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1 NAME
2 MolecularComplexityDescriptors
3
4 SYNOPSIS
5 use MolecularDescriptors::MolecularComplexityDescriptors;
6
7 use MolecularDescriptors::MolecularComplexityDescriptors qw(:all);
8
9 DESCRIPTION
10 MolecularComplexityDescriptors class provides the following methods:
11
12 new, GenerateDescriptors, GetDescriptorNames,
13 GetMolecularComplexityTypeAbbreviation, MACCSKeysSize,
14 SetAtomIdentifierType, SetAtomicInvariantsToUse, SetDistanceBinSize,
15 SetFunctionalClassesToUse, SetMaxDistance, SetMaxPathLength,
16 SetMinDistance, SetMinPathLength, SetMolecularComplexityType,
17 SetNeighborhoodRadius, SetNormalizationMethodology,
18 StringifyMolecularComplexityDescriptors
19
20 MolecularComplexityDescriptors is derived from MolecularDescriptors
21 class which in turn is derived from ObjectProperty base class that
22 provides methods not explicitly defined in
23 MolecularComplexityDescriptors, MolecularDescriptors or ObjectProperty
24 classes using Perl's AUTOLOAD functionality. These methods are generated
25 on-the-fly for a specified object property:
26
27 Set<PropertyName>(<PropertyValue>);
28 $PropertyValue = Get<PropertyName>();
29 Delete<PropertyName>();
30
31 The current release of MayaChemTools supports calculation of molecular
32 complexity using *MolecularComplexityType* parameter corresponding to
33 number of bits-set or unique keys [ Ref 117-119 ] in molecular
34 fingerprints. The valid values for *MolecularComplexityType* are:
35
36 AtomTypesFingerprints
37 ExtendedConnectivityFingerprints
38 MACCSKeys
39 PathLengthFingerprints
40 TopologicalAtomPairsFingerprints
41 TopologicalAtomTripletsFingerprints
42 TopologicalAtomTorsionsFingerprints
43 TopologicalPharmacophoreAtomPairsFingerprints
44 TopologicalPharmacophoreAtomTripletsFingerprints
45
46 Default value for *MolecularComplexityType*: *MACCSKeys*.
47
48 *AtomIdentifierType* parameter name corresponds to atom types used
49 during generation of fingerprints. The valid values for
50 *AtomIdentifierType* are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
51 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
52 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
53 *AtomicInvariantsAtomTypes* is not supported for following values of
54 *MolecularComplexityType*: *MACCSKeys,
55 TopologicalPharmacophoreAtomPairsFingerprints,
56 TopologicalPharmacophoreAtomTripletsFingerprints*.
57 *FunctionalClassAtomTypes* is the only valid value of
58 *AtomIdentifierType* for topological pharmacophore fingerprints.
59
60 Default value for *AtomIdentifierType*: *AtomicInvariantsAtomTypes* for
61 all fingerprints; *FunctionalClassAtomTypes* for topological
62 pharmacophore fingerprints.
63
64 *AtomicInvariantsToUse* parameter name and values are used during
65 *AtomicInvariantsAtomTypes* value of parameter *AtomIdentifierType*.
66 It's a list of space separated valid atomic invariant atom types.
67
68 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB, TB,
69 H, Ar, RA, FC, MN, SM*. Default value for *AtomicInvariantsToUse*
70 parameter are set differently for different fingerprints using
71 *MolecularComplexityType* parameter as shown below:
72
73 MolecularComplexityType AtomicInvariantsToUse
74
75 AtomTypesFingerprints AS X BO H FC
76 TopologicalAtomPairsFingerprints AS X BO H FC
77 TopologicalAtomTripletsFingerprints AS X BO H FC
78 TopologicalAtomTorsionsFingerprints AS X BO H FC
79
80 ExtendedConnectivityFingerprints AS X BO H FC MN
81 PathLengthFingerprints AS
82
83 *FunctionalClassesToUse* parameter name and values are used during
84 *FunctionalClassAtomTypes* value of parameter *AtomIdentifierType*. It's
85 a list of space separated valid atomic invariant atom types.
86
87 Possible values for atom functional classes are: *Ar, CA, H, HBA, HBD,
88 Hal, NI, PI, RA*.
89
90 Default value for *FunctionalClassesToUse* parameter is set to:
91
92 HBD HBA PI NI Ar Hal
93
94 for all fingerprints except for the following two
95 *MolecularComplexityType* fingerints:
96
97 MolecularComplexityType FunctionalClassesToUse
98
99 TopologicalPharmacophoreAtomPairsFingerprints HBD HBA P, NI H
100 TopologicalPharmacophoreAtomTripletsFingerprints HBD HBA PI NI H Ar
101
102 *MACCSKeysSize* parameter name is only used during *MACCSKeys* value of
103 *MolecularComplexityType* and corresponds to size of MACCS key set.
104 Possible values: *166 or 322*. Default value: *166*.
105
106 *NeighborhoodRadius* parameter name is only used during
107 *ExtendedConnectivityFingerprints* value of *MolecularComplexityType*
108 and corresponds to atomic neighborhoods radius for generating extended
109 connectivity fingerprints. Possible values: positive integer. Default
110 value: *2*.
111
112 *MinPathLength* and *MaxPathLength* parameters are only used during
113 *PathLengthFingerprints* value of *MolecularComplexityType* and
114 correspond to minimum and maximum path lengths to use for generating
115 path length fingerprints. Possible values: positive integers. Default
116 value: *MinPathLength - 1*; *MaxPathLength - 8*.
117
118 *UseBondSymbols* parameter is only used during *PathLengthFingerprints*
119 value of *MolecularComplexityType* and indicates whether bond symbols
120 are included in atom path strings used to generate path length
121 fingerprints. Possible value: *Yes or No*. Default value: *Yes*.
122
123 *MinDistance* and *MaxDistance* parameters are only used during
124 *TopologicalAtomPairsFingerprints* and
125 *TopologicalAtomTripletsFingerprints* values of
126 *MolecularComplexityType* and correspond to minimum and maximum bond
127 distance between atom pairs during topological pharmacophore
128 fingerprints. Possible values: positive integers. Default value:
129 *MinDistance - 1*; *MaxDistance - 10*.
130
131 *UseTriangleInequality* parameter is used during these values for
132 *MolecularComplexityType*: *TopologicalAtomTripletsFingerprints* and
133 *TopologicalPharmacophoreAtomTripletsFingerprints*. Possible values:
134 *Yes or No*. It determines wheter to apply triangle inequality to
135 distance triplets. Default value: *TopologicalAtomTripletsFingerprints -
136 No*; *TopologicalPharmacophoreAtomTripletsFingerprints - Yes*.
137
138 *DistanceBinSize* parameter is used during
139 *TopologicalPharmacophoreAtomTripletsFingerprints* value of
140 *MolecularComplexityType* and corresponds to distance bin size used for
141 binning distances during generation of topological pharmacophore atom
142 triplets fingerprints. Possible value: positive integer. Default value:
143 *2*.
144
145 *NormalizationMethodology* is only used for these values for
146 *MolecularComplexityType*: *ExtendedConnectivityFingerprints*,
147 *TopologicalPharmacophoreAtomPairsFingerprints* and
148 *TopologicalPharmacophoreAtomTripletsFingerprints*. It corresponds to
149 normalization methodology to use for scaling the number of bits-set or
150 unique keys during generation of fingerprints. Possible values during
151 *ExtendedConnectivityFingerprints*: *None or ByHeavyAtomsCount*; Default
152 value: *None*. Possible values during topological pharmacophore atom
153 pairs and triplets fingerprints: *None or ByPossibleKeysCount*; Default
154 value: *None*. *ByPossibleKeysCount* corresponds to total number of
155 possible topological pharmacophore atom pairs or triplets in a molecule.
156
157 METHODS
158 new
159 $NewMolecularComplexityDescriptors = new MolecularDescriptors::
160 MolecularComplexityDescriptors(
161 %NamesAndValues);
162
163 Using specified *MolecularComplexityDescriptors* property names and
164 values hash, new method creates a new object and returns a reference
165 to newly created MolecularComplexityDescriptors object. By default,
166 the following properties are initialized:
167
168 Molecule = ''
169 Type = 'MolecularComplexity'
170 MolecularComplexityType = 'MACCSKeys'
171 AtomIdentifierType = ''
172 MACCSKeysSize = 166
173 NeighborhoodRadius = 2
174 MinPathLength = 1
175 MaxPathLength = 8
176 UseBondSymbols = 1
177 MinDistance = 1
178 MaxDistance = 10
179 UseTriangleInequality = ''
180 DistanceBinSize = 2
181 NormalizationMethodology = 'None'
182 @DescriptorNames = ('MolecularComplexity')
183 @DescriptorValues = ('None')
184
185 Examples:
186
187 $MolecularComplexityDescriptors = new MolecularDescriptors::
188 MolecularComplexityDescriptors(
189 'Molecule' => $Molecule);
190
191 $MolecularComplexityDescriptors = new MolecularDescriptors::
192 MolecularComplexityDescriptors();
193
194 $MolecularComplexityDescriptors->SetMolecule($Molecule);
195 $MolecularComplexityDescriptors->GenerateDescriptors();
196 print "MolecularComplexityDescriptors: $MolecularComplexityDescriptors\n";
197
198 GenerateDescriptors
199 $MolecularComplexityDescriptors->GenerateDescriptors();
200
201 Calculates MolecularComplexity value for a molecule and returns
202 *MolecularComplexityDescriptors*.
203
204 GetDescriptorNames
205 @DescriptorNames = $MolecularComplexityDescriptors->GetDescriptorNames();
206 @DescriptorNames = MolecularDescriptors::MolecularComplexityDescriptors::
207 GetDescriptorNames();
208
209 Returns all available descriptor names as an array.
210
211 GetMolecularComplexityTypeAbbreviation
212 $Abbrev = $MolecularComplexityDescriptors->
213 GetMolecularComplexityTypeAbbreviation();
214 $Abbrev = MolecularDescriptors::MolecularComplexityDescriptors::
215 GetMolecularComplexityTypeAbbreviation($ComplexityType);
216
217 Returns abbreviation for a specified molecular complexity type or
218 corresponding to *MolecularComplexityDescriptors* object.
219
220 SetMACCSKeysSize
221 $MolecularComplexityDescriptors->MACCSKeysSize($Size);
222
223 Sets MACCS keys size and returns *MolecularComplexityDescriptors*.
224
225 SetAtomIdentifierType
226 $MolecularComplexityDescriptors->SetAtomIdentifierType($IdentifierType);
227
228 Sets atom *IdentifierType* to use during fingerprints generation
229 corresponding to *MolecularComplexityType* and returns
230 *MolecularComplexityDescriptors*.
231
232 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
233 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
234 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
235
236 SetAtomicInvariantsToUse
237 $MolecularComplexityDescriptors->SetAtomicInvariantsToUse($ValuesRef);
238 $MolecularComplexityDescriptors->SetAtomicInvariantsToUse(@Values);
239
240 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
241 value of *AtomIdentifierType* for fingerprints generation and
242 returns *MolecularComplexityDescriptors*.
243
244 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
245 TB, H, Ar, RA, FC, MN, SM*. Default value [ Ref 24 ]:
246 *AS,X,BO,H,FC,MN*.
247
248 The atomic invariants abbreviations correspond to:
249
250 AS = Atom symbol corresponding to element symbol
251
252 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
253 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
254 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
255 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
256 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
257 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
258 H<n> = Number of implicit and explicit hydrogens for atom
259 Ar = Aromatic annotation indicating whether atom is aromatic
260 RA = Ring atom annotation indicating whether atom is a ring
261 FC<+n/-n> = Formal charge assigned to atom
262 MN<n> = Mass number indicating isotope other than most abundant isotope
263 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
264 3 (triplet)
265
266 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
267 corresponds to:
268
269 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
270
271 Except for AS which is a required atomic invariant in atom types,
272 all other atomic invariants are optional. Atom type specification
273 doesn't include atomic invariants with zero or undefined values.
274
275 In addition to usage of abbreviations for specifying atomic
276 invariants, the following descriptive words are also allowed:
277
278 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
279 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
280 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
281 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
282 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
283 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
284 H : NumOfImplicitAndExplicitHydrogens
285 Ar : Aromatic
286 RA : RingAtom
287 FC : FormalCharge
288 MN : MassNumber
289 SM : SpinMultiplicity
290
291 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
292 atomic invariant atom types.
293
294 SetDistanceBinSize
295 $MolecularComplexityDescriptors->SetDistanceBinSize($BinSize);
296
297 Sets distance bin size used to bin distances between atom pairs in
298 atom triplets for topological pharmacophore atom triplets
299 fingerprints generation and returns
300 *MolecularComplexityDescriptors*.
301
302 SetFunctionalClassesToUse
303 $MolecularComplexityDescriptors->SetFunctionalClassesToUse($ValuesRef);
304 $MolecularComplexityDescriptors->SetFunctionalClassesToUse(@Values);
305
306 Sets functional classes invariants to use during
307 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
308 fingerprints generation and returns
309 *MolecularComplexityDescriptors*.
310
311 Possible values for atom functional classes are: *Ar, CA, H, HBA,
312 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
313 *HBD,HBA,PI,NI,Ar,Hal*.
314
315 The functional class abbreviations correspond to:
316
317 HBD: HydrogenBondDonor
318 HBA: HydrogenBondAcceptor
319 PI : PositivelyIonizable
320 NI : NegativelyIonizable
321 Ar : Aromatic
322 Hal : Halogen
323 H : Hydrophobic
324 RA : RingAtom
325 CA : ChainAtom
326
327 Functional class atom type specification for an atom corresponds to:
328
329 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
330
331 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
332 functional class atom types. It uses following definitions [ Ref
333 60-61, Ref 65-66 ]:
334
335 HydrogenBondDonor: NH, NH2, OH
336 HydrogenBondAcceptor: N[!H], O
337 PositivelyIonizable: +, NH2
338 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
339
340 SetMaxDistance
341 $MolecularComplexityDescriptors->SetMaxDistance($MaxDistance);
342
343 Sets maximum distance to use during topological atom pairs and
344 triplets fingerprints generation and returns
345 *MolecularComplexityDescriptors*.
346
347 SetMaxPathLength
348 $MolecularComplexityDescriptors->SetMaxPathLength($Length);
349
350 Sets maximum path length to use during path length fingerprints
351 generation and returns *MolecularComplexityDescriptors*.
352
353 SetMinDistance
354 $MolecularComplexityDescriptors->SetMinDistance($MinDistance);
355
356 Sets minimum distance to use during topological atom pairs and
357 triplets fingerprints generation and returns
358 *MolecularComplexityDescriptors*.
359
360 SetMinPathLength
361 $MolecularComplexityDescriptors->SetMinPathLength($MinPathLength);
362
363 Sets minimum path length to use during path length fingerprints
364 generation and returns *MolecularComplexityDescriptors*.
365
366 SetMolecularComplexityType
367 $MolecularComplexityDescriptors->SetMolecularComplexityType($ComplexityType);
368
369 Sets molecular complexity type to use for calculating its value and
370 returns *MolecularComplexityDescriptors*.
371
372 SetNeighborhoodRadius
373 $MolecularComplexityDescriptors->SetNeighborhoodRadius($Radius);
374
375 Sets neighborhood radius to use during extended connectivity
376 fingerprints generation and returns
377 *MolecularComplexityDescriptors*.
378
379 SetNormalizationMethodology
380 $MolecularComplexityDescriptors->SetNormalizationMethodology($Methodology);
381
382 Sets normalization methodology to use during calculation of
383 molecular complexity corresponding to extended connectivity,
384 topological pharmacophore atom pairs and tripletes fingerprints
385 returns *MolecularComplexityDescriptors*.
386
387 StringifyMolecularComplexityDescriptors
388 $String = $MolecularComplexityDescriptors->
389 StringifyMolecularComplexityDescriptors();
390
391 Returns a string containing information about
392 *MolecularComplexityDescriptors* object.
393
394 AUTHOR
395 Manish Sud <msud@san.rr.com>
396
397 SEE ALSO
398 MolecularDescriptors.pm, MolecularDescriptorsGenerator.pm
399
400 COPYRIGHT
401 Copyright (C) 2015 Manish Sud. All rights reserved.
402
403 This file is part of MayaChemTools.
404
405 MayaChemTools is free software; you can redistribute it and/or modify it
406 under the terms of the GNU Lesser General Public License as published by
407 the Free Software Foundation; either version 3 of the License, or (at
408 your option) any later version.
409