Mercurial > repos > deepakjadmin > mayatool3_test3
diff mayachemtools/docs/modules/html/code/HydrogenBondsDescriptors.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/HydrogenBondsDescriptors.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,250 @@ +<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>