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<html> <head> <title>MayaChemTools:Code:MolecularDescriptors::HydrogenBondsDescriptors.pm</title> <meta http-equiv="content-type" content="text/html;charset=utf-8"> <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> </head> <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> <br/> <center> <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> </center> <br/> <pre> <a name="package-MolecularDescriptors::HydrogenBondsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::HydrogenBondsDescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: HydrogenBondsDescriptors.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</span> 5 <span class="c"># $Revision: 1.18 $</span> 6 <span class="c">#</span> 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> 8 <span class="c">#</span> 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> 10 <span class="c">#</span> 11 <span class="c"># This file is part of MayaChemTools.</span> 12 <span class="c">#</span> 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> 16 <span class="c"># later version.</span> 17 <span class="c">#</span> 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> 21 <span class="c"># details.</span> 22 <span class="c">#</span> 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> 27 <span class="c">#</span> 28 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 33 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> 37 38 <span class="k">use</span> <span class="w">vars</span> <span class="q">qw(@ISA @EXPORT @EXPORT_OK %EXPORT_TAGS)</span><span class="sc">;</span> 39 40 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> 41 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 42 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span> 43 44 <span class="i">%EXPORT_TAGS</span> = <span class="s">(</span><span class="w">all</span> <span class="cm">=></span> <span class="s">[</span><span class="i">@EXPORT</span><span class="cm">,</span> <span class="i">@EXPORT_OK</span><span class="s">]</span><span class="s">)</span><span class="sc">;</span> 45 46 <span class="c"># Setup class variables...</span> 47 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 48 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 49 50 <span class="c"># Overload Perl functions...</span> 51 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyHydrogenBondsDescriptors'</span><span class="sc">;</span> 52 53 <span class="c"># Class constructor...</span> <a name="new-"></a> 54 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 55 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 56 57 <span class="c"># Initialize object...</span> 58 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 59 <span class="k">bless</span> <span class="i">$This</span><span class="cm">,</span> <span class="k">ref</span><span class="s">(</span><span class="i">$Class</span><span class="s">)</span> || <span class="i">$Class</span><span class="sc">;</span> 60 <span class="i">$This</span><span class="i">->_InitializeHydrogenBondsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 61 62 <span class="i">$This</span><span class="i">->_InitializeHydrogenBondsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 63 64 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 65 <span class="s">}</span> 66 67 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 68 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 69 <span class="c">#Class name...</span> 70 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 71 72 <span class="c"># Descriptor names...</span> 73 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'HydrogenBondDonors'</span><span class="cm">,</span> <span class="q">'HydrogenBondAcceptors'</span><span class="s">)</span><span class="sc">;</span> 74 75 <span class="s">}</span> 76 77 <span class="c"># Get descriptor names as an array.</span> 78 <span class="c">#</span> 79 <span class="c"># This functionality can be either invoked as a class function or an</span> 80 <span class="c"># object method.</span> 81 <span class="c">#</span> <a name="GetDescriptorNames-"></a> 82 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> 83 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> 84 <span class="s">}</span> 85 86 <span class="c"># Initialize object data...</span> 87 <span class="c">#</span> <a name="_InitializeHydrogenBondsDescriptors-"></a> 88 <span class="k">sub </span><span class="m">_InitializeHydrogenBondsDescriptors</span> <span class="s">{</span> 89 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 90 91 <span class="c"># Type of MolecularDescriptor...</span> 92 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'HydrogenBonds'</span><span class="sc">;</span> 93 94 <span class="c"># The currrent release of MayaChemTools supports identification of two types of</span> 95 <span class="c"># hydrogen bond donor and acceptor atoms with these names:</span> 96 <span class="c">#</span> 97 <span class="c"># HBondsType1 or HydrogenBondsType1</span> 98 <span class="c"># HBondsType2 or HydrogenBondsType2</span> 99 <span class="c">#</span> 100 <span class="c"># The names of these hydrogen bond types are rather arbirary. However, their</span> 101 <span class="c"># definitions have specific meaning and are as follows:</span> 102 <span class="c">#</span> 103 <span class="c"># HydrogenBondsType1 [ Ref 60-61, Ref 65-66 ]:</span> 104 <span class="c"># . Donor: NH, NH2, OH - Any N and O with available H</span> 105 <span class="c"># . Acceptor: N[!H], O - Any N without available H and any O</span> 106 <span class="c">#</span> 107 <span class="c"># HydrogenBondsType2 [ Ref 91 ]:</span> 108 <span class="c"># . Donor: NH, NH2, OH - N and O with availabe H</span> 109 <span class="c"># . Acceptor: N, O - Add N and O</span> 110 <span class="c">#</span> 111 <span class="c"># Note:</span> 112 <span class="c"># . HydrogenBondsType2 definition corresponds to Rule of 5.</span> 113 <span class="c">#</span> 114 <span class="i">$This</span>->{<span class="w">HydrogenBondsType</span>} = <span class="q">'HBondsType2'</span><span class="sc">;</span> 115 116 <span class="c"># Intialize descriptor names and values...</span> 117 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 118 119 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 120 <span class="s">}</span> 121 122 <span class="c"># Initialize object properties...</span> 123 <span class="c">#</span> <a name="_InitializeHydrogenBondsDescriptorsProperties-"></a> 124 <span class="k">sub </span><span class="m">_InitializeHydrogenBondsDescriptorsProperties</span> <span class="s">{</span> 125 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 126 127 <span class="k">my</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="cm">,</span> <span class="i">$MethodName</span><span class="s">)</span><span class="sc">;</span> 128 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> 129 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 130 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 131 <span class="s">}</span> 132 133 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 134 <span class="s">}</span> 135 136 <span class="c"># Set hydrogen bonds type...</span> 137 <span class="c">#</span> <a name="SetHydrogenBondsType-"></a> 138 <span class="k">sub </span><span class="m">SetHydrogenBondsType</span> <span class="s">{</span> 139 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$HydrogenBondsType</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 140 141 <span class="k">if</span> <span class="s">(</span><span class="i">$HydrogenBondsType</span> !~ <span class="q">/^(HBondsType1|HBondsType2|HydrogenBondsType1|HydrogenBondsType2)$/i</span><span class="s">)</span> <span class="s">{</span> 142 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetHydrogenBondsType: Specified hydrogen bonds type, $HydrogenBondsType, is not supported. Valid values: HBondsType1, HBondsType2, HydrogenBondsType1, HydrogenBondsType2 ...\n "</span><span class="sc">;</span> 143 <span class="s">}</span> 144 145 <span class="i">$This</span>->{<span class="w">HydrogenBondsType</span>} = <span class="i">$HydrogenBondsType</span><span class="sc">;</span> 146 147 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 148 <span class="s">}</span> 149 150 <span class="c"># Calculate number of hydrogen bond donors and acceptors in a molecule...</span> 151 <span class="c">#</span> <a name="GenerateDescriptors-"></a> 152 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> 153 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 154 155 <span class="c"># Initialize descriptor values...</span> 156 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 157 158 <span class="c"># Check availability of molecule...</span> 159 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 160 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> 161 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 162 <span class="s">}</span> 163 164 <span class="c"># Calculate descriptor values...</span> 165 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 166 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->CalculateDescriptorValues: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate number of hydrogen bond donor and accepror values..."</span><span class="sc">;</span> 167 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 168 <span class="s">}</span> 169 170 <span class="c"># Set final descriptor values...</span> 171 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 172 173 <span class="s">}</span> 174 175 <span class="c"># Calculate number of hydrogen bond donors and acceptors...</span> 176 <span class="c">#</span> <a name="_CalculateDescriptorValues-"></a> 177 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> 178 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 179 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenBondDonors</span><span class="cm">,</span> <span class="i">$HydrogenBondAcceptors</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 180 181 <span class="i">$HydrogenBondDonors</span> = <span class="n">0</span><span class="sc">;</span> 182 <span class="i">$HydrogenBondAcceptors</span> = <span class="n">0</span><span class="sc">;</span> 183 184 <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 185 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogenBondDonor</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">HydrogenBondsType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 186 <span class="i">$HydrogenBondDonors</span>++<span class="sc">;</span> 187 <span class="s">}</span> 188 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogenBondAcceptor</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">HydrogenBondsType</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> 189 <span class="i">$HydrogenBondAcceptors</span>++<span class="sc">;</span> 190 <span class="s">}</span> 191 <span class="s">}</span> 192 193 <span class="c"># Track the calculated values...</span> 194 <span class="i">$This</span>->{<span class="w">HydrogenBondDonors</span>} = <span class="i">$HydrogenBondDonors</span><span class="sc">;</span> 195 <span class="i">$This</span>->{<span class="w">HydrogenBondAcceptors</span>} = <span class="i">$HydrogenBondAcceptors</span><span class="sc">;</span> 196 197 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 198 <span class="s">}</span> 199 200 <span class="c"># Setup final descriptor values...</span> 201 <span class="c">#</span> <a name="_SetFinalDescriptorValues-"></a> 202 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> 203 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 204 205 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 206 207 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">HydrogenBondDonors</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">HydrogenBondAcceptors</span>}<span class="s">)</span><span class="sc">;</span> 208 209 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 210 <span class="s">}</span> 211 212 <span class="c"># Return a string containg data for HydrogenBondsDescriptors object...</span> 213 <span class="c">#</span> <a name="StringifyHydrogenBondsDescriptors-"></a> 214 <span class="k">sub </span><span class="m">StringifyHydrogenBondsDescriptors</span> <span class="s">{</span> 215 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 216 <span class="k">my</span><span class="s">(</span><span class="i">$HydrogenBondsDescriptorsString</span><span class="s">)</span><span class="sc">;</span> 217 218 <span class="i">$HydrogenBondsDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; HydrogenBondsType: $This->{HydrogenBondsType}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 219 220 <span class="k">return</span> <span class="i">$HydrogenBondsDescriptorsString</span><span class="sc">;</span> 221 <span class="s">}</span> 222 223 <span class="c"># Is it a HydrogenBondsDescriptors object?</span> <a name="_IsHydrogenBondsDescriptors-"></a> 224 <span class="k">sub </span><span class="m">_IsHydrogenBondsDescriptors</span> <span class="s">{</span> 225 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 226 227 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> && <span class="i">$Object</span><span class="i">->isa</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 228 <span class="s">}</span> 229 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>