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124 .\" ========================================================================
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125 .\"
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126 .IX Title "MOLECULARDESCRIPTORS 1"
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127 .TH MOLECULARDESCRIPTORS 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 MolecularDescriptors \- MolecularDescriptors class
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use MolecularDescriptors::MolecularDescriptors;
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137 .PP
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138 use MolecularDescriptors::MolecularDescriptors qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBMolecularDescriptors\fR base class used to derive all other molecular descriptors classes provides the following methods:
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142 .PP
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143 new, AddDescriptorNames, AddDescriptorValues, GetDescriptorNames,
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144 GetDescriptorNamesAndValues, GetDescriptorValueByName, GetDescriptorValues,
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145 IsDescriptorsGenerationSuccessful, SetDescriptorNames, SetDescriptorValues,
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146 SetMolecule, SetType
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147 .PP
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148 \&\fBMolecularDescriptors\fR class is derived from \fBObjectProperty\fR base class which provides methods not
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149 explicitly defined in \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's \s-1AUTOLOAD\s0 functionality.
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150 These methods are generated on-the-fly for a specified object property:
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151 .PP
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152 .Vb 3
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153 \& Set<PropertyName>(<PropertyValue>);
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154 \& $PropertyValue = Get<PropertyName>();
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155 \& Delete<PropertyName>();
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156 .Ve
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157 .SS "\s-1METHODS\s0"
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158 .IX Subsection "METHODS"
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159 .IP "\fBnew\fR" 4
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160 .IX Item "new"
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161 .Vb 2
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162 \& $NewMolecularDescriptors = new MolecularDescriptors::
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163 \& MolecularDescriptors(%NamesAndValues);
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164 .Ve
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165 .Sp
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166 Using specified \fIMolecularDescriptors\fR property names and values hash, \fBnew\fR method creates a new object
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167 and returns a reference to newly created \fBMolecularDescriptors\fR object. By default, following properties are
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168 initialized:
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169 .Sp
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170 .Vb 2
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171 \& Molecule = \*(Aq\*(Aq;
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172 \& Type = \*(Aq\*(Aq;
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173 .Ve
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174 .IP "\fBAddDescriptorNames\fR" 4
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175 .IX Item "AddDescriptorNames"
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176 .Vb 1
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177 \& $MolecularDescriptors\->AddDescriptorNames(@Name);
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178 .Ve
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179 .Sp
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180 Adds specified descriptor \fINames\fR to the list of available descriptor names and returns
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181 \&\fIMolecularDescriptors\fR.
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182 .IP "\fBAddDescriptorValues\fR" 4
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183 .IX Item "AddDescriptorValues"
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184 .Vb 1
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185 \& $MolecularDescriptors\->AddDescriptorValues(@Values);
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186 .Ve
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187 .Sp
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188 Adds specified descriptor \fIValues\fR to the list of calculated descriptor values and returns
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189 \&\fIMolecularDescriptors\fR.
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190 .IP "\fBGetDescriptorNames\fR" 4
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191 .IX Item "GetDescriptorNames"
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192 .Vb 1
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193 \& @Names = $MolecularDescriptors\->GetDescriptorNames();
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194 .Ve
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195 .Sp
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196 Returns an array containing all available descriptor names.
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197 .IP "\fBGetDescriptorNamesAndValues\fR" 4
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198 .IX Item "GetDescriptorNamesAndValues"
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199 .Vb 2
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200 \& %NamesAndValuesReturn = $MolecularDescriptors\->
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201 \& GetDescriptorNamesAndValues();
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202 .Ve
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203 .Sp
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204 Returns a hash containing all available descriptor names and calculated values.
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205 .IP "\fBGetDescriptorValueByName\fR" 4
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206 .IX Item "GetDescriptorValueByName"
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207 .Vb 2
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208 \& $Value = $MolecularDescriptors\->
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209 \& GetDescriptorValueByName($Name);
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210 .Ve
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211 .Sp
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212 Returns calculated value for a specified descriptor name. A string \fBNone\fR is returned for
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213 unknown descriptor names or for those descriptors whose values haven't been calculated.
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214 .IP "\fBGetDescriptorValues\fR" 4
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215 .IX Item "GetDescriptorValues"
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216 .Vb 1
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217 \& @Values = $MolecularDescriptors\->GetDescriptorValues();
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218 .Ve
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219 .Sp
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220 Returns an array containing calculated descriptor values for all available descriptors.
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221 Unless \fBCalculateDescriptorsValues\fR method has been successfully invoked on a
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222 \&\fIMolecularDescriptors\fR object, value of each descriptor corresponds to string \fBNone\fR.
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223 .IP "\fBIsDescriptorsGenerationSuccessful\fR" 4
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224 .IX Item "IsDescriptorsGenerationSuccessful"
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225 .Vb 2
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226 \& $Status = $MolecularDescriptors\->
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227 \& IsDescriptorsGenerationSuccessful();
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228 .Ve
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229 .Sp
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230 Returns 1 or 0 based on whether molecular descriptors generation was successful.
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231 For a successful molecular descriptors calculation, all available descriptors must have
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232 a values other than a string \fINone\fR which are set by \fBCalculateDescriptorsValues\fR
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233 method after successful completion of descriptors calculation.
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234 .IP "\fBSetDescriptorNames\fR" 4
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235 .IX Item "SetDescriptorNames"
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236 .Vb 1
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237 \& $MolecularDescriptors\->SetDescriptorNames(@Names);
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238 .Ve
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239 .Sp
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240 Sets names of available descriptors to specified names and returns \fIMolecularDescriptors\fR.
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241 .IP "\fBSetDescriptorValues\fR" 4
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242 .IX Item "SetDescriptorValues"
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243 .Vb 1
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244 \& $MolecularDescriptors\->SetDescriptorValues(@Values);
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245 .Ve
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246 .Sp
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247 Sets values of available descriptors to specified values and returns \fIMolecularDescriptors\fR.
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248 .IP "\fBSetMolecule\fR" 4
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249 .IX Item "SetMolecule"
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250 .Vb 1
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251 \& $MolecularDescriptors\->SetMolecule($Molecule);
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252 .Ve
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253 .Sp
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254 Sets molecule to use during calculation of molecular descriptors and returns \fIMolecularDescriptors\fR.
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255 .IP "\fBSetType\fR" 4
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256 .IX Item "SetType"
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257 .Vb 1
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258 \& $MolecularDescriptors\->SetType($Type);
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259 .Ve
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260 .Sp
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261 Sets \fIType\fR for \fIMolecularDescriptors\fR object and returns \fIMolecularDescriptors\fR.
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262 .SH "AUTHOR"
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263 .IX Header "AUTHOR"
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264 Manish Sud <msud@san.rr.com>
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265 .SH "SEE ALSO"
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266 .IX Header "SEE ALSO"
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267 MolecularDescriptorsGenerator.pm
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268 .SH "COPYRIGHT"
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269 .IX Header "COPYRIGHT"
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270 Copyright (C) 2015 Manish Sud. All rights reserved.
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271 .PP
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272 This file is part of MayaChemTools.
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273 .PP
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274 MayaChemTools is free software; you can redistribute it and/or modify it under
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275 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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276 Software Foundation; either version 3 of the License, or (at your option)
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277 any later version.
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