode =~ /^AllAtomPathsWithLengthUpto$/i) { @Paths = $This->GetAllPathsStartingAtWithLengthUpto($StartAtomID, $Length, $AllowCycles); last MODE; }
|
|
|
4116 if ($Mode =~ /^AllAtomPathsWithLength$/i) { @Paths = $This->GetAllPathsStartingAtWithLength($StartAtomID, $Length, $AllowCycles); last MODE; }
|
|
|
4117 if ($Mode =~ /^AllAtomPathsWithAllLengths$/i) { @Paths = $This->GetAllPathsStartingAt($StartAtomID, $AllowCycles); last MODE; }
|
|
|
4118
|
|
|
4119 print "Warn: ${ClassName}->_GetAtomPathsStartingAt: No atom paths retrieved: Mode, $Mode, is not supported...";
|
|
|
4120 return @AtomPaths;
|
|
|
4121 }
|
|
|
4122 return $This->_GetAtomPathsFromPaths(\@Paths);
|
|
|
4123 }
|
|
|
4124
|
|
|
4125 # Get atom paths for all atoms as a reference to an array containing references to arrays with
|
|
|
4126 # path atoms.
|
|
|
4127 #
|
|
|
4128 # Path atoms correspond to to all possible paths for each atom in molecule with length
|
|
|
4129 # upto a specified length and sharing of bonds in paths traversed. By default, rings are
|
|
|
4130 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4131 #
|
|
|
4132 # Notes:
|
|
|
4133 # . For molecule without any rings, this method returns the same set of atom paths
|
|
|
4134 # as GetAtomPathsWithLengthUpto method.
|
|
|
4135 #
|
|
|
4136 sub GetAllAtomPathsWithLengthUpto {
|
|
|
4137 my($This, $Length, $AllowCycles) = @_;
|
|
|
4138
|
|
|
4139 return $This->_GetAtomPaths('AllAtomPathsWithLengthUpto', $Length, $AllowCycles);
|
|
|
4140 }
|
|
|
4141
|
|
|
4142 # Get atom paths for all atoms as a reference to an array containing references to arrays with
|
|
|
4143 # path atoms.
|
|
|
4144 #
|
|
|
4145 # Path atoms correspond to to all possible paths for each atom in molecule with
|
|
|
4146 # a specified length and sharing of bonds in paths traversed. By default, rings are
|
|
|
4147 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4148 #
|
|
|
4149 # Notes:
|
|
|
4150 # . For molecule without any rings, this method returns the same set of atom paths
|
|
|
4151 # as GetAtomPathsWithLengthUpto method.
|
|
|
4152 #
|
|
|
4153 sub GetAllAtomPathsWithLength {
|
|
|
4154 my($This, $Length, $AllowCycles) = @_;
|
|
|
4155
|
|
|
4156 return $This->_GetAtomPaths('AllAtomPathsWithLength', $Length, $AllowCycles);
|
|
|
4157 }
|
|
|
4158
|
|
|
4159 # Get atom paths for all atoms as a reference to an array containing references to arrays with
|
|
|
4160 # path atoms.
|
|
|
4161 #
|
|
|
4162 # Path atoms correspond to to all possible paths for each atom in molecule with all
|
|
|
4163 # possible lengths and sharing of bonds in paths traversed. By default, rings are
|
|
|
4164 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4165 #
|
|
|
4166 # Notes:
|
|
|
4167 # . For molecule without any rings, this method returns the same set of atom paths
|
|
|
4168 # as GetAtomPaths method.
|
|
|
4169 #
|
|
|
4170 sub GetAllAtomPaths {
|
|
|
4171 my($This, $AllowCycles) = @_;
|
|
|
4172
|
|
|
4173 return $This->_GetAtomPaths('AllAtomPathsWithAllLengths', undef, $AllowCycles);
|
|
|
4174 }
|
|
|
4175
|
|
|
4176 # Get atom paths for all atoms as a reference to an array containing references to arrays with
|
|
|
4177 # path atoms.
|
|
|
4178 #
|
|
|
4179 # Path atoms correspond to to all possible paths for each atom in molecule with length
|
|
|
4180 # upto a specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
4181 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4182 #
|
|
|
4183 sub GetAtomPathsWithLengthUpto {
|
|
|
4184 my($This, $Length, $AllowCycles) = @_;
|
|
|
4185
|
|
|
4186 return $This->_GetAtomPaths('AtomPathsWithLengthUpto', $Length, $AllowCycles);
|
|
|
4187 }
|
|
|
4188
|
|
|
4189 # Get atom paths for all atoms as a reference to an array containing references to arrays with
|
|
|
4190 # path atoms.
|
|
|
4191 #
|
|
|
4192 # Path atoms correspond to to all possible paths for each atom in molecule with
|
|
|
4193 # a specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
4194 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4195 #
|
|
|
4196 sub GetAtomPathsWithLength {
|
|
|
4197 my($This, $Length, $AllowCycles) = @_;
|
|
|
4198
|
|
|
4199 return $This->_GetAtomPaths('AtomPathsWithLength', $Length, $AllowCycles);
|
|
|
4200 }
|
|
|
4201
|
|
|
4202
|
|
|
4203 # Get atom paths for all atoms as a reference to an array containing references to arrays with
|
|
|
4204 # path atoms.
|
|
|
4205 #
|
|
|
4206 # Path atoms correspond to to all possible paths for each atom in molecule with all
|
|
|
4207 # possible lengths and no sharing of bonds in paths traversed. By default, rings are
|
|
|
4208 # included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
4209 #
|
|
|
4210 sub GetAtomPaths {
|
|
|
4211 my($This, $AllowCycles) = @_;
|
|
|
4212
|
|
|
4213 return $This->_GetAtomPaths('AtomPathsWithAllLengths', undef, $AllowCycles);
|
|
|
4214 }
|
|
|
4215
|
|
|
4216 # Get atom paths for all atoms as a reference to an array containing references to arrays with
|
|
|
4217 # path atoms.
|
|
|
4218 #
|
|
|
4219 sub _GetAtomPaths {
|
|
|
4220 my($This, $Mode, $Length, $AllowCycles) = @_;
|
|
|
4221 my($PathsRef, @AtomPaths);
|
|
|
4222
|
|
|
4223 @AtomPaths = ();
|
|
|
4224 # Collect appropriate atom paths...
|
|
|
4225 MODE: {
|
|
|
4226 if ($Mode =~ /^AtomPathsWithLengthUpto$/i) { $PathsRef = $This->GetPathsWithLengthUpto($Length, $AllowCycles); last MODE; }
|
|
|
4227 if ($Mode =~ /^AtomPathsWithLength$/i) { $PathsRef = $This->GetPathsWithLength($Length, $AllowCycles); last MODE; }
|
|
|
4228 if ($Mode =~ /^AtomPathsWithAllLengths$/i) { $PathsRef = $This->GetPaths($AllowCycles); last MODE; }
|
|
|
4229
|
|
|
4230 if ($Mode =~ /^AllAtomPathsWithLengthUpto$/i) { $PathsRef = $This->GetAllPathsWithLengthUpto($Length, $AllowCycles); last MODE; }
|
|
|
4231 if ($Mode =~ /^AllAtomPathsWithLength$/i) { $PathsRef = $This->GetAllPathsWithLength($Length, $AllowCycles); last MODE; }
|
|
|
4232 if ($Mode =~ /^AllAtomPathsWithAllLengths$/i) { $PathsRef = $This->GetAllPaths($AllowCycles); last MODE; }
|
|
|
4233
|
|
|
4234 print "Warn: ${ClassName}->_GetAtomPaths: No atom paths retrieved: Mode, $Mode, is not supported...";
|
|
|
4235 return \@AtomPaths;
|
|
|
4236 }
|
|
|
4237 return $This->_GetAtomPathsFromPaths($PathsRef);
|
|
|
4238 }
|
|
|
4239
|
|
|
4240 # Get atom paths as an array reference containing references to arrays with path atoms...
|
|
|
4241 #
|
|
|
4242 sub _GetAtomPathsFromPaths {
|
|
|
4243 my($This, $PathsRef) = @_;
|
|
|
4244 my($Path, @AtomPaths);
|
|
|
4245
|
|
|
4246 @AtomPaths = ();
|
|
|
4247 if (!defined $PathsRef) {
|
|
|
4248 return \@AtomPaths;
|
|
|
4249 }
|
|
|
4250 if (!@{$PathsRef}) {
|
|
|
4251 # Return an empty atom paths list...
|
|
|
4252 return \@AtomPaths;
|
|
|
4253 }
|
|
|
4254 for $Path (@{$PathsRef}) {
|
|
|
4255 my(@PathAtoms);
|
|
|
4256 @PathAtoms = ();
|
|
|
4257 @PathAtoms = $This->_GetAtomPathFromPath($Path);
|
|
|
4258
|
|
|
4259 push @AtomPaths, \@PathAtoms;
|
|
|
4260 }
|
|
|
4261 return \@AtomPaths;
|
|
|
4262 }
|
|
|
4263
|
|
|
4264 # Generate an array of bond objects for an array of path atoms and return an array
|
|
|
4265 # of bond objects...
|
|
|
4266 #
|
|
|
4267 sub GetAtomPathBonds {
|
|
|
4268 my($This, @PathAtoms) = @_;
|
|
|
4269 my(@Bonds);
|
|
|
4270
|
|
|
4271 if (!@PathAtoms) {
|
|
|
4272 # Return an empty ring bonds list...
|
|
|
4273 return @Bonds;
|
|
|
4274 }
|
|
|
4275 my(@PathAtomIDs);
|
|
|
4276
|
|
|
4277 @PathAtomIDs = ();
|
|
|
4278 @PathAtomIDs = $This->_GetAtomsIDsFromAtoms(@PathAtoms);
|
|
|
4279
|
|
|
4280 return $This->_GetPathBonds(@PathAtomIDs);
|
|
|
4281 }
|
|
|
4282
|
|
|
4283 # Map atom IDs in path to atoms and return a reference to an array containing ring atoms...
|
|
|
4284 #
|
|
|
4285 sub _GetAtomPathFromPath {
|
|
|
4286 my($This, $Path) = @_;
|
|
|
4287 my(@PathAtoms);
|
|
|
4288
|
|
|
4289 @PathAtoms = ();
|
|
|
4290 if (!defined $Path) {
|
|
|
4291 # Return an empty atoms list...
|
|
|
4292 return @PathAtoms;
|
|
|
4293 }
|
|
|
4294
|
|
|
4295 return $This->_GetPathAtoms($Path);
|
|
|
4296 }
|
|
|
4297
|
|
|
4298 # Get atom paths between two specified atoms as a reference to an array containing references
|
|
|
4299 # to arrays with path atoms. For molecules with rings, atom paths array contains may contain
|
|
|
4300 # two paths.
|
|
|
4301 #
|
|
|
4302 sub GetAtomPathsBetween {
|
|
|
4303 my($This, $StartAtom, $EndAtom) = @_;
|
|
|
4304 my(@AtomPaths);
|
|
|
4305
|
|
|
4306 @AtomPaths = ();
|
|
|
4307 if (!(defined($StartAtom) && $This->HasAtom($StartAtom))) {
|
|
|
4308 carp "Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: Start atom is not defined or it doesn't exist...";
|
|
|
4309 return @AtomPaths;
|
|
|
4310 }
|
|
|
4311 if (!(defined($EndAtom) && $This->HasAtom($EndAtom))) {
|
|
|
4312 carp "Warning: ${ClassName}->_GetAtomPathsBetween: No atom paths retrieved: End atom is not defined or it doesn't exist...";
|
|
|
4313 return @AtomPaths;
|
|
|
4314 }
|
|
|
4315 return $This->_GetAtomPathsBetween($StartAtom, $EndAtom);
|
|
|
4316 }
|
|
|
4317
|
|
|
4318 # Get atom paths between two specified atoms as a reference to an array containing references
|
|
|
4319 # to arrays with path atoms.
|
|
|
4320 #
|
|
|
4321 sub _GetAtomPathsBetween {
|
|
|
4322 my($This, $StartAtom, $EndAtom) = @_;
|
|
|
4323 my($StartAtomID, $EndAtomID, @Paths);
|
|
|
4324
|
|
|
4325 $StartAtomID = $StartAtom->GetID();
|
|
|
4326 $EndAtomID = $EndAtom->GetID();
|
|
|
4327
|
|
|
4328 @Paths = ();
|
|
|
4329 @Paths = $This->GetPathsBetween($StartAtomID, $EndAtomID);
|
|
|
4330
|
|
|
4331 return $This->_GetAtomPathsFromPaths(\@Paths);
|
|
|
4332 }
|
|
|
4333
|
|
|
4334 # Get atom neighborhoods around a specified atom as an array containing references
|
|
|
4335 # to arrays with neighborhood atoms at different radii upto specified radius...
|
|
|
4336 #
|
|
|
4337 sub GetAtomNeighborhoodsWithRadiusUpto {
|
|
|
4338 my($This, $StartAtom, $Radius) = @_;
|
|
|
4339
|
|
|
4340 return $This->_GetAtomNeighborhoods('RadiusUpto', $StartAtom, $Radius);
|
|
|
4341 }
|
|
|
4342
|
|
|
4343 # Get atom neighborhoods around a specified atom as an array containing references
|
|
|
4344 # to arrays with neighborhood atoms at possible radii...
|
|
|
4345 #
|
|
|
4346 sub GetAtomNeighborhoods {
|
|
|
4347 my($This, $StartAtom) = @_;
|
|
|
4348
|
|
|
4349 return $This->_GetAtomNeighborhoods('AllRadii', $StartAtom, undef);
|
|
|
4350 }
|
|
|
4351
|
|
|
4352 # Get atom neighborhood around a specified atom, along with their successor connected atoms, collected
|
|
|
4353 # with in a specified radius as a list containing references to lists with first value corresponding to neighborhood
|
|
|
4354 # atom at a specific radius and second value as reference to a list containing its successor connected atoms.
|
|
|
4355 #
|
|
|
4356 # For a neighborhood atom at each radius level, the successor connected atoms correspond to the
|
|
|
4357 # neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last
|
|
|
4358 # radius level don't contain any successor atoms which fall outside the range of specified radius.
|
|
|
4359 #
|
|
|
4360 sub GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto {
|
|
|
4361 my($This, $StartAtom, $Radius) = @_;
|
|
|
4362
|
|
|
4363 return $This->_GetAtomNeighborhoods('WithSuccessorsAndRadiusUpto', $StartAtom, $Radius);
|
|
|
4364 }
|
|
|
4365
|
|
|
4366 # Get atom neighborhood around a specified atom, along with their successor connected atoms, collected
|
|
|
4367 # at all radii as a list containing references to lists with first value corresponding to neighborhood
|
|
|
4368 # atom at a specific radius and second value as reference to a list containing its successor connected atoms.
|
|
|
4369 #
|
|
|
4370 # For a neighborhood atom at each radius level, the successor connected atoms correspond to the
|
|
|
4371 # neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last
|
|
|
4372 # radius level don't contain any successor atoms which fall outside the range of specified radius.
|
|
|
4373 #
|
|
|
4374 #
|
|
|
4375 sub GetAtomNeighborhoodsWithSuccessorAtoms {
|
|
|
4376 my($This, $StartAtom) = @_;
|
|
|
4377
|
|
|
4378 return $This->_GetAtomNeighborhoods('WithSuccessorsAndAllRadii', $StartAtom, undef);
|
|
|
4379 }
|
|
|
4380
|
|
|
4381 # Get atom neighborhoods...
|
|
|
4382 #
|
|
|
4383 sub _GetAtomNeighborhoods {
|
|
|
4384 my($This, $Mode, $StartAtom, $Radius) = @_;
|
|
|
4385 my(@AtomNeighborhoods);
|
|
|
4386
|
|
|
4387 @AtomNeighborhoods = ();
|
|
|
4388
|
|
|
4389 if (!(defined($StartAtom) && $This->HasAtom($StartAtom))) {
|
|
|
4390 carp "Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Start atom is not defined or it doesn't exist...";
|
|
|
4391 return @AtomNeighborhoods;
|
|
|
4392 }
|
|
|
4393 if ($Mode =~ /^(RadiusUpto|WithSuccessorsAndRadiusUpto)$/i) {
|
|
|
4394 if (!(defined($Radius) && $Radius > 0)) {
|
|
|
4395 carp "Warning: ${ClassName}->_GetAtomNeighborhoods: No atom neighborhoods retrieved: Radius is not defined or it's <= 0 ...";
|
|
|
4396 return @AtomNeighborhoods;
|
|
|
4397 }
|
|
|
4398 }
|
|
|
4399
|
|
|
4400 # Collect neighborhood atom IDs...
|
|
|
4401 my($StartAtomID, @NeighborhoodAtomIDs, @NeighborhoodAtomIDsWithSuccessors);
|
|
|
4402
|
|
|
4403 @NeighborhoodAtomIDs = (); @NeighborhoodAtomIDsWithSuccessors = ();
|
|
|
4404 $StartAtomID = $StartAtom->GetID();
|
|
|
4405
|
|
|
4406 MODE: {
|
|
|
4407 if ($Mode =~ /^RadiusUpto$/i) { @NeighborhoodAtomIDs = $This->GetNeighborhoodVerticesWithRadiusUpto($StartAtomID, $Radius); last MODE; }
|
|
|
4408 if ($Mode =~ /^AllRadii$/i) { @NeighborhoodAtomIDs = $This->GetNeighborhoodVertices($StartAtomID); last MODE; }
|
|
|
4409
|
|
|
4410 if ($Mode =~ /^WithSuccessorsAndRadiusUpto$/i) { @NeighborhoodAtomIDsWithSuccessors = $This->GetNeighborhoodVerticesWithSuccessorsAndRadiusUpto($StartAtomID, $Radius); last MODE; }
|
|
|
4411 if ($Mode =~ /^WithSuccessorsAndAllRadii$/i) { @NeighborhoodAtomIDsWithSuccessors = $This->GetNeighborhoodVerticesWithSuccessors($StartAtomID); last MODE; }
|
|
|
4412
|
|
|
4413 print "Warn: ${ClassName}->_GetAtomNeighborhood: No atom neighborhoods retrieved: Mode, $Mode, is not supported...";
|
|
|
4414 return @AtomNeighborhoods;
|
|
|
4415 }
|
|
|
4416 if ($Mode =~ /^(RadiusUpto|AllRadii)$/i) {
|
|
|
4417 return $This->_GetNeighborhoodAtomsFromAtomIDs(\@NeighborhoodAtomIDs);
|
|
|
4418 }
|
|
|
4419 elsif ($Mode =~ /^(WithSuccessorsAndRadiusUpto|WithSuccessorsAndAllRadii)$/i) {
|
|
|
4420 return $This->_GetNeighborhoodAtomsWithSuccessorsFromAtomIDs(\@NeighborhoodAtomIDsWithSuccessors);
|
|
|
4421 }
|
|
|
4422
|
|
|
4423 return @AtomNeighborhoods;
|
|
|
4424 }
|
|
|
4425
|
|
|
4426 # Map neighborhood atom IDs to atoms...
|
|
|
4427 #
|
|
|
4428 sub _GetNeighborhoodAtomsFromAtomIDs {
|
|
|
4429 my($This, $NeighborhoodsAtomIDsRef) = @_;
|
|
|
4430 my($NeighborhoodAtomIDsRef, @AtomNeighborhoods);
|
|
|
4431
|
|
|
4432 @AtomNeighborhoods = ();
|
|
|
4433 for $NeighborhoodAtomIDsRef (@{$NeighborhoodsAtomIDsRef}) {
|
|
|
4434 my(@AtomNeighborhood);
|
|
|
4435
|
|
|
4436 @AtomNeighborhood = ();
|
|
|
4437 @AtomNeighborhood = $This->_GetAtomsFromAtomIDs(@{$NeighborhoodAtomIDsRef});
|
|
|
4438 push @AtomNeighborhoods, \@AtomNeighborhood;
|
|
|
4439 }
|
|
|
4440 return @AtomNeighborhoods;
|
|
|
4441 }
|
|
|
4442
|
|
|
4443 # Map neighborhood atom IDs with successors to atoms...
|
|
|
4444 #
|
|
|
4445 sub _GetNeighborhoodAtomsWithSuccessorsFromAtomIDs {
|
|
|
4446 my($This, $NeighborhoodsAtomIDsWithSuccessorsRef) = @_;
|
|
|
4447 my($Depth, $NeighborhoodAtomIDsWithSuccessorsRef, $NeighborhoodAtomIDWithSuccessorsRef, $NeighborhoodAtomID, $NeighborhoodAtomSuccessorsIDsRef, @AtomNeighborhoods);
|
|
|
4448
|
|
|
4449 $Depth = 0;
|
|
|
4450 @AtomNeighborhoods = ();
|
|
|
4451
|
|
|
4452 # Go over neighborhoods at each level...
|
|
|
4453 for $NeighborhoodAtomIDsWithSuccessorsRef (@{$NeighborhoodsAtomIDsWithSuccessorsRef}) {
|
|
|
4454 @{$AtomNeighborhoods[$Depth]} = ();
|
|
|
4455
|
|
|
4456 # Go over the neighborhood atoms and their successors at a specific level..
|
|
|
4457 for $NeighborhoodAtomIDWithSuccessorsRef (@{$NeighborhoodAtomIDsWithSuccessorsRef}) {
|
|
|
4458 my($NeighborhoodAtom, @NeighborhoodAtomWithSuccessors, @NeighborhoodAtomSuccessorAtoms);
|
|
|
4459
|
|
|
4460 @NeighborhoodAtomWithSuccessors = (); @NeighborhoodAtomSuccessorAtoms = ();
|
|
|
4461 ($NeighborhoodAtomID, $NeighborhoodAtomSuccessorsIDsRef) = @{$NeighborhoodAtomIDWithSuccessorsRef};
|
|
|
4462
|
|
|
4463 # Map atom IDs to atoms...
|
|
|
4464 $NeighborhoodAtom = $This->_GetAtomFromAtomID($NeighborhoodAtomID);
|
|
|
4465 if (@{$NeighborhoodAtomSuccessorsIDsRef}) {
|
|
|
4466 @NeighborhoodAtomSuccessorAtoms = $This->_GetAtomsFromAtomIDs(@{$NeighborhoodAtomSuccessorsIDsRef});
|
|
|
4467 }
|
|
|
4468
|
|
|
4469 # Store an atom and its successors at each level in an array...
|
|
|
4470 push @NeighborhoodAtomWithSuccessors, ($NeighborhoodAtom, \@NeighborhoodAtomSuccessorAtoms);
|
|
|
4471
|
|
|
4472 push @{$AtomNeighborhoods[$Depth]} , \@NeighborhoodAtomWithSuccessors;
|
|
|
4473 }
|
|
|
4474 $Depth++;
|
|
|
4475 }
|
|
|
4476 return @AtomNeighborhoods;
|
|
|
4477 }
|
|
|
4478
|
|
|
4479 # Get next object ID...
|
|
|
4480 sub _GetNewObjectID {
|
|
|
4481 $ObjectID++;
|
|
|
4482 return $ObjectID;
|
|
|
4483 }
|
|
|
4484
|
|
|
4485 # Is aromatic property set for the molecule?
|
|
|
4486 sub IsAromatic {
|
|
|
4487 my($This) = @_;
|
|
|
4488 my($Aromatic);
|
|
|
4489
|
|
|
4490 $Aromatic = $This->GetAromatic();
|
|
|
4491
|
|
|
4492 return (defined($Aromatic) && $Aromatic) ? 1 : 0;
|
|
|
4493 }
|
|
|
4494
|
|
|
4495 # Does molecule contains any atoms with non-zero Z coordiantes?
|
|
|
4496 sub IsThreeDimensional {
|
|
|
4497 my($This) = @_;
|
|
|
4498 my($Atom, @Atoms);
|
|
|
4499
|
|
|
4500 @Atoms = $This->GetAtoms();
|
|
|
4501 ATOM: for $Atom (@Atoms) {
|
|
|
4502 if ($Atom->GetZ() != 0) {
|
|
|
4503 return 1;
|
|
|
4504 }
|
|
|
4505 }
|
|
|
4506 return 0;
|
|
|
4507 }
|
|
|
4508
|
|
|
4509 # Does molecule contains any atoms with non-zero X or Y coordinates
|
|
|
4510 # and only zero Z-coordinates?
|
|
|
4511 sub IsTwoDimensional {
|
|
|
4512 my($This) = @_;
|
|
|
4513 my($Atom, @Atoms);
|
|
|
4514
|
|
|
4515 @Atoms = $This->GetAtoms();
|
|
|
4516 ATOM: for $Atom (@Atoms) {
|
|
|
4517 if ($Atom->GetZ() != 0) {
|
|
|
4518 return 0;
|
|
|
4519 }
|
|
|
4520 if ($Atom->GetX() != 0 || $Atom->GetY() != 0) {
|
|
|
4521 return 1;
|
|
|
4522 }
|
|
|
4523 }
|
|
|
4524 return 0;
|
|
|
4525 }
|
|
|
4526
|
|
|
4527 # Get dimensionality of the molecule using one of the following two methods:
|
|
|
4528 # . Using explicitly set Dimensionality
|
|
|
4529 # . Going over atomic coordinates
|
|
|
4530 #
|
|
|
4531 # The valid dimensionality values are:
|
|
|
4532 # . 3D - Three dimensional: One of X, Y or Z coordinate is non-zero
|
|
|
4533 # . 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z coordinates are zero
|
|
|
4534 # . 0D - Zero dimensional: All atomic coordinates are zero
|
|
|
4535 #
|
|
|
4536 sub GetDimensionality {
|
|
|
4537 my($This) = @_;
|
|
|
4538
|
|
|
4539 # Is Dimensionality property explicitly set?
|
|
|
4540 if ($This->HasProperty('Dimensionality')) {
|
|
|
4541 return $This->GetProperty('Dimensionality');
|
|
|
4542 }
|
|
|
4543 my($Atom, @Atoms);
|
|
|
4544
|
|
|
4545 @Atoms = $This->GetAtoms();
|
|
|
4546 ATOM: for $Atom (@Atoms) {
|
|
|
4547 if ($Atom->GetZ() != 0) {
|
|
|
4548 return '3D';
|
|
|
4549 }
|
|
|
4550 if ($Atom->GetX() != 0 || $Atom->GetY() != 0) {
|
|
|
4551 return '2D';
|
|
|
4552 }
|
|
|
4553 }
|
|
|
4554 return '0D';
|
|
|
4555 }
|
|
|
4556
|
|
|
4557 # Is it a molecule object?
|
|
|
4558 sub IsMolecule ($) {
|
|
|
4559 my($Object) = @_;
|
|
|
4560
|
|
|
4561 return _IsMolecule($Object);
|
|
|
4562 }
|
|
|
4563
|
|
|
4564 # Return a string containing vertices, edges and other properties...
|
|
|
4565 sub StringifyMolecule {
|
|
|
4566 my($This) = @_;
|
|
|
4567 my($MoleculeString, $ID, $Name, $NumOfAtoms, $NumOfBonds, $MolecularFormula, $NumOfRings, $MolecularWeight, $ExactMass, $FormalCharge, $SpinMultiplicity, $FreeRadicalElectrons, $Charge, $ElementsRef, $ElementsCompositionRef, $ElementalComposition);
|
|
|
4568
|
|
|
4569 $ID = $This->GetID();
|
|
|
4570 $Name = $This->GetName();
|
|
|
4571 $NumOfAtoms = $This->GetNumOfAtoms();
|
|
|
4572 $NumOfBonds = $This->GetNumOfBonds();
|
|
|
4573
|
|
|
4574 $NumOfRings = $This->GetNumOfRings();
|
|
|
4575 if (!defined $NumOfRings) {
|
|
|
4576 $NumOfRings = 'undefined';
|
|
|
4577 }
|
|
|
4578
|
|
|
4579 $MolecularFormula = $This->GetMolecularFormula();
|
|
|
4580
|
|
|
4581 $MolecularWeight = $This->GetMolecularWeight();
|
|
|
4582 $MolecularWeight = round($MolecularWeight, 4) + 0;
|
|
|
4583
|
|
|
4584 $ExactMass = $This->GetExactMass();
|
|
|
4585 $ExactMass = round($ExactMass, 4) + 0;
|
|
|
4586
|
|
|
4587 $FormalCharge = $This->GetFormalCharge();
|
|
|
4588 $Charge = $This->GetCharge();
|
|
|
4589
|
|
|
4590 $SpinMultiplicity = $This->GetSpinMultiplicity();
|
|
|
4591 $FreeRadicalElectrons = $This->GetFreeRadicalElectrons();
|
|
|
4592
|
|
|
4593 ($ElementsRef, $ElementsCompositionRef) = $This->GetElementalComposition();
|
|
|
4594 $ElementalComposition = 'None';
|
|
|
4595 if (defined($ElementsRef) && @{$ElementsRef}) {
|
|
|
4596 $ElementalComposition = "[ " . FormatElementalCompositionInformation($ElementsRef, $ElementsCompositionRef) . " ]";
|
|
|
4597 }
|
|
|
4598
|
|
|
4599 $MoleculeString = "Molecule: ID: $ID; Name: \"$Name\"; NumOfAtoms: $NumOfAtoms; NumOfBonds: $NumOfBonds; NumOfRings: $NumOfRings; MolecularFormula: $MolecularFormula; MolecularWeight: $MolecularWeight; ExactMass: $ExactMass; FormalCharge: $FormalCharge; Charge: $Charge; SpinMultiplicity: $SpinMultiplicity; FreeRadicalElectrons: $FreeRadicalElectrons; ElementalComposition: $ElementalComposition";
|
|
|
4600
|
|
|
4601 return $MoleculeString;
|
|
|
4602 }
|
|
|
4603
|
|
|
4604 # Load appropriate atom data files from <MayaChemTools>/lib directory used by various
|
|
|
4605 # object methods in the current class...
|
|
|
4606 #
|
|
|
4607 sub _LoadMoleculeClassData {
|
|
|
4608 my($MayaChemToolsLibDir);
|
|
|
4609
|
|
|
4610 $MayaChemToolsLibDir = GetMayaChemToolsLibDirName();
|
|
|
4611
|
|
|
4612 # Load and process data for aromaticity models...
|
|
|
4613 _LoadAromaticityModelsData($MayaChemToolsLibDir);
|
|
|
4614 _ProcessAromaticityModelsData();
|
|
|
4615 }
|
|
|
4616
|
|
|
4617 #
|
|
|
4618 # Load data for supported aromaticity models...
|
|
|
4619 #
|
|
|
4620 sub _LoadAromaticityModelsData {
|
|
|
4621 my($MayaChemToolsLibDir) = @_;
|
|
|
4622 my($DataFile, $Index, $InDelim, $Line, $NumOfCols, $ParameterName, $ParameterValue, $ModelName, @ColLabels, @LineWords, %ParameterNames, %ColIndexToModelName, %SupportedParameterNames);
|
|
|
4623
|
|
|
4624 %AromaticityModelsDataMap = ();
|
|
|
4625 %CanonicalAromaticityModelNamesMap = ();
|
|
|
4626
|
|
|
4627 # File format:
|
|
|
4628 #
|
|
|
4629 # "ParameterName","MDLAromaticityModel","TriposAromaticityModel","MMFFAromaticityModel","ChemAxonBasicAromaticityModel","ChemAxonGeneralAromaticityModel","DaylightAromaticityModel","MayaChemToolsAromaticityModel"
|
|
|
4630 # "AllowHeteroRingAtoms","No","No","Yes","Yes","Yes","Yes","Yes"
|
|
|
4631 #
|
|
|
4632 $DataFile = $MayaChemToolsLibDir . "/data/AromaticityModelsData.csv";
|
|
|
4633 if (! -e "$DataFile") {
|
|
|
4634 croak "Error: ${ClassName}::_LoadAromaticityModelsData: MayaChemTools package file, $DataFile, is missing: Possible installation problems...";
|
|
|
4635 }
|
|
|
4636
|
|
|
4637 # Setup a list of currently supported aromaticity parameters...
|
|
|
4638 #
|
|
|
4639 my(@KnownNames);
|
|
|
4640 @KnownNames = qw(AllowHeteroRingAtoms HeteroRingAtomsList AllowExocyclicDoubleBonds AllowHomoNuclearExocyclicDoubleBonds AllowElectronegativeRingAtomExocyclicDoubleBonds AllowRingAtomFormalCharge AllowHeteroRingAtomFormalCharge MinimumRingSize);
|
|
|
4641
|
|
|
4642 %SupportedParameterNames = ();
|
|
|
4643 for $ParameterName (@KnownNames) {
|
|
|
4644 $SupportedParameterNames{$ParameterName} = $ParameterName;
|
|
|
4645 }
|
|
|
4646
|
|
|
4647 $InDelim = "\,";
|
|
|
4648 open DATAFILE, "$DataFile" or croak "Couldn't open $DataFile: $! ...";
|
|
|
4649
|
|
|
4650 # Skip lines up to column labels...
|
|
|
4651 LINE: while ($Line = GetTextLine(\*DATAFILE)) {
|
|
|
4652 if ($Line !~ /^#/) {
|
|
|
4653 last LINE;
|
|
|
4654 }
|
|
|
4655 }
|
|
|
4656 @ColLabels= quotewords($InDelim, 0, $Line);
|
|
|
4657 $NumOfCols = @ColLabels;
|
|
|
4658
|
|
|
4659 %ColIndexToModelName = ();
|
|
|
4660
|
|
|
4661 # Process names of aromaticity models...
|
|
|
4662 for $Index (1 .. $#ColLabels) {
|
|
|
4663 $ModelName = $ColLabels[$Index];
|
|
|
4664 $ModelName =~ s/ //g;
|
|
|
4665
|
|
|
4666 if (exists $AromaticityModelsDataMap{$ModelName}) {
|
|
|
4667 croak "Error: ${ClassName}::_LoadAromaticityModelsData: The aromaticity model name, $ModelName, in $DataFile has already exists.\nLine: $Line...";
|
|
|
4668 }
|
|
|
4669 %{$AromaticityModelsDataMap{$ModelName}} = ();
|
|
|
4670
|
|
|
4671 # Cannonicalize aromatic model name by converting into all lowercase...
|
|
|
4672 $CanonicalAromaticityModelNamesMap{lc($ModelName)} = $ModelName;
|
|
|
4673
|
|
|
4674 $ColIndexToModelName{$Index} = $ModelName;
|
|
|
4675 }
|
|
|
4676
|
|
|
4677 # Process paramater name and their values for specified aromaticity models...
|
|
|
4678 #
|
|
|
4679 %ParameterNames = ();
|
|
|
4680 LINE: while ($Line = GetTextLine(\*DATAFILE)) {
|
|
|
4681 if ($Line =~ /^#/) {
|
|
|
4682 next LINE;
|
|
|
4683 }
|
|
|
4684 @LineWords = ();
|
|
|
4685 @LineWords = quotewords($InDelim, 0, $Line);
|
|
|
4686 if (@LineWords != $NumOfCols) {
|
|
|
4687 croak "Error: ${ClassName}::_LoadAromaticityModelsData: The number of data fields, @LineWords, in $DataFile must be $NumOfCols.\nLine: $Line...";
|
|
|
4688 }
|
|
|
4689
|
|
|
4690 # Process parameter name and values for aromaticity models...
|
|
|
4691 #
|
|
|
4692 $ParameterName = $LineWords[0];
|
|
|
4693
|
|
|
4694 if (!exists $SupportedParameterNames{$ParameterName}) {
|
|
|
4695 carp "Warning: ${ClassName}::_LoadAromaticityModelsData: The current release of MayaChemTools doesn't support aromaticity model parameter name, $ParameterName, specified in $DataFile. It would be ignore during aromaticity detection.\nLine: $Line...";
|
|
|
4696 }
|
|
|
4697
|
|
|
4698 if (exists $ParameterNames{$ParameterName}) {
|
|
|
4699 carp "Warning: ${ClassName}::_LoadAromaticityModelsData: Ignoring aromaticity model data for parameter name, $ParameterName, in $DataFile. It has already been loaded.\nLine: $Line...";
|
|
|
4700 next LINE;
|
|
|
4701 }
|
|
|
4702 $ParameterNames{$ParameterName} = $ParameterName;
|
|
|
4703
|
|
|
4704 for $Index (1 .. $#LineWords) {
|
|
|
4705 $ModelName = $ColIndexToModelName{$Index};
|
|
|
4706 $ParameterValue = $LineWords[$Index];
|
|
|
4707 $AromaticityModelsDataMap{$ModelName}{$ParameterName} = $ParameterValue;
|
|
|
4708 }
|
|
|
4709 }
|
|
|
4710 close DATAFILE;
|
|
|
4711 }
|
|
|
4712
|
|
|
4713 # Process already loaded aromaticity model data...
|
|
|
4714 #
|
|
|
4715 sub _ProcessAromaticityModelsData {
|
|
|
4716 my($ParameterName, $ParameterValue, $ModelName, $NewParameterValue);
|
|
|
4717
|
|
|
4718 for $ModelName (keys %AromaticityModelsDataMap) {
|
|
|
4719 for $ParameterName (keys %{$AromaticityModelsDataMap{$ModelName}}) {
|
|
|
4720 $ParameterValue = $AromaticityModelsDataMap{$ModelName}{$ParameterName};
|
|
|
4721 $ParameterValue =~ s/ //g;
|
|
|
4722
|
|
|
4723 VALUE: {
|
|
|
4724 if ($ParameterValue =~ /^Yes$/i) {
|
|
|
4725 $NewParameterValue = 1;
|
|
|
4726 last VALUE;
|
|
|
4727 }
|
|
|
4728 if ($ParameterValue =~ /^(NA|No)$/i) {
|
|
|
4729 $NewParameterValue = 0;
|
|
|
4730 last VALUE;
|
|
|
4731 }
|
|
|
4732 if ($ParameterValue =~ /^None$/i) {
|
|
|
4733 $NewParameterValue = '';
|
|
|
4734 last VALUE;
|
|
|
4735 }
|
|
|
4736 $NewParameterValue = $ParameterValue;
|
|
|
4737 }
|
|
|
4738 $AromaticityModelsDataMap{$ModelName}{$ParameterName} = $NewParameterValue;
|
|
|
4739
|
|
|
4740 if ($ParameterName =~ /List/i) {
|
|
|
4741 # Setup a new parameter conatining a reference to a hash for the specified values...
|
|
|
4742 my($DataMapRefName, $DataValue, %DataMap);
|
|
|
4743
|
|
|
4744 $DataMapRefName = "${ParameterName}MapRef";
|
|
|
4745
|
|
|
4746 %DataMap = ();
|
|
|
4747 for $DataValue (split /\,/, $NewParameterValue) {
|
|
|
4748 $DataMap{$DataValue} = $DataValue;
|
|
|
4749 }
|
|
|
4750 $AromaticityModelsDataMap{$ModelName}{$DataMapRefName} = \%DataMap;
|
|
|
4751 }
|
|
|
4752 }
|
|
|
4753 }
|
|
|
4754 }
|
|
|
4755
|
|
|
4756 # Is it a molecule object?
|
|
|
4757 sub _IsMolecule {
|
|
|
4758 my($Object) = @_;
|
|
|
4759
|
|
|
4760 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
|
|
|
4761 }
|
|
|
4762
|
|
|
4763 1;
|
|
|
4764
|
|
|
4765 __END__
|
|
|
4766
|
|
|
4767 =head1 NAME
|
|
|
4768
|
|
|
4769 Molecule - Molecule class
|
|
|
4770
|
|
|
4771 =head1 SYNOPSIS
|
|
|
4772
|
|
|
4773 use Molecule;
|
|
|
4774
|
|
|
4775 use Molecule qw(:all);
|
|
|
4776
|
|
|
4777 =head1 DESCRIPTION
|
|
|
4778
|
|
|
4779 B<Molecule> class provides the following methods:
|
|
|
4780
|
|
|
4781 new, AddAtom, AddAtoms, AddBond, AddBonds, AddHydrogens, AddPolarHydrogens,
|
|
|
4782 ClearRings, Copy, DeleteAromaticity, DeleteAtom, DeleteAtoms, DeleteBond,
|
|
|
4783 DeleteBonds, DeleteHydrogens, DeletePolarHydrogens, DetectAromaticity,
|
|
|
4784 DetectRings, FormatElementalCompositionInformation, GetAllAtomPaths,
|
|
|
4785 GetAllAtomPathsStartingAt, GetAllAtomPathsStartingAtWithLength,
|
|
|
4786 GetAllAtomPathsStartingAtWithLengthUpto, GetAllAtomPathsWithLength,
|
|
|
4787 GetAllAtomPathsWithLengthUpto, GetAromaticRings, GetAromaticityModel,
|
|
|
4788 GetAtomNeighborhoods, GetAtomNeighborhoodsWithRadiusUpto,
|
|
|
4789 GetAtomNeighborhoodsWithSuccessorAtoms,
|
|
|
4790 GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto, GetAtomPathBonds,
|
|
|
4791 GetAtomPaths, GetAtomPathsBetween, GetAtomPathsStartingAt,
|
|
|
4792 GetAtomPathsStartingAtWithLength, GetAtomPathsStartingAtWithLengthUpto,
|
|
|
4793 GetAtomPathsWithLength, GetAtomPathsWithLengthUpto, GetAtoms, GetBonds, GetCharge,
|
|
|
4794 GetConnectedComponents, GetConnectedComponentsAtoms, GetDimensionality,
|
|
|
4795 GetElementalComposition, GetElementsAndNonElements, GetExactMass, GetFormalCharge,
|
|
|
4796 GetFreeRadicalElectrons, GetFusedAndNonFusedRings, GetLargestConnectedComponent,
|
|
|
4797 GetLargestConnectedComponentAtoms, GetLargestRing, GetMolecularFormula,
|
|
|
4798 GetMolecularWeight, GetNumOfAromaticRings, GetNumOfAtoms, GetNumOfBonds,
|
|
|
4799 GetNumOfConnectedComponents, GetNumOfElementsAndNonElements, GetNumOfHeavyAtoms,
|
|
|
4800 GetNumOfHydrogenAtoms, GetNumOfMissingHydrogenAtoms, GetNumOfNonHydrogenAtoms,
|
|
|
4801 GetNumOfRings, GetNumOfRingsWithEvenSize, GetNumOfRingsWithOddSize,
|
|
|
4802 GetNumOfRingsWithSize, GetNumOfRingsWithSizeGreaterThan,
|
|
|
4803 GetNumOfRingsWithSizeLessThan, GetRingBonds, GetRingBondsFromRings, GetRings,
|
|
|
4804 GetRingsWithEvenSize, GetRingsWithOddSize, GetRingsWithSize,
|
|
|
4805 GetRingsWithSizeGreaterThan, GetRingsWithSizeLessThan, GetSizeOfLargestRing,
|
|
|
4806 GetSizeOfSmallestRing, GetSmallestRing, GetSpinMultiplicity,
|
|
|
4807 GetSupportedAromaticityModels, GetTopologicallySortedAtoms, GetValenceModel,
|
|
|
4808 HasAromaticAtomsInRings, HasAromaticAtomsNotInRings, HasAromaticRings, HasAtom,
|
|
|
4809 HasBond, HasFusedRings, HasNoRings, HasOnlyOneRing, HasRings, IsAromatic,
|
|
|
4810 IsMolecule, IsRingAromatic, IsSupportedAromaticityModel, IsThreeDimensional,
|
|
|
4811 IsTwoDimensional, KeepLargestComponent, KekulizeAromaticAtoms, NewAtom, NewBond,
|
|
|
4812 SetActiveRings, SetAromaticityModel, SetID, SetValenceModel, StringifyMolecule
|
|
|
4813
|
|
|
4814 The following methods can also be used as functions:
|
|
|
4815
|
|
|
4816 FormatElementalCompositionInformation, IsMolecule
|
|
|
4817
|
|
|
4818 B<Molecule> class is derived from B<ObjectProperty> base class which provides methods not explicitly
|
|
|
4819 defined in B<Molecule> or B<ObjectProperty> class using Perl's AUTOLOAD functionality. These methods
|
|
|
4820 are generated on-the-fly for a specified object property:
|
|
|
4821
|
|
|
4822 Set<PropertyName>(<PropertyValue>);
|
|
|
4823 $PropertyValue = Get<PropertyName>();
|
|
|
4824 Delete<PropertyName>();
|
|
|
4825
|
|
|
4826 =head2 METHODS
|
|
|
4827
|
|
|
4828 =over 4
|
|
|
4829
|
|
|
4830 =item B<new>
|
|
|
4831
|
|
|
4832 $NewMolecule = new Molecule([%PropertyNameAndValues]);
|
|
|
4833
|
|
|
4834 Using specified I<Atom> property names and values hash, B<new> method creates a new object
|
|
|
4835 and returns a reference to newly created B<Atom> object. By default, the following properties are
|
|
|
4836 initialized:
|
|
|
4837
|
|
|
4838 ID = SequentialObjectID
|
|
|
4839 Name = "Molecule <SequentialObjectID>"
|
|
|
4840
|
|
|
4841 Examples:
|
|
|
4842
|
|
|
4843 $Molecule = new Molecule();
|
|
|
4844
|
|
|
4845 $WaterMolecule = new Molecule('Name' => 'Water');
|
|
|
4846
|
|
|
4847 $Oxygen = new Atom('AtomSymbol' => 'O', 'XYZ' => [0, 0, 0]);
|
|
|
4848 $Hydrogen1 = new Atom('AtomSymbol' => 'H',
|
|
|
4849 'XYZ' => [0.7144, 0.4125, 0]);
|
|
|
4850 $Hydrogen2 = new Atom('AtomSymbol' => 'H',
|
|
|
4851 'XYZ' => [1.1208, -0.2959, 0]);
|
|
|
4852 $WaterMolecule->AddAtoms($Oxygen, $Hydrogen1, $Hydrogen2);
|
|
|
4853
|
|
|
4854 $Bond1 = new Bond('Atoms' => [$Oxygen, $Hydrogen1],
|
|
|
4855 'BondOrder' => 1);
|
|
|
4856 $Bond2 = new Bond('Atoms' => [$Oxygen, $Hydrogen2],
|
|
|
4857 'BondOrder' => 1);
|
|
|
4858 $WaterMolecule->AddBonds($Bond1, $Bond2);
|
|
|
4859
|
|
|
4860 =item B<AddAtom>
|
|
|
4861
|
|
|
4862 $Molecule->AddAtom($Atom);
|
|
|
4863
|
|
|
4864 Adds an I<Atom> to a I<Molecule> and returns I<Molecule>.
|
|
|
4865
|
|
|
4866 =item B<AddAtoms>
|
|
|
4867
|
|
|
4868 $Molecule->AddAtoms(@Atoms);
|
|
|
4869
|
|
|
4870 Adds I<Atoms> to a I<Molecule> and returns I<Molecule>.
|
|
|
4871
|
|
|
4872 =item B<AddBond>
|
|
|
4873
|
|
|
4874 $Molecule->AddBond($Bond);
|
|
|
4875
|
|
|
4876 Adds a I<Bond> to a I<Molecule> and returns I<Molecule>.
|
|
|
4877
|
|
|
4878 =item B<AddBonds>
|
|
|
4879
|
|
|
4880 $Molecule->AddBonds(@Bonds);
|
|
|
4881
|
|
|
4882 Adds I<Bonds> to a I<Molecule> and returns I<Molecule>.
|
|
|
4883
|
|
|
4884 =item B<AddHydrogens>
|
|
|
4885
|
|
|
4886 $NumOfHydrogensAdded = $Molecule->AddHydrogens();
|
|
|
4887
|
|
|
4888 Adds hydrogens to each atom in a I<Molecule> and returns total number of hydrogens
|
|
|
4889 added. The current release of MayaChemTools doesn't assign hydrogen positions.
|
|
|
4890
|
|
|
4891 =item B<AddPolarHydrogens>
|
|
|
4892
|
|
|
4893 $NumOfHydrogensAdded = $Molecule->AddPolarHydrogens();
|
|
|
4894
|
|
|
4895 Adds hydrogens to each polar atom - N, O, P or S - in a I<Molecule> and returns total
|
|
|
4896 number of polar hydrogens added. The current release of MayaChemTools doesn't
|
|
|
4897 assign hydrogen positions.
|
|
|
4898
|
|
|
4899 =item B<ClearRings>
|
|
|
4900
|
|
|
4901 $Molecule->ClearRings();
|
|
|
4902
|
|
|
4903 Deletes all rings associated with I<Molecule> and returns I<Molecule>.
|
|
|
4904
|
|
|
4905 =item B<Copy>
|
|
|
4906
|
|
|
4907 $MoleculeCopy = $Molecule->Copy();
|
|
|
4908
|
|
|
4909 Copies I<Molecule> and its associated data using B<Storable::dclone> and returns a new
|
|
|
4910 B<Molecule> object.
|
|
|
4911
|
|
|
4912 =item B<DeleteAromaticity>
|
|
|
4913
|
|
|
4914 $Molecule->DeleteAromaticity();
|
|
|
4915
|
|
|
4916 Deletes aromatic property associated with all atoms and bonds in a I<Molecule> and returns
|
|
|
4917 I<Molecule>.
|
|
|
4918
|
|
|
4919 =item B<DeleteAtom>
|
|
|
4920
|
|
|
4921 $Molecule->DeleteAtom($Atom);
|
|
|
4922
|
|
|
4923 Deletes I<Atom> from a I<Molecule> and returns I<Molecule>.
|
|
|
4924
|
|
|
4925 =item B<DeleteAtoms>
|
|
|
4926
|
|
|
4927 $Molecule->DeleteAtoms(@Atoms);
|
|
|
4928
|
|
|
4929 Deletes I<Atoms> from a I<Molecule> and returns I<Molecule>.
|
|
|
4930
|
|
|
4931 =item B<DeleteBond>
|
|
|
4932
|
|
|
4933 $Molecule->DeleteBond($Bond);
|
|
|
4934
|
|
|
4935 Deletes I<Bond> from a I<Molecule> and returns I<Molecule>.
|
|
|
4936
|
|
|
4937 =item B<DeleteBonds>
|
|
|
4938
|
|
|
4939 $Molecule->DeleteBonds(@Bonds);
|
|
|
4940
|
|
|
4941 Deletes I<Bonds> from a I<Molecule> and returns I<Molecule>.
|
|
|
4942
|
|
|
4943 =item B<DeleteHydrogens>
|
|
|
4944
|
|
|
4945 $NumOfHydrogensDeleted = $Molecule->DeleteHydrogens();
|
|
|
4946
|
|
|
4947 Removes hydrogens from each atom in a I<Molecule> and returns total number of hydrogens
|
|
|
4948 deleted.
|
|
|
4949
|
|
|
4950 =item B<DeletePolarHydrogens>
|
|
|
4951
|
|
|
4952 $NumOfHydrogensDeleted = $Molecule->DeletePolarHydrogens();
|
|
|
4953
|
|
|
4954 Removes hydrogens to each polar atom - N, O, P or S - in a I<Molecule> and returns total
|
|
|
4955 number of polar hydrogens deleted.
|
|
|
4956
|
|
|
4957 =item B<DetectAromaticity>
|
|
|
4958
|
|
|
4959 $Molecule->DetectAromaticity();
|
|
|
4960
|
|
|
4961 Associates I<Aromatic> property to atoms and bonds involved in aromatic rings or ring
|
|
|
4962 systems in a I<Molecule> and returns I<Molecule>.
|
|
|
4963
|
|
|
4964 This method assumes the ring detection has already been perfomed using B<DetectRings>.
|
|
|
4965 And any existing I<Aromatic> property associated with atoms and bonds is deleted before
|
|
|
4966 performing aromaticity detection.
|
|
|
4967
|
|
|
4968 What is aromaticity? [ Ref 124 ] It's in the code of the implementer, did you
|
|
|
4969 say? Agree. The implementation of aromaticity varies widely across different
|
|
|
4970 packages [ Ref 125 ]; additionally, the implementation details are not always
|
|
|
4971 completely available, and it's not possible to figure out the exact implementation
|
|
|
4972 of aromaticity across various packages. Using the publicly available information,
|
|
|
4973 however, one can try to reproduce the available results to the extent possible,
|
|
|
4974 along with parameterizing all the control parameters used to implement different
|
|
|
4975 aromaticity models, and that's exactly what the current release of MayaChemTools
|
|
|
4976 does.
|
|
|
4977
|
|
|
4978 The implementation of aromaticity corresponding to various aromaticity models in
|
|
|
4979 MayaChemTools package is driven by an external CSV file AromaticityModelsData.csv,
|
|
|
4980 which is distributed with the package and is available in lib/data directory. The CSV
|
|
|
4981 files contains names of supported aromaticity models, along with various control
|
|
|
4982 parameters and their values. This file is loaded and processed during instantiation
|
|
|
4983 of Molecule class and data corresponding to specific aromaticity model are used
|
|
|
4984 to detect aromaticity for that model. Any new aromaticity model added to the
|
|
|
4985 aromaticity data file, using different combinations of values for existing control
|
|
|
4986 parameters, would work without any changes to the code; the addition of any new
|
|
|
4987 control parameters, however, requires its implementation in the code used to
|
|
|
4988 calculate number of pi electrons available towards delocalization in a ring or ring
|
|
|
4989 systems.
|
|
|
4990
|
|
|
4991 The current release of MayaChemTools package supports these aromaticity
|
|
|
4992 models: MDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
4993 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
|
|
|
4994 DaylightAromaticityModel, MayaChemToolsAromaticityModel.
|
|
|
4995
|
|
|
4996 The current list of control parameters available to detect aromaticity corresponding
|
|
|
4997 to different aromaticity models are: AllowHeteroRingAtoms, HeteroRingAtomsList,
|
|
|
4998 AllowExocyclicDoubleBonds, AllowHomoNuclearExocyclicDoubleBonds,
|
|
|
4999 AllowElectronegativeRingAtomExocyclicDoubleBonds, AllowRingAtomFormalCharge,
|
|
|
5000 AllowHeteroRingAtomFormalCharge, MinimumRingSize. The values for these control
|
|
|
5001 parameters are specified in AromaticityModelsData.csv file.
|
|
|
5002
|
|
|
5003 Although definition of aromaticity differs across various aromaticity models, a ring
|
|
|
5004 or a ring system containing 4n + 2 pi electrons (Huckel's rule) corresponding to
|
|
|
5005 alternate single and double bonds, in general, is considered aromatic.
|
|
|
5006
|
|
|
5007 The available valence free electrons on heterocyclic ring atoms, involved in two single
|
|
|
5008 ring bonds, are also allowed to participate in pi electron delocalizaiton for most of
|
|
|
5009 the supported aromaticity models.
|
|
|
5010
|
|
|
5011 The presence of exocyclic terminal double bond on ring atoms involved in pi electron
|
|
|
5012 delocalization is only allowed for some of the aromaticity models. Additionally, the type
|
|
|
5013 atoms involved in exocyclic terminal double bonds may result in making a ring or ring
|
|
|
5014 system non-aromatic.
|
|
|
5015
|
|
|
5016 For molecules containing fused rings, each fused ring set is considered as one aromatic
|
|
|
5017 system for counting pi electrons to satisfy Huckel's rule; In case of a failure, rings in
|
|
|
5018 fused set are treated individually for aromaticity detection. Additionally, non-fused
|
|
|
5019 rings are handled on their own during aromaticity detection.
|
|
|
5020
|
|
|
5021 =item B<DetectRings>
|
|
|
5022
|
|
|
5023 $Molecule->DetectRings();
|
|
|
5024
|
|
|
5025 Detects rings in a I<Molecule> and returns I<Molecule>. Ring detection is performed using
|
|
|
5026 B<DetectCycles> method avaible in B<Graph> class which in turn uses methods available
|
|
|
5027 B<Graph::CyclesDetection> class. B<Graph::CyclesDetection> class implements collapsing path graph
|
|
|
5028 [Ref 31] methodology to detect all cycles in a graph.
|
|
|
5029
|
|
|
5030 =item B<FormatElementalCompositionInformation>
|
|
|
5031
|
|
|
5032 $FormattedInfo = $Molecule->FormatElementalCompositionInformation(
|
|
|
5033 $ElementsRef, $ElementCompositionRef,
|
|
|
5034 [$Precision]);
|
|
|
5035 $FormattedInfo = Molecule::FormatElementalCompositionInformation(
|
|
|
5036 $ElementsRef, $ElementCompositionRef,
|
|
|
5037 [$Precision]);
|
|
|
5038
|
|
|
5039 Using I<ElementsRef> and I<ElementCompositionRef> arrays referneces containg informatio
|
|
|
5040 about elements and their composition, formats elemental composition information and returns
|
|
|
5041 a I<FormattedInfo> string. Defaule I<Precision> value: I<2>.
|
|
|
5042
|
|
|
5043 =item B<GetAromaticityModel>
|
|
|
5044
|
|
|
5045 $AromaticityModel = $Molecule->GetAromaticityModel();
|
|
|
5046
|
|
|
5047 Returns name of B<AromaticityModel> set for I<Molecule> corresponding to B<AromaticityModel>
|
|
|
5048 property or default model name of B<MayaChemToolsAromaticityModel>.
|
|
|
5049
|
|
|
5050 =item B<GetAllAtomPaths>
|
|
|
5051
|
|
|
5052 $AtomPathsRef = $Molecule->GetAllAtomPaths([$AllowCycles]);
|
|
|
5053
|
|
|
5054 Returns all paths as a reference to an array containing reference to arrays with path
|
|
|
5055 B<Atom> objects.
|
|
|
5056
|
|
|
5057 Path atoms correspond to to all possible paths for each atom in molecule with all
|
|
|
5058 possible lengths and sharing of bonds in paths traversed. By default, rings are
|
|
|
5059 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5060
|
|
|
5061 For molecule without any rings, this method returns the same set of atom paths as
|
|
|
5062 B<GetAtomPaths> method.
|
|
|
5063
|
|
|
5064 =item B<GetAllAtomPathsStartingAt>
|
|
|
5065
|
|
|
5066 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAt($StartAtom,
|
|
|
5067 [$AllowCycles]);
|
|
|
5068
|
|
|
5069 Returns all atom paths starting from I<StartAtom> as a reference to an array containing
|
|
|
5070 reference to arrays with path B<Atom> objects.
|
|
|
5071
|
|
|
5072 Path atoms atoms correspond to to all possible paths for specified atom in molecule with all
|
|
|
5073 possible lengths and sharing of bonds in paths traversed. By default, rings are
|
|
|
5074 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5075
|
|
|
5076 For molecule without any rings, this method returns the same set of atom paths as
|
|
|
5077 B<GetAtomPathsStartingAt> method.
|
|
|
5078
|
|
|
5079 =item B<GetAllAtomPathsStartingAtWithLength>
|
|
|
5080
|
|
|
5081 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLength(
|
|
|
5082 $StartAtom, $Length, [$AllowCycles]);
|
|
|
5083
|
|
|
5084 Returns all atom paths starting from I<StartAtom> with specified I<Length>as a reference
|
|
|
5085 to an array containing reference to arrays with path B<Atom> objects.
|
|
|
5086
|
|
|
5087 Path atoms atoms correspond to to all possible paths for specified atom in molecule with all
|
|
|
5088 possible lengths and sharing of bonds in paths traversed. By default, rings are
|
|
|
5089 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5090
|
|
|
5091 For molecule without any rings, this method returns the same set of atom paths as
|
|
|
5092 B<GetAtomPathsStartingAtWithLength> method.
|
|
|
5093
|
|
|
5094 =item B<GetAllAtomPathsStartingAtWithLengthUpto>
|
|
|
5095
|
|
|
5096 $AtomPathsRef = $Molecule->GetAllAtomPathsStartingAtWithLengthUpto(
|
|
|
5097 $StartAtom, $Length, [$AllowCycles]);
|
|
|
5098
|
|
|
5099 Returns atom paths starting from I<StartAtom> with length up to I<Length> as a reference
|
|
|
5100 to an array containing reference to arrays with path B<Atom> objects.
|
|
|
5101
|
|
|
5102 Path atoms atoms correspond to all possible paths for specified atom in molecule with length
|
|
|
5103 up to a specified length and sharing of bonds in paths traversed. By default, rings are
|
|
|
5104 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5105
|
|
|
5106 For molecule without any rings, this method returns the same set of atom paths as
|
|
|
5107 I<GetAtomPathsStartingAtWithLengthUpto> method.
|
|
|
5108
|
|
|
5109 =item B<GetAllAtomPathsWithLength>
|
|
|
5110
|
|
|
5111 $AtomPathsRef = $Molecule->GetAllAtomPathsWithLength($Length,
|
|
|
5112 [$AllowCycles]);
|
|
|
5113
|
|
|
5114 Returns all atom paths with specified I<Length> as a reference to an array containing
|
|
|
5115 reference to arrays with path B<Atom> objects.
|
|
|
5116
|
|
|
5117 Path atoms correspond to to all possible paths for each atom in molecule with length
|
|
|
5118 up to a specified length and sharing of bonds in paths traversed. By default, rings are
|
|
|
5119 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5120
|
|
|
5121 For molecule without any rings, this method returns the same set of atom paths as
|
|
|
5122 as I<GetAtomPathsWithLength> method.
|
|
|
5123
|
|
|
5124 =item B<GetAllAtomPathsWithLengthUpto>
|
|
|
5125
|
|
|
5126 $AtomPathsRef = $Molecule->GetAllAtomPathsWithLengthUpto($Length,
|
|
|
5127 [$AllowCycles]);
|
|
|
5128
|
|
|
5129 Returns all atom paths with length up to I<Length> as a reference to an array containing
|
|
|
5130 reference to arrays with path B<Atom> objects.
|
|
|
5131
|
|
|
5132 Path atoms correspond to to all possible paths for each atom in molecule with length
|
|
|
5133 up to a specified length and sharing of bonds in paths traversed. By default, rings are
|
|
|
5134 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5135
|
|
|
5136 For molecule without any rings, this method returns the same set of atom paths as
|
|
|
5137 as I<GetAtomPathsWithLengthUpto> method.
|
|
|
5138
|
|
|
5139 =item B<GetAromaticRings>
|
|
|
5140
|
|
|
5141 @AtomaticRings = $Molecule->GetAromaticRings();
|
|
|
5142
|
|
|
5143 Returns aromatic rings as an array containing references to arrays of ring I<Atom> objects
|
|
|
5144 in a I<Molecule>.
|
|
|
5145
|
|
|
5146 =item B<GetAtomNeighborhoods>
|
|
|
5147
|
|
|
5148 @Neighborhoods = $Molecule->GetAtomNeighborhoods($StartAtom);
|
|
|
5149
|
|
|
5150 Returns atom neighborhoods around a I<StartAtom> as an array containing references
|
|
|
5151 to arrays with neighborhood I<Atom> objects at possible radii.
|
|
|
5152
|
|
|
5153 =item B<GetAtomNeighborhoodsWithRadiusUpto>
|
|
|
5154
|
|
|
5155 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithRadiusUpto($StartAtom,
|
|
|
5156 $Radius);
|
|
|
5157
|
|
|
5158 Returns atom neighborhoods around a I<StartAtom> as an array containing references
|
|
|
5159 to arrays with neighborhood I<Atom> objects up to I<Radius>.
|
|
|
5160
|
|
|
5161 =item B<GetAtomNeighborhoodsWithSuccessorAtoms>
|
|
|
5162
|
|
|
5163 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtoms(
|
|
|
5164 $StartAtom);
|
|
|
5165
|
|
|
5166 Returns atom neighborhood around a specified I<StartAtom>, along with their successor
|
|
|
5167 connected atoms, collected at all radii as an array containing references to arrays with first
|
|
|
5168 value corresponding to neighborhood atom at a specific radius and second value as reference
|
|
|
5169 to an array containing its successor connected atoms.
|
|
|
5170
|
|
|
5171 For a neighborhood atom at each radius level, the successor connected atoms correspond to the
|
|
|
5172 neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last
|
|
|
5173 radius level don't contain any successor atoms which fall outside the range of specified radius.
|
|
|
5174
|
|
|
5175 =item B<GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto>
|
|
|
5176
|
|
|
5177 @Neighborhoods = $Molecule->GetAtomNeighborhoodsWithSuccessorAtomsAndRadiusUpto(
|
|
|
5178 $StartAtom, $Radius);
|
|
|
5179
|
|
|
5180 Returns atom neighborhood around a specified I<StartAtom>, along with their successor
|
|
|
5181 connected atoms, collected upto specified I<Radiud> as an array containing references to arrays
|
|
|
5182 with first value corresponding to neighborhood atom at a specific radius and second value as
|
|
|
5183 reference to an array containing its successor connected atoms.
|
|
|
5184
|
|
|
5185 For a neighborhood atom at each radius level, the successor connected atoms correspond to the
|
|
|
5186 neighborhood atoms at the next radius level. Consequently, the neighborhood atoms at the last
|
|
|
5187 radius level don't contain any successor atoms which fall outside the range of specified radius.
|
|
|
5188
|
|
|
5189 =item B<GetAtomPathBonds>
|
|
|
5190
|
|
|
5191 $Return = $Molecule->GetAtomPathBonds(@PathAtoms);
|
|
|
5192
|
|
|
5193 Returns an array containing B<Bond> objects corresponding to successive pair of
|
|
|
5194 atoms in I<PathAtoms>
|
|
|
5195
|
|
|
5196 =item B<GetAtomPaths>
|
|
|
5197
|
|
|
5198 $AtomPathsRef = $Molecule->GetAtomPaths([$AllowCycles]);
|
|
|
5199
|
|
|
5200 Returns all paths as a reference to an array containing reference to arrays with path
|
|
|
5201 B<Atom> objects.
|
|
|
5202
|
|
|
5203 Path atoms correspond to to all possible paths for each atom in molecule with all
|
|
|
5204 possible lengths and no sharing of bonds in paths traversed. By default, rings are
|
|
|
5205 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5206
|
|
|
5207 =item B<GetAtomPathsBetween>
|
|
|
5208
|
|
|
5209 $AtomPathsRef = $Molecule->GetAtomPathsBetween($StartAtom, $EndAtom);
|
|
|
5210
|
|
|
5211 Returns all paths as between I<StartAtom> and I<EndAtom> as a reference to an array
|
|
|
5212 containing reference to arrays with path B<Atom> objects.
|
|
|
5213
|
|
|
5214 For molecules with rings, atom paths array contains may contain two paths.
|
|
|
5215
|
|
|
5216 =item B<GetAtomPathsStartingAt>
|
|
|
5217
|
|
|
5218 $AtomPathsRef = $Molecule->GetAtomPathsStartingAt($StartAtom, [$AllowCycles]);
|
|
|
5219
|
|
|
5220 Returns paths starting at I<StartAtom> as a reference to an array containing reference to
|
|
|
5221 arrays with path B<Atom> objects.
|
|
|
5222
|
|
|
5223 Path atoms correspond to all possible paths for specified atom in molecule with all
|
|
|
5224 possible lengths and no sharing of bonds in paths traversed. By default, rings are
|
|
|
5225 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5226
|
|
|
5227 =item B<GetAtomPathsStartingAtWithLength>
|
|
|
5228
|
|
|
5229 $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLength($StartAtom,
|
|
|
5230 $Length, [$AllowCycles]);
|
|
|
5231
|
|
|
5232 Returns paths starting at I<StartAtom> with length I<Length> as a reference to an array
|
|
|
5233 containing reference to arrays with path B<Atom> objects.
|
|
|
5234
|
|
|
5235 Path atoms correspond to all possible paths for specified atom in molecule with length
|
|
|
5236 upto a specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
5237 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5238
|
|
|
5239 =item B<GetAtomPathsStartingAtWithLengthUpto>
|
|
|
5240
|
|
|
5241 $AtomPathsRef = $Molecule->GetAtomPathsStartingAtWithLengthUpto($StartAtom,
|
|
|
5242 $Length, [$AllowCycles]);
|
|
|
5243
|
|
|
5244 Returns paths starting at I<StartAtom> with length up to I<Length> as a reference to an array
|
|
|
5245 containing reference to arrays with path B<Atom> objects.
|
|
|
5246
|
|
|
5247 Path atoms correspond to all possible paths for specified atom in molecule with length
|
|
|
5248 upto a specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
5249 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5250
|
|
|
5251 =item B<GetAtomPathsWithLength>
|
|
|
5252
|
|
|
5253 $AtomPathsRef = $Molecule->GetAtomPathsWithLength($Length, [$AllowCycles]);
|
|
|
5254
|
|
|
5255 Returns all paths with specified I<Length> as a reference to an array containing reference
|
|
|
5256 to arrays with path B<Atom> objects.
|
|
|
5257
|
|
|
5258 Path atoms correspond to all possible paths for each atom in molecule with length
|
|
|
5259 upto a specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
5260 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5261
|
|
|
5262 =item B<GetAtomPathsWithLengthUpto>
|
|
|
5263
|
|
|
5264 $AtomPathsRef = $Molecule->GetAtomPathsWithLengthUpto($Length, [$AllowCycles]);
|
|
|
5265
|
|
|
5266 Returns all paths with length up to I<Length> as a reference to an array containing reference
|
|
|
5267 to arrays with path B<Atom> objects.
|
|
|
5268
|
|
|
5269 Path atoms correspond to all possible paths for each atom in molecule with length
|
|
|
5270 upto a specified length and no sharing of bonds in paths traversed. By default, rings are
|
|
|
5271 included in paths. A path containing a ring is terminated at an atom completing the ring.
|
|
|
5272
|
|
|
5273 =item B<GetAtoms>
|
|
|
5274
|
|
|
5275 @AllAtoms = $Molecule->GetAtoms();
|
|
|
5276 @PolarAtoms = $Molecule->GetAtoms('IsPolarAtom');
|
|
|
5277
|
|
|
5278 $NegateMethodResult = 1;
|
|
|
5279 @NonHydrogenAtoms = $Molecule->GetAtoms('IsHydrogenAtom',
|
|
|
5280 $NegateMethodResult);
|
|
|
5281
|
|
|
5282 $AtomsCount = $Molecule->GetAtoms();
|
|
|
5283
|
|
|
5284 Returns an array of I<Atoms> in a I<Molecule>. In scalar context, it returns number of atoms.
|
|
|
5285 Additionally, B<Atoms> array can be filtered by any user specifiable valid B<Atom> class method
|
|
|
5286 and the result of the B<Atom> class method used to filter the atoms can also be negated by
|
|
|
5287 an optional negate results flag as third parameter.
|
|
|
5288
|
|
|
5289 =item B<GetBonds>
|
|
|
5290
|
|
|
5291 @Bonds = $Molecule->GetBonds();
|
|
|
5292 $BondsCount = $Molecule->GetBonds();
|
|
|
5293
|
|
|
5294 Returns an array of I<Bonds> in a I<Molecule>. In scalar context, it returns number of bonds.
|
|
|
5295
|
|
|
5296 =item B<GetCharge>
|
|
|
5297
|
|
|
5298 $Charge = $Molecule->GetCharge();
|
|
|
5299
|
|
|
5300 Returns net charge on a I<Molecule> using one of the following two methods: explicitly
|
|
|
5301 set B<Charge> property or sum of partial atomic charges on each atom.
|
|
|
5302
|
|
|
5303 =item B<GetConnectedComponents>
|
|
|
5304
|
|
|
5305 @ConnectedComponents = $Molecule->GetConnectedComponents();
|
|
|
5306
|
|
|
5307 Returns a reference to an array containing I<Molecule> objects corresponding
|
|
|
5308 to connected components sorted in decreasing order of component size in a I<Molecule>.
|
|
|
5309
|
|
|
5310 =item B<GetConnectedComponentsAtoms>
|
|
|
5311
|
|
|
5312 @ConnectedComponentsAtoms =
|
|
|
5313 $Molecule->GetConnectedComponentsAtoms();
|
|
|
5314
|
|
|
5315 Returns an array containing references to arrays with I<Atom> objects corresponding to
|
|
|
5316 atoms of connected components sorted in order of component decreasing size in a
|
|
|
5317 I<Molecule>.
|
|
|
5318
|
|
|
5319 =item B<GetDimensionality>
|
|
|
5320
|
|
|
5321 $Dimensionality = $Molecule->GetDimensionality();
|
|
|
5322
|
|
|
5323 Returns I<Dimensionality> of a I<Molecule> corresponding to explicitly set
|
|
|
5324 I<Dimensionality> property value or by processing atomic.
|
|
|
5325
|
|
|
5326 The I<Dimensionality> value from atomic coordinates is calculated as follows:
|
|
|
5327
|
|
|
5328 3D - Three dimensional: One of X, Y or Z coordinate is non-zero
|
|
|
5329 2D - Two dimensional: One of X or Y coordinate is non-zero; All Z
|
|
|
5330 coordinates are zero
|
|
|
5331 0D - Zero dimensional: All atomic coordinates are zero
|
|
|
5332
|
|
|
5333 =item B<GetElementalComposition>
|
|
|
5334
|
|
|
5335 ($ElementsRef, $CompositionRef) =
|
|
|
5336 $Molecule->GetElementalComposition([$IncludeMissingHydrogens]);
|
|
|
5337
|
|
|
5338 Calculates elemental composition and returns references to arrays containing elements
|
|
|
5339 and their percent composition in a I<Molecule>. By default, missing hydrogens are included
|
|
|
5340 during the calculation.
|
|
|
5341
|
|
|
5342 =item B<GetElementsAndNonElements>
|
|
|
5343
|
|
|
5344 ($ElementsRef, $NonElementsRef) =
|
|
|
5345 $Molecule->GetElementsAndNonElements([$IncludeMissingHydrogens]);
|
|
|
5346
|
|
|
5347 Counts elements and non-elements in a I<Molecule> and returns references to hashes
|
|
|
5348 containing element and non-element as hash keys with values corresponding to their
|
|
|
5349 count. By default, missing hydrogens are not added to the element hash.
|
|
|
5350
|
|
|
5351 =item B<GetExactMass>
|
|
|
5352
|
|
|
5353 $ExactMass = $Molecule->GetExactMass();
|
|
|
5354
|
|
|
5355 Returns exact mass of a I<Molecule> corresponding to sum of exact masses of all
|
|
|
5356 the atoms.
|
|
|
5357
|
|
|
5358 =item B<GetFormalCharge>
|
|
|
5359
|
|
|
5360 $FormalCharge = $Molecule->GetFormalCharge();
|
|
|
5361
|
|
|
5362 Returns net formal charge on a I<Molecule> using one of the following two methods: explicitly
|
|
|
5363 set B<FormalCharge> property or sum of formal charges on each atom.
|
|
|
5364
|
|
|
5365 B<FormalCharge> is different from B<Charge> property of the molecule which corresponds to
|
|
|
5366 sum of partial atomic charges explicitly set for each atom using a specific methodology.
|
|
|
5367
|
|
|
5368 =item B<GetFreeRadicalElectrons>
|
|
|
5369
|
|
|
5370 $FreeRadicalElectrons = $Molecule->GetFreeRadicalElectrons();
|
|
|
5371
|
|
|
5372 Returns total number of free radical electrons available in a I<Molecule> using one of the
|
|
|
5373 following two methods: explicitly set B<FreeRadicalElectrons> property or sum of available
|
|
|
5374 free radical electrons on each atom.
|
|
|
5375
|
|
|
5376 =item B<GetFusedAndNonFusedRings>
|
|
|
5377
|
|
|
5378 ($FusedRingSetRef, $NonFusedRingsRef) =
|
|
|
5379 $Molecule->GetFusedAndNonFusedRings();
|
|
|
5380
|
|
|
5381 Returns references to array of fused ring sets and non-fused rings in a I<Molecule>. Fused ring sets
|
|
|
5382 array reference contains refernces to arrays of rings corresponding to ring I<Atom> objects;
|
|
|
5383 Non-fused rings array reference contains references to arrays of ring I<Atom> objects.
|
|
|
5384
|
|
|
5385 =item B<GetLargestConnectedComponent>
|
|
|
5386
|
|
|
5387 $ComponentMolecule = $Molecule->GetLargestConnectedComponent();
|
|
|
5388
|
|
|
5389 Returns a reference to B<Molecule> object corresponding to a largest connected component
|
|
|
5390 in a I<Molecule>.
|
|
|
5391
|
|
|
5392 =item B<GetLargestConnectedComponentAtoms>
|
|
|
5393
|
|
|
5394 @ComponentAtoms = $Molecule->GetLargestConnectedComponentAtoms();
|
|
|
5395
|
|
|
5396 Returns a reference to an array of B<Atom> objects corresponding to a largest connected
|
|
|
5397 component in a I<Molecule>.
|
|
|
5398
|
|
|
5399 =item B<GetLargestRing>
|
|
|
5400
|
|
|
5401 @RingAtoms = $Molecule->GetLargestRing();
|
|
|
5402
|
|
|
5403 Returns an array of I<Atoms> objects corresponding to a largest ring in a I<Molecule>.
|
|
|
5404
|
|
|
5405 =item B<GetMolecularFormula>
|
|
|
5406
|
|
|
5407 $FormulaString = $Molecule->GetMolecularFormula(
|
|
|
5408 [$IncludeMissingHydrogens,
|
|
|
5409 $IncludeNonElements]);
|
|
|
5410
|
|
|
5411 Returns molecular formula of a I<Molecule> by collecting information about all atoms in
|
|
|
5412 the molecule and composing the formula using Hills ordering system:
|
|
|
5413
|
|
|
5414 o C shows up first and H follows assuming C is present.
|
|
|
5415 o All other standard elements are sorted alphanumerically.
|
|
|
5416 o All other non-stanard atom symbols are also sorted
|
|
|
5417 alphanumerically and follow standard elements.
|
|
|
5418
|
|
|
5419 Notes:
|
|
|
5420
|
|
|
5421 o By default, missing hydrogens and nonelements are also included.
|
|
|
5422 o Elements for disconnected fragments are combined into the same
|
|
|
5423 formula.
|
|
|
5424 o Formal charge is also used during compoisiton of molecular formula.
|
|
|
5425
|
|
|
5426 =item B<GetMolecularWeight>
|
|
|
5427
|
|
|
5428 $MolWeight = $Molecule->GetMolecularWeight();
|
|
|
5429
|
|
|
5430 Returns molecular weight of a I<Molecule> corresponding to sum of atomic weights of all
|
|
|
5431 the atoms.
|
|
|
5432
|
|
|
5433 =item B<GetNumOfAromaticRings>
|
|
|
5434
|
|
|
5435 $NumOfAromaticRings = $Molecule->GetNumOfAromaticRings();
|
|
|
5436
|
|
|
5437 Returns number of aromatic rings in a I<Molecule>.
|
|
|
5438
|
|
|
5439 =item B<GetNumOfAtoms>
|
|
|
5440
|
|
|
5441 $NumOfAtoms = $Molecule->GetNumOfAtoms();
|
|
|
5442
|
|
|
5443 Returns number of atoms in a I<Molecule>.
|
|
|
5444
|
|
|
5445 =item B<GetNumOfBonds>
|
|
|
5446
|
|
|
5447 $NumOfBonds = $Molecule->GetNumOfBonds();
|
|
|
5448
|
|
|
5449 Returns number of bonds in a I<Molecule>.
|
|
|
5450
|
|
|
5451 =item B<GetNumOfConnectedComponents>
|
|
|
5452
|
|
|
5453 $NumOfComponents = $Molecule->GetNumOfConnectedComponents();
|
|
|
5454
|
|
|
5455 Returns number of connected components in a I<Molecule>.
|
|
|
5456
|
|
|
5457 =item B<GetNumOfElementsAndNonElements>
|
|
|
5458
|
|
|
5459 ($NumOfElements, $NumOfNonElements) = $Molecule->
|
|
|
5460 GetNumOfElementsAndNonElements();
|
|
|
5461 ($NumOfElements, $NumOfNonElements) = $Molecule->
|
|
|
5462 GetNumOfElementsAndNonElements($IncludeMissingHydrogens);
|
|
|
5463
|
|
|
5464 Returns number of elements and non-elements in a I<Molecule>. By default, missing
|
|
|
5465 hydrogens are not added to element count.
|
|
|
5466
|
|
|
5467 =item B<GetNumOfHeavyAtoms>
|
|
|
5468
|
|
|
5469 $NumOfHeavyAtoms = $Molecule->GetNumOfHeavyAtoms();
|
|
|
5470
|
|
|
5471 Returns number of heavy atoms, non-hydrogen atoms, in a I<Molecule>.
|
|
|
5472
|
|
|
5473 =item B<GetNumOfHydrogenAtoms>
|
|
|
5474
|
|
|
5475 $NumOfHydrogenAtoms = $Molecule->GetNumOfHydrogenAtoms();
|
|
|
5476
|
|
|
5477 Returns number of hydrogen atoms in a I<Molecule>.
|
|
|
5478
|
|
|
5479 =item B<GetNumOfMissingHydrogenAtoms>
|
|
|
5480
|
|
|
5481 $NumOfMissingHydrogenAtoms = $Molecule->GetNumOfMissingHydrogenAtoms();
|
|
|
5482
|
|
|
5483 Returns number of hydrogen atoms in a I<Molecule>.
|
|
|
5484
|
|
|
5485 =item B<GetNumOfNonHydrogenAtoms>
|
|
|
5486
|
|
|
5487 $NumOfNonHydrogenAtoms = $Molecule->GetNumOfNonHydrogenAtoms();
|
|
|
5488
|
|
|
5489 Returns number of non-hydrogen atoms in a I<Molecule>.
|
|
|
5490
|
|
|
5491 =item B<GetNumOfRings>
|
|
|
5492
|
|
|
5493 $RingCount = $Molecule->GetNumOfRings();
|
|
|
5494
|
|
|
5495 Returns number of rings in a I<Molecule>.
|
|
|
5496
|
|
|
5497 =item B<GetNumOfRingsWithEvenSize>
|
|
|
5498
|
|
|
5499 $RingCount = $Molecule->GetNumOfRingsWithEvenSize();
|
|
|
5500
|
|
|
5501 Returns number of rings with even size in a I<Molecule>.
|
|
|
5502
|
|
|
5503 =item B<GetNumOfRingsWithOddSize>
|
|
|
5504
|
|
|
5505 $RingCount = $Molecule->GetNumOfRingsWithOddSize();
|
|
|
5506
|
|
|
5507 Returns number of rings with odd size in a I<Molecule>.
|
|
|
5508
|
|
|
5509 =item B<GetNumOfRingsWithSize>
|
|
|
5510
|
|
|
5511 $RingCount = $Molecule->GetNumOfRingsWithSize($Size);
|
|
|
5512
|
|
|
5513 Returns number of rings with I<Size> in a I<Molecule>.
|
|
|
5514
|
|
|
5515 =item B<GetNumOfRingsWithSizeGreaterThan>
|
|
|
5516
|
|
|
5517 $RingCount = $Molecule->GetNumOfRingsWithSizeGreaterThan($Size);
|
|
|
5518
|
|
|
5519 Returns number of rings with size greater than I<Size> in a I<Molecule>.
|
|
|
5520
|
|
|
5521 =item B<GetNumOfRingsWithSizeLessThan>
|
|
|
5522
|
|
|
5523 $RingCount = $Molecule->GetNumOfRingsWithSizeLessThan($Size);
|
|
|
5524
|
|
|
5525 Returns number of rings with size less than I<Size> in a I<Molecule>.
|
|
|
5526
|
|
|
5527 =item B<GetRingBonds>
|
|
|
5528
|
|
|
5529 @RingBonds = $Molecule->GetRingBonds(@RingAtoms);
|
|
|
5530
|
|
|
5531 Returns an array of ring B<Bond> objects correponding to an array of ring I<Atoms> in a
|
|
|
5532 I<Molecule>.
|
|
|
5533
|
|
|
5534 =item B<GetRingBondsFromRings>
|
|
|
5535
|
|
|
5536 @RingBondsSets = $Molecule->GetRingBondsFromRings(@RingAtomsSets);
|
|
|
5537
|
|
|
5538 Returns an array containing references to arrays of ring B<Bond> objects for rings specified
|
|
|
5539 in an array of references to ring I<Atom> objects.
|
|
|
5540
|
|
|
5541 =item B<GetRings>
|
|
|
5542
|
|
|
5543 @Rings = $Molecule->GetRings();
|
|
|
5544
|
|
|
5545 Returns rings as an array containing references to arrays of ring I<Atom> objects in a I<Molecule>.
|
|
|
5546
|
|
|
5547 =item B<GetRingsWithEvenSize>
|
|
|
5548
|
|
|
5549 @Rings = $Molecule->GetRingsWithEvenSize();
|
|
|
5550
|
|
|
5551 Returns even size rings as an array containing references to arrays of ring I<Atom> objects in
|
|
|
5552 a I<Molecule>.
|
|
|
5553
|
|
|
5554 =item B<GetRingsWithOddSize>
|
|
|
5555
|
|
|
5556 @Rings = $Molecule->GetRingsWithOddSize();
|
|
|
5557
|
|
|
5558 Returns odd size rings as an array containing references to arrays of ring I<Atom> objects in
|
|
|
5559 a I<Molecule>.
|
|
|
5560
|
|
|
5561 =item B<GetRingsWithSize>
|
|
|
5562
|
|
|
5563 @Rings = $Molecule->GetRingsWithSize($Size);
|
|
|
5564
|
|
|
5565 Returns rings with I<Size> as an array containing references to arrays of ring I<Atom> objects in
|
|
|
5566 a I<Molecule>.
|
|
|
5567
|
|
|
5568 =item B<GetRingsWithSizeGreaterThan>
|
|
|
5569
|
|
|
5570 @Rings = $Molecule->GetRingsWithSizeGreaterThan($Size);
|
|
|
5571
|
|
|
5572 Returns rings with size greater than I<Size> as an array containing references to arrays of
|
|
|
5573 ring I<Atom> objects in a I<Molecule>.
|
|
|
5574
|
|
|
5575 =item B<GetRingsWithSizeLessThan>
|
|
|
5576
|
|
|
5577 @Rings = $Molecule->GetRingsWithSizeLessThan($Size);
|
|
|
5578
|
|
|
5579 Returns rings with size less than I<Size> as an array containing references to arrays of
|
|
|
5580 ring I<Atom> objects in a I<Molecule>.
|
|
|
5581
|
|
|
5582 =item B<GetSizeOfLargestRing>
|
|
|
5583
|
|
|
5584 $Size = $Molecule->GetSizeOfLargestRing();
|
|
|
5585
|
|
|
5586 Returns size of the largest ring in a I<Molecule>.
|
|
|
5587
|
|
|
5588 =item B<GetSizeOfSmallestRing>
|
|
|
5589
|
|
|
5590 $Size = $Molecule->GetSizeOfSmallestRing();
|
|
|
5591
|
|
|
5592 Returns size of the smalles ring in a I<Molecule>.
|
|
|
5593
|
|
|
5594 =item B<GetSmallestRing>
|
|
|
5595
|
|
|
5596 @RingAtoms = $Molecule->GetSmallestRing();
|
|
|
5597
|
|
|
5598 Returns an array containing I<Atom> objects corresponding to the smallest ring in
|
|
|
5599 a I<Molecule>.
|
|
|
5600
|
|
|
5601 =item B<GetSpinMultiplicity>
|
|
|
5602
|
|
|
5603 $SpinMultiplicity = $Molecule->GetSpinMultiplicity();
|
|
|
5604
|
|
|
5605 Returns net spin multiplicity of a I<Molecule> using one of the following two methods: explicitly
|
|
|
5606 set B<SpinMultiplicity> property or sum of spin multiplicity on each atom.
|
|
|
5607
|
|
|
5608 =item B<GetSupportedAromaticityModels>
|
|
|
5609
|
|
|
5610 @SupportedModels = $Molecule->GetSupportedAromaticityModels();
|
|
|
5611
|
|
|
5612 Returns an array containing a list of supported aromaticity models.
|
|
|
5613
|
|
|
5614 =item B<GetValenceModel>
|
|
|
5615
|
|
|
5616 $ValenceModel = $Molecule->GetValenceModel();
|
|
|
5617
|
|
|
5618 Returns valence model for I<Molecule> using one of the following two methods: explicitly
|
|
|
5619 set B<ValenceModel> property or defaul value of I<InternalValenceModel>.
|
|
|
5620
|
|
|
5621 =item B<GetTopologicallySortedAtoms>
|
|
|
5622
|
|
|
5623 @SortedAtoms = $Molecule->GetTopologicallySortedAtoms([$StartAtom]);
|
|
|
5624
|
|
|
5625 Returns an array of topologically sorted I<Atom> objects starting from I<StartAtom> or
|
|
|
5626 an arbitrary atom in a I<Molecule>.
|
|
|
5627
|
|
|
5628 =item B<HasAromaticRings>
|
|
|
5629
|
|
|
5630 $Status = $Molecule->HasAromaticRings();
|
|
|
5631
|
|
|
5632 Returns 1 or 0 based on whether any aromatic ring is present in a I<Molecule>.
|
|
|
5633
|
|
|
5634 =item B<HasAromaticAtomsInRings>
|
|
|
5635
|
|
|
5636 $Status = $Molecule->HasAromaticAtomsInRings();
|
|
|
5637
|
|
|
5638 Returns 1 or 0 based on whether any aromatic ring atom is present in a I<Molecule>.
|
|
|
5639
|
|
|
5640 =item B<HasAromaticAtomsNotInRings>
|
|
|
5641
|
|
|
5642 $Status = $Molecule->HasAromaticAtomsNotInRings();
|
|
|
5643
|
|
|
5644 Returns 1 or 0 based on whether any non-ring atom is marked aromatic in a I<Molecule>.
|
|
|
5645
|
|
|
5646 =item B<HasAtom>
|
|
|
5647
|
|
|
5648 $Status = $Molecule->HasAtom($Atom);
|
|
|
5649
|
|
|
5650 Returns 1 or 0 based on whether I<Atom> is present in a I<Molecule>.
|
|
|
5651
|
|
|
5652 =item B<HasBond>
|
|
|
5653
|
|
|
5654 $Status = $Molecule->HasBond($Bond);
|
|
|
5655
|
|
|
5656 Returns 1 or 0 based on whether I<Bond> is present in a I<Molecule>.
|
|
|
5657
|
|
|
5658 =item B<HasFusedRings>
|
|
|
5659
|
|
|
5660 $Status = $Molecule->HasFusedRings();
|
|
|
5661
|
|
|
5662 Returns 1 or 0 based on whether any fused rings set is present in a I<Molecule>.
|
|
|
5663
|
|
|
5664 =item B<HasNoRings>
|
|
|
5665
|
|
|
5666 $Status = $Molecule->HasNoRings();
|
|
|
5667
|
|
|
5668 Returns 0 or 1 based on whether any ring is present in a I<Molecule>.
|
|
|
5669
|
|
|
5670 =item B<HasOnlyOneRing>
|
|
|
5671
|
|
|
5672 $Status = $Molecule->HasOnlyOneRing();
|
|
|
5673
|
|
|
5674 Returns 1 or 0 based on whether only one ring is present in a I<Molecule>.
|
|
|
5675
|
|
|
5676 =item B<HasRings>
|
|
|
5677
|
|
|
5678 $Status = $Molecule->HasRings();
|
|
|
5679
|
|
|
5680 Returns 1 or 0 based on whether rings are present in a I<Molecule>.
|
|
|
5681
|
|
|
5682 =item B<IsAromatic>
|
|
|
5683
|
|
|
5684 $Status = $Molecule->IsAromatic();
|
|
|
5685
|
|
|
5686 Returns 1 or 0 based on whether I<Molecule> is aromatic.
|
|
|
5687
|
|
|
5688 =item B<IsMolecule>
|
|
|
5689
|
|
|
5690 $Status = Molecule::IsMolecule();
|
|
|
5691
|
|
|
5692 Returns 1 or 0 based on whether I<Object> is a B<Molecule> object.
|
|
|
5693
|
|
|
5694 =item B<IsRingAromatic>
|
|
|
5695
|
|
|
5696 $Status = $Molecule->IsRingAromatic(@RingAtoms);
|
|
|
5697
|
|
|
5698 Returns 1 or 0 based on whether all I<RingAtoms> are aromatic.
|
|
|
5699
|
|
|
5700 =item B<IsSupportedAromaticityModel>
|
|
|
5701
|
|
|
5702 $Status = $Molecule->IsSupportedAromaticityModel($AromaticityModel);
|
|
|
5703 $Status = Molecule::IsSupportedAromaticityModel($AromaticityModel);
|
|
|
5704
|
|
|
5705 Returns 1 or 0 based on whether specified I<AromaticityModel> is supported.
|
|
|
5706
|
|
|
5707 =item B<IsTwoDimensional>
|
|
|
5708
|
|
|
5709 $Status = $Molecule->IsTwoDimensional();
|
|
|
5710
|
|
|
5711 Returns 1 or 0 based on whether any atom in I<Molecule> has a non-zero value
|
|
|
5712 for X or Y coordinate and all atoms have zero value for Z coordinates.
|
|
|
5713
|
|
|
5714 =item B<IsThreeDimensional>
|
|
|
5715
|
|
|
5716 $Status = $Molecule->IsThreeDimensional();
|
|
|
5717
|
|
|
5718 Returns 1 or 0 based on whether any atom in I<Molecule> has a non-zero value
|
|
|
5719 for Z coordinate.
|
|
|
5720
|
|
|
5721 =item B<KeepLargestComponent>
|
|
|
5722
|
|
|
5723 $Molecule->KeepLargestComponent();
|
|
|
5724
|
|
|
5725 Deletes atoms corresponding to all other connected components Except for the largest
|
|
|
5726 connected component in a I<Molecule> and returns I<Molecule>.
|
|
|
5727
|
|
|
5728 =item B<KekulizeAromaticAtoms>
|
|
|
5729
|
|
|
5730 $Status = $Molecule->KekulizeAromaticAtoms();
|
|
|
5731
|
|
|
5732 Kekulize marked ring and non-ring aromatic atoms in a molecule and return 1 or 1 based
|
|
|
5733 on whether the kekulization succeeded.
|
|
|
5734
|
|
|
5735 =item B<NewAtom>
|
|
|
5736
|
|
|
5737 $NewAtom = $Molecule->NewAtom(%AtomPropertyNamesAndValues);
|
|
|
5738
|
|
|
5739 Creates a new atom using I<AtomPropertyNamesAndValues>, add its to I<Molecule>, and returns
|
|
|
5740 new B<Atom> object.
|
|
|
5741
|
|
|
5742 =item B<NewBond>
|
|
|
5743
|
|
|
5744 $NewBond = $Molecule->NewBond(%BondPropertyNamesAndValues);
|
|
|
5745
|
|
|
5746 Creates a new bond using I<AtomPropertyNamesAndValues>, add its to I<Molecule>, and returns
|
|
|
5747 new B<Bond> object.
|
|
|
5748
|
|
|
5749 =item B<SetActiveRings>
|
|
|
5750
|
|
|
5751 $Molecule->SetActiveRings($RingsType);
|
|
|
5752
|
|
|
5753 Sets up type of detected ring sets to use during all ring related methods and returns I<Molecule>.
|
|
|
5754 Possible I<RingType> values: I<Independent or All>. By default, I<Independent> ring set is used
|
|
|
5755 during all ring methods.
|
|
|
5756
|
|
|
5757 =item B<SetAromaticityModel>
|
|
|
5758
|
|
|
5759 $Molecule = $Molecule->SetAromaticityModel($AromaticityModel);
|
|
|
5760
|
|
|
5761 Sets up I<AromaticityModel> property value for I<Molecule> and retrurns I<Molecule>.
|
|
|
5762
|
|
|
5763 =item B<SetValenceModel>
|
|
|
5764
|
|
|
5765 $Molecule = $Molecule->SetValenceModel(ValenceModel);
|
|
|
5766
|
|
|
5767 Sets up I<ValenceModel> property value for I<Molecule> and retrurns I<Molecule>.
|
|
|
5768
|
|
|
5769 =item B<StringifyMolecule>
|
|
|
5770
|
|
|
5771 $MoleculeString = $Molecule->StringifyMolecule();
|
|
|
5772
|
|
|
5773 Returns a string containing information about I<Molecule> object
|
|
|
5774
|
|
|
5775 =back
|
|
|
5776
|
|
|
5777 =head1 AUTHOR
|
|
|
5778
|
|
|
5779 Manish Sud <msud@san.rr.com>
|
|
|
5780
|
|
|
5781 =head1 SEE ALSO
|
|
|
5782
|
|
|
5783 Atom.pm, Bond.pm, MoleculeFileIO.pm, MolecularFormula.pm
|
|
|
5784
|
|
|
5785 =head1 COPYRIGHT
|
|
|
5786
|
|
|
5787 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
5788
|
|
|
5789 This file is part of MayaChemTools.
|
|
|
5790
|
|
|
5791 MayaChemTools is free software; you can redistribute it and/or modify it under
|
|
|
5792 the terms of the GNU Lesser General Public License as published by the Free
|
|
|
5793 Software Foundation; either version 3 of the License, or (at your option)
|
|
|
5794 any later version.
|
|
|
5795
|
|
|
5796 =cut
|
