1 package MolecularDescriptors::HydrogenBondsDescriptors; 2 # 3 # $RCSfile: HydrogenBondsDescriptors.pm,v $ 4 # $Date: 2015/02/28 20:49:20 $ 5 # $Revision: 1.18 $ 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 Atom; 35 use Molecule; 36 use MolecularDescriptors::MolecularDescriptors; 37 38 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS); 39 40 @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter); 41 @EXPORT = qw(); 42 @EXPORT_OK = qw(GetDescriptorNames); 43 44 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]); 45 46 # Setup class variables... 47 my($ClassName, @DescriptorNames); 48 _InitializeClass(); 49 50 # Overload Perl functions... 51 use overload '""' => 'StringifyHydrogenBondsDescriptors'; 52 53 # Class constructor... 54 sub new { 55 my($Class, %NamesAndValues) = @_; 56 57 # Initialize object... 58 my $This = $Class->SUPER::new(); 59 bless $This, ref($Class) || $Class; 60 $This->_InitializeHydrogenBondsDescriptors(); 61 62 $This->_InitializeHydrogenBondsDescriptorsProperties(%NamesAndValues); 63 64 return $This; 65 } 66 67 # Initialize class ... 68 sub _InitializeClass { 69 #Class name... 70 $ClassName = __PACKAGE__; 71 72 # Descriptor names... 73 @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors'); 74 75 } 76 77 # Get descriptor names as an array. 78 # 79 # This functionality can be either invoked as a class function or an 80 # object method. 81 # 82 sub GetDescriptorNames { 83 return @DescriptorNames; 84 } 85 86 # Initialize object data... 87 # 88 sub _InitializeHydrogenBondsDescriptors { 89 my($This) = @_; 90 91 # Type of MolecularDescriptor... 92 $This->{Type} = 'HydrogenBonds'; 93 94 # The currrent release of MayaChemTools supports identification of two types of 95 # hydrogen bond donor and acceptor atoms with these names: 96 # 97 # HBondsType1 or HydrogenBondsType1 98 # HBondsType2 or HydrogenBondsType2 99 # 100 # The names of these hydrogen bond types are rather arbirary. However, their 101 # definitions have specific meaning and are as follows: 102 # 103 # HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]: 104 # . Donor: NH, NH2, OH - Any N and O with available H 105 # . Acceptor: N[!H], O - Any N without available H and any O 106 # 107 # HydrogenBondsType2 [ Ref 91 ]: 108 # . Donor: NH, NH2, OH - N and O with availabe H 109 # . Acceptor: N, O - Add N and O 110 # 111 # Note: 112 # . HydrogenBondsType2 definition corresponds to Rule of 5. 113 # 114 $This->{HydrogenBondsType} = 'HBondsType2'; 115 116 # Intialize descriptor names and values... 117 $This->_InitializeDescriptorNamesAndValues(@DescriptorNames); 118 119 return $This; 120 } 121 122 # Initialize object properties... 123 # 124 sub _InitializeHydrogenBondsDescriptorsProperties { 125 my($This, %NamesAndValues) = @_; 126 127 my($Name, $Value, $MethodName); 128 while (($Name, $Value) = each %NamesAndValues) { 129 $MethodName = "Set${Name}"; 130 $This->$MethodName($Value); 131 } 132 133 return $This; 134 } 135 136 # Set hydrogen bonds type... 137 # 138 sub SetHydrogenBondsType { 139 my($This, $HydrogenBondsType) = @_; 140 141 if ($HydrogenBondsType !~ /^(HBondsType1|HBondsType2|HydrogenBondsType1|HydrogenBondsType2)$/i) { 142 croak "Error: ${ClassName}->SetHydrogenBondsType: Specified hydrogen bonds type, $HydrogenBondsType, is not supported. Valid values: HBondsType1, HBondsType2, HydrogenBondsType1, HydrogenBondsType2 ...\n "; 143 } 144 145 $This->{HydrogenBondsType} = $HydrogenBondsType; 146 147 return $This; 148 } 149 150 # Calculate number of hydrogen bond donors and acceptors in a molecule... 151 # 152 sub GenerateDescriptors { 153 my($This) = @_; 154 155 # Initialize descriptor values... 156 $This->_InitializeDescriptorValues(); 157 158 # Check availability of molecule... 159 if (!$This->{Molecule}) { 160 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."; 161 return undef; 162 } 163 164 # Calculate descriptor values... 165 if (!$This->_CalculateDescriptorValues()) { 166 carp "Warning: ${ClassName}->CalculateDescriptorValues: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate number of hydrogen bond donor and accepror values..."; 167 return undef; 168 } 169 170 # Set final descriptor values... 171 $This->_SetFinalDescriptorValues(); 172 173 } 174 175 # Calculate number of hydrogen bond donors and acceptors... 176 # 177 sub _CalculateDescriptorValues { 178 my($This) = @_; 179 my($HydrogenBondDonors, $HydrogenBondAcceptors, $Atom); 180 181 $HydrogenBondDonors = 0; 182 $HydrogenBondAcceptors = 0; 183 184 for $Atom ($This->{Molecule}->GetAtoms()) { 185 if ($Atom->IsHydrogenBondDonor($This->{HydrogenBondsType})) { 186 $HydrogenBondDonors++; 187 } 188 if ($Atom->IsHydrogenBondAcceptor($This->{HydrogenBondsType})) { 189 $HydrogenBondAcceptors++; 190 } 191 } 192 193 # Track the calculated values... 194 $This->{HydrogenBondDonors} = $HydrogenBondDonors; 195 $This->{HydrogenBondAcceptors} = $HydrogenBondAcceptors; 196 197 return $This; 198 } 199 200 # Setup final descriptor values... 201 # 202 sub _SetFinalDescriptorValues { 203 my($This) = @_; 204 205 $This->{DescriptorsGenerated} = 1; 206 207 $This->SetDescriptorValues($This->{HydrogenBondDonors}, $This->{HydrogenBondAcceptors}); 208 209 return $This; 210 } 211 212 # Return a string containg data for HydrogenBondsDescriptors object... 213 # 214 sub StringifyHydrogenBondsDescriptors { 215 my($This) = @_; 216 my($HydrogenBondsDescriptorsString); 217 218 $HydrogenBondsDescriptorsString = "MolecularDescriptorType: $This->{Type}; HydrogenBondsType: $This->{HydrogenBondsType}; " . $This->_StringifyDescriptorNamesAndValues(); 219 220 return $HydrogenBondsDescriptorsString; 221 } 222 223 # Is it a HydrogenBondsDescriptors object? 224 sub _IsHydrogenBondsDescriptors { 225 my($Object) = @_; 226 227 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0; 228 } 229