Mercurial > repos > deepakjadmin > mayatool3_test3
view mayachemtools/docs/modules/html/code/Fsp3CarbonsDescriptors.html @ 0:73ae111cf86f draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 11:55:01 -0500 |
| parents | |
| children |
line wrap: on
line source
<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>