Mercurial > repos > deepakjadmin > mayatool3_test1
comparison docs/modules/html/code/EStateValuesDescriptors.html @ 1:2abf0d43254d draft
Uploaded
| author | deepakjadmin |
|---|---|
| date | Wed, 20 Jan 2016 09:10:43 -0500 |
| parents | |
| children |
comparison
equal
deleted
inserted
replaced
| 0:1791cb0984a7 | 1:2abf0d43254d |
|---|---|
| 1 <html> | |
| 2 <head> | |
| 3 <title>MayaChemTools:Code:AtomicDescriptors::EStateValuesDescriptors.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::EStateValuesDescriptors-"></a> 1 <span class="k">package </span><span class="i">AtomicDescriptors::EStateValuesDescriptors</span><span class="sc">;</span> | |
| 15 2 <span class="c">#</span> | |
| 16 3 <span class="c"># $RCSfile: EStateValuesDescriptors.pm,v $</span> | |
| 17 4 <span class="c"># $Date: 2015/02/28 20:47:49 $</span> | |
| 18 5 <span class="c"># $Revision: 1.16 $</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">Matrix</span><span class="sc">;</span> | |
| 47 34 <span class="k">use</span> <span class="w">Constants</span><span class="sc">;</span> | |
| 48 35 <span class="k">use</span> <span class="w">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 49 36 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 50 37 <span class="k">use</span> <span class="w">StatisticsUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 51 38 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> | |
| 52 39 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> | |
| 53 40 <span class="k">use</span> <span class="w">AtomicDescriptors::AtomicDescriptors</span><span class="sc">;</span> | |
| 54 41 | |
| 55 42 <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> | |
| 56 43 | |
| 57 44 <span class="i">@ISA</span> = <span class="q">qw(AtomicDescriptors::AtomicDescriptors Exporter)</span><span class="sc">;</span> | |
| 58 45 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 59 46 <span class="i">@EXPORT_OK</span> = <span class="q">qw()</span><span class="sc">;</span> | |
| 60 47 | |
| 61 48 <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> | |
| 62 49 | |
| 63 50 <span class="c"># Setup class variables...</span> | |
| 64 51 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="s">)</span><span class="sc">;</span> | |
| 65 52 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 66 53 | |
| 67 54 <span class="c"># Overload Perl functions...</span> | |
| 68 55 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyEStateValuesDescriptors'</span><span class="sc">;</span> | |
| 69 56 | |
| 70 57 <span class="c"># Class constructor...</span> | |
| 71 <a name="new-"></a> 58 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> | |
| 72 59 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 73 60 | |
| 74 61 <span class="c"># Initialize object...</span> | |
| 75 62 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 76 63 <span class="k">bless</span> <span class="i">$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> | |
| 77 64 <span class="i">$This</span><span class="i">->_InitializeEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 78 65 | |
| 79 66 <span class="i">$This</span><span class="i">->_InitializeEStateValuesDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> | |
| 80 67 | |
| 81 68 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 82 69 <span class="s">}</span> | |
| 83 70 | |
| 84 71 <span class="c"># Initialize class ...</span> | |
| 85 <a name="_InitializeClass-"></a> 72 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> | |
| 86 73 <span class="c">#Class name...</span> | |
| 87 74 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> | |
| 88 75 <span class="s">}</span> | |
| 89 76 | |
| 90 77 | |
| 91 78 <span class="c"># Initialize object data...</span> | |
| 92 79 <span class="c">#</span> | |
| 93 <a name="_InitializeEStateValuesDescriptors-"></a> 80 <span class="k">sub </span><span class="m">_InitializeEStateValuesDescriptors</span> <span class="s">{</span> | |
| 94 81 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 95 82 | |
| 96 83 <span class="c"># Type of AtomicDescriptor...</span> | |
| 97 84 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'EStateValue'</span><span class="sc">;</span> | |
| 98 85 | |
| 99 86 <span class="c"># Intrinsic state values calculated for non-hydrogen atom...</span> | |
| 100 87 <span class="c">#</span> | |
| 101 88 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">IStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 102 89 | |
| 103 90 <span class="c"># Calculatetion of E-state values for types for hydrogens is not supported...</span> | |
| 104 91 <span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} = <span class="n">1</span><span class="sc">;</span> | |
| 105 92 | |
| 106 93 <span class="c"># Perturbation to intrinsic state values of atoms corresponding to all non-hydrogen</span> | |
| 107 94 <span class="c"># atom pairs...</span> | |
| 108 95 <span class="c">#</span> | |
| 109 96 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 110 97 | |
| 111 98 <span class="c"># E-state values calculated for non-hydrogen atoms...</span> | |
| 112 99 <span class="c">#</span> | |
| 113 100 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 114 101 | |
| 115 102 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 116 103 <span class="s">}</span> | |
| 117 104 | |
| 118 105 <span class="c"># Initialize object properties...</span> | |
| 119 106 <span class="c">#</span> | |
| 120 <a name="_InitializeEStateValuesDescriptorsProperties-"></a> 107 <span class="k">sub </span><span class="m">_InitializeEStateValuesDescriptorsProperties</span> <span class="s">{</span> | |
| 121 108 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 122 109 | |
| 123 110 <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">$MethodName</span><span class="s">)</span><span class="sc">;</span> | |
| 124 111 <span class="k">while</span> <span class="s">(</span><span class="s">(</span><span class="i">$Name</span><span class="cm">,</span> <span class="i">$Value</span><span class="s">)</span> = <span class="k">each</span> <span class="i">%NamesAndValues</span><span class="s">)</span> <span class="s">{</span> | |
| 125 112 <span class="i">$MethodName</span> = <span class="q">"Set${Name}"</span><span class="sc">;</span> | |
| 126 113 <span class="i">$This</span><span class="i">->$MethodName</span><span class="s">(</span><span class="i">$Value</span><span class="s">)</span><span class="sc">;</span> | |
| 127 114 <span class="s">}</span> | |
| 128 115 | |
| 129 116 <span class="c"># Make sure molecule object was specified...</span> | |
| 130 117 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$NamesAndValues</span>{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> | |
| 131 118 <span class="w">croak</span> <span class="q">"Error: ${ClassName}->New: Object can't be instantiated without specifying molecule..."</span><span class="sc">;</span> | |
| 132 119 <span class="s">}</span> | |
| 133 120 | |
| 134 121 <span class="c"># Intialize atomic descriptor values...</span> | |
| 135 122 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 136 123 | |
| 137 124 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 138 125 <span class="s">}</span> | |
| 139 126 | |
| 140 127 <span class="c"># Disable change of ignore hydrogens...</span> | |
| 141 128 <span class="c">#</span> | |
| 142 <a name="SetIgnoreHydrogens-"></a> 129 <span class="k">sub </span><span class="m">SetIgnoreHydrogens</span> <span class="s">{</span> | |
| 143 130 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="cm">,</span> <span class="i">$IgnoreHydrogens</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 144 131 | |
| 145 132 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->SetIgnoreHydrogens: Ignore hydrogens value can't be changed: It's not supported..."</span><span class="sc">;</span> | |
| 146 133 | |
| 147 134 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 148 135 <span class="s">}</span> | |
| 149 136 | |
| 150 137 <span class="c"># Generate electrotopological state (E-state) values [ Ref 75-78 ] for all atoms</span> | |
| 151 138 <span class="c"># in the molecule...</span> | |
| 152 139 <span class="c">#</span> | |
| 153 140 <span class="c"># Calculation of E-state values for non-hydrogen atoms:</span> | |
| 154 141 <span class="c">#</span> | |
| 155 142 <span class="c"># Let:</span> | |
| 156 143 <span class="c">#</span> | |
| 157 144 <span class="c"># N = Principal quantum number or period number corresponding to element symbol</span> | |
| 158 145 <span class="c">#</span> | |
| 159 146 <span class="c"># Sigma = Number of sigma electrons involves in bonds to hydrogen and non-hydrogen atoms</span> | |
| 160 147 <span class="c"># attached to atom</span> | |
| 161 148 <span class="c"># = Number of sigma bonds to hydrogen and non-hydrogen atoms attached to atom</span> | |
| 162 149 <span class="c"># PI = Number of PI electrons involved in bonds to non-hydrogen atoms attached to atom</span> | |
| 163 150 <span class="c"># = Number of PI bonds to non-hydrogen atoms attached to atom</span> | |
| 164 151 <span class="c">#</span> | |
| 165 152 <span class="c"># LP = Number of lone pair electrons on atom</span> | |
| 166 153 <span class="c">#</span> | |
| 167 154 <span class="c"># Zv = Number of electrons in valence shell of atom</span> | |
| 168 155 <span class="c">#</span> | |
| 169 156 <span class="c"># X = Number of non-hydrogen atom neighbors or heavy atoms attached to atom</span> | |
| 170 157 <span class="c"># H = Number of implicit and explicit hydrogens for atom</span> | |
| 171 158 <span class="c">#</span> | |
| 172 159 <span class="c"># Delta = Number of sigma electrons involved to bonds to non-hydrogen atoms</span> | |
| 173 160 <span class="c"># DeltaV = ValenceDelta = Number of valence shell electrons not involved in bonding to hydrogen atoms</span> | |
| 174 161 <span class="c">#</span> | |
| 175 162 <span class="c"># Ii = Intrinsic state value for atom i</span> | |
| 176 163 <span class="c">#</span> | |
| 177 164 <span class="c"># DeltaIi = Sum of perturbations to intrinsic state value Ii of atom i by all other atoms besides atom i</span> | |
| 178 165 <span class="c">#</span> | |
| 179 166 <span class="c"># DeltaIij = Perturbation to intrinsic state value Ii of atom i by atom j</span> | |
| 180 167 <span class="c">#</span> | |
| 181 168 <span class="c"># Dij = Graph/bond distance between atom i and j</span> | |
| 182 169 <span class="c"># Rij = Dij + 1</span> | |
| 183 170 <span class="c">#</span> | |
| 184 171 <span class="c"># Si = E-state value for atom i</span> | |
| 185 172 <span class="c">#</span> | |
| 186 173 <span class="c">#</span> | |
| 187 174 <span class="c"># Then:</span> | |
| 188 175 <span class="c">#</span> | |
| 189 176 <span class="c"># Delta = Sigma - H = X</span> | |
| 190 177 <span class="c">#</span> | |
| 191 178 <span class="c"># DeltaV = Zv - H</span> | |
| 192 179 <span class="c"># = Sigma + PI + LP - H</span> | |
| 193 180 <span class="c">#</span> | |
| 194 181 <span class="c"># Ii = ( ( ( 2 / N ) ** 2 ) * DeltaV + 1 ) / Delta</span> | |
| 195 182 <span class="c">#</span> | |
| 196 183 <span class="c"># Si = Ii + DeltaIi</span> | |
| 197 184 <span class="c">#</span> | |
| 198 185 <span class="c"># DeltaIij = (Ii - Ij) / (Rij ** 2) for j not equal to i</span> | |
| 199 186 <span class="c">#</span> | |
| 200 187 <span class="c"># DeltaIji = - DeltaIij</span> | |
| 201 188 <span class="c">#</span> | |
| 202 189 <span class="c"># DeltaIi = SUM ( (Ii - Ij) / (Rij ** 2) ) for j = 1 to num of atoms skipping atom i</span> | |
| 203 190 <span class="c">#</span> | |
| 204 191 <span class="c"># Methodology:</span> | |
| 205 192 <span class="c"># . Calculate intrinsic state values for atoms.</span> | |
| 206 193 <span class="c"># . Generate a distance matrix.</span> | |
| 207 194 <span class="c"># . Use distance matrix to calculate DeltaIij matrix with each row i containing</span> | |
| 208 195 <span class="c"># DeltaIij values corresponding to perturbation to intrinsic state value of atom</span> | |
| 209 196 <span class="c"># i by atom j.</span> | |
| 210 197 <span class="c"># . Calculate E-state values using DeltaIij matrix.</span> | |
| 211 198 <span class="c"># . Assign E-state values to atoms.</span> | |
| 212 199 <span class="c">#</span> | |
| 213 200 <span class="c"># Notes:</span> | |
| 214 201 <span class="c"># . The current release of MayaChemTools doesn't support calculation of Hydrogen</span> | |
| 215 202 <span class="c"># E-state values.</span> | |
| 216 203 <span class="c">#</span> | |
| 217 <a name="GenerateDescriptors-"></a> 204 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> | |
| 218 205 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 219 206 | |
| 220 207 <span class="c"># Cache appropriate molecule data...</span> | |
| 221 208 <span class="i">$This</span><span class="i">->_SetupMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 222 209 | |
| 223 210 <span class="c"># Generate distance matrix...</span> | |
| 224 211 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_SetupDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 225 212 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: E-state values description generation didn't succeed: Couldn't generate a distance matrix..."</span><span class="sc">;</span> | |
| 226 213 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 227 214 <span class="s">}</span> | |
| 228 215 | |
| 229 216 <span class="c"># Calculate EState values..</span> | |
| 230 217 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateEStateValuesDescriptors</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 231 218 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: E-state values description generation didn't succeed: Couldn't calculate IState values for all atoms..."</span><span class="sc">;</span> | |
| 232 219 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 233 220 <span class="s">}</span> | |
| 234 221 | |
| 235 222 <span class="c"># Set final descriptor values...</span> | |
| 236 223 <span class="i">$This</span><span class="i">->_SetFinalValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 237 224 | |
| 238 225 <span class="c"># Clear cached molecule data...</span> | |
| 239 226 <span class="i">$This</span><span class="i">->_ClearMoleculeDataCache</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 240 227 | |
| 241 228 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 242 229 <span class="s">}</span> | |
| 243 230 | |
| 244 231 <span class="c"># Calculate E-state values for non-hydrogen atoms...</span> | |
| 245 232 <span class="c">#</span> | |
| 246 <a name="_CalculateEStateValuesDescriptors-"></a> 233 <span class="k">sub </span><span class="m">_CalculateEStateValuesDescriptors</span> <span class="s">{</span> | |
| 247 234 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 248 235 <span class="k">my</span><span class="s">(</span><span class="i">$DeltaIStateMatrix</span><span class="cm">,</span> <span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="cm">,</span> <span class="i">$IStateValue</span><span class="cm">,</span> <span class="i">$DeltaIStateValue</span><span class="cm">,</span> <span class="i">@DeltaIStateMatrixRowValues</span><span class="s">)</span><span class="sc">;</span> | |
| 249 236 | |
| 250 237 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">EStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 251 238 | |
| 252 239 <span class="c"># Calculate intrinsic state values for non-hydrogen atoms...</span> | |
| 253 240 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateIStateValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 254 241 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 255 242 <span class="s">}</span> | |
| 256 243 | |
| 257 244 <span class="c"># Calculate delta intrinsic state matrix for non-hydrogen atoms...</span> | |
| 258 245 <span class="i">$This</span><span class="i">->_CalculateDeltaIStateMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 259 246 | |
| 260 247 <span class="c"># Get DeltaIState matrix information...</span> | |
| 261 248 <span class="i">$DeltaIStateMatrix</span> = <span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>}<span class="sc">;</span> | |
| 262 249 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DeltaIStateMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 263 250 | |
| 264 251 <span class="c"># Calculate EState values...</span> | |
| 265 252 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 266 253 <span class="i">$AtomID</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span> | |
| 267 254 <span class="k">if</span> <span class="s">(</span> !<span class="s">(</span><span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 268 255 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span> | |
| 269 256 <span class="s">}</span> | |
| 270 257 <span class="i">$IStateValue</span> = <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 271 258 | |
| 272 259 <span class="i">@DeltaIStateMatrixRowValues</span> = <span class="i">$DeltaIStateMatrix</span><span class="i">->GetRowValues</span><span class="s">(</span><span class="i">$RowIndex</span><span class="s">)</span><span class="sc">;</span> | |
| 273 260 <span class="i">$DeltaIStateValue</span> = <span class="i">StatisticsUtil::Sum</span><span class="s">(</span>\<span class="i">@DeltaIStateMatrixRowValues</span><span class="s">)</span><span class="sc">;</span> | |
| 274 261 | |
| 275 262 <span class="i">$EStateValue</span> = <span class="i">$IStateValue</span> + <span class="i">$DeltaIStateValue</span><span class="sc">;</span> | |
| 276 263 | |
| 277 264 <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$EStateValue</span><span class="sc">;</span> | |
| 278 265 <span class="s">}</span> | |
| 279 266 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 280 267 <span class="s">}</span> | |
| 281 268 | |
| 282 269 <span class="c"># Calculate intrinsic state values for non-hydrogen atoms...</span> | |
| 283 270 <span class="c">#</span> | |
| 284 <a name="_CalculateIStateValues-"></a> 271 <span class="k">sub </span><span class="m">_CalculateIStateValues</span> <span class="s">{</span> | |
| 285 272 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 286 273 <span class="k">my</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$AtomID</span><span class="s">)</span><span class="sc">;</span> | |
| 287 274 | |
| 288 275 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">IStateValues</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 289 276 | |
| 290 277 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 291 278 <span class="c"># Irrespective of IgoreHydrogens value, just ignore hydrogens...</span> | |
| 292 279 <span class="k">if</span> <span class="s">(</span><span class="i">$Atom</span><span class="i">->IsHydrogen</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 293 280 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 294 281 <span class="s">}</span> | |
| 295 282 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 296 283 <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>} = <span class="i">$This</span><span class="i">->_CalculateIStateValue</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 297 284 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 298 285 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 299 286 <span class="s">}</span> | |
| 300 287 <span class="s">}</span> | |
| 301 288 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 302 289 <span class="s">}</span> | |
| 303 290 | |
| 304 291 <span class="c"># Calculation intrinsic state value for non-hydrogen...</span> | |
| 305 292 <span class="c">#</span> | |
| 306 <a name="_CalculateIStateValue-"></a> 293 <span class="k">sub </span><span class="m">_CalculateIStateValue</span> <span class="s">{</span> | |
| 307 294 <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> | |
| 308 295 <span class="k">my</span><span class="s">(</span><span class="i">$IStateValue</span><span class="cm">,</span> <span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="cm">,</span> <span class="i">$PeriodNumber</span><span class="s">)</span><span class="sc">;</span> | |
| 309 296 | |
| 310 297 <span class="i">$PeriodNumber</span> = <span class="i">$Atom</span><span class="i">->GetPeriodNumber</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 311 298 <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span> = <span class="i">$This</span><span class="i">->_GetDeltaValues</span><span class="s">(</span><span class="i">$Atom</span><span class="s">)</span><span class="sc">;</span> | |
| 312 299 | |
| 313 300 <span class="k">if</span> <span class="s">(</span>!<span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$Delta</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$PeriodNumber</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$DeltaV</span><span class="s">)</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 314 301 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 315 302 <span class="s">}</span> | |
| 316 303 | |
| 317 304 <span class="i">$IStateValue</span> = <span class="s">(</span><span class="i">$PeriodNumber</span> && <span class="i">$Delta</span><span class="s">)</span> ? <span class="s">(</span><span class="s">(</span><span class="s">(</span><span class="n">2</span>/<span class="i">$PeriodNumber</span><span class="s">)</span>**<span class="n">2</span><span class="s">)</span>*<span class="i">$DeltaV</span> + <span class="n">1</span><span class="s">)</span>/<span class="i">$Delta</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> | |
| 318 305 | |
| 319 306 <span class="k">return</span> <span class="i">$IStateValue</span><span class="sc">;</span> | |
| 320 307 <span class="s">}</span> | |
| 321 308 | |
| 322 309 <span class="c"># Get Delta and DeltaV values for atom...</span> | |
| 323 310 <span class="c">#</span> | |
| 324 <a name="_GetDeltaValues-"></a> 311 <span class="k">sub </span><span class="m">_GetDeltaValues</span> <span class="s">{</span> | |
| 325 312 <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> | |
| 326 313 <span class="k">my</span><span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="cm">,</span> <span class="i">$ValenceElectrons</span><span class="cm">,</span> <span class="i">$NumOfHydrogens</span><span class="s">)</span><span class="sc">;</span> | |
| 327 314 | |
| 328 315 <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span> = <span class="s">(</span><span class="k">undef</span><span class="cm">,</span> <span class="k">undef</span><span class="s">)</span><span class="sc">;</span> | |
| 329 316 | |
| 330 317 <span class="i">$ValenceElectrons</span> = <span class="i">$Atom</span><span class="i">->GetValenceElectrons</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 331 318 <span class="i">$NumOfHydrogens</span> = <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'H'</span><span class="s">)</span><span class="sc">;</span> | |
| 332 319 | |
| 333 320 <span class="i">$Delta</span> = <span class="i">$Atom</span><span class="i">->GetAtomicInvariantValue</span><span class="s">(</span><span class="q">'X'</span><span class="s">)</span><span class="sc">;</span> | |
| 334 321 <span class="k">if</span> <span class="s">(</span><span class="k">defined</span><span class="s">(</span><span class="i">$ValenceElectrons</span><span class="s">)</span> && <span class="k">defined</span><span class="s">(</span><span class="i">$NumOfHydrogens</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 335 322 <span class="i">$DeltaV</span> = <span class="i">$ValenceElectrons</span> - <span class="i">$NumOfHydrogens</span><span class="sc">;</span> | |
| 336 323 <span class="s">}</span> | |
| 337 324 | |
| 338 325 <span class="k">return</span> <span class="s">(</span><span class="i">$Delta</span><span class="cm">,</span> <span class="i">$DeltaV</span><span class="s">)</span><span class="sc">;</span> | |
| 339 326 <span class="s">}</span> | |
| 340 327 | |
| 341 328 <span class="c"># Calculate DeltaIState matrix for atoms with each row i containing DeltaIij values</span> | |
| 342 329 <span class="c"># corresponding atom atoms i and j.</span> | |
| 343 330 <span class="c">#</span> | |
| 344 331 <span class="c"># Notes:</span> | |
| 345 332 <span class="c"># . Matrix elements corresponding to hydrogen atoms or unconnected</span> | |
| 346 333 <span class="c"># are assigned zero value.</span> | |
| 347 334 <span class="c">#</span> | |
| 348 <a name="_CalculateDeltaIStateMatrix-"></a> 335 <span class="k">sub </span><span class="m">_CalculateDeltaIStateMatrix</span> <span class="s">{</span> | |
| 349 336 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 350 337 <span class="k">my</span><span class="s">(</span><span class="i">$DistanceMatrix</span><span class="cm">,</span> <span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$AtomID1</span><span class="cm">,</span> <span class="i">$AtomID2</span><span class="cm">,</span> <span class="i">$DeltaIStateMatrix</span><span class="cm">,</span> <span class="i">$IStateValue1</span><span class="cm">,</span> <span class="i">$IStateValue2</span><span class="cm">,</span> <span class="i">$GraphDistance</span><span class="cm">,</span> <span class="i">$DeltaIState12</span><span class="cm">,</span> <span class="i">$DeltaIState21</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 351 338 | |
| 352 339 <span class="c"># Get distance matrix information...</span> | |
| 353 340 <span class="i">$DistanceMatrix</span> = <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="sc">;</span> | |
| 354 341 <span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetSize</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 355 342 | |
| 356 343 <span class="c"># Initialize DeltaIState matrix...</span> | |
| 357 344 <span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>} = <span class="i">new</span> <span class="i">Matrix</span><span class="s">(</span><span class="i">$NumOfRows</span><span class="cm">,</span> <span class="i">$NumOfCols</span><span class="s">)</span><span class="sc">;</span> | |
| 358 345 <span class="i">$DeltaIStateMatrix</span> = <span class="i">$This</span>->{<span class="w">DeltaIStateMatrix</span>}<span class="sc">;</span> | |
| 359 346 | |
| 360 347 <span class="i">$SkipIndexCheck</span> = <span class="n">1</span><span class="sc">;</span> | |
| 361 348 | |
| 362 349 <span class="c"># Calculate DeltaIState matrix values...</span> | |
| 363 350 <span class="j">ROWINDEX:</span> <span class="k">for</span> <span class="i">$RowIndex</span> <span class="s">(</span><span class="n">0</span> .. <span class="s">(</span><span class="i">$NumOfRows</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 364 351 <span class="i">$AtomID1</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$RowIndex</span>}<span class="sc">;</span> | |
| 365 352 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID1</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 366 353 <span class="k">next</span> <span class="j">ROWINDEX</span><span class="sc">;</span> | |
| 367 354 <span class="s">}</span> | |
| 368 355 <span class="i">$IStateValue1</span> = <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID1</span>}<span class="sc">;</span> | |
| 369 356 | |
| 370 357 <span class="j">COLINDEX:</span> <span class="k">for</span> <span class="i">$ColIndex</span> <span class="s">(</span><span class="s">(</span><span class="i">$RowIndex</span> + <span class="n">1</span><span class="s">)</span> .. <span class="s">(</span><span class="i">$NumOfCols</span> - <span class="n">1</span><span class="s">)</span> <span class="s">)</span> <span class="s">{</span> | |
| 371 358 <span class="i">$AtomID2</span> = <span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}{<span class="i">$ColIndex</span>}<span class="sc">;</span> | |
| 372 359 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID2</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 373 360 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> | |
| 374 361 <span class="s">}</span> | |
| 375 362 <span class="i">$IStateValue2</span> = <span class="i">$This</span>->{<span class="w">IStateValues</span>}{<span class="i">$AtomID2</span>}<span class="sc">;</span> | |
| 376 363 | |
| 377 364 <span class="c"># Make sure it's a connected atom...</span> | |
| 378 365 <span class="i">$GraphDistance</span> = <span class="i">$DistanceMatrix</span><span class="i">->GetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 379 366 <span class="k">if</span> <span class="s">(</span><span class="i">$GraphDistance</span> >= <span class="w">BigNumber</span><span class="s">)</span> <span class="s">{</span> | |
| 380 367 <span class="k">next</span> <span class="j">COLINDEX</span><span class="sc">;</span> | |
| 381 368 <span class="s">}</span> | |
| 382 369 | |
| 383 370 <span class="i">$DeltaIState12</span> = <span class="s">(</span><span class="i">$IStateValue1</span> - <span class="i">$IStateValue2</span><span class="s">)</span>/<span class="s">(</span><span class="s">(</span><span class="i">$GraphDistance</span> + <span class="n">1</span><span class="s">)</span>**<span class="n">2</span><span class="s">)</span><span class="sc">;</span> | |
| 384 371 <span class="i">$DeltaIState21</span> = -<span class="i">$DeltaIState12</span><span class="sc">;</span> | |
| 385 372 | |
| 386 373 <span class="c"># Set DeltaIState values...</span> | |
| 387 374 <span class="i">$DeltaIStateMatrix</span><span class="i">->SetValue</span><span class="s">(</span><span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$DeltaIState12</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 388 375 <span class="i">$DeltaIStateMatrix</span><span class="i">->SetValue</span><span class="s">(</span><span class="i">$ColIndex</span><span class="cm">,</span> <span class="i">$RowIndex</span><span class="cm">,</span> <span class="i">$DeltaIState21</span><span class="cm">,</span> <span class="i">$SkipIndexCheck</span><span class="s">)</span><span class="sc">;</span> | |
| 389 376 <span class="s">}</span> | |
| 390 377 <span class="s">}</span> | |
| 391 378 <span class="s">}</span> | |
| 392 379 | |
| 393 380 <span class="c"># Setup distance matrix...</span> | |
| 394 381 <span class="c">#</span> | |
| 395 <a name="_SetupDistanceMatrix-"></a> 382 <span class="k">sub </span><span class="m">_SetupDistanceMatrix</span> <span class="s">{</span> | |
| 396 383 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 397 384 | |
| 398 385 <span class="i">$This</span>->{<span class="w">DistanceMatrix</span>} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetDistanceMatrix</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 399 386 | |
| 400 387 <span class="k">if</span> <span class="s">(</span>!<span class="k">defined</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">DistanceMatrix</span>}<span class="s">)</span><span class="s">)</span> <span class="s">{</span> | |
| 401 388 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> | |
| 402 389 <span class="s">}</span> | |
| 403 390 | |
| 404 391 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 405 392 <span class="s">}</span> | |
| 406 393 | |
| 407 394 <span class="c"># Setup final descriptor values...</span> | |
| 408 395 <span class="c">#</span> | |
| 409 <a name="_SetFinalValues-"></a> 396 <span class="k">sub </span><span class="m">_SetFinalValues</span> <span class="s">{</span> | |
| 410 397 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 411 398 <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">$EStateValue</span><span class="s">)</span><span class="sc">;</span> | |
| 412 399 | |
| 413 400 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="s">)</span> <span class="s">{</span> | |
| 414 401 <span class="i">$AtomID</span> = <span class="i">$Atom</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 415 402 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="s">)</span> <span class="s">{</span> | |
| 416 403 <span class="k">next</span> <span class="j">ATOM</span><span class="sc">;</span> | |
| 417 404 <span class="s">}</span> | |
| 418 405 <span class="i">$EStateValue</span> = <span class="i">$This</span>->{<span class="w">EStateValues</span>}{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 419 406 <span class="i">$This</span><span class="i">->SetDescriptorValue</span><span class="s">(</span><span class="i">$Atom</span><span class="cm">,</span> <span class="i">$EStateValue</span><span class="s">)</span><span class="sc">;</span> | |
| 420 407 <span class="s">}</span> | |
| 421 408 | |
| 422 409 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 423 410 <span class="s">}</span> | |
| 424 411 | |
| 425 412 <span class="c"># Cache appropriate molecule data...</span> | |
| 426 413 <span class="c">#</span> | |
| 427 <a name="_SetupMoleculeDataCache-"></a> 414 <span class="k">sub </span><span class="m">_SetupMoleculeDataCache</span> <span class="s">{</span> | |
| 428 415 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 429 416 | |
| 430 417 <span class="c"># Get all atoms including hydrogens to correctly map atom indicies to atom IDs for</span> | |
| 431 418 <span class="c"># usage of distance matrix.</span> | |
| 432 419 <span class="c">#</span> | |
| 433 420 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="i">$This</span><span class="i">->GetMolecule</span><span class="s">(</span><span class="s">)</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 434 421 | |
| 435 422 <span class="c"># Get all atom IDs...</span> | |
| 436 423 <span class="k">my</span><span class="s">(</span><span class="i">@AtomIDs</span><span class="s">)</span><span class="sc">;</span> | |
| 437 424 <span class="i">@AtomIDs</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 438 425 <span class="i">@AtomIDs</span> = <span class="k">map</span> <span class="s">{</span> <span class="i">$_</span><span class="i">->GetID</span><span class="s">(</span><span class="s">)</span> <span class="s">}</span> <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}}<span class="sc">;</span> | |
| 439 426 | |
| 440 427 <span class="c"># Set AtomIndex to AtomID hash...</span> | |
| 441 428 <span class="i">%</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 442 429 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">AtomIndexToID</span>}}{ <span class="s">(</span><span class="n">0</span> .. <span class="i">$#AtomIDs</span><span class="s">)</span> } = <span class="i">@AtomIDs</span><span class="sc">;</span> | |
| 443 430 | |
| 444 431 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 445 432 <span class="s">}</span> | |
| 446 433 | |
| 447 434 <span class="c"># Clear cached molecule data...</span> | |
| 448 435 <span class="c">#</span> | |
| 449 <a name="_ClearMoleculeDataCache-"></a> 436 <span class="k">sub </span><span class="m">_ClearMoleculeDataCache</span> <span class="s">{</span> | |
| 450 437 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 451 438 | |
| 452 439 <span class="i">@</span>{<span class="i">$This</span>->{<span class="w">Atoms</span>}} = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 453 440 | |
| 454 441 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> | |
| 455 442 <span class="s">}</span> | |
| 456 443 | |
| 457 444 <span class="c"># Return a string containg data for EStateValuesDescriptors object...</span> | |
| 458 445 <span class="c">#</span> | |
| 459 <a name="StringifyEStateValuesDescriptors-"></a> 446 <span class="k">sub </span><span class="m">StringifyEStateValuesDescriptors</span> <span class="s">{</span> | |
| 460 447 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 461 448 <span class="k">my</span><span class="s">(</span><span class="i">$EStateValuesDescriptorsString</span><span class="s">)</span><span class="sc">;</span> | |
| 462 449 | |
| 463 450 <span class="c"># Type of AtomicValues...</span> | |
| 464 451 <span class="i">$EStateValuesDescriptorsString</span> = <span class="q">"AtomicDescriptorType: $This->{Type}; IgnoreHydrogens: "</span> . <span class="s">(</span><span class="i">$This</span>->{<span class="w">IgnoreHydrogens</span>} ? <span class="q">"Yes"</span> <span class="co">:</span> <span class="q">"No"</span><span class="s">)</span><span class="sc">;</span> | |
| 465 452 | |
| 466 453 <span class="c"># Setup atomic descriptor information...</span> | |
| 467 454 <span class="k">my</span><span class="s">(</span><span class="i">$AtomID</span><span class="cm">,</span> <span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="i">%DescriptorValues</span><span class="s">)</span><span class="sc">;</span> | |
| 468 455 | |
| 469 456 <span class="i">@DescriptorValuesInfo</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 470 457 <span class="i">%DescriptorValues</span> = <span class="i">$This</span><span class="i">->GetDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> | |
| 471 458 | |
| 472 459 <span class="k">for</span> <span class="i">$AtomID</span> <span class="s">(</span><span class="k">sort</span> <span class="s">{</span> <span class="i">$a</span> <=> <span class="i">$b</span> <span class="s">}</span> <span class="k">keys</span> <span class="i">%DescriptorValues</span><span class="s">)</span> <span class="s">{</span> | |
| 473 460 <span class="i">$DescriptorValue</span> = <span class="i">$DescriptorValues</span>{<span class="i">$AtomID</span>}<span class="sc">;</span> | |
| 474 461 <span class="i">$DescriptorValue</span> = <span class="s">(</span><span class="i">TextUtil::IsEmpty</span><span class="s">(</span><span class="i">$DescriptorValue</span><span class="s">)</span> || <span class="i">$DescriptorValue</span> =~ <span class="q">/^None$/i</span><span class="s">)</span> ? <span class="q">'None'</span> <span class="co">:</span> <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$DescriptorValue</span><span class="cm">,</span> <span class="n">3</span><span class="s">)</span> + <span class="n">0</span><span class="sc">;</span> | |
| 475 462 <span class="k">push</span> <span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="q">"$AtomID:$DescriptorValue"</span><span class="sc">;</span> | |
| 476 463 <span class="s">}</span> | |
| 477 464 <span class="i">$EStateValuesDescriptorsString</span> .= <span class="q">"; AtomIDs:EStateValuesDescriptors: <"</span> . <span class="i">TextUtil::JoinWords</span><span class="s">(</span>\<span class="i">@DescriptorValuesInfo</span><span class="cm">,</span> <span class="q">", "</span><span class="cm">,</span> <span class="n">0</span><span class="s">)</span> . <span class="q">">"</span><span class="sc">;</span> | |
| 478 465 | |
| 479 466 <span class="k">return</span> <span class="i">$EStateValuesDescriptorsString</span><span class="sc">;</span> | |
| 480 467 <span class="s">}</span> | |
| 481 468 | |
| 482 469 <span class="c"># Is it a EStateValuesDescriptors object?</span> | |
| 483 <a name="_IsEStateValuesDescriptors-"></a> 470 <span class="k">sub </span><span class="m">_IsEStateValuesDescriptors</span> <span class="s">{</span> | |
| 484 471 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> | |
| 485 472 | |
| 486 473 <span class="k">return</span> <span class="s">(</span><span class="i">Scalar::Util::blessed</span><span class="s">(</span><span class="i">$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> | |
| 487 474 <span class="s">}</span> | |
| 488 475 | |
| 489 <a name="EOF-"></a></pre> | |
| 490 <p> </p> | |
| 491 <br /> | |
| 492 <center> | |
| 493 <img src="../../../images/h2o2.png"> | |
| 494 </center> | |
| 495 </body> | |
| 496 </html> |