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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> | |
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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> |