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124 .\" ========================================================================
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125 .\"
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126 .IX Title "MOLECULARVOLUMEDESCRIPTORS 1"
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127 .TH MOLECULARVOLUMEDESCRIPTORS 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
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128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
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129 .\" way too many mistakes in technical documents.
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130 .if n .ad l
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131 .nh
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132 .SH "NAME"
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133 MolecularVolumeDescriptors
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use MolecularDescriptors::MolecularVolumeDescriptors;
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137 .PP
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138 use MolecularDescriptors::MolecularVolumeDescriptors qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBMolecularVolumeDescriptors\fR class provides the following methods:
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142 .PP
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143 new, GenerateDescriptors, GetDescriptorNames,
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144 GetVDWAtomRadiiAndVolumesData, StringifyMolecularVolumeDescriptors
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145 .PP
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146 \&\fBMolecularVolumeDescriptors\fR is derived from \fBMolecularDescriptors\fR class which in turn
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147 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
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148 in \fBMolecularVolumeDescriptors\fR, \fBMolecularDescriptors\fR or \fBObjectProperty\fR classes using Perl's
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149 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
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150 .PP
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151 .Vb 3
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152 \& Set<PropertyName>(<PropertyValue>);
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153 \& $PropertyValue = Get<PropertyName>();
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154 \& Delete<PropertyName>();
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155 .Ve
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156 .PP
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157 van der Waals molecular volume [ Ref 93 ] (A**3/molecule) of a molecule is
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158 calculated using atomic and bonds contributions along with adjustments for
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159 aromatic and non-aromatic rings using the following equation:
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160 .PP
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161 .Vb 4
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162 \& vdwMolecularVolume = SumOfAtomicVDWVolumeContributions
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163 \& \- 5.92 * NumOfBonds
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164 \& \- 14.7 * NumOfAromaticRings
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165 \& \- 3.8 * NumOfNonAromaticRings
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166 .Ve
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167 .PP
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168 van der Waals atomic volume for atoms is taken from data file VDWAtomRadiiAndVolumes.csv
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169 distributed with MayaChemTools. It contains van der Waals atom radii and atom and volumes
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170 data for 38 elements; Table 2 [ Ref 93 ] contains data for only 15 elements. After converting
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171 valid van der Waals atom radius data from pm (picometer) to A (Angstrom) available under column
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172 name VanderWaalsRadius in PeriodicTableElementsData.csv data file, van der Waals atom volume
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173 is calculated using: 4/3 * \s-1PI\s0 * (Radius ** 3). For elements specified in Table 2 [ Ref 93 ] \-
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174 H, B, C, N, O, F, Si, P, S, Cl, As, Se, Br, Te, I \- the van der Waals atom radii and calculated
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175 atom volumes match the values in the table.
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176 .SS "\s-1METHODS\s0"
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177 .IX Subsection "METHODS"
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178 .IP "\fBnew\fR" 4
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179 .IX Item "new"
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180 .Vb 3
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181 \& $NewMolecularVolumeDescriptors = new MolecularDescriptors::
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182 \& MolecularVolumeDescriptors(
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183 \& %NamesAndValues);
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184 .Ve
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185 .Sp
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186 Using specified \fIMolecularVolumeDescriptors\fR property names and values hash, \fBnew\fR
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187 method creates a new object and returns a reference to newly created \fBMolecularVolumeDescriptors\fR
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188 object. By default, the following properties are initialized:
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189 .Sp
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190 .Vb 4
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191 \& Molecule = \*(Aq\*(Aq
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192 \& Type = \*(AqMolecularVolume\*(Aq
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193 \& @DescriptorNames = (\*(AqMolecularVolume\*(Aq)
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194 \& @DescriptorValues = (\*(AqNone\*(Aq)
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195 .Ve
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196 .Sp
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197 Examples:
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198 .Sp
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199 .Vb 2
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200 \& $MolecularVolumeDescriptors = new MolecularDescriptors::
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201 \& MolecularVolumeDescriptors();
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202 \&
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203 \& $MolecularVolumeDescriptors\->SetMolecule($Molecule);
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204 \& $MolecularVolumeDescriptors\->GenerateDescriptors();
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205 \& print "MolecularVolumeDescriptors: $MolecularVolumeDescriptors\en";
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206 .Ve
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207 .IP "\fBGenerateDescriptors\fR" 4
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208 .IX Item "GenerateDescriptors"
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209 .Vb 1
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210 \& $MolecularVolumeDescriptors\->GenerateDescriptors();
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211 .Ve
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212 .Sp
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213 Calculate van der Waals molecular volume descriptor for a molecule and returns
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214 \&\fIMolecularVolumeDescriptors\fR.
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215 .IP "\fBGetDescriptorNames\fR" 4
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216 .IX Item "GetDescriptorNames"
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217 .Vb 3
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218 \& @DescriptorNames = $MolecularVolumeDescriptors\->GetDescriptorNames();
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219 \& @DescriptorNames = MolecularDescriptors::MolecularVolumeDescriptors::
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220 \& GetDescriptorNames();
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221 .Ve
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222 .Sp
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223 Returns all available descriptor names as an array.
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224 .IP "\fBGetVDWAtomRadiiAndVolumesData\fR" 4
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225 .IX Item "GetVDWAtomRadiiAndVolumesData"
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226 .Vb 4
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227 \& $VDWVolumeDataMapRef = $MolecularVolumeDescriptors\->
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228 \& GetVDWAtomRadiiAndVolumesData();
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229 \& $VDWVolumeDataMapRef = MolecularDescriptors::MolecularVolumeDescriptors::
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230 \& GetVDWAtomRadiiAndVolumesData();
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231 .Ve
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232 .Sp
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233 Returns a hash reference to van der Waals atom symbols corresponding to atom types
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234 and associated data loaded from VDWAtomRadiiAndVolumes.csv data file as a reference
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235 to hash with the following hash data format:
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236 .Sp
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237 .Vb 5
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238 \& @{$VDWVolumeDataMap{AtomTypes}} \- Array of all possible atom
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239 \& types for all atom symbols
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240 \& @{$VDWVolumeDataMap\->{ColLabels}} \- Array of column labels
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241 \& %{$VDWVolumeDataMap\->{DataCol<Num>}} \- Hash keys pair:
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242 \& DataCol<Num>, AtomType
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243 .Ve
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244 .IP "\fBStringifyMolecularVolumeDescriptors\fR" 4
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245 .IX Item "StringifyMolecularVolumeDescriptors"
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246 .Vb 2
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247 \& $String = $MolecularVolumeDescriptors\->
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248 \& StringifyMolecularVolumeDescriptors();
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249 .Ve
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250 .Sp
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251 Returns a string containing information about \fIMolecularVolumeDescriptors\fR object.
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252 .SH "AUTHOR"
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253 .IX Header "AUTHOR"
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254 Manish Sud <msud@san.rr.com>
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255 .SH "SEE ALSO"
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256 .IX Header "SEE ALSO"
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257 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
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258 .SH "COPYRIGHT"
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259 .IX Header "COPYRIGHT"
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260 Copyright (C) 2015 Manish Sud. All rights reserved.
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261 .PP
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262 This file is part of MayaChemTools.
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263 .PP
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264 MayaChemTools is free software; you can redistribute it and/or modify it under
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265 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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266 Software Foundation; either version 3 of the License, or (at your option)
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267 any later version.
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