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comparison mayachemtools/docs/modules/man3/AtomNeighborhoodsFingerprints.3 @ 0:73ae111cf86f draft
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date | Wed, 20 Jan 2016 11:55:01 -0500 |
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124 .\" ======================================================================== | |
125 .\" | |
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. |