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