Mercurial > repos > deepakjadmin > mayatool3_test3
view mayachemtools/docs/modules/html/code/AtomicDescriptors.html @ 9:ab29fa5c8c1f draft default tip
Uploaded
| author | deepakjadmin |
|---|---|
| date | Thu, 15 Dec 2016 14:18:03 -0500 |
| parents | 73ae111cf86f |
| children |
line wrap: on
line source
<html> <head> <title>MayaChemTools:Code:AtomicDescriptors::AtomicDescriptors.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-AtomicDescriptors::AtomicDescriptors-"></a> 1 <span class="k">package </span><span class="i">AtomicDescriptors::AtomicDescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: AtomicDescriptors.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:47:48 $</span> 5 <span class="c"># $Revision: 1.17 $</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">ObjectProperty</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 36 <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> 37 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> 41 42 <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> 43 44 <span class="c"># Setup class variables...</span> 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 47 48 <span class="c"># Class constructor...</span> <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%PropertyNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 51 52 <span class="c"># Initialize object...</span> 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> 54 <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">$Class</span><span class="sc">;</span> 55 <span class="i">$This</span><span class="i">->_InitializeAtomicDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 56 57 <span class="i">$This</span><span class="i">->_InitializeAtomicDescriptorsProperties</span><span class="s">(</span><span class="i">%PropertyNamesAndValues</span><span class="s">)</span><span class="sc">;</span> 58 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 60 <span class="s">}</span> 61 62 <span class="c"># Initialize object data...</span> 63 <span class="c">#</span> <a name="_InitializeAtomicDescriptors-"></a> 64 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptors</span> <span class="s">{</span> 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 66 67 <span class="c"># Molecule object...</span> 68 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span> 69 70 <span class="c"># Type of atomic descriptors...</span> 71 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> 72 73 <span class="c"># By default, atomic decriptor values are also calculated for hydrogens...</span> 74 <span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} = <span class="n">0</span><span class="sc">;</span> 75 76 <span class="c"># Calculated atomic descriptor values hash. Instead of assigning the calculated values to Atom</span> 77 <span class="c"># objects, these values are stored in the current object in a hash with atom ID and atomic descriptor</span> 78 <span class="c"># values as key/value pairs.</span> 79 <span class="c">#</span> 80 <span class="c"># Unlike molecular descriptors, no descriptor names are assigned to individual atomic descriptor</span> 81 <span class="c"># values.</span> 82 <span class="c">#</span> 83 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 84 <span class="s">}</span> 85 86 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 87 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 88 <span class="c">#Class name...</span> 89 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 90 <span class="s">}</span> 91 92 <span class="c"># Initialize object properties....</span> <a name="_InitializeAtomicDescriptorsProperties-"></a> 93 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptorsProperties</span> <span class="s">{</span> 94 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%PropertiesNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 95 96 <span class="k">my</span><span class="s">(</span><span class="i">$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> 97 <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">%PropertiesNamesAndValues</span><span class="s">)</span> <span class="s">{</span> 98 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> 99 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> 100 <span class="s">}</span> 101 102 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 103 <span class="s">}</span> 104 105 <span class="c"># Initialize descriptor values for all atoms in a molecule...</span> 106 <span class="c">#</span> <a name="_InitializeDescriptorValues-"></a> 107 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span> 108 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 109 110 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 111 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 112 <span class="s">}</span> 113 114 <span class="c"># Assign 'None' to all atomic descriptor values...</span> 115 <span class="c">#</span> 116 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 117 118 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 119 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 120 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="q">'None'</span><span class="sc">;</span> 121 <span class="s">}</span> 122 123 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 124 <span class="s">}</span> 125 126 <span class="c"># Set molecule object and make sure it's not already set...</span> 127 <span class="c">#</span> <a name="SetMolecule-"></a> 128 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> 129 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 130 131 <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> 132 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set..."</span><span class="sc">;</span> 133 <span class="s">}</span> 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> 135 136 <span class="c"># Weaken the reference to disable increment of reference count...</span> 137 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> 138 139 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 140 <span class="s">}</span> 141 142 <span class="c"># Set type and make sure it's not already set...</span> 143 <span class="c">#</span> <a name="SetType-"></a> 144 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> 145 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 146 147 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> 148 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change AtomicDescriptors type: It's already set..."</span><span class="sc">;</span> 149 <span class="s">}</span> 150 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span> 151 152 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 153 <span class="s">}</span> 154 155 <span class="c"># Set specific atomic descriptor value...</span> 156 <span class="c">#</span> <a name="SetDescriptorValue-"></a> 157 <span class="k">sub </span><span class="m">SetDescriptorValue</span> <span class="s">{</span> 158 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomicDescriptor</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 159 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 160 161 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 162 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomicDescriptor</span><span class="sc">;</span> 163 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 165 <span class="s">}</span> 166 167 <span class="c"># Get specific atomic descriptor value...</span> 168 <span class="c">#</span> <a name="GetDescriptorValue-"></a> 169 <span class="k">sub </span><span class="m">GetDescriptorValue</span> <span class="s">{</span> 170 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Atom</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 171 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> 172 173 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 174 175 <span class="k">return</span> <span class="k">exists</span> <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} ? <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> 176 <span class="s">}</span> 177 178 <span class="c"># Get calculated atomic descriptor values as a hash with atom ID and atomic descriptor</span> 179 <span class="c"># values as key/value pairs...</span> 180 <span class="c">#</span> <a name="GetDescriptorValues-"></a> 181 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span> 182 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 183 184 <span class="k">return</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span> 185 <span class="s">}</span> 186 187 <span class="c"># Are all atomic descriptor values successfully calculated?</span> 188 <span class="c">#</span> 189 <span class="c"># Notes:</span> 190 <span class="c"># . Dynamic checking of calculated descriptor values for atoms eliminates the need</span> 191 <span class="c"># to check and synchronize valid descriptor values during SetDescriptorValue.</span> 192 <span class="c">#</span> <a name="IsDescriptorsGenerationSuccessful-"></a> 193 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span> 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 195 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="i">@Atoms</span><span class="s">)</span><span class="sc">;</span> 196 197 <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> 198 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} && <span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 199 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> 200 <span class="s">}</span> 201 <span class="i">$DescriptorValue</span> = <span class="i">$This</span><span class="i">->GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> 202 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> 203 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> 204 <span class="s">}</span> 205 <span class="s">}</span> 206 207 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> 208 <span class="s">}</span> 209 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>