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124 .\" ========================================================================
125 .\"
126 .IX Title "MOLECULARDESCRIPTORSGENERATOR 1"
127 .TH MOLECULARDESCRIPTORSGENERATOR 1 "2015-03-29" "perl v5.14.2" "MayaChemTools"
128 .\" For nroff, turn off justification. Always turn off hyphenation; it makes
129 .\" way too many mistakes in technical documents.
130 .if n .ad l
131 .nh
132 .SH "NAME"
133 MolecularDescriptorsGenerator
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use MolecularDescriptors::MolecularDescriptorsGenerator;
137 .PP
138 use MolecularDescriptors::MolecularDescriptorsGenerator qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBMolecularDescriptorsGenerator\fR class provides the following methods:
142 .PP
143 new, GenerateDescriptors, GetAvailableClassAndDescriptorNames,
144 GetAvailableClassNameForDescriptorName, GetAvailableDescriptorClassNames,
145 GetAvailableDescriptorNames, GetAvailableDescriptorNamesForDescriptorClass,
146 GetDescriptorClassParameters, GetDescriptorNames, GetDescriptorNamesAndValues,
147 GetDescriptorValueByName, GetDescriptorValues, GetRuleOf3DescriptorNames,
148 GetRuleOf5DescriptorNames, IsDescriptorClassNameAvailable,
149 IsDescriptorNameAvailable, IsDescriptorsGenerationSuccessful,
150 SetDescriptorClassParameters, SetDescriptorNames, SetMode, SetMolecule,
151 StringifyMolecularDescriptorsGenerator
152 .PP
153 \&\fBMolecularDescriptorsGenerator\fR is derived from is derived from \fBObjectProperty\fR
154 base class that provides methods not explicitly defined in \fBMolecularDescriptorsGenerator\fR
155 or \fBObjectProperty\fR classes using Perl's \s-1AUTOLOAD\s0 functionality. These methods are
156 generated on-the-fly for a specified object property:
157 .PP
158 .Vb 3
159 \& Set<PropertyName>(<PropertyValue>);
160 \& $PropertyValue = Get<PropertyName>();
161 \& Delete<PropertyName>();
162 .Ve
163 .PP
164 \&\fBMolecularDescriptorsGenerator\fR is designed to provide a plug-in environment for
165 molecular descriptors development. The molecular descriptor class modules available
166 in \fBMolecularDescriptors\fR directory under \fBMayaChemTools/lib\fR directory are
167 automatically detected and loaded into the system. The descriptor names provided
168 by each descriptor class module through its \fBGetDescriptorNames\fR function are
169 retrieved and are made available for calculations of their values for a specified
170 molecule.
171 .PP
172 Any combination of available descriptor names can be specified during calculation
173 of descriptor values using \fBGenerateDescriptors\fR method. The current release of
174 MayaChemTools supports generation of four sets of descriptors: All available
175 descriptors, rule of 5 or 3 descriptors, or a specified set of descriptor names.
176 .PP
177 RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
178 HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
179 HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
180 .PP
181 RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
182 HydrogenBondDonors, HydrogenBondAcceptors, SLogP, \s-1TPSA\s0. RuleOf3 states:
183 MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
184 HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
185 .PP
186 Before calculation of a specified set of descriptors by \fBGenerateDescriptors\fR
187 method, a set of descriptor calculation control parameters for a specific descriptor
188 class name can be set using \fBSetDescriptorClassParameters\fR method. The specified
189 control parameter names and values are simply passed on to specified descriptor
190 class during instantiation of descriptor class object without performing any validation
191 of parameter names and associated values. It's up to the appropriate descriptor class methods
192 to validate these parameters and values. In addition to specified parameter names and
193 values, the parameter hash must also contain descriptor class name as key and
194 value pair with DescriptorClassName as key with class name as value.
195 .SS "\s-1METHODS\s0"
196 .IX Subsection "METHODS"
197 .IP "\fBnew\fR" 4
198 .IX Item "new"
199 .Vb 3
200 \& $NewMolecularDescriptorsGenerator = new MolecularDescriptors::
201 \& MolecularDescriptorsGenerator(
202 \& %NamesAndValues);
203 .Ve
204 .Sp
205 Using specified \fIMolecularDescriptorsGenerator\fR property names and values hash, \fBnew\fR
206 method creates a new object and returns a reference to newly created \fBMolecularDescriptorsGenerator\fR
207 object. By default, the following properties are initialized:
208 .Sp
209 .Vb 6
210 \& Mode = \*(AqAll\*(Aq
211 \& @{$This\->{DescriptorNames}} = ()
212 \& %{$This\->{DescriptorClassParameters}} = ()
213 \& @{$This\->{DescriptorClassNames}} = ()
214 \& %{$This\->{DescriptorClassObjects}} = ()
215 \& @{$This\->{DescriptorValues}} = ()
216 .Ve
217 .Sp
218 Examples:
219 .Sp
220 .Vb 3
221 \& $MolecularDescriptorsGenerator = new MolecularDescriptors::
222 \& MolecularDescriptorsGenerator(
223 \& \*(AqMolecule\*(Aq => $Molecule);
224 \&
225 \& @DescriptorNames = qw(MolecularWeight HydrogenBondDonors Fsp3Carbons)
226 \& $MolecularDescriptorsGenerator = new MolecularDescriptors::
227 \& MolecularDescriptorsGenerator(
228 \& \*(AqMode\*(Aq => \*(AqSpecify\*(Aq,
229 \& \*(AqDescriptorNames\*(Aq => \e@DescriptorNames);
230 \&
231 \& $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
232 \& \*(AqDescriptorClassName\*(Aq => \*(AqWeightAndMassDescriptors\*(Aq,
233 \& \*(AqWeightPrecision\*(Aq => 2,
234 \& \*(AqMassPrecision\*(Aq => 2);
235 \&
236 \& $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
237 \& \*(AqDescriptorClassName\*(Aq => \*(AqHydrogenBondsDescriptors\*(Aq,
238 \& \*(AqHydrogenBondsType\*(Aq => \*(AqHBondsType1\*(Aq);
239 \&
240 \& $MolecularDescriptorsGenerator\->SetMolecule($Molecule);
241 \& $MolecularDescriptorsGenerator\->GenerateDescriptors();
242 \& print "MolecularDescriptorsGenerator: $MolecularDescriptorsGenerator\en";
243 .Ve
244 .IP "\fBGenerateDescriptors\fR" 4
245 .IX Item "GenerateDescriptors"
246 .Vb 1
247 \& $MolecularDescriptorsGenerator\->GenerateDescriptors();
248 .Ve
249 .Sp
250 Calculates descriptor values for specified descriptors and returns \fIMolecularDescriptorsGenerator\fR.
251 .Sp
252 Descriptor class objects are instantiated only once at first invocation. During
253 subsequent calls to \fBGenerateDescriptors\fR method, descriptor values are
254 initialized and \fBGenerateDescriptors\fR method provided by descriptor class is
255 used to calculate descriptor values for specified descriptors.
256 .IP "\fBGetAvailableClassAndDescriptorNames\fR" 4
257 .IX Item "GetAvailableClassAndDescriptorNames"
258 .Vb 5
259 \& %ClassAndDescriptorNames = $MolecularDescriptorsGenerator\->
260 \& GetAvailableClassAndDescriptorNames();
261 \& %ClassAndDescriptorNames = MolecularDescriptors::
262 \& MolecularDescriptorsGenerator::
263 \& GetAvailableClassAndDescriptorNames();
264 .Ve
265 .Sp
266 Returns available descriptors class and descriptors names as a hash containing key
267 and value pairs corresponding to class name and an array of descriptor names
268 available for the class.
269 .IP "\fBGetAvailableClassNameForDescriptorName\fR" 4
270 .IX Item "GetAvailableClassNameForDescriptorName"
271 .Vb 2
272 \& $DescriptorClassName = $MolecularDescriptorsGenerator\->
273 \& GetAvailableClassNameForDescriptorName($DescriptorName);
274 \&
275 \& $DescriptorClassName = MolecularDescriptors::MolecularDescriptorsGenerator::
276 \& GetAvailableClassNameForDescriptorName($DescriptorName);
277 .Ve
278 .Sp
279 Returns available descriptor class name for a descriptor name.
280 .IP "\fBGetAvailableDescriptorClassNames\fR" 4
281 .IX Item "GetAvailableDescriptorClassNames"
282 .Vb 1
283 \& $Return = $MolecularDescriptorsGenerator\->GetAvailableDescriptorClassNames();
284 \&
285 \& @DescriptorClassNames = $MolecularDescriptorsGenerator\->
286 \& GetAvailableDescriptorClassNames();
287 \& @DescriptorClassNames = MolecularDescriptors::
288 \& MolecularDescriptorsGenerator::
289 \& GetAvailableDescriptorClassNames();
290 .Ve
291 .Sp
292 Returns available descriptor class names as an array or number of available descriptor
293 class names in scalar context.
294 .IP "\fBGetAvailableDescriptorNames\fR" 4
295 .IX Item "GetAvailableDescriptorNames"
296 .Vb 5
297 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
298 \& GetAvailableDescriptorNames();
299 \& @DescriptorNames = MolecularDescriptors::
300 \& MolecularDescriptorsGenerator::
301 \& GetAvailableDescriptorNames();
302 .Ve
303 .Sp
304 Returns available descriptor names as an array or number of available descriptor
305 names in scalar context.
306 .IP "\fBGetAvailableDescriptorNamesForDescriptorClass\fR" 4
307 .IX Item "GetAvailableDescriptorNamesForDescriptorClass"
308 .Vb 5
309 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
310 \& GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
311 \& @DescriptorNames = MolecularDescriptors::
312 \& MolecularDescriptorsGenerator::
313 \& GetAvailableDescriptorNamesForDescriptorClass($DescriptorClassName);
314 .Ve
315 .Sp
316 Returns available descriptors names for a descriptor class as an array or number
317 of available descriptor names in scalar context.
318 .IP "\fBGetDescriptorClassParameters\fR" 4
319 .IX Item "GetDescriptorClassParameters"
320 .Vb 5
321 \& $DescriptorClassParametersRef = $MolecularDescriptorsGenerator\->
322 \& GetDescriptorClassParameters();
323 \& $DescriptorClassParametersRef = MolecularDescriptors::
324 \& MolecularDescriptorsGenerator::
325 \& GetDescriptorClassParameters();
326 .Ve
327 .Sp
328 Returns descriptor name parameters as a reference to hash of hashes with hash
329 keys corresponding to class name and class parameter name with hash value
330 as class parameter value.
331 .IP "\fBGetDescriptorNames\fR" 4
332 .IX Item "GetDescriptorNames"
333 .Vb 3
334 \& @DescriptorNames = $MolecularDescriptorsGenerator\->GetDescriptorNames();
335 \& @DescriptorNames = MolecularDescriptors::MolecularDescriptorsGenerator::
336 \& GetDescriptorNames();
337 .Ve
338 .Sp
339 Returns all available descriptor names as an array or number of available descriptors
340 in scalar context.
341 .IP "\fBGetDescriptorNamesAndValues\fR" 4
342 .IX Item "GetDescriptorNamesAndValues"
343 .Vb 2
344 \& %NamesAndValues = $MolecularDescriptorsGenerator\->
345 \& GetDescriptorNamesAndValues();
346 .Ve
347 .Sp
348 Returns calculated molecular descriptor names and values as a hash with descriptor
349 names and values as hash key and value pairs.
350 .IP "\fBGetDescriptorValueByName\fR" 4
351 .IX Item "GetDescriptorValueByName"
352 .Vb 2
353 \& $Value = $MolecularDescriptorsGenerator\->
354 \& GetDescriptorValueByName($Name);
355 .Ve
356 .Sp
357 Returns calculated descriptor values for a specified descriptor name.
358 .IP "\fBGetDescriptorValues\fR" 4
359 .IX Item "GetDescriptorValues"
360 .Vb 1
361 \& @DescriptorValues = $MolecularDescriptorsGenerator\->GetDescriptorValues();
362 .Ve
363 .Sp
364 Returns all calculated descriptor values as an array corresponding to specified
365 descriptor names.
366 .IP "\fBGetRuleOf3DescriptorNames\fR" 4
367 .IX Item "GetRuleOf3DescriptorNames"
368 .Vb 5
369 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
370 \& GetRuleOf3DescriptorNames();
371 \& @DescriptorNames = MolecularDescriptors::
372 \& MolecularDescriptorsGenerator::
373 \& GetRuleOf3DescriptorNames();
374 .Ve
375 .Sp
376 Returns rule of 3 descriptor names as an array or number of rule of 3 descriptors in scalar
377 context.
378 .Sp
379 RuleOf3 [ Ref 92 ] descriptor names are: MolecularWeight, RotatableBonds,
380 HydrogenBondDonors, HydrogenBondAcceptors, SLogP, \s-1TPSA\s0. RuleOf3 states:
381 MolecularWeight <= 300, RotatableBonds <= 3, HydrogenBondDonors <= 3,
382 HydrogenBondAcceptors <= 3, logP <= 3, and \s-1TPSA\s0 <= 60.
383 .IP "\fBGetRuleOf5DescriptorNames\fR" 4
384 .IX Item "GetRuleOf5DescriptorNames"
385 .Vb 4
386 \& @DescriptorNames = $MolecularDescriptorsGenerator\->
387 \& GetRuleOf5DescriptorNames();
388 \& @DescriptorNames = $MolecularDescriptorsGenerator::
389 \& GetRuleOf5DescriptorNames();
390 .Ve
391 .Sp
392 Returns rule of 5 descriptor names as an array or number of rule of 4 descriptors in scalar
393 context.
394 .Sp
395 RuleOf5 [ Ref 91 ] descriptor names are: MolecularWeight, HydrogenBondDonors,
396 HydrogenBondAcceptors, SLogP. RuleOf5 states: MolecularWeight <= 500,
397 HydrogenBondDonors <= 5, HydrogenBondAcceptors <= 10, and logP <= 5.
398 .IP "\fBIsDescriptorClassNameAvailable\fR" 4
399 .IX Item "IsDescriptorClassNameAvailable"
400 .Vb 5
401 \& $Status = $MolecularDescriptorsGenerator\->
402 \& IsDescriptorClassNameAvailable($ClassName);
403 \& $Status = MolecularDescriptors::
404 \& MolecularDescriptorsGenerator::
405 \& IsDescriptorClassNameAvailable($ClassName);
406 .Ve
407 .Sp
408 Returns 1 or 0 based on whether specified descriptor class name is available.
409 .IP "\fBIsDescriptorNameAvailable\fR" 4
410 .IX Item "IsDescriptorNameAvailable"
411 .Vb 5
412 \& $Status = $MolecularDescriptorsGenerator\->
413 \& IsDescriptorNameAvailable($DescriptorName);
414 \& $Status = MolecularDescriptors::
415 \& MolecularDescriptorsGenerator::
416 \& IsDescriptorNameAvailable($DescriptorName);
417 .Ve
418 .Sp
419 Returns 1 or 0 based on whether specified descriptor name is available.
420 .IP "\fBIsDescriptorsGenerationSuccessful\fR" 4
421 .IX Item "IsDescriptorsGenerationSuccessful"
422 .Vb 2
423 \& $Status = $MolecularDescriptorsGenerator\->
424 \& IsDescriptorsGenerationSuccessful();
425 .Ve
426 .Sp
427 Returns 1 or 0 based on whether descriptors generation is successful.
428 .IP "\fBSetDescriptorClassParameters\fR" 4
429 .IX Item "SetDescriptorClassParameters"
430 .Vb 2
431 \& $MolecularDescriptorsGenerator\->SetDescriptorClassParameters(
432 \& %NamesAndValues);
433 .Ve
434 .Sp
435 Sets descriptor calculation control parameters for a specified descriptor class name
436 and returns \fIMolecularDescriptorsGenerator\fR.
437 .Sp
438 The specified parameter names and values are simply passed on to specified descriptor
439 class during instantiation of descriptor class object without any performing any validation
440 of parameter names and associated values. It's up to the appropriate descriptor class methods
441 to validate these parameters and values.
442 .Sp
443 In addition to specified parameter names and values, the parameter hash must also contain
444 descriptor class name as key and value pair with DescriptorClassName as key with class
445 name as value.
446 .IP "\fBSetDescriptorNames\fR" 4
447 .IX Item "SetDescriptorNames"
448 .Vb 2
449 \& $MolecularDescriptorsGenerator\->SetDescriptorNames(@Names);
450 \& $MolecularDescriptorsGenerator\->SetDescriptorNames(\e@Names);
451 .Ve
452 .Sp
453 Sets descriptor names to use for generating descriptor values using an array
454 or reference to an array and returns \fIMolecularDescriptorsGenerator\fR.
455 .IP "\fBSetMode\fR" 4
456 .IX Item "SetMode"
457 .Vb 1
458 \& $MolecularDescriptorsGenerator\->SetMode($Mode);
459 .Ve
460 .Sp
461 Sets descriptors generation mode and returns \fIMolecularDescriptorsGenerator\fR.
462 Possible \fIMode\fR values: \fIAll, RuleOf5, RuleOf3, Specify\fR.
463 .IP "\fBSetMolecule\fR" 4
464 .IX Item "SetMolecule"
465 .Vb 1
466 \& $MolecularDescriptorsGenerator\->SetMolecule($Molecule);
467 .Ve
468 .Sp
469 Sets molecule to use during calculation of molecular descriptors and returns
470 \&\fIMolecularDescriptorsGenerator\fR.
471 .IP "\fBStringifyMolecularDescriptorsGenerator\fR" 4
472 .IX Item "StringifyMolecularDescriptorsGenerator"
473 .Vb 1
474 \& $String = $MolecularDescriptorsGenerator\->StringifyMolecularDescriptorsGenerator();
475 .Ve
476 .Sp
477 Returns a string containing information about \fIMolecularDescriptorsGenerator\fR object.
478 .SH "AUTHOR"
479 .IX Header "AUTHOR"
480 Manish Sud <msud@san.rr.com>
481 .SH "SEE ALSO"
482 .IX Header "SEE ALSO"
483 MolecularDescriptors.pm
484 .SH "COPYRIGHT"
485 .IX Header "COPYRIGHT"
486 Copyright (C) 2015 Manish Sud. All rights reserved.
487 .PP
488 This file is part of MayaChemTools.
489 .PP
490 MayaChemTools is free software; you can redistribute it and/or modify it under
491 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
492 Software Foundation; either version 3 of the License, or (at your option)
493 any later version.