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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/mayachemtools/docs/modules/html/code/Fsp3CarbonsDescriptors.html Wed Jan 20 11:55:01 2016 -0500 @@ -0,0 +1,224 @@ +<html> +<head> +<title>MayaChemTools:Code:MolecularDescriptors::Fsp3CarbonsDescriptors.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::Fsp3CarbonsDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::Fsp3CarbonsDescriptors</span><span class="sc">;</span> + 2 <span class="c">#</span> + 3 <span class="c"># $RCSfile: Fsp3CarbonsDescriptors.pm,v $</span> + 4 <span class="c"># $Date: 2015/02/28 20:49:19 $</span> + 5 <span class="c"># $Revision: 1.12 $</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">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> + 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> + 37 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> + 38 + 39 <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> + 40 + 41 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> + 42 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> + 43 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames)</span><span class="sc">;</span> + 44 + 45 <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> + 46 + 47 <span class="c"># Setup class variables...</span> + 48 <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> + 49 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 50 + 51 <span class="c"># Overload Perl functions...</span> + 52 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyFsp3CarbonsDescriptors'</span><span class="sc">;</span> + 53 + 54 <span class="c"># Class constructor...</span> +<a name="new-"></a> 55 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> + 56 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 57 + 58 <span class="c"># Initialize object...</span> + 59 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 60 <span class="k">bless</span> <span class="i">$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> + 61 <span class="i">$This</span><span class="i">->_InitializeFsp3CarbonsDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 62 + 63 <span class="i">$This</span><span class="i">->_InitializeFsp3CarbonsDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> + 64 + 65 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 66 <span class="s">}</span> + 67 + 68 <span class="c"># Initialize class ...</span> +<a name="_InitializeClass-"></a> 69 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> + 70 <span class="c">#Class name...</span> + 71 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> + 72 + 73 <span class="c"># Descriptor names...</span> + 74 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'Fsp3Carbons'</span><span class="cm">,</span> <span class="q">'Sp3Carbons'</span><span class="s">)</span><span class="sc">;</span> + 75 + 76 <span class="s">}</span> + 77 + 78 <span class="c"># Get descriptor names as an array.</span> + 79 <span class="c">#</span> + 80 <span class="c"># This functionality can be either invoked as a class function or an</span> + 81 <span class="c"># object method.</span> + 82 <span class="c">#</span> +<a name="GetDescriptorNames-"></a> 83 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> + 84 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> + 85 <span class="s">}</span> + 86 + 87 <span class="c"># Initialize object data...</span> + 88 <span class="c">#</span> +<a name="_InitializeFsp3CarbonsDescriptors-"></a> 89 <span class="k">sub </span><span class="m">_InitializeFsp3CarbonsDescriptors</span> <span class="s">{</span> + 90 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 91 + 92 <span class="c"># Type of MolecularDescriptor...</span> + 93 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'Fsp3Carbons'</span><span class="sc">;</span> + 94 + 95 <span class="c"># Intialize descriptor names and values...</span> + 96 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> + 97 + 98 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 99 <span class="s">}</span> + 100 + 101 <span class="c"># Initialize object properties...</span> + 102 <span class="c">#</span> +<a name="_InitializeFsp3CarbonsDescriptorsProperties-"></a> 103 <span class="k">sub </span><span class="m">_InitializeFsp3CarbonsDescriptorsProperties</span> <span class="s">{</span> + 104 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 105 + 106 <span class="k">my</span><span class="s">(</span><span class="i">$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> + 107 <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> + 108 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> + 109 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> + 110 <span class="s">}</span> + 111 + 112 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 113 <span class="s">}</span> + 114 + 115 <span class="c"># Calculate fraction of SP3 carbons (Fsp3Carbons) [ Ref 115-116, Ref 119 ] in a molecule...</span> + 116 <span class="c">#</span> + 117 <span class="c"># It is defined as follows:</span> + 118 <span class="c">#</span> + 119 <span class="c"># Fsp3 = Number of SP3 carbons/Total number of carbons</span> + 120 <span class="c">#</span> +<a name="GenerateDescriptors-"></a> 121 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> + 122 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 123 + 124 <span class="c"># Initialize descriptor values...</span> + 125 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 126 + 127 <span class="c"># Check availability of molecule...</span> + 128 <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> + 129 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> + 130 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 131 <span class="s">}</span> + 132 + 133 <span class="c"># Calculate descriptor values...</span> + 134 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 135 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate Fsp3Carbons values corresponding to assigned Fsp3Carbons atom types..."</span><span class="sc">;</span> + 136 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> + 137 <span class="s">}</span> + 138 + 139 <span class="c"># Set final descriptor values...</span> + 140 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 141 + 142 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 143 <span class="s">}</span> + 144 + 145 <span class="c"># Calculate Fsp3Carbons value...</span> + 146 <span class="c">#</span> +<a name="_CalculateDescriptorValues-"></a> 147 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> + 148 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 149 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$TotalCarbons</span><span class="cm">,</span> <span class="i">$NumOfSp3Carbons</span><span class="cm">,</span> <span class="i">$Fsp3Carbons</span><span class="s">)</span><span class="sc">;</span> + 150 + 151 <span class="i">$TotalCarbons</span> = <span class="n">0</span><span class="sc">;</span> + 152 <span class="i">$NumOfSp3Carbons</span> = <span class="n">0</span><span class="sc">;</span> + 153 + 154 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 155 <span class="k">if</span> <span class="s">(</span>!<span class="i">$Atom</span><span class="i">->IsCarbon</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 156 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> + 157 <span class="s">}</span> + 158 <span class="i">$TotalCarbons</span> += <span class="n">1</span><span class="sc">;</span> + 159 + 160 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->DoesAtomNeighborhoodMatch</span><span class="s">(</span><span class="q">'C.T4.TSB4'</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> + 161 <span class="i">$NumOfSp3Carbons</span> += <span class="n">1</span><span class="sc">;</span> + 162 <span class="s">}</span> + 163 <span class="s">}</span> + 164 + 165 <span class="i">$Fsp3Carbons</span> = <span class="i">$NumOfSp3Carbons</span> ? <span class="i">$NumOfSp3Carbons</span>/<span class="i">$TotalCarbons</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> + 166 + 167 <span class="c"># Track values...</span> + 168 <span class="i">$This</span>->{<span class="w">Fsp3Carbons</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$Fsp3Carbons</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> + 169 <span class="i">$This</span>->{<span class="w">Sp3Carbons</span>} = <span class="i">$NumOfSp3Carbons</span><span class="sc">;</span> + 170 + 171 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 172 <span class="s">}</span> + 173 + 174 <span class="c"># Setup final descriptor values...</span> + 175 <span class="c">#</span> +<a name="_SetFinalDescriptorValues-"></a> 176 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> + 177 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 178 + 179 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> + 180 + 181 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Fsp3Carbons</span>}<span class="cm">,</span> <span class="i">$This</span>->{<span class="w">Sp3Carbons</span>}<span class="s">)</span><span class="sc">;</span> + 182 + 183 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> + 184 <span class="s">}</span> + 185 + 186 <span class="c"># Return a string containg data for Fsp3CarbonsDescriptors object...</span> + 187 <span class="c">#</span> +<a name="StringifyFsp3CarbonsDescriptors-"></a> 188 <span class="k">sub </span><span class="m">StringifyFsp3CarbonsDescriptors</span> <span class="s">{</span> + 189 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 190 <span class="k">my</span><span class="s">(</span><span class="i">$Fsp3CarbonsDescriptorsString</span><span class="s">)</span><span class="sc">;</span> + 191 + 192 <span class="i">$Fsp3CarbonsDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> + 193 + 194 <span class="k">return</span> <span class="i">$Fsp3CarbonsDescriptorsString</span><span class="sc">;</span> + 195 <span class="s">}</span> + 196 + 197 <span class="c"># Is it a Fsp3CarbonsDescriptors object?</span> +<a name="_IsFsp3CarbonsDescriptors-"></a> 198 <span class="k">sub </span><span class="m">_IsFsp3CarbonsDescriptors</span> <span class="s">{</span> + 199 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> + 200 + 201 <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> + 202 <span class="s">}</span> + 203 +<a name="EOF-"></a></pre> +<p> </p> +<br /> +<center> +<img src="../../../images/h2o2.png"> +</center> +</body> +</html>