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comparison mayachemtools/docs/modules/html/code/AtomicDescriptors.html @ 0:73ae111cf86f draft
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| author | deepakjadmin |
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| date | Wed, 20 Jan 2016 11:55:01 -0500 |
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| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:AtomicDescriptors::AtomicDescriptors.pm</title> | |
| 4 <meta http-equiv="content-type" content="text/html;charset=utf-8"> | |
| 5 <link rel="stylesheet" type="text/css" href="../../../css/MayaChemToolsCode.css"> | |
| 6 </head> | |
| 7 <body leftmargin="20" rightmargin="20" topmargin="10" bottommargin="10"> | |
| 8 <br/> | |
| 9 <center> | |
| 10 <a href="http://www.mayachemtools.org" title="MayaChemTools Home"><img src="../../../images/MayaChemToolsLogo.gif" border="0" alt="MayaChemTools"></a> | |
| 11 </center> | |
| 12 <br/> | |
| 13 <pre> | |
| 14 <a name="package-AtomicDescriptors::AtomicDescriptors-"></a> 1 <span class="k">package </span><span class="i">AtomicDescriptors::AtomicDescriptors</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: AtomicDescriptors.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:48 $</span> | |
| 18 5 <span class="c"># $Revision: 1.17 $</span> | |
| 19 6 <span class="c">#</span> | |
| 20 7 <span class="c"># Author: Manish Sud <msud@san.rr.com></span> | |
| 21 8 <span class="c">#</span> | |
| 22 9 <span class="c"># Copyright (C) 2015 Manish Sud. All rights reserved.</span> | |
| 23 10 <span class="c">#</span> | |
| 24 11 <span class="c"># This file is part of MayaChemTools.</span> | |
| 25 12 <span class="c">#</span> | |
| 26 13 <span class="c"># MayaChemTools is free software; you can redistribute it and/or modify it under</span> | |
| 27 14 <span class="c"># the terms of the GNU Lesser General Public License as published by the Free</span> | |
| 28 15 <span class="c"># Software Foundation; either version 3 of the License, or (at your option) any</span> | |
| 29 16 <span class="c"># later version.</span> | |
| 30 17 <span class="c">#</span> | |
| 31 18 <span class="c"># MayaChemTools is distributed in the hope that it will be useful, but without</span> | |
| 32 19 <span class="c"># any warranty; without even the implied warranty of merchantability of fitness</span> | |
| 33 20 <span class="c"># for a particular purpose. See the GNU Lesser General Public License for more</span> | |
| 34 21 <span class="c"># details.</span> | |
| 35 22 <span class="c">#</span> | |
| 36 23 <span class="c"># You should have received a copy of the GNU Lesser General Public License</span> | |
| 37 24 <span class="c"># along with MayaChemTools; if not, see <http://www.gnu.org/licenses/> or</span> | |
| 38 25 <span class="c"># write to the Free Software Foundation Inc., 59 Temple Place, Suite 330,</span> | |
| 39 26 <span class="c"># Boston, MA, 02111-1307, USA.</span> | |
| 40 27 <span class="c">#</span> | |
| 41 28 | |
| 42 29 <span class="k">use</span> <span class="w">strict</span><span class="sc">;</span> | |
| 43 30 <span class="k">use</span> <span class="w">Carp</span><span class="sc">;</span> | |
| 44 31 <span class="k">use</span> <span class="w">Exporter</span><span class="sc">;</span> | |
| 45 32 <span class="k">use</span> <span class="w">Scalar::Util</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 46 33 <span class="k">use</span> <span class="w">ObjectProperty</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 48 35 | |
| 49 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> | |
| 50 37 | |
| 51 38 <span class="i">@ISA</span> = <span class="q">qw(ObjectProperty Exporter)</span><span class="sc">;</span> | |
| 52 39 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 53 40 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 54 41 | |
| 55 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> | |
| 56 43 | |
| 57 44 <span class="c"># Setup class variables...</span> | |
| 58 45 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 59 46 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 60 47 | |
| 61 48 <span class="c"># Class constructor...</span> | |
| 62 <a name="new-"></a> 49 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 63 50 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%PropertyNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 64 51 | |
| 65 52 <span class="c"># Initialize object...</span> | |
| 66 53 <span class="k">my</span> <span class="i">$This</span> = <span class="s">{</span><span class="s">}</span><span class="sc">;</span> | |
| 67 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">$Class</span><span class="sc">;</span> | |
| 68 55 <span class="i">$This</span><span class="i">->_InitializeAtomicDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="i">$This</span><span class="i">->_InitializeAtomicDescriptorsProperties</span><span class="s">(</span><span class="i">%PropertyNamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 71 58 | |
| 72 59 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 73 60 <span class="s">}</span> | |
| 74 61 | |
| 75 62 <span class="c"># Initialize object data...</span> | |
| 76 63 <span class="c">#</span> | |
| 77 <a name="_InitializeAtomicDescriptors-"></a> 64 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptors</span> <span class="s">{</span> | |
| 78 65 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 79 66 | |
| 80 67 <span class="c"># Molecule object...</span> | |
| 81 68 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 82 69 | |
| 83 70 <span class="c"># Type of atomic descriptors...</span> | |
| 84 71 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">''</span><span class="sc">;</span> | |
| 85 72 | |
| 86 73 <span class="c"># By default, atomic decriptor values are also calculated for hydrogens...</span> | |
| 87 74 <span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} = <span class="n">0</span><span class="sc">;</span> | |
| 88 75 | |
| 89 76 <span class="c"># Calculated atomic descriptor values hash. Instead of assigning the calculated values to Atom</span> | |
| 90 77 <span class="c"># objects, these values are stored in the current object in a hash with atom ID and atomic descriptor</span> | |
| 91 78 <span class="c"># values as key/value pairs.</span> | |
| 92 79 <span class="c">#</span> | |
| 93 80 <span class="c"># Unlike molecular descriptors, no descriptor names are assigned to individual atomic descriptor</span> | |
| 94 81 <span class="c"># values.</span> | |
| 95 82 <span class="c">#</span> | |
| 96 83 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 97 84 <span class="s">}</span> | |
| 98 85 | |
| 99 86 <span class="c"># Initialize class ...</span> | |
| 100 <a name="_InitializeClass-"></a> 87 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 101 88 <span class="c">#Class name...</span> | |
| 102 89 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 103 90 <span class="s">}</span> | |
| 104 91 | |
| 105 92 <span class="c"># Initialize object properties....</span> | |
| 106 <a name="_InitializeAtomicDescriptorsProperties-"></a> 93 <span class="k">sub </span><span class="m">_InitializeAtomicDescriptorsProperties</span> <span class="s">{</span> | |
| 107 94 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%PropertiesNamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 108 95 | |
| 109 96 <span class="k">my</span><span class="s">(</span><span class="i">$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> | |
| 110 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> | |
| 111 98 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 112 99 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 113 100 <span class="s">}</span> | |
| 114 101 | |
| 115 102 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 116 103 <span class="s">}</span> | |
| 117 104 | |
| 118 105 <span class="c"># Initialize descriptor values for all atoms in a molecule...</span> | |
| 119 106 <span class="c">#</span> | |
| 120 <a name="_InitializeDescriptorValues-"></a> 107 <span class="k">sub </span><span class="m">_InitializeDescriptorValues</span> <span class="s">{</span> | |
| 121 108 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 122 109 | |
| 123 110 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 124 111 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 125 112 <span class="s">}</span> | |
| 126 113 | |
| 127 114 <span class="c"># Assign 'None' to all atomic descriptor values...</span> | |
| 128 115 <span class="c">#</span> | |
| 129 116 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 130 117 | |
| 131 118 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 132 119 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 133 120 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="q">'None'</span><span class="sc">;</span> | |
| 134 121 <span class="s">}</span> | |
| 135 122 | |
| 136 123 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 137 124 <span class="s">}</span> | |
| 138 125 | |
| 139 126 <span class="c"># Set molecule object and make sure it's not already set...</span> | |
| 140 127 <span class="c">#</span> | |
| 141 <a name="SetMolecule-"></a> 128 <span class="k">sub </span><span class="m">SetMolecule</span> <span class="s">{</span> | |
| 142 129 <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> | |
| 143 130 | |
| 144 131 <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> | |
| 145 132 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetMolecule: Can't change molecule object: It's already set..."</span><span class="sc">;</span> | |
| 146 133 <span class="s">}</span> | |
| 147 134 <span class="i">$This</span>->{<span class="w">Molecule</span>} = <span class="i">$Molecule</span><span class="sc">;</span> | |
| 148 135 | |
| 149 136 <span class="c"># Weaken the reference to disable increment of reference count...</span> | |
| 150 137 <span class="i">Scalar::Util::weaken</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span><span class="sc">;</span> | |
| 151 138 | |
| 152 139 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 153 140 <span class="s">}</span> | |
| 154 141 | |
| 155 142 <span class="c"># Set type and make sure it's not already set...</span> | |
| 156 143 <span class="c">#</span> | |
| 157 <a name="SetType-"></a> 144 <span class="k">sub </span><span class="m">SetType</span> <span class="s">{</span> | |
| 158 145 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$Type</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 159 146 | |
| 160 147 <span class="k">if</span> <span class="s">(</span><span class="i">$This</span>->{<span class="w">Type</span>}<span class="s">)</span> <span class="s">{</span> | |
| 161 148 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->SetType: Can't change AtomicDescriptors type: It's already set..."</span><span class="sc">;</span> | |
| 162 149 <span class="s">}</span> | |
| 163 150 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="i">$Type</span><span class="sc">;</span> | |
| 164 151 | |
| 165 152 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 166 153 <span class="s">}</span> | |
| 167 154 | |
| 168 155 <span class="c"># Set specific atomic descriptor value...</span> | |
| 169 156 <span class="c">#</span> | |
| 170 <a name="SetDescriptorValue-"></a> 157 <span class="k">sub </span><span class="m">SetDescriptorValue</span> <span class="s">{</span> | |
| 171 158 <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">$AtomicDescriptor</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 172 159 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 173 160 | |
| 174 161 <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> | |
| 175 162 <span class="i">$This</span>->{<span class="w">DescriptorValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$AtomicDescriptor</span><span class="sc">;</span> | |
| 176 163 | |
| 177 164 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 178 165 <span class="s">}</span> | |
| 179 166 | |
| 180 167 <span class="c"># Get specific atomic descriptor value...</span> | |
| 181 168 <span class="c">#</span> | |
| 182 <a name="GetDescriptorValue-"></a> 169 <span class="k">sub </span><span class="m">GetDescriptorValue</span> <span class="s">{</span> | |
| 183 170 <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> | |
| 184 171 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 185 172 | |
| 186 173 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 187 174 | |
| 188 175 <span class="k">return</span> <span class="k">exists</span> <span class="i">$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">$AtomID</span>} <span class="co">:</span> <span class="q">'None'</span><span class="sc">;</span> | |
| 189 176 <span class="s">}</span> | |
| 190 177 | |
| 191 178 <span class="c"># Get calculated atomic descriptor values as a hash with atom ID and atomic descriptor</span> | |
| 192 179 <span class="c"># values as key/value pairs...</span> | |
| 193 180 <span class="c">#</span> | |
| 194 <a name="GetDescriptorValues-"></a> 181 <span class="k">sub </span><span class="m">GetDescriptorValues</span> <span class="s">{</span> | |
| 195 182 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 196 183 | |
| 197 184 <span class="k">return</span> <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DescriptorValues</span>}}<span class="sc">;</span> | |
| 198 185 <span class="s">}</span> | |
| 199 186 | |
| 200 187 <span class="c"># Are all atomic descriptor values successfully calculated?</span> | |
| 201 188 <span class="c">#</span> | |
| 202 189 <span class="c"># Notes:</span> | |
| 203 190 <span class="c"># . Dynamic checking of calculated descriptor values for atoms eliminates the need</span> | |
| 204 191 <span class="c"># to check and synchronize valid descriptor values during SetDescriptorValue.</span> | |
| 205 192 <span class="c">#</span> | |
| 206 <a name="IsDescriptorsGenerationSuccessful-"></a> 193 <span class="k">sub </span><span class="m">IsDescriptorsGenerationSuccessful</span> <span class="s">{</span> | |
| 207 194 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 208 195 <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> | |
| 209 196 | |
| 210 197 <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> | |
| 211 198 <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> | |
| 212 199 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 213 200 <span class="s">}</span> | |
| 214 201 <span class="i">$DescriptorValue</span> = <span class="i">$This</span><span class="i">->GetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 215 202 <span class="k">if</span> <span class="s">(</span><span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> <span class="s">{</span> | |
| 216 203 <span class="k">return</span> <span class="n">0</span><span class="sc">;</span> | |
| 217 204 <span class="s">}</span> | |
| 218 205 <span class="s">}</span> | |
| 219 206 | |
| 220 207 <span class="k">return</span> <span class="n">1</span><span class="sc">;</span> | |
| 221 208 <span class="s">}</span> | |
| 222 209 | |
| 223 <a name="EOF-"></a></pre> | |
| 224 <p> </p> | |
| 225 <br /> | |
| 226 <center> | |
| 227 <img src="../../../images/h2o2.png"> | |
| 228 </center> | |
| 229 </body> | |
| 230 </html> |