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<html> <head> <title>MayaChemTools:Code:MolecularDescriptors::MolecularVolumeDescriptors.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-MolecularDescriptors::MolecularVolumeDescriptors-"></a> 1 <span class="k">package </span><span class="i">MolecularDescriptors::MolecularVolumeDescriptors</span><span class="sc">;</span> 2 <span class="c">#</span> 3 <span class="c"># $RCSfile: MolecularVolumeDescriptors.pm,v $</span> 4 <span class="c"># $Date: 2015/02/28 20:49:20 $</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">TextUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 34 <span class="k">use</span> <span class="w">MathUtil</span> <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 35 <span class="k">use</span> <span class="w">Atom</span><span class="sc">;</span> 36 <span class="k">use</span> <span class="w">Molecule</span><span class="sc">;</span> 37 <span class="k">use</span> <span class="w">AtomTypes::AtomTypes</span><span class="sc">;</span> 38 <span class="k">use</span> <span class="w">MolecularDescriptors::MolecularDescriptors</span><span class="sc">;</span> 39 40 <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> 41 42 <span class="i">@ISA</span> = <span class="q">qw(MolecularDescriptors::MolecularDescriptors Exporter)</span><span class="sc">;</span> 43 <span class="i">@EXPORT</span> = <span class="q">qw()</span><span class="sc">;</span> 44 <span class="i">@EXPORT_OK</span> = <span class="q">qw(GetDescriptorNames GetVDWAtomRadiiAndVolumesData)</span><span class="sc">;</span> 45 46 <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> 47 48 <span class="c"># Setup class variables...</span> 49 <span class="k">my</span><span class="s">(</span><span class="i">$ClassName</span><span class="cm">,</span> <span class="i">@DescriptorNames</span><span class="cm">,</span> <span class="i">%VDWAtomRadiiAndVolumesDataMap</span><span class="s">)</span><span class="sc">;</span> 50 <span class="i">_InitializeClass</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 51 52 <span class="c"># Overload Perl functions...</span> 53 <span class="k">use</span> <span class="w">overload</span> <span class="q">'""'</span> <span class="cm">=></span> <span class="q">'StringifyMolecularVolumeDescriptors'</span><span class="sc">;</span> 54 55 <span class="c"># Class constructor...</span> <a name="new-"></a> 56 <span class="k">sub </span><span class="m">new</span> <span class="s">{</span> 57 <span class="k">my</span><span class="s">(</span><span class="i">$Class</span><span class="cm">,</span> <span class="i">%NamesAndValues</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 58 59 <span class="c"># Initialize object...</span> 60 <span class="k">my</span> <span class="i">$This</span> = <span class="i">$Class</span><span class="i">->SUPER::new</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 61 <span class="k">bless</span> <span class="i">$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> 62 <span class="i">$This</span><span class="i">->_InitializeMolecularVolumeDescriptors</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 63 64 <span class="i">$This</span><span class="i">->_InitializeMolecularVolumeDescriptorsProperties</span><span class="s">(</span><span class="i">%NamesAndValues</span><span class="s">)</span><span class="sc">;</span> 65 66 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 67 <span class="s">}</span> 68 69 <span class="c"># Initialize class ...</span> <a name="_InitializeClass-"></a> 70 <span class="k">sub </span><span class="m">_InitializeClass</span> <span class="s">{</span> 71 <span class="c">#Class name...</span> 72 <span class="i">$ClassName</span> = <span class="w">__PACKAGE__</span><span class="sc">;</span> 73 74 <span class="c"># Descriptor names...</span> 75 <span class="i">@DescriptorNames</span> = <span class="s">(</span><span class="q">'MolecularVolume'</span><span class="s">)</span><span class="sc">;</span> 76 77 <span class="c"># Initialize the data hash. It'll be loaded on demand later...</span> 78 <span class="i">%VDWAtomRadiiAndVolumesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 79 80 <span class="s">}</span> 81 82 <span class="c"># Get descriptor names as an array.</span> 83 <span class="c">#</span> 84 <span class="c"># This functionality can be either invoked as a class function or an</span> 85 <span class="c"># object method.</span> 86 <span class="c">#</span> <a name="GetDescriptorNames-"></a> 87 <span class="k">sub </span><span class="m">GetDescriptorNames</span> <span class="s">{</span> 88 <span class="k">return</span> <span class="i">@DescriptorNames</span><span class="sc">;</span> 89 <span class="s">}</span> 90 91 <span class="c"># Initialize object data...</span> 92 <span class="c">#</span> <a name="_InitializeMolecularVolumeDescriptors-"></a> 93 <span class="k">sub </span><span class="m">_InitializeMolecularVolumeDescriptors</span> <span class="s">{</span> 94 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 95 96 <span class="c"># Type of MolecularDescriptor...</span> 97 <span class="i">$This</span>->{<span class="w">Type</span>} = <span class="q">'MolecularVolume'</span><span class="sc">;</span> 98 99 <span class="c"># Intialize descriptor names and values...</span> 100 <span class="i">$This</span><span class="i">->_InitializeDescriptorNamesAndValues</span><span class="s">(</span><span class="i">@DescriptorNames</span><span class="s">)</span><span class="sc">;</span> 101 102 <span class="k">return</span> <span class="i">$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="_InitializeMolecularVolumeDescriptorsProperties-"></a> 107 <span class="k">sub </span><span class="m">_InitializeMolecularVolumeDescriptorsProperties</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">$Value</span><span class="s">)</span><span class="sc">;</span> 114 <span class="s">}</span> 115 116 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 117 <span class="s">}</span> 118 119 <span class="c"># Get VDW atom data loaded from VDW atom radii and and volumes data file as</span> 120 <span class="c"># a reference to hash with the following hash data format:</span> 121 <span class="c">#</span> 122 <span class="c"># @{$VDWAtomRadiiAndVolumesDataMap{AtomTypes}} - Array of all possible atom type symbols for all atoms</span> 123 <span class="c"># @{$VDWAtomRadiiAndVolumesDataMap->{ColLabels}} - Array of column labels</span> 124 <span class="c"># %{$VDWAtomRadiiAndVolumesDataMap->{DataCol<Num>}} - Hash keys pair: <DataCol<Num>, AtomType></span> 125 <span class="c">#</span> 126 <span class="c"># This functionality can be either invoked as a class function or an</span> 127 <span class="c"># object method.</span> 128 <span class="c">#</span> <a name="GetVDWAtomRadiiAndVolumesData-"></a> 129 <span class="k">sub </span><span class="m">GetVDWAtomRadiiAndVolumesData</span> <span class="s">{</span> 130 131 <span class="c"># Make sure data is loaded...</span> 132 <span class="i">_CheckAndLoadVDWAtomRadiiAndVolumesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 133 134 <span class="k">return</span> \<span class="i">%VDWAtomRadiiAndVolumesDataMap</span><span class="sc">;</span> 135 <span class="s">}</span> 136 137 <span class="c"># Calculate van der Waals molecular volume [ Ref 93 ] of a molecule using</span> 138 <span class="c"># atomic and bonds contributions...</span> 139 <span class="c">#</span> 140 <span class="c"># van der Waals molecular volume (A**3/molecule) is defined as:</span> 141 <span class="c">#</span> 142 <span class="c"># vdwMolecularVolume = SumOfAtomicVDWVolumeContributions - 5.92 * NumOfBonds</span> 143 <span class="c"># - 14.7 * NumOfAromaticRings - 3.8 * NumOfNonAromaticRings</span> 144 <span class="c">#</span> 145 <span class="c"># Methodology:</span> 146 <span class="c"># . Add up van der Waals atom volumne of all atoms</span> 147 <span class="c"># . Calculate molecular volume by correcting sum of atom volumes for num of</span> 148 <span class="c"># bonds and rings</span> 149 <span class="c">#</span> 150 <span class="c"># Caveats:</span> 151 <span class="c"># . All hydrogens must be added to molecule before calling GenerateDescriptors.</span> 152 <span class="c">#</span> <a name="GenerateDescriptors-"></a> 153 <span class="k">sub </span><span class="m">GenerateDescriptors</span> <span class="s">{</span> 154 <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> 155 156 <span class="c"># Initialize descriptor values...</span> 157 <span class="i">$This</span><span class="i">->_InitializeDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 158 159 <span class="c"># Check availability of molecule...</span> 160 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="s">)</span> <span class="s">{</span> 161 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Molecule data is not available: Molecule object hasn't been set..."</span><span class="sc">;</span> 162 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 163 <span class="s">}</span> 164 165 <span class="c"># Calculate descriptor values...</span> 166 <span class="k">if</span> <span class="s">(</span>!<span class="i">$This</span><span class="i">->_CalculateDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 167 <span class="w">carp</span> <span class="q">"Warning: ${ClassName}->GenerateDescriptors: $This->{Type} molecular descriptors generation didn't succeed: Couldn't calculate MolecularVolume values: van der Waals atom volume data is not available for all atoms..."</span><span class="sc">;</span> 168 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 169 <span class="s">}</span> 170 171 <span class="c"># Set final descriptor values...</span> 172 <span class="i">$This</span><span class="i">->_SetFinalDescriptorValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 173 174 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 175 <span class="s">}</span> 176 177 <span class="c"># Calculate MolecularVolume value...</span> 178 <span class="c">#</span> <a name="_CalculateDescriptorValues-"></a> 179 <span class="k">sub </span><span class="m">_CalculateDescriptorValues</span> <span class="s">{</span> 180 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 181 <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">$AtomSymbol</span><span class="cm">,</span> <span class="i">$SumOfVDWAtomVolumes</span><span class="cm">,</span> <span class="i">$Molecule</span><span class="cm">,</span> <span class="i">$MolecularVolume</span><span class="cm">,</span> <span class="i">$NumOfBonds</span><span class="cm">,</span> <span class="i">$NumOfAromaticRings</span><span class="cm">,</span> <span class="i">$NumOfNonAromaticRings</span><span class="cm">,</span> <span class="i">$VDWAtomRadiiAndVolumesDataMapRef</span><span class="s">)</span><span class="sc">;</span> 182 183 <span class="i">$MolecularVolume</span> = <span class="n">0</span><span class="sc">;</span> 184 185 <span class="i">$VDWAtomRadiiAndVolumesDataMapRef</span> = <span class="i">$This</span><span class="i">->GetVDWAtomRadiiAndVolumesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 186 <span class="i">$Molecule</span> = <span class="i">$This</span>->{<span class="w">Molecule</span>}<span class="sc">;</span> 187 188 <span class="c"># Calculate atom volumes contribution to molecular volume...</span> 189 <span class="c">#</span> 190 <span class="i">$SumOfVDWAtomVolumes</span> = <span class="n">0</span><span class="sc">;</span> 191 192 <span class="j">ATOM:</span> <span class="k">for</span> <span class="i">$Atom</span> <span class="s">(</span><span class="i">$Molecule</span><span class="i">->GetAtoms</span><span class="s">(</span><span class="s">)</span><span class="s">)</span> <span class="s">{</span> 193 <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> 194 <span class="i">$AtomSymbol</span> = <span class="i">$Atom</span><span class="i">->GetAtomSymbol</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 195 196 <span class="c"># Make sure van der Waals atom volume is available...</span> 197 <span class="k">if</span> <span class="s">(</span>!<span class="k">exists</span> <span class="i">$VDWAtomRadiiAndVolumesDataMap</span>{<span class="w">DataCol3</span>}{<span class="i">$AtomSymbol</span>}<span class="s">)</span> <span class="s">{</span> 198 <span class="k">return</span> <span class="k">undef</span><span class="sc">;</span> 199 <span class="s">}</span> 200 <span class="i">$SumOfVDWAtomVolumes</span> += <span class="i">$VDWAtomRadiiAndVolumesDataMapRef</span>->{<span class="w">DataCol3</span>}{<span class="i">$AtomSymbol</span>}<span class="sc">;</span> 201 <span class="s">}</span> 202 203 <span class="i">$NumOfBonds</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfBonds</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 204 <span class="i">$NumOfAromaticRings</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfAromaticRings</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 205 <span class="i">$NumOfNonAromaticRings</span> = <span class="i">$Molecule</span><span class="i">->GetNumOfRings</span><span class="s">(</span><span class="s">)</span> - <span class="i">$NumOfAromaticRings</span><span class="sc">;</span> 206 207 <span class="c"># Apply correction for bonds and rings...</span> 208 <span class="i">$MolecularVolume</span> = <span class="i">$SumOfVDWAtomVolumes</span> - <span class="n">5.92</span> * <span class="i">$NumOfBonds</span> - <span class="n">14.7</span> * <span class="i">$NumOfAromaticRings</span> - <span class="n">3.8</span> * <span class="i">$NumOfNonAromaticRings</span><span class="sc">;</span> 209 210 <span class="c"># Track the calculated values...</span> 211 <span class="i">$This</span>->{<span class="w">MolecularVolume</span>} = <span class="i">MathUtil::round</span><span class="s">(</span><span class="i">$MolecularVolume</span><span class="cm">,</span> <span class="n">2</span><span class="s">)</span><span class="sc">;</span> 212 213 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 214 <span class="s">}</span> 215 216 <span class="c"># Setup final descriptor values...</span> 217 <span class="c">#</span> <a name="_SetFinalDescriptorValues-"></a> 218 <span class="k">sub </span><span class="m">_SetFinalDescriptorValues</span> <span class="s">{</span> 219 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 220 221 <span class="i">$This</span>->{<span class="w">DescriptorsGenerated</span>} = <span class="n">1</span><span class="sc">;</span> 222 223 <span class="i">$This</span><span class="i">->SetDescriptorValues</span><span class="s">(</span><span class="i">$This</span>->{<span class="w">MolecularVolume</span>}<span class="s">)</span><span class="sc">;</span> 224 225 <span class="k">return</span> <span class="i">$This</span><span class="sc">;</span> 226 <span class="s">}</span> 227 228 <span class="c"># Return a string containg data for MolecularVolumeDescriptors object...</span> 229 <span class="c">#</span> <a name="StringifyMolecularVolumeDescriptors-"></a> 230 <span class="k">sub </span><span class="m">StringifyMolecularVolumeDescriptors</span> <span class="s">{</span> 231 <span class="k">my</span><span class="s">(</span><span class="i">$This</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 232 <span class="k">my</span><span class="s">(</span><span class="i">$MolecularVolumeDescriptorsString</span><span class="s">)</span><span class="sc">;</span> 233 234 <span class="i">$MolecularVolumeDescriptorsString</span> = <span class="q">"MolecularDescriptorType: $This->{Type}; "</span> . <span class="i">$This</span><span class="i">->_StringifyDescriptorNamesAndValues</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 235 236 <span class="k">return</span> <span class="i">$MolecularVolumeDescriptorsString</span><span class="sc">;</span> 237 <span class="s">}</span> 238 239 <span class="c"># Is it a MolecularVolumeDescriptors object?</span> <a name="_IsMolecularVolumeDescriptors-"></a> 240 <span class="k">sub </span><span class="m">_IsMolecularVolumeDescriptors</span> <span class="s">{</span> 241 <span class="k">my</span><span class="s">(</span><span class="i">$Object</span><span class="s">)</span> = <span class="i">@_</span><span class="sc">;</span> 242 243 <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">$ClassName</span><span class="s">)</span><span class="s">)</span> ? <span class="n">1</span> <span class="co">:</span> <span class="n">0</span><span class="sc">;</span> 244 <span class="s">}</span> 245 246 <span class="c"># Check and load van der Waals atom radii and volumes data...</span> 247 <span class="c">#</span> <a name="_CheckAndLoadVDWAtomRadiiAndVolumesData-"></a> 248 <span class="k">sub </span><span class="m">_CheckAndLoadVDWAtomRadiiAndVolumesData</span> <span class="s">{</span> 249 250 <span class="c"># Is it already loaded?</span> 251 <span class="k">if</span> <span class="s">(</span><span class="k">exists</span> <span class="i">$VDWAtomRadiiAndVolumesDataMap</span>{<span class="w">AtomTypes</span>}<span class="s">)</span> <span class="s">{</span> 252 <span class="k">return</span><span class="sc">;</span> 253 <span class="s">}</span> 254 255 <span class="i">_LoadVDWAtomRadiiAndVolumesData</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 256 <span class="s">}</span> 257 258 <span class="c"># Initialize van der Waals atom radii and volumes data from the file...</span> 259 <span class="c">#</span> 260 <span class="c"># Format:</span> 261 <span class="c">#</span> 262 <span class="c"># "AtomTypeSymbol","VDWAtomRadius(A)","VDWAtomVolume(A**3)/molecule"</span> 263 <span class="c"># "H","1.20","7.24"</span> 264 <span class="c"># "He","1.40","11.49"</span> 265 <span class="c">#</span> <a name="_LoadVDWAtomRadiiAndVolumesData-"></a> 266 <span class="k">sub </span><span class="m">_LoadVDWAtomRadiiAndVolumesData</span> <span class="s">{</span> 267 <span class="k">my</span><span class="s">(</span><span class="i">$VDWAtomDataFile</span><span class="cm">,</span> <span class="i">$MayaChemToolsLibDir</span><span class="s">)</span><span class="sc">;</span> 268 269 <span class="i">$MayaChemToolsLibDir</span> = <span class="i">FileUtil::GetMayaChemToolsLibDirName</span><span class="s">(</span><span class="s">)</span><span class="sc">;</span> 270 271 <span class="i">$VDWAtomDataFile</span> = <span class="q">"$MayaChemToolsLibDir"</span> . <span class="q">"/data/VDWAtomRadiiAndVolumes.csv"</span><span class="sc">;</span> 272 <span class="k">if</span> <span class="s">(</span>! <span class="k">-e</span> <span class="q">"$VDWAtomDataFile"</span><span class="s">)</span> <span class="s">{</span> 273 <span class="w">croak</span> <span class="q">"Error: MayaChemTools package file, $VDWAtomDataFile, is missing: Possible installation problems..."</span><span class="sc">;</span> 274 <span class="s">}</span> 275 276 <span class="i">%VDWAtomRadiiAndVolumesDataMap</span> = <span class="s">(</span><span class="s">)</span><span class="sc">;</span> 277 <span class="i">AtomTypes::AtomTypes::LoadAtomTypesData</span><span class="s">(</span><span class="i">$VDWAtomDataFile</span><span class="cm">,</span> \<span class="i">%VDWAtomRadiiAndVolumesDataMap</span><span class="s">)</span><span class="sc">;</span> 278 <span class="s">}</span><span class="sc">;</span> 279 <a name="EOF-"></a></pre> <p> </p> <br /> <center> <img src="../../../images/h2o2.png"> </center> </body> </html>