1 package MolecularDescriptors::MolecularVolumeDescriptors; 2 # 3 # $RCSfile: MolecularVolumeDescriptors.pm,v $ 4 # $Date: 2015/02/28 20:49:20 $ 5 # $Revision: 1.16 $ 6 # 7 # Author: Manish Sud <msud@san.rr.com> 8 # 9 # Copyright (C) 2015 Manish Sud. All rights reserved. 10 # 11 # This file is part of MayaChemTools. 12 # 13 # MayaChemTools is free software; you can redistribute it and/or modify it under 14 # the terms of the GNU Lesser General Public License as published by the Free 15 # Software Foundation; either version 3 of the License, or (at your option) any 16 # later version. 17 # 18 # MayaChemTools is distributed in the hope that it will be useful, but without 19 # any warranty; without even the implied warranty of merchantability of fitness 20 # for a particular purpose. See the GNU Lesser General Public License for more 21 # details. 22 # 23 # You should have received a copy of the GNU Lesser General Public License 24 # along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or 25 # write to the Free Software Foundation Inc., 59 Temple Place, Suite 330, 26 # Boston, MA, 02111-1307, USA. 27 # 28 29 use strict; 30 use Carp; 31 use Exporter; 32 use Scalar::Util (); 33 use TextUtil (); 34 use MathUtil (); 35 use Atom; 36 use Molecule; 37 use AtomTypes::AtomTypes; 38 use MolecularDescriptors::MolecularDescriptors; 39 40 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS); 41 42 @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter); 43 @EXPORT = qw(); 44 @EXPORT_OK = qw(GetDescriptorNames GetVDWAtomRadiiAndVolumesData); 45 46 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]); 47 48 # Setup class variables... 49 my($ClassName, @DescriptorNames, %VDWAtomRadiiAndVolumesDataMap); 50 _InitializeClass(); 51 52 # Overload Perl functions... 53 use overload '""' => 'StringifyMolecularVolumeDescriptors'; 54 55 # Class constructor... 56 sub new { 57 my($Class, %NamesAndValues) = @_; 58 59 # Initialize object... 60 my $This = $Class->SUPER::new(); 61 bless $This, ref($Class) || $Class; 62 $This->_InitializeMolecularVolumeDescriptors(); 63 64 $This->_InitializeMolecularVolumeDescriptorsProperties(%NamesAndValues); 65 66 return $This; 67 } 68 69 # Initialize class ... 70 sub _InitializeClass { 71 #Class name... 72 $ClassName = __PACKAGE__; 73 74 # Descriptor names... 75 @DescriptorNames = ('MolecularVolume'); 76 77 # Initialize the data hash. It'll be loaded on demand later... 78 %VDWAtomRadiiAndVolumesDataMap = (); 79 80 } 81 82 # Get descriptor names as an array. 83 # 84 # This functionality can be either invoked as a class function or an 85 # object method. 86 # 87 sub GetDescriptorNames { 88 return @DescriptorNames; 89 } 90 91 # Initialize object data... 92 # 93 sub _InitializeMolecularVolumeDescriptors { 94 my($This) = @_; 95 96 # Type of MolecularDescriptor... 97 $This->{Type} = 'MolecularVolume'; 98 99 # Intialize descriptor names and values... 100 $This->_InitializeDescriptorNamesAndValues(@DescriptorNames); 101 102 return $This; 103 } 104 105 # Initialize object properties... 106 # 107 sub _InitializeMolecularVolumeDescriptorsProperties { 108 my($This, %NamesAndValues) = @_; 109 110 my($Name, $Value, $MethodName); 111 while (($Name, $Value) = each %NamesAndValues) { 112 $MethodName = "Set${Name}"; 113 $This->$MethodName($Value); 114 } 115 116 return $This; 117 } 118 119 # Get VDW atom data loaded from VDW atom radii and and volumes data file as 120 # a reference to hash with the following hash data format: 121 # 122 # @{$VDWAtomRadiiAndVolumesDataMap{AtomTypes}} - Array of all possible atom type symbols for all atoms 123 # @{$VDWAtomRadiiAndVolumesDataMap->{ColLabels}} - Array of column labels 124 # %{$VDWAtomRadiiAndVolumesDataMap->{DataCol<Num>}} - Hash keys pair: <DataCol<Num>, AtomType> 125 # 126 # This functionality can be either invoked as a class function or an 127 # object method. 128 # 129 sub GetVDWAtomRadiiAndVolumesData { 130 131 # Make sure data is loaded... 132 _CheckAndLoadVDWAtomRadiiAndVolumesData(); 133 134 return \%VDWAtomRadiiAndVolumesDataMap; 135 } 136 137 # Calculate van der Waals molecular volume [ Ref 93 ] of a molecule using 138 # atomic and bonds contributions... 139 # 140 # van der Waals molecular volume (A**3/molecule) is defined as: 141 # 142 # vdwMolecularVolume = SumOfAtomicVDWVolumeContributions - 5.92 * NumOfBonds 143 # - 14.7 * NumOfAromaticRings - 3.8 * NumOfNonAromaticRings 144 # 145 # Methodology: 146 # . Add up van der Waals atom volumne of all atoms 147 # . Calculate molecular volume by correcting sum of atom volumes for num of 148 # bonds and rings 149 # 150 # Caveats: 151 # . All hydrogens must be added to molecule before calling GenerateDescriptors. 152 # 153 sub GenerateDescriptors { 154 my($This) = @_; 155 156 # Initialize descriptor values... 157 $This->_InitializeDescriptorValues(); 158 159 # Check availability of molecule... 160 if (!$This->{Molecule}) { 161 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."; 162 return undef; 163 } 164 165 # Calculate descriptor values... 166 if (!$This->_CalculateDescriptorValues()) { 167 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularVolume values: van der Waals atom volume data is not available for all atoms..."; 168 return undef; 169 } 170 171 # Set final descriptor values... 172 $This->_SetFinalDescriptorValues(); 173 174 return $This; 175 } 176 177 # Calculate MolecularVolume value... 178 # 179 sub _CalculateDescriptorValues { 180 my($This) = @_; 181 my($Atom, $AtomID, $AtomSymbol, $SumOfVDWAtomVolumes, $Molecule, $MolecularVolume, $NumOfBonds, $NumOfAromaticRings, $NumOfNonAromaticRings, $VDWAtomRadiiAndVolumesDataMapRef); 182 183 $MolecularVolume = 0; 184 185 $VDWAtomRadiiAndVolumesDataMapRef = $This->GetVDWAtomRadiiAndVolumesData(); 186 $Molecule = $This->{Molecule}; 187 188 # Calculate atom volumes contribution to molecular volume... 189 # 190 $SumOfVDWAtomVolumes = 0; 191 192 ATOM: for $Atom ($Molecule->GetAtoms()) { 193 $AtomID = $Atom->GetID(); 194 $AtomSymbol = $Atom->GetAtomSymbol(); 195 196 # Make sure van der Waals atom volume is available... 197 if (!exists $VDWAtomRadiiAndVolumesDataMap{DataCol3}{$AtomSymbol}) { 198 return undef; 199 } 200 $SumOfVDWAtomVolumes += $VDWAtomRadiiAndVolumesDataMapRef->{DataCol3}{$AtomSymbol}; 201 } 202 203 $NumOfBonds = $Molecule->GetNumOfBonds(); 204 $NumOfAromaticRings = $Molecule->GetNumOfAromaticRings(); 205 $NumOfNonAromaticRings = $Molecule->GetNumOfRings() - $NumOfAromaticRings; 206 207 # Apply correction for bonds and rings... 208 $MolecularVolume = $SumOfVDWAtomVolumes - 5.92 * $NumOfBonds - 14.7 * $NumOfAromaticRings - 3.8 * $NumOfNonAromaticRings; 209 210 # Track the calculated values... 211 $This->{MolecularVolume} = MathUtil::round($MolecularVolume, 2); 212 213 return $This; 214 } 215 216 # Setup final descriptor values... 217 # 218 sub _SetFinalDescriptorValues { 219 my($This) = @_; 220 221 $This->{DescriptorsGenerated} = 1; 222 223 $This->SetDescriptorValues($This->{MolecularVolume}); 224 225 return $This; 226 } 227 228 # Return a string containg data for MolecularVolumeDescriptors object... 229 # 230 sub StringifyMolecularVolumeDescriptors { 231 my($This) = @_; 232 my($MolecularVolumeDescriptorsString); 233 234 $MolecularVolumeDescriptorsString = "MolecularDescriptorType: $This->{Type}; " . $This->_StringifyDescriptorNamesAndValues(); 235 236 return $MolecularVolumeDescriptorsString; 237 } 238 239 # Is it a MolecularVolumeDescriptors object? 240 sub _IsMolecularVolumeDescriptors { 241 my($Object) = @_; 242 243 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0; 244 } 245 246 # Check and load van der Waals atom radii and volumes data... 247 # 248 sub _CheckAndLoadVDWAtomRadiiAndVolumesData { 249 250 # Is it already loaded? 251 if (exists $VDWAtomRadiiAndVolumesDataMap{AtomTypes}) { 252 return; 253 } 254 255 _LoadVDWAtomRadiiAndVolumesData(); 256 } 257 258 # Initialize van der Waals atom radii and volumes data from the file... 259 # 260 # Format: 261 # 262 # "AtomTypeSymbol","VDWAtomRadius(A)","VDWAtomVolume(A**3)/molecule" 263 # "H","1.20","7.24" 264 # "He","1.40","11.49" 265 # 266 sub _LoadVDWAtomRadiiAndVolumesData { 267 my($VDWAtomDataFile, $MayaChemToolsLibDir); 268 269 $MayaChemToolsLibDir = FileUtil::GetMayaChemToolsLibDirName(); 270 271 $VDWAtomDataFile = "$MayaChemToolsLibDir" . "/data/VDWAtomRadiiAndVolumes.csv"; 272 if (! -e "$VDWAtomDataFile") { 273 croak "Error: MayaChemTools package file, $VDWAtomDataFile, is missing: Possible installation problems..."; 274 } 275 276 %VDWAtomRadiiAndVolumesDataMap = (); 277 AtomTypes::AtomTypes::LoadAtomTypesData($VDWAtomDataFile, \%VDWAtomRadiiAndVolumesDataMap); 278 }; 279