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1 package MolecularDescriptors::HydrogenBondsDescriptors;
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2 #
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3 # $RCSfile: HydrogenBondsDescriptors.pm,v $
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4 # $Date: 2015/02/28 20:49:20 $
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5 # $Revision: 1.18 $
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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 Scalar::Util ();
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33 use TextUtil ();
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34 use Atom;
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35 use Molecule;
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36 use MolecularDescriptors::MolecularDescriptors;
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37
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38 use vars qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS);
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39
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40 @ISA = qw(MolecularDescriptors::MolecularDescriptors Exporter);
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41 @EXPORT = qw();
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42 @EXPORT_OK = qw(GetDescriptorNames);
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43
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44 %EXPORT_TAGS = (all => [@EXPORT, @EXPORT_OK]);
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45
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46 # Setup class variables...
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47 my($ClassName, @DescriptorNames);
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48 _InitializeClass();
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49
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50 # Overload Perl functions...
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51 use overload '""' => 'StringifyHydrogenBondsDescriptors';
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52
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53 # Class constructor...
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54 sub new {
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55 my($Class, %NamesAndValues) = @_;
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56
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57 # Initialize object...
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58 my $This = $Class->SUPER::new();
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59 bless $This, ref($Class) || $Class;
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60 $This->_InitializeHydrogenBondsDescriptors();
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61
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62 $This->_InitializeHydrogenBondsDescriptorsProperties(%NamesAndValues);
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63
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64 return $This;
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65 }
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66
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67 # Initialize class ...
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68 sub _InitializeClass {
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69 #Class name...
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70 $ClassName = __PACKAGE__;
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71
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72 # Descriptor names...
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73 @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors');
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74
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75 }
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76
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77 # Get descriptor names as an array.
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78 #
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79 # This functionality can be either invoked as a class function or an
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80 # object method.
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81 #
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82 sub GetDescriptorNames {
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83 return @DescriptorNames;
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84 }
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85
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86 # Initialize object data...
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87 #
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88 sub _InitializeHydrogenBondsDescriptors {
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89 my($This) = @_;
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90
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91 # Type of MolecularDescriptor...
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92 $This->{Type} = 'HydrogenBonds';
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93
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94 # The currrent release of MayaChemTools supports identification of two types of
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95 # hydrogen bond donor and acceptor atoms with these names:
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96 #
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97 # HBondsType1 or HydrogenBondsType1
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98 # HBondsType2 or HydrogenBondsType2
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99 #
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100 # The names of these hydrogen bond types are rather arbirary. However, their
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101 # definitions have specific meaning and are as follows:
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102 #
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103 # HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:
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104 # . Donor: NH, NH2, OH - Any N and O with available H
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105 # . Acceptor: N[!H], O - Any N without available H and any O
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106 #
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107 # HydrogenBondsType2 [ Ref 91 ]:
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108 # . Donor: NH, NH2, OH - N and O with availabe H
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109 # . Acceptor: N, O - Add N and O
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110 #
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111 # Note:
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112 # . HydrogenBondsType2 definition corresponds to Rule of 5.
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113 #
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114 $This->{HydrogenBondsType} = 'HBondsType2';
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115
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116 # Intialize descriptor names and values...
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117 $This->_InitializeDescriptorNamesAndValues(@DescriptorNames);
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118
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119 return $This;
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120 }
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121
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122 # Initialize object properties...
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123 #
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124 sub _InitializeHydrogenBondsDescriptorsProperties {
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125 my($This, %NamesAndValues) = @_;
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126
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127 my($Name, $Value, $MethodName);
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128 while (($Name, $Value) = each %NamesAndValues) {
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129 $MethodName = "Set${Name}";
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130 $This->$MethodName($Value);
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131 }
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132
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133 return $This;
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134 }
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135
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136 # Set hydrogen bonds type...
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137 #
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138 sub SetHydrogenBondsType {
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139 my($This, $HydrogenBondsType) = @_;
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140
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141 if ($HydrogenBondsType !~ /^(HBondsType1|HBondsType2|HydrogenBondsType1|HydrogenBondsType2)$/i) {
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142 croak "Error: ${ClassName}->SetHydrogenBondsType: Specified hydrogen bonds type, $HydrogenBondsType, is not supported. Valid values: HBondsType1, HBondsType2, HydrogenBondsType1, HydrogenBondsType2 ...\n ";
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143 }
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144
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145 $This->{HydrogenBondsType} = $HydrogenBondsType;
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146
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147 return $This;
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148 }
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149
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150 # Calculate number of hydrogen bond donors and acceptors in a molecule...
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151 #
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152 sub GenerateDescriptors {
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153 my($This) = @_;
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154
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155 # Initialize descriptor values...
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156 $This->_InitializeDescriptorValues();
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157
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158 # Check availability of molecule...
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159 if (!$This->{Molecule}) {
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160 carp "Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set...";
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161 return undef;
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162 }
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163
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164 # Calculate descriptor values...
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165 if (!$This->_CalculateDescriptorValues()) {
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166 carp "Warning: ${ClassName}->CalculateDescriptorValues: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate number of hydrogen bond donor and accepror values...";
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167 return undef;
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168 }
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169
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170 # Set final descriptor values...
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171 $This->_SetFinalDescriptorValues();
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172
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173 }
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174
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175 # Calculate number of hydrogen bond donors and acceptors...
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176 #
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177 sub _CalculateDescriptorValues {
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178 my($This) = @_;
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179 my($HydrogenBondDonors, $HydrogenBondAcceptors, $Atom);
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180
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181 $HydrogenBondDonors = 0;
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182 $HydrogenBondAcceptors = 0;
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183
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184 for $Atom ($This->{Molecule}->GetAtoms()) {
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185 if ($Atom->IsHydrogenBondDonor($This->{HydrogenBondsType})) {
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186 $HydrogenBondDonors++;
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187 }
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188 if ($Atom->IsHydrogenBondAcceptor($This->{HydrogenBondsType})) {
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189 $HydrogenBondAcceptors++;
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190 }
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191 }
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192
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193 # Track the calculated values...
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194 $This->{HydrogenBondDonors} = $HydrogenBondDonors;
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195 $This->{HydrogenBondAcceptors} = $HydrogenBondAcceptors;
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196
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197 return $This;
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198 }
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199
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200 # Setup final descriptor values...
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201 #
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202 sub _SetFinalDescriptorValues {
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203 my($This) = @_;
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204
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205 $This->{DescriptorsGenerated} = 1;
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206
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207 $This->SetDescriptorValues($This->{HydrogenBondDonors}, $This->{HydrogenBondAcceptors});
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208
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209 return $This;
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210 }
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211
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212 # Return a string containg data for HydrogenBondsDescriptors object...
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213 #
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214 sub StringifyHydrogenBondsDescriptors {
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215 my($This) = @_;
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216 my($HydrogenBondsDescriptorsString);
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217
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218 $HydrogenBondsDescriptorsString = "MolecularDescriptorType: $This->{Type}; HydrogenBondsType: $This->{HydrogenBondsType}; " . $This->_StringifyDescriptorNamesAndValues();
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219
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220 return $HydrogenBondsDescriptorsString;
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221 }
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222
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223 # Is it a HydrogenBondsDescriptors object?
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224 sub _IsHydrogenBondsDescriptors {
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225 my($Object) = @_;
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226
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227 return (Scalar::Util::blessed($Object) && $Object->isa($ClassName)) ? 1 : 0;
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228 }
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229
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230 1;
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231
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232 __END__
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233
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234 =head1 NAME
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235
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236 HydrogenBondsDescriptors
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237
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238 =head1 SYNOPSIS
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239
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240 use MolecularDescriptors::HydrogenBondsDescriptors;
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241
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242 use MolecularDescriptors::HydrogenBondsDescriptors qw(:all);
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243
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244 =head1 DESCRIPTION
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245
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246 B<HydrogenBondsDescriptors> class provides the following methods:
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247
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248 new, GenerateDescriptors, GetDescriptorNames, SetHydrogenBondsType,
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249 StringifyHydrogenBondsDescriptors
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250
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251 B<HydrogenBondsDescriptors> is derived from B<MolecularDescriptors> class which in turn
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252 is derived from B<ObjectProperty> base class that provides methods not explicitly defined
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253 in B<HydrogenBondsDescriptors>, B<MolecularDescriptors> or B<ObjectProperty> classes using Perl's
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254 AUTOLOAD functionality. These methods are generated on-the-fly for a specified object property:
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255
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256 Set<PropertyName>(<PropertyValue>);
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257 $PropertyValue = Get<PropertyName>();
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258 Delete<PropertyName>();
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259
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260 The current release of MayaChemTools supports identification of two types of hydrogen bond
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261 donor and acceptor atoms with these names:
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262
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263 HBondsType1 or HydrogenBondsType1
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264 HBondsType2 or HydrogenBondsType2
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265
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266 The names of these hydrogen bond types are rather arbitrary. However, their definitions have
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267 specific meaning and are as follows:
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268
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269 HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:
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270
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271 Donor: NH, NH2, OH - Any N and O with available H
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272 Acceptor: N[!H], O - Any N without available H and any O
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273
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274 HydrogenBondsType2 [ Ref 91 ]:
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275
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276 Donor: NH, NH2, OH - N and O with available H
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277 Acceptor: N, O - And N and O
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278
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279 By default, I<HydrogenBondsType2> is used to calculate number hydrogen bond donor
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280 and acceptor atoms. This corresponds to B<RuleOf5> definition of hydrogen bond donors
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281 and acceptors.
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282
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283 =head2 METHODS
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284
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285 =over 4
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286
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287 =item B<new>
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288
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289 $HydrogenBondsDescriptors = new MolecularDescriptors::
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290 HydrogenBondsDescriptors(%NamesAndValues);
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291
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292 Using specified I<HydrogenBondsDescriptors> property names and values hash, B<new>
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293 method creates a new object and returns a reference to newly created B<HydrogenBondsDescriptors>
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294 object. By default, the following properties are initialized:
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295
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296 Molecule = ''
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297 Type = 'HydrogenBonds'
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298 HydrogenBondsType = 'HBondsType2'
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299 @DescriptorNames = ('HydrogenBondDonors', 'HydrogenBondAcceptors')
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300 @DescriptorValues = ('None', 'None')
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301
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302 Examples:
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303
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304 $HydrogenBondsDescriptors = new MolecularDescriptors::
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305 HydrogenBondsDescriptors();
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306
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307 $HydrogenBondsDescriptors = new MolecularDescriptors::
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308 HydrogenBondsDescriptors(
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309 'HydrogenBondsType' => 'HBondsType2');
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310
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311 $HydrogenBondsDescriptors->SetMolecule($Molecule);
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312 $HydrogenBondsDescriptors->GenerateDescriptors();
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313 print "HydrogenBondsDescriptors: $HydrogenBondsDescriptors\n";
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314
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315 =item B<GenerateDescriptors>
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316
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317 $HydrogenBondsDescriptors->GenerateDescriptors();
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318
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319 Calculates number of hydrogen bond donors and acceptors a molecule and returns
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320 I<HydrogenBondsDescriptors>.
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321
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322 =item B<GetDescriptorNames>
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323
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324 @DescriptorNames = $HydrogenBondsDescriptors->GetDescriptorNames();
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325 @DescriptorNames = MolecularDescriptors::HydrogenBondsDescriptors::
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326 GetDescriptorNames();
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327
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328 Returns all available descriptor names as an array.
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329
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330 =item B<SetHydrogenBondsType>
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331
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332 $HydrogenBondsDescriptors->SetHydrogenBondsType($HBondsType);
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333
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334 Sets value of hydrogen bonds type to use during calculation of descriptors and returns
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335 I<HydrogenBondsDescriptors>. Possible values: I<HBondsType1, HydrogenBondsType1,
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336 HBondsType2, HydrogenBondsType2>.
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337
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338 =item B<StringifyHydrogenBondsDescriptors>
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339
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340 $String = $HydrogenBondsDescriptors->
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341 StringifyHydrogenBondsDescriptors();
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342
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343 Returns a string containing information about I<HydrogenBondsDescriptors> object.
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344
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345 =back
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346
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347 =head1 AUTHOR
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348
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349 Manish Sud <msud@san.rr.com>
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350
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351 =head1 SEE ALSO
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352
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353 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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354
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355 =head1 COPYRIGHT
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356
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357 Copyright (C) 2015 Manish Sud. All rights reserved.
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358
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359 This file is part of MayaChemTools.
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360
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361 MayaChemTools is free software; you can redistribute it and/or modify it under
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362 the terms of the GNU Lesser General Public License as published by the Free
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363 Software Foundation; either version 3 of the License, or (at your option)
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364 any later version.
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365
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366 =cut
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