comparison mayachemtools/docs/modules/man3/AtomNeighborhoodsFingerprints.3 @ 0:73ae111cf86f draft

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126 .IX Title "ATOMNEIGHBORHOODSFINGERPRINTS 1"
127 .TH ATOMNEIGHBORHOODSFINGERPRINTS 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 AtomNeighborhoodsFingerprints
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 use Fingerprints::AtomNeighborhoodsFingerprints;
137 .PP
138 use Fingerprints::AtomNeighborhoodsFingerprints qw(:all);
139 .SH "DESCRIPTION"
140 .IX Header "DESCRIPTION"
141 \&\fBAtomNeighborhoodsFingerprints\fR [ Ref 53\-56, Ref 73 ] class provides the following methods:
142 .PP
143 new, GenerateFingerprints, GetDescription, SetAtomIdentifierType,
144 SetAtomicInvariantsToUse, SetFunctionalClassesToUse, SetMaxNeighborhoodRadius,
145 SetMinNeighborhoodRadius, StringifyAtomNeighborhoodsFingerprints
146 .PP
147 \&\fBAtomNeighborhoodsFingerprints\fR is derived from \fBFingerprints\fR class which in turn
148 is derived from \fBObjectProperty\fR base class that provides methods not explicitly defined
149 in \fBAtomNeighborhoodsFingerprints\fR, \fBFingerprints\fR or \fBObjectProperty\fR classes using Perl's
150 \&\s-1AUTOLOAD\s0 functionality. These methods are generated on-the-fly for a specified object property:
151 .PP
152 .Vb 3
153 \& Set<PropertyName>(<PropertyValue>);
154 \& $PropertyValue = Get<PropertyName>();
155 \& Delete<PropertyName>();
156 .Ve
157 .PP
158 The current release of MayaChemTools supports generation of \fBAtomNeighborhoodsFingerprints\fR
159 corresponding to following \fBAtomIdentifierTypes\fR:
160 .PP
161 .Vb 3
162 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
163 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
164 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
165 .Ve
166 .PP
167 Based on the values specified for \fBAtomIdentifierType\fR along with other specified
168 sucb as \fBAtomicInvariantsToUse\fR and \fBFunctionalClassesToUse\fR, initial atom types are
169 assigned to all non-hydrogen atoms in a molecule. Using atom neighborhoods
170 around each non-hydrogen central atom corresponding to radii between specified values
171 \&\fBMinNeighborhoodRadius\fR and \fBMaxNeighborhoodRadius\fR, unique atom types at each radii
172 level are counted and an atom neighborhood identifier is generated.
173 .PP
174 The format of an atom neighborhood identifier around a central non-hydrogen atom at a
175 specific radius is:
176 .PP
177 .Vb 1
178 \& NR<n>\-<AtomType>\-ATC<n>
179 \&
180 \& NR: Neighborhood radius
181 \& AtomType: Assigned atom type
182 \& ATC: Atom type count
183 .Ve
184 .PP
185 The atom neighborhood identifier for non-hydrogen central atom corresponding to all specified radii
186 is generated by concatenating neighborhood identifiers at each radii by colon as a delimiter:
187 .PP
188 .Vb 1
189 \& NR<n>\-<AtomType>\-ATC<n>:NR<n>\-<AtomType>\-ATC<n>:...
190 .Ve
191 .PP
192 The atom neighborhood identifiers for all non-hydrogen central atoms at all specified radii are
193 concatenated using space as a delimiter and constitute atom neighborhood fingerprint of the molecule.
194 .PP
195 The current release of MayaChemTools generates the following types of atom neighborhoods
196 fingerprints vector strings:
197 .PP
198 .Vb 6
199 \& FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
200 \& us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-C.X1.BO1.H3\-AT
201 \& C1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-ATC1 NR0\-C.X
202 \& 1.BO1.H3\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2\-C.X1.BO1.H3\-ATC1:NR2\-C.X3.BO4\-A
203 \& TC1 NR0\-C.X2.BO2.H2\-ATC1:NR1\-C.X2.BO2.H2\-ATC1:NR1\-C.X3.BO3.H1\-ATC1:NR2
204 \& \-C.X2.BO2.H2\-ATC1:NR2\-N.X3.BO3\-ATC1:NR2\-O.X1.BO1.H1\-ATC1 NR0\-C.X2.B...
205 \&
206 \& FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
207 \& adius2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:
208 \& NR1\-O_2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N
209 \& _3\-ATC1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-AT
210 \& C1:NR2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR
211 \& 1\-N_R\-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-...
212 \&
213 \& FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
214 \& ius2;41;AlphaNumericalValues;ValuesString;NR0\-aaCH\-ATC1:NR1\-aaCH\-ATC1:
215 \& NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-aaCH\-ATC1:NR
216 \& 1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC1:NR2\-sF\-ATC1 NR0\-
217 \& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 NR0\-
218 \& aaCH\-ATC1:NR1\-aaCH\-ATC1:NR1\-aasC\-ATC1:NR2\-aaCH\-ATC1:NR2\-aasC\-ATC2 N...
219 \&
220 \& FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
221 \& s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0\-Ar\-ATC1:NR1\-Ar\-
222 \& ATC1:NR1\-Ar.HBA\-ATC1:NR1\-None\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC4 NR0\-Ar\-AT
223 \& C1:NR1\-Ar\-ATC2:NR1\-Ar.HBA\-ATC1:NR2\-Ar\-ATC5:NR2\-None\-ATC1 NR0\-Ar\-ATC1:N
224 \& R1\-Ar\-ATC2:NR1\-HBD\-ATC1:NR2\-Ar\-ATC2:NR2\-None\-ATC1 NR0\-Ar\-ATC1:NR1\-Ar\-A
225 \& TC2:NR1\-Hal\-ATC1:NR2\-Ar\-ATC2 NR0\-Ar\-ATC1:NR1\-Ar\-ATC2:NR1\-None\-ATC1:...
226 \&
227 \& FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
228 \& ius2;41;AlphaNumericalValues;ValuesString;NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR
229 \& 1\-CB\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C5B\-ATC1:NR2\-CB\-ATC3:NR2\-CR\-ATC
230 \& 1 NR0\-C5A\-ATC1:NR1\-C5B\-ATC1:NR1\-CR\-ATC1:NR1\-N5\-ATC1:NR2\-C5A\-ATC1:NR2\-C
231 \& 5B\-ATC1:NR2\-C=ON\-ATC1:NR2\-CR\-ATC3 NR0\-C5B\-ATC1:NR1\-C5A\-ATC1:NR1\-C5B\-AT
232 \& C1:NR1\-C=ON\-ATC1:NR2\-C5A\-ATC1:NR2\-CB\-ATC1:NR2\-CR\-ATC1:NR2\-N5\-ATC1:N...
233 \&
234 \& FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
235 \& us2;41;AlphaNumericalValues;ValuesString;NR0\-C1\-ATC1:NR1\-C10\-ATC1:NR1\-
236 \& CS\-ATC1:NR2\-C1\-ATC1:NR2\-N11\-ATC1:NR2\-O2\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:
237 \& NR2\-C1\-ATC1:NR2\-C21\-ATC1 NR0\-C1\-ATC1:NR1\-C11\-ATC1:NR2\-C1\-ATC1:NR2\-C21\-
238 \& ATC1 NR0\-C1\-ATC1:NR1\-C5\-ATC1:NR1\-CS\-ATC1:NR2\-C1\-ATC1:NR2\-O2\-ATC2:NR2\-O
239 \& 9\-ATC1 NR0\-C1\-ATC1:NR1\-CS\-ATC2:NR2\-C1\-ATC2:NR2\-O2\-ATC2 NR0\-C10\-ATC1...
240 \&
241 \& FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
242 \& us2;41;AlphaNumericalValues;ValuesString;NR0\-C.2\-ATC1:NR1\-C.3\-ATC1:NR1
243 \& \-O.co2\-ATC2:NR2\-C.3\-ATC1 NR0\-C.2\-ATC1:NR1\-C.ar\-ATC1:NR1\-N.am\-ATC1:NR1\-
244 \& O.2\-ATC1:NR2\-C.ar\-ATC3 NR0\-C.3\-ATC1:NR1\-C.2\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-
245 \& ATC1:NR2\-O.3\-ATC1:NR2\-O.co2\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR1\-N.ar\-AT
246 \& C1:NR2\-C.3\-ATC1:NR2\-C.ar\-ATC2 NR0\-C.3\-ATC1:NR1\-C.3\-ATC1:NR2\-C.3\-ATC...
247 \&
248 \& FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
249 \& s2;41;AlphaNumericalValues;ValuesString;NR0\-N21\-ATC1:NR1\-None\-ATC3:NR2
250 \& \-None\-ATC5 NR0\-N7\-ATC1:NR1\-None\-ATC2:NR2\-None\-ATC3:NR2\-O3\-ATC1 NR0\-Non
251 \& e\-ATC1:NR1\-N21\-ATC1:NR1\-None\-ATC1:NR2\-None\-ATC3 NR0\-None\-ATC1:NR1\-N21\-
252 \& ATC1:NR1\-None\-ATC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N21\-ATC1:NR1\-None\-A
253 \& TC2:NR2\-None\-ATC6 NR0\-None\-ATC1:NR1\-N7\-ATC1:NR1\-None\-ATC1:NR1\-O3\-AT...
254 \&
255 \& FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
256 \& 2;41;AlphaNumericalValues;ValuesString;NR0\-C_2\-ATC1:NR1\-C_3\-ATC1:NR1\-O
257 \& _2\-ATC1:NR1\-O_3\-ATC1:NR2\-C_3\-ATC1 NR0\-C_2\-ATC1:NR1\-C_R\-ATC1:NR1\-N_3\-AT
258 \& C1:NR1\-O_2\-ATC1:NR2\-C_R\-ATC3 NR0\-C_3\-ATC1:NR1\-C_2\-ATC1:NR1\-C_3\-ATC1:NR
259 \& 2\-C_3\-ATC1:NR2\-O_2\-ATC1:NR2\-O_3\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR1\-N_R
260 \& \-ATC1:NR2\-C_3\-ATC1:NR2\-C_R\-ATC2 NR0\-C_3\-ATC1:NR1\-C_3\-ATC1:NR2\-C_3\-A...
261 .Ve
262 .SS "\s-1METHODS\s0"
263 .IX Subsection "METHODS"
264 .IP "\fBnew\fR" 4
265 .IX Item "new"
266 .Vb 2
267 \& $NewAtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
268 \& %NamesAndValues);
269 .Ve
270 .Sp
271 Using specified \fIAtomNeighborhoodsFingerprints\fR property names and values hash, \fBnew\fR
272 method creates a new object and returns a reference to newly created \fBAtomNeighborhoodsFingerprints\fR
273 object. By default, the following properties are initialized:
274 .Sp
275 .Vb 7
276 \& Molecule = \*(Aq\*(Aq
277 \& Type = \*(AqAtomNeighborhoods\*(Aq
278 \& MinNeighborhoodRadius = 0
279 \& MaxNeighborhoodRadius = 2
280 \& AtomIdentifierType = \*(Aq\*(Aq
281 \& AtomicInvariantsToUse = [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq, \*(AqMN\*(Aq]
282 \& FunctionalClassesToUse = [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq]
283 .Ve
284 .Sp
285 Examples:
286 .Sp
287 .Vb 4
288 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
289 \& \*(AqMolecule\*(Aq => $Molecule,
290 \& \*(AqAtomIdentifierType\*(Aq =>
291 \& "AtomicInvariantsAtomTypes");
292 \&
293 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
294 \& \*(AqMolecule\*(Aq => $Molecule,
295 \& \*(AqMinNeighborhoodRadius\*(Aq => 0,
296 \& \*(AqMaxNeighborhoodRadius\*(Aq => 2,
297 \& \*(AqAtomIdentifierType\*(Aq =>
298 \& \*(AqAtomicInvariantsAtomTypes\*(Aq,
299 \& \*(AqAtomicInvariantsToUse\*(Aq =>
300 \& [\*(AqAS\*(Aq, \*(AqX\*(Aq, \*(AqBO\*(Aq, \*(AqH\*(Aq, \*(AqFC\*(Aq] );
301 \&
302 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
303 \& \*(AqMolecule\*(Aq => $Molecule,
304 \& \*(AqAtomIdentifierType\*(Aq =>
305 \& \*(AqSYBYLAtomTypes\*(Aq);
306 \&
307 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
308 \& \*(AqMolecule\*(Aq => $Molecule,
309 \& \*(AqAtomIdentifierType\*(Aq =>
310 \& \*(AqMMFF94AtomTypes\*(Aq);
311 \&
312 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
313 \& \*(AqMolecule\*(Aq => $Molecule,
314 \& \*(AqAtomIdentifierType\*(Aq =>
315 \& \*(AqAtomicInvariantsAtomTypes\*(Aq);
316 \&
317 \& $AtomNeighborhoodsFingerprints = new AtomNeighborhoodsFingerprints(
318 \& \*(AqMolecule\*(Aq => $Molecule,
319 \& \*(AqMinNeighborhoodRadius\*(Aq => 0,
320 \& \*(AqMaxNeighborhoodRadius\*(Aq => 2,
321 \& \*(AqAtomIdentifierType\*(Aq =>
322 \& \*(AqFunctionalClassAtomTypes\*(Aq,
323 \& \*(AqFunctionalClassesToUse\*(Aq =>
324 \& [\*(AqHBD\*(Aq, \*(AqHBA\*(Aq, \*(AqPI\*(Aq, \*(AqNI\*(Aq, \*(AqAr\*(Aq, \*(AqHal\*(Aq] );
325 \&
326 \& $AtomNeighborhoodsFingerprints\->GenerateFingerprints();
327 \& print "$AtomNeighborhoodsFingerprints\en";
328 .Ve
329 .IP "\fBGenerateFingerprints\fR" 4
330 .IX Item "GenerateFingerprints"
331 .Vb 1
332 \& $AtomNeighborhoodsFingerprints\->GenerateFingerprints();
333 .Ve
334 .Sp
335 Generates atom neighborhood fingerprints and returns \fIAtomNeighborhoodsFingerprints\fR.
336 .IP "\fBGetDescription\fR" 4
337 .IX Item "GetDescription"
338 .Vb 1
339 \& $Description = $AtomNeighborhoodsFingerprints\->GetDescription();
340 .Ve
341 .Sp
342 Returns a string containing description of atom neighborhood fingerprints.
343 .IP "\fBSetAtomIdentifierType\fR" 4
344 .IX Item "SetAtomIdentifierType"
345 .Vb 1
346 \& $AtomNeighborhoodsFingerprints\->SetAtomIdentifierType($IdentifierType);
347 .Ve
348 .Sp
349 Sets atom \fIIdentifierType\fR to use during atom neighborhood fingerprints generation and
350 returns \fIAtomNeighborhoodsFingerprints\fR.
351 .Sp
352 Possible values: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
353 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
354 TPSAAtomTypes, UFFAtomTypes\fR.
355 .IP "\fBSetAtomicInvariantsToUse\fR" 4
356 .IX Item "SetAtomicInvariantsToUse"
357 .Vb 2
358 \& $AtomNeighborhoodsFingerprints\->SetAtomicInvariantsToUse($ValuesRef);
359 \& $AtomNeighborhoodsFingerprints\->SetAtomicInvariantsToUse(@Values);
360 .Ve
361 .Sp
362 Sets atomic invariants to use during \fIAtomicInvariantsAtomTypes\fR value of \fIAtomIdentifierType\fR
363 for atom neighborhood fingerprints generation and returns \fIAtomNeighborhoodsFingerprints\fR.
364 .Sp
365 Possible values for atomic invariants are: \fI\s-1AS\s0, X, \s-1BO\s0, \s-1LBO\s0, \s-1SB\s0, \s-1DB\s0, \s-1TB\s0,
366 H, Ar, \s-1RA\s0, \s-1FC\s0, \s-1MN\s0, \s-1SM\s0\fR. Default value: \fI\s-1AS\s0,X,BO,H,FC\fR.
367 .Sp
368 The atomic invariants abbreviations correspond to:
369 .Sp
370 .Vb 1
371 \& AS = Atom symbol corresponding to element symbol
372 \&
373 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
374 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
375 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
376 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
377 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
378 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
379 \& H<n> = Number of implicit and explicit hydrogens for atom
380 \& Ar = Aromatic annotation indicating whether atom is aromatic
381 \& RA = Ring atom annotation indicating whether atom is a ring
382 \& FC<+n/\-n> = Formal charge assigned to atom
383 \& MN<n> = Mass number indicating isotope other than most abundant isotope
384 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
385 \& 3 (triplet)
386 .Ve
387 .Sp
388 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
389 .Sp
390 .Vb 1
391 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
392 .Ve
393 .Sp
394 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
395 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
396 .Sp
397 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
398 are also allowed:
399 .Sp
400 .Vb 12
401 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
402 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
403 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
404 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
405 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
406 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
407 \& H : NumOfImplicitAndExplicitHydrogens
408 \& Ar : Aromatic
409 \& RA : RingAtom
410 \& FC : FormalCharge
411 \& MN : MassNumber
412 \& SM : SpinMultiplicity
413 .Ve
414 .Sp
415 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
416 atom types.
417 .IP "\fBSetFunctionalClassesToUse\fR" 4
418 .IX Item "SetFunctionalClassesToUse"
419 .Vb 2
420 \& $AtomNeighborhoodsFingerprints\->SetFunctionalClassesToUse($ValuesRef);
421 \& $AtomNeighborhoodsFingerprints\->SetFunctionalClassesToUse(@Values);
422 .Ve
423 .Sp
424 Sets functional classes invariants to use during \fIFunctionalClassAtomTypes\fR value of \fIAtomIdentifierType\fR
425 for atom neighborhoods fingerprints generation and returns \fIAtomNeighborhoodsFingerprints\fR.
426 .Sp
427 Possible values for atom functional classes are: \fIAr, \s-1CA\s0, H, \s-1HBA\s0, \s-1HBD\s0, Hal, \s-1NI\s0, \s-1PI\s0, \s-1RA\s0\fR.
428 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
429 .Sp
430 The functional class abbreviations correspond to:
431 .Sp
432 .Vb 9
433 \& HBD: HydrogenBondDonor
434 \& HBA: HydrogenBondAcceptor
435 \& PI : PositivelyIonizable
436 \& NI : NegativelyIonizable
437 \& Ar : Aromatic
438 \& Hal : Halogen
439 \& H : Hydrophobic
440 \& RA : RingAtom
441 \& CA : ChainAtom
442 \&
443 \& Functional class atom type specification for an atom corresponds to:
444 \&
445 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
446 .Ve
447 .Sp
448 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
449 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
450 .Sp
451 .Vb 4
452 \& HydrogenBondDonor: NH, NH2, OH
453 \& HydrogenBondAcceptor: N[!H], O
454 \& PositivelyIonizable: +, NH2
455 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
456 .Ve
457 .IP "\fBSetMaxNeighborhoodRadius\fR" 4
458 .IX Item "SetMaxNeighborhoodRadius"
459 .Vb 1
460 \& $AtomNeighborhoodsFingerprints\->SetMaxNeighborhoodRadius($Radius);
461 .Ve
462 .Sp
463 Sets maximum neighborhood radius to use during atom neighborhood fingerprints generation and
464 returns \fIAtomNeighborhoodsFingerprints\fR.
465 .IP "\fBSetMinNeighborhoodRadius\fR" 4
466 .IX Item "SetMinNeighborhoodRadius"
467 .Vb 1
468 \& $AtomNeighborhoodsFingerprints\->SetMinNeighborhoodRadius($Radius);
469 .Ve
470 .Sp
471 Sets minimum neighborhood radius to use during atom neighborhood fingerprints generation and
472 returns \fIAtomNeighborhoodsFingerprints\fR.
473 .IP "\fBStringifyAtomNeighborhoodsFingerprints\fR" 4
474 .IX Item "StringifyAtomNeighborhoodsFingerprints"
475 .Vb 1
476 \& $String = $Fingerprints\->StringifyAtomNeighborhoodsFingerprints();
477 .Ve
478 .Sp
479 Returns a string containing information about \fIAtomNeighborhoodsFingerprints\fR object.
480 .SH "AUTHOR"
481 .IX Header "AUTHOR"
482 Manish Sud <msud@san.rr.com>
483 .SH "SEE ALSO"
484 .IX Header "SEE ALSO"
485 Fingerprints.pm, FingerprintsStringUtil.pm, AtomTypesFingerprints.pm, EStateIndiciesFingerprints.pm,
486 ExtendedConnectivityFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
487 TopologicalAtomPairsFingerprints.pm, TopologicalAtomTripletsFingerprints.pm,
488 TopologicalAtomTorsionsFingerprints.pm, TopologicalPharmacophoreAtomPairsFingerprints.pm,
489 TopologicalPharmacophoreAtomTripletsFingerprints.pm
490 .SH "COPYRIGHT"
491 .IX Header "COPYRIGHT"
492 Copyright (C) 2015 Manish Sud. All rights reserved.
493 .PP
494 This file is part of MayaChemTools.
495 .PP
496 MayaChemTools is free software; you can redistribute it and/or modify it under
497 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
498 Software Foundation; either version 3 of the License, or (at your option)
499 any later version.