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124 .\" ========================================================================
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125 .\"
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126 .IX Title "MOLECULARDESCRIPTORSGENERATOR 1"
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127 .TH MOLECULARDESCRIPTORSGENERATOR 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 MolecularDescriptorsGenerator
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134 .SH "SYNOPSIS"
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135 .IX Header "SYNOPSIS"
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136 use MolecularDescriptors::MolecularDescriptorsGenerator;
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137 .PP
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138 use MolecularDescriptors::MolecularDescriptorsGenerator qw(:all);
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139 .SH "DESCRIPTION"
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140 .IX Header "DESCRIPTION"
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141 \&\fBMolecularDescriptorsGenerator\fR class provides the following methods:
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142 .PP
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143 new, GenerateDescriptors, GetAvailableClassAndDescriptorNames,
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144 GetAvailableClassNameForDescriptorName, GetAvailableDescriptorClassNames,
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145 GetAvailableDescriptorNames, GetAvailableDescriptorNamesForDescriptorClass,
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146 GetDescriptorClassParameters, GetDescriptorNames, GetDescriptorNamesAndValues,
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147 GetDescriptorValueByName, GetDescriptorValues, GetRuleOf3DescriptorNames,
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148 GetRuleOf5DescriptorNames, IsDescriptorClassNameAvailable,
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149 IsDescriptorNameAvailable, IsDescriptorsGenerationSuccessful,
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150 SetDescriptorClassParameters, SetDescriptorNames, SetMode, SetMolecule,
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151 StringifyMolecularDescriptorsGenerator
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152 .PP
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153 \&\fBMolecularDescriptorsGenerator\fR is derived from is derived from \fBObjectProperty\fR
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154 base class that provides methods not explicitly defined in \fBMolecularDescriptorsGenerator\fR
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155 or \fBObjectProperty\fR classes using Perl's \s-1AUTOLOAD\s0 functionality. These methods are
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156 generated on-the-fly for a specified object property:
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157 .PP
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158 .Vb 3
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159 \& Set<PropertyName>(<PropertyValue>);
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160 \& $PropertyValue = Get<PropertyName>();
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161 \& Delete<PropertyName>();
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162 .Ve
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163 .PP
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164 \&\fBMolecularDescriptorsGenerator\fR is designed to provide a plug-in environment for
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165 molecular descriptors development. The molecular descriptor class modules available
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166 in \fBMolecularDescriptors\fR directory under \fBMayaChemTools/lib\fR directory are
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167 automatically detected and loaded into the system. The descriptor names provided
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168 by each descriptor class module through its \fBGetDescriptorNames\fR function are
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169 retrieved and are made available for calculations of their values for a specified
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170 molecule.
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171 .PP
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172 Any combination of available descriptor names can be specified during calculation
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173 of descriptor values using \fBGenerateDescriptors\fR method. The current release of
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174 MayaChemTools supports generation of four sets of descriptors: All available
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175 descriptors, rule of 5 or 3 descriptors, or a specified set of descriptor names.
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176 .PP
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177 RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
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178 HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
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179 HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
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180 .PP
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181 RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
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182 HydrogenBondDonors, HydrogenBondAcceptors, SLogP, \s-1TPSA\s0. RuleOf3 states:
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183 MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
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184 HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
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185 .PP
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186 Before calculation of a specified set of descriptors by \fBGenerateDescriptors\fR
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187 method, a set of descriptor calculation control parameters for a specific descriptor
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188 class name can be set using \fBSetDescriptorClassParameters\fR method. The specified
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189 control parameter names and values are simply passed on to specified descriptor
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190 class during instantiation of descriptor class object without performing any validation
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191 of parameter names and associated values. It's up to the appropriate descriptor class methods
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192 to validate these parameters and values. In addition to specified parameter names and
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193 values, the parameter hash must also contain descriptor class name as key and
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194 value pair with DescriptorClassName as key with class name as value.
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195 .SS "\s-1METHODS\s0"
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196 .IX Subsection "METHODS"
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197 .IP "\fBnew\fR" 4
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198 .IX Item "new"
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199 .Vb 3
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200 \& $NewMolecularDescriptorsGenerator = new MolecularDescriptors::
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201 \& MolecularDescriptorsGenerator(
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202 \& %NamesAndValues);
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203 .Ve
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204 .Sp
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205 Using specified \fIMolecularDescriptorsGenerator\fR property names and values hash, \fBnew\fR
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206 method creates a new object and returns a reference to newly created \fBMolecularDescriptorsGenerator\fR
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207 object. By default, the following properties are initialized:
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208 .Sp
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209 .Vb 6
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210 \& Mode = \*(AqAll\*(Aq
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211 \& @{$This\->{DescriptorNames}} = ()
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212 \& %{$This\->{DescriptorClassParameters}} = ()
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213 \& @{$This\->{DescriptorClassNames}} = ()
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214 \& %{$This\->{DescriptorClassObjects}} = ()
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215 \& @{$This\->{DescriptorValues}} = ()
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216 .Ve
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217 .Sp
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218 Examples:
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219 .Sp
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220 .Vb 3
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221 \& $MolecularDescriptorsGenerator = new MolecularDescriptors::
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222 \& MolecularDescriptorsGenerator(
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223 \& \*(AqMolecule\*(Aq => $Molecule);
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224 \&
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225 \& @DescriptorNames = qw(MolecularWeight HydrogenBondDonors Fsp3Carbons)
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226 \& $MolecularDescriptorsGenerator = new MolecularDescriptors::
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227 \& MolecularDescriptorsGenerator(
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228 \& \*(AqMode\*(Aq => \*(AqSpecify\*(Aq,
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229 \& \*(AqDescriptorNames\*(Aq => \e@DescriptorNames);
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230 \&
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231 \& $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
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232 \& \*(AqDescriptorClassName\*(Aq => \*(AqWeightAndMassDescriptors\*(Aq,
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233 \& \*(AqWeightPrecision\*(Aq => 2,
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234 \& \*(AqMassPrecision\*(Aq => 2);
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235 \&
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236 \& $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
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237 \& \*(AqDescriptorClassName\*(Aq => \*(AqHydrogenBondsDescriptors\*(Aq,
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238 \& \*(AqHydrogenBondsType\*(Aq => \*(AqHBondsType1\*(Aq);
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239 \&
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240 \& $MolecularDescriptorsGenerator\->SetMolecule($Molecule);
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241 \& $MolecularDescriptorsGenerator\->GenerateDescriptors();
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242 \& print "MolecularDescriptorsGenerator: $MolecularDescriptorsGenerator\en";
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243 .Ve
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244 .IP "\fBGenerateDescriptors\fR" 4
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245 .IX Item "GenerateDescriptors"
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246 .Vb 1
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247 \& $MolecularDescriptorsGenerator\->GenerateDescriptors();
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248 .Ve
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249 .Sp
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250 Calculates descriptor values for specified descriptors and returns \fIMolecularDescriptorsGenerator\fR.
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251 .Sp
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252 Descriptor class objects are instantiated only once at first invocation. During
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253 subsequent calls to \fBGenerateDescriptors\fR method, descriptor values are
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254 initialized and \fBGenerateDescriptors\fR method provided by descriptor class is
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255 used to calculate descriptor values for specified descriptors.
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256 .IP "\fBGetAvailableClassAndDescriptorNames\fR" 4
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257 .IX Item "GetAvailableClassAndDescriptorNames"
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258 .Vb 5
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259 \& %ClassAndDescriptorNames = $MolecularDescriptorsGenerator\->
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260 \& GetAvailableClassAndDescriptorNames();
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261 \& %ClassAndDescriptorNames = MolecularDescriptors::
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262 \& MolecularDescriptorsGenerator::
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263 \& GetAvailableClassAndDescriptorNames();
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264 .Ve
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265 .Sp
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266 Returns available descriptors class and descriptors names as a hash containing key
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267 and value pairs corresponding to class name and an array of descriptor names
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268 available for the class.
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269 .IP "\fBGetAvailableClassNameForDescriptorName\fR" 4
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270 .IX Item "GetAvailableClassNameForDescriptorName"
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271 .Vb 2
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272 \& $DescriptorClassName = $MolecularDescriptorsGenerator\->
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273 \& GetAvailableClassNameForDescriptorName($DescriptorName);
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274 \&
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275 \& $DescriptorClassName = MolecularDescriptors::MolecularDescriptorsGenerator::
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276 \& GetAvailableClassNameForDescriptorName($DescriptorName);
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277 .Ve
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278 .Sp
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279 Returns available descriptor class name for a descriptor name.
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280 .IP "\fBGetAvailableDescriptorClassNames\fR" 4
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281 .IX Item "GetAvailableDescriptorClassNames"
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282 .Vb 1
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283 \& $Return = $MolecularDescriptorsGenerator\->GetAvailableDescriptorClassNames();
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284 \&
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285 \& @DescriptorClassNames = $MolecularDescriptorsGenerator\->
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286 \& GetAvailableDescriptorClassNames();
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287 \& @DescriptorClassNames = MolecularDescriptors::
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288 \& MolecularDescriptorsGenerator::
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289 \& GetAvailableDescriptorClassNames();
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290 .Ve
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291 .Sp
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292 Returns available descriptor class names as an array or number of available descriptor
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293 class names in scalar context.
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294 .IP "\fBGetAvailableDescriptorNames\fR" 4
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295 .IX Item "GetAvailableDescriptorNames"
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296 .Vb 5
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297 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
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298 \& GetAvailableDescriptorNames();
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299 \& @DescriptorNames = MolecularDescriptors::
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300 \& MolecularDescriptorsGenerator::
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301 \& GetAvailableDescriptorNames();
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302 .Ve
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303 .Sp
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304 Returns available descriptor names as an array or number of available descriptor
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305 names in scalar context.
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306 .IP "\fBGetAvailableDescriptorNamesForDescriptorClass\fR" 4
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307 .IX Item "GetAvailableDescriptorNamesForDescriptorClass"
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308 .Vb 5
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309 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
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310 \& GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
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311 \& @DescriptorNames = MolecularDescriptors::
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312 \& MolecularDescriptorsGenerator::
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313 \& GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
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314 .Ve
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315 .Sp
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316 Returns available descriptors names for a descriptor class as an array or number
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317 of available descriptor names in scalar context.
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318 .IP "\fBGetDescriptorClassParameters\fR" 4
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319 .IX Item "GetDescriptorClassParameters"
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320 .Vb 5
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321 \& $DescriptorClassParametersRef = $MolecularDescriptorsGenerator\->
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322 \& GetDescriptorClassParameters();
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323 \& $DescriptorClassParametersRef = MolecularDescriptors::
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324 \& MolecularDescriptorsGenerator::
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325 \& GetDescriptorClassParameters();
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326 .Ve
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327 .Sp
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328 Returns descriptor name parameters as a reference to hash of hashes with hash
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329 keys corresponding to class name and class parameter name with hash value
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330 as class parameter value.
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331 .IP "\fBGetDescriptorNames\fR" 4
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332 .IX Item "GetDescriptorNames"
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333 .Vb 3
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334 \& @DescriptorNames = $MolecularDescriptorsGenerator\->GetDescriptorNames();
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335 \& @DescriptorNames = MolecularDescriptors::MolecularDescriptorsGenerator::
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336 \& GetDescriptorNames();
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337 .Ve
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338 .Sp
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339 Returns all available descriptor names as an array or number of available descriptors
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340 in scalar context.
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341 .IP "\fBGetDescriptorNamesAndValues\fR" 4
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342 .IX Item "GetDescriptorNamesAndValues"
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343 .Vb 2
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344 \& %NamesAndValues = $MolecularDescriptorsGenerator\->
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345 \& GetDescriptorNamesAndValues();
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346 .Ve
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347 .Sp
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348 Returns calculated molecular descriptor names and values as a hash with descriptor
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349 names and values as hash key and value pairs.
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350 .IP "\fBGetDescriptorValueByName\fR" 4
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351 .IX Item "GetDescriptorValueByName"
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352 .Vb 2
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353 \& $Value = $MolecularDescriptorsGenerator\->
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354 \& GetDescriptorValueByName($Name);
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355 .Ve
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356 .Sp
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357 Returns calculated descriptor values for a specified descriptor name.
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358 .IP "\fBGetDescriptorValues\fR" 4
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359 .IX Item "GetDescriptorValues"
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360 .Vb 1
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361 \& @DescriptorValues = $MolecularDescriptorsGenerator\->GetDescriptorValues();
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362 .Ve
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363 .Sp
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364 Returns all calculated descriptor values as an array corresponding to specified
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365 descriptor names.
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366 .IP "\fBGetRuleOf3DescriptorNames\fR" 4
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367 .IX Item "GetRuleOf3DescriptorNames"
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368 .Vb 5
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369 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
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370 \& GetRuleOf3DescriptorNames();
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371 \& @DescriptorNames = MolecularDescriptors::
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372 \& MolecularDescriptorsGenerator::
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373 \& GetRuleOf3DescriptorNames();
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374 .Ve
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375 .Sp
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376 Returns rule of 3 descriptor names as an array or number of rule of 3 descriptors in scalar
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377 context.
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378 .Sp
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379 RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
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380 HydrogenBondDonors, HydrogenBondAcceptors, SLogP, \s-1TPSA\s0. RuleOf3 states:
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381 MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
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382 HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
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383 .IP "\fBGetRuleOf5DescriptorNames\fR" 4
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384 .IX Item "GetRuleOf5DescriptorNames"
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385 .Vb 4
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386 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
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387 \& GetRuleOf5DescriptorNames();
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388 \& @DescriptorNames = $MolecularDescriptorsGenerator::
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389 \& GetRuleOf5DescriptorNames();
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390 .Ve
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391 .Sp
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392 Returns rule of 5 descriptor names as an array or number of rule of 4 descriptors in scalar
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393 context.
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394 .Sp
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395 RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
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396 HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
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397 HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
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398 .IP "\fBIsDescriptorClassNameAvailable\fR" 4
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399 .IX Item "IsDescriptorClassNameAvailable"
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400 .Vb 5
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401 \& $Status = $MolecularDescriptorsGenerator\->
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402 \& IsDescriptorClassNameAvailable($ClassName);
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403 \& $Status = MolecularDescriptors::
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404 \& MolecularDescriptorsGenerator::
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405 \& IsDescriptorClassNameAvailable($ClassName);
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406 .Ve
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407 .Sp
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408 Returns 1 or 0 based on whether specified descriptor class name is available.
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409 .IP "\fBIsDescriptorNameAvailable\fR" 4
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410 .IX Item "IsDescriptorNameAvailable"
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411 .Vb 5
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412 \& $Status = $MolecularDescriptorsGenerator\->
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413 \& IsDescriptorNameAvailable($DescriptorName);
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414 \& $Status = MolecularDescriptors::
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415 \& MolecularDescriptorsGenerator::
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416 \& IsDescriptorNameAvailable($DescriptorName);
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417 .Ve
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418 .Sp
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419 Returns 1 or 0 based on whether specified descriptor name is available.
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420 .IP "\fBIsDescriptorsGenerationSuccessful\fR" 4
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421 .IX Item "IsDescriptorsGenerationSuccessful"
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422 .Vb 2
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423 \& $Status = $MolecularDescriptorsGenerator\->
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424 \& IsDescriptorsGenerationSuccessful();
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425 .Ve
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426 .Sp
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427 Returns 1 or 0 based on whether descriptors generation is successful.
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428 .IP "\fBSetDescriptorClassParameters\fR" 4
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429 .IX Item "SetDescriptorClassParameters"
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430 .Vb 2
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431 \& $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
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432 \& %NamesAndValues);
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433 .Ve
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434 .Sp
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435 Sets descriptor calculation control parameters for a specified descriptor class name
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436 and returns \fIMolecularDescriptorsGenerator\fR.
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437 .Sp
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438 The specified parameter names and values are simply passed on to specified descriptor
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439 class during instantiation of descriptor class object without any performing any validation
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440 of parameter names and associated values. It's up to the appropriate descriptor class methods
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441 to validate these parameters and values.
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442 .Sp
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443 In addition to specified parameter names and values, the parameter hash must also contain
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444 descriptor class name as key and value pair with DescriptorClassName as key with class
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445 name as value.
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446 .IP "\fBSetDescriptorNames\fR" 4
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447 .IX Item "SetDescriptorNames"
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448 .Vb 2
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449 \& $MolecularDescriptorsGenerator\->SetDescriptorNames(@Names);
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450 \& $MolecularDescriptorsGenerator\->SetDescriptorNames(\e@Names);
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451 .Ve
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452 .Sp
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453 Sets descriptor names to use for generating descriptor values using an array
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454 or reference to an array and returns \fIMolecularDescriptorsGenerator\fR.
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455 .IP "\fBSetMode\fR" 4
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456 .IX Item "SetMode"
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457 .Vb 1
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458 \& $MolecularDescriptorsGenerator\->SetMode($Mode);
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459 .Ve
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460 .Sp
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461 Sets descriptors generation mode and returns \fIMolecularDescriptorsGenerator\fR.
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462 Possible \fIMode\fR values: \fIAll, RuleOf5, RuleOf3, Specify\fR.
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463 .IP "\fBSetMolecule\fR" 4
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464 .IX Item "SetMolecule"
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465 .Vb 1
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466 \& $MolecularDescriptorsGenerator\->SetMolecule($Molecule);
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467 .Ve
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468 .Sp
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469 Sets molecule to use during calculation of molecular descriptors and returns
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470 \&\fIMolecularDescriptorsGenerator\fR.
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471 .IP "\fBStringifyMolecularDescriptorsGenerator\fR" 4
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472 .IX Item "StringifyMolecularDescriptorsGenerator"
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473 .Vb 1
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474 \& $String = $MolecularDescriptorsGenerator\->StringifyMolecularDescriptorsGenerator();
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475 .Ve
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476 .Sp
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477 Returns a string containing information about \fIMolecularDescriptorsGenerator\fR object.
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478 .SH "AUTHOR"
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479 .IX Header "AUTHOR"
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480 Manish Sud <msud@san.rr.com>
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481 .SH "SEE ALSO"
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482 .IX Header "SEE ALSO"
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483 MolecularDescriptors.pm
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484 .SH "COPYRIGHT"
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485 .IX Header "COPYRIGHT"
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486 Copyright (C) 2015 Manish Sud. All rights reserved.
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487 .PP
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488 This file is part of MayaChemTools.
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489 .PP
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490 MayaChemTools is free software; you can redistribute it and/or modify it under
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491 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
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492 Software Foundation; either version 3 of the License, or (at your option)
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493 any later version.
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