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124 .\" ========================================================================
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126 .IX Title "TOPOLOGICALATOMTORSIONSFINGERPRINTS 1"
127 .TH TOPOLOGICALATOMTORSIONSFINGERPRINTS 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 TopologicalAtomTorsionsFingerprints.pl \- Generate topological atom torsions fingerprints for SD files
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 TopologicalAtomTorsionsFingerprints.pl SDFile(s)...
137 .PP
138 TopologicalAtomTorsionsFingerprints.pl [\fB\-\-AromaticityModel\fR \fIAromaticityModelType\fR]
139 [\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes\fR]
140 [\fB\-\-AtomicInvariantsToUse\fR \fI\*(L"AtomicInvariant,AtomicInvariant...\*(R"\fR]
141 [\fB\-\-FunctionalClassesToUse\fR \fI\*(L"FunctionalClass1,FunctionalClass2...\*(R"\fR]
142 [\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR] [\fB\-\-CompoundIDLabel\fR \fItext\fR]
143 [\fB\-\-CompoundIDMode\fR] [\fB\-\-DataFields\fR \fI\*(L"FieldLabel1,FieldLabel2,...\*(R"\fR]
144 [\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR] [\fB\-f, \-\-Filter\fR \fIYes | No\fR]
145 [\fB\-\-FingerprintsLabel\fR \fItext\fR] [\fB\-h, \-\-help\fR] [\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR]
146 [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-o, \-\-overwrite\fR]
147 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR] [\fB\-v, \-\-VectorStringFormat\fR]
148 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
149 .SH "DESCRIPTION"
150 .IX Header "DESCRIPTION"
151 Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for \fISDFile(s)\fR and create
152 appropriate \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector strings corresponding to
153 molecular fingerprints.
154 .PP
155 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
156 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
157 can be specified either by \fI*.sdf\fR or the current directory name.
158 .PP
159 The current release of MayaChemTools supports generation of topological atom torsions
160 fingerprints corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
161 .PP
162 .Vb 3
163 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
164 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
165 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
166 .Ve
167 .PP
168 Based on the values specified for \fB\-a, \-\-AtomIdentifierType\fR and \fB\-\-AtomicInvariantsToUse\fR,
169 initial atom types are assigned to all non-hydrogen atoms in a molecule. All unique atom torsions
170 are identified and an atom torsion identifier is generated; the format of atom torsion identifier is:
171 .PP
172 .Vb 1
173 \& <AtomType1>\-<AtomType2>\-<AtomType3>\-<AtomType4>
174 \&
175 \& AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
176 \&
177 \& where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
178 .Ve
179 .PP
180 The atom torsion identifiers for all unique atom torsions corresponding to non-hydrogen atoms constitute
181 topological atom torsions fingerprints of the molecule.
182 .PP
183 Example of \fI\s-1SD\s0\fR file containing topological atom torsions fingerprints string data:
184 .PP
185 .Vb 10
186 \& ... ...
187 \& ... ...
188 \& $$$$
189 \& ... ...
190 \& ... ...
191 \& ... ...
192 \& 41 44 0 0 0 0 0 0 0 0999 V2000
193 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
194 \& ... ...
195 \& 2 3 1 0 0 0 0
196 \& ... ...
197 \& M END
198 \& > <CmpdID>
199 \& Cmpd1
200 \&
201 \& > <TopologicalAtomTorsionsFingerprints>
202 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
203 \& ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-C.
204 \& X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO2.H
205 \& 2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O.X1....;
206 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
207 \&
208 \& $$$$
209 \& ... ...
210 \& ... ...
211 .Ve
212 .PP
213 Example of \fI\s-1FP\s0\fR file containing topological atom torsions fingerprints string data:
214 .PP
215 .Vb 10
216 \& #
217 \& # Package = MayaChemTools 7.4
218 \& # Release Date = Oct 21, 2010
219 \& #
220 \& # TimeStamp = Fri Mar 11 15:17:20 2011
221 \& #
222 \& # FingerprintsStringType = FingerprintsVector
223 \& #
224 \& # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
225 \& # VectorStringFormat = IDsAndValuesString
226 \& # VectorValuesType = NumericalValues
227 \& #
228 \& Cmpd1 33;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-C.X3.BO4...;2 2 1 1 2 2 ...
229 \& Cmpd2 23;C.X1.BO1.H3\-C.X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2...;2 2 1 5 ...
230 \& ... ...
231 \& ... ..
232 .Ve
233 .PP
234 Example of \s-1CSV\s0 \fIText\fR file containing topological atom torsions fingerprints string data:
235 .PP
236 .Vb 8
237 \& "CompoundID","TopologicalAtomTorsionsFingerprints"
238 \& "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
239 \& mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.
240 \& X3.BO4\-C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C
241 \& .X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3....;
242 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
243 \& ... ...
244 \& ... ...
245 .Ve
246 .PP
247 The current release of MayaChemTools generates the following types of topological atom torsions
248 fingerprints vector strings:
249 .PP
250 .Vb 5
251 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
252 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
253 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
254 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
255 \& ;2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
256 \&
257 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
258 \& 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3
259 \& .BO4\-C.X3.BO4 2 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 2 C.X2.BO2.H
260 \& 2\-C.X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.B
261 \& O3.H1\-O.X1.BO1.H1 1 C.X2.BO2.H2\-C.X2.BO2.H2\-N.X3.BO3\-C.X3.BO4 2 C.X2.B
262 \& O2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2\-C.X3.BO3.H1 2 C.X2.BO2.H2\-C.X3.BO3.H1...
263 \&
264 \& FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
265 \& calValues;IDsAndValuesString;C_2\-C_3\-C_3\-C_3 C_2\-C_3\-C_3\-O_3 C_2\-C_R\-C
266 \& _R\-C_3 C_2\-C_R\-C_R\-C_R C_2\-C_R\-C_R\-N_R C_2\-N_3\-C_R\-C_R C_3\-C_3\-C_2\-O_2
267 \& C_3\-C_3\-C_2\-O_3 C_3\-C_3\-C_3\-C_3 C_3\-C_3\-C_3\-N_R C_3\-C_3\-C_3\-O_3 C_...;
268 \& 1 1 1 2 1 2 1 1 3 1 3 2 2 2 1 1 1 3 1 2 2 32 2 2 5 3 1
269 \&
270 \& FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
271 \& lValues;IDsAndValuesString;aaCH\-aaCH\-aaCH\-aaCH aaCH\-aaCH\-aaCH\-aasC aaC
272 \& H\-aaCH\-aasC\-aaCH aaCH\-aaCH\-aasC\-aasC aaCH\-aaCH\-aasC\-sF aaCH\-aaCH\-aasC\-
273 \& ssNH aaCH\-aasC\-aasC\-aasC aaCH\-aasC\-aasC\-aasN aaCH\-aasC\-ssNH\-dssC a...;
274 \& 4 4 8 4 2 2 6 2 2 2 4 3 2 1 3 3 2 2 2 1 2 1 1 1 2 1 1 1 1 1 1 1 2 1 1 2
275 \&
276 \& FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
277 \& ;NumericalValues;IDsAndValuesString;Ar\-Ar\-Ar\-Ar Ar\-Ar\-Ar\-Ar.HBA Ar\-Ar\-
278 \& Ar\-HBD Ar\-Ar\-Ar\-Hal Ar\-Ar\-Ar\-None Ar\-Ar\-Ar.HBA\-Ar Ar\-Ar\-Ar.HBA\-None Ar
279 \& \-Ar\-HBD\-None Ar\-Ar\-None\-HBA Ar\-Ar\-None\-HBD Ar\-Ar\-None\-None Ar\-Ar.H...;
280 \& 32 5 2 2 3 3 3 2 2 2 2 1 2 1 1 1 2 1 1 1 1 3 1 1 1 3
281 \&
282 \& FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
283 \& lValues;IDsAndValuesString;C5A\-C5B\-C5B\-C5A C5A\-C5B\-C5B\-C=ON C5A\-C5B\-C5
284 \& B\-CB C5A\-C5B\-C=ON\-NC=O C5A\-C5B\-C=ON\-O=CN C5A\-C5B\-CB\-CB C5A\-CB\-CB\-CB C5
285 \& A\-N5\-C5A\-C5B C5A\-N5\-C5A\-CB C5A\-N5\-C5A\-CR C5A\-N5\-CR\-CR C5B\-C5A\-CB\-C...;
286 \& 1 1 1 1 1 2 2 2 1 1 2 2 2 2 1 1 2 1 1 2 1 2 1 1 1 2 1 1 1 2 18 2 2 1 1
287 \& 1 1 2 1 1 3 1 3
288 \&
289 \& FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
290 \& Values;IDsAndValuesPairsString;C1\-C10\-N11\-C20 1 C1\-C10\-N11\-C21 1 C1\-C1
291 \& 1\-C21\-C21 2 C1\-C11\-C21\-N11 2 C1\-CS\-C1\-C10 1 C1\-CS\-C1\-C5 1 C1\-CS\-C1\-CS
292 \& 2 C10\-C1\-CS\-O2 1 C10\-N11\-C20\-C20 2 C10\-N11\-C21\-C11 1 C10\-N11\-C21\-C21 1
293 \& C11\-C21\-C21\-C20 1 C11\-C21\-C21\-C5 1 C11\-C21\-N11\-C20 1 C14\-C18\-C18\-C20
294 \& 2 C18\-C14\-C18\-C18 2 C18\-C18\-C14\-F 2 C18\-C18\-C18\-C18 4 C18\-C18\-C18\-C...
295 \&
296 \& FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
297 \& Values;IDsAndValuesPairsString;C.2\-C.3\-C.3\-C.3 1 C.2\-C.3\-C.3\-O.3 1 C.2
298 \& \-C.ar\-C.ar\-C.3 1 C.2\-C.ar\-C.ar\-C.ar 2 C.2\-C.ar\-C.ar\-N.ar 1 C.2\-N.am\-C.
299 \& ar\-C.ar 2 C.3\-C.3\-C.2\-O.co2 2 C.3\-C.3\-C.3\-C.3 3 C.3\-C.3\-C.3\-N.ar 1 C.3
300 \& \-C.3\-C.3\-O.3 3 C.3\-C.3\-C.ar\-C.ar 2 C.3\-C.3\-C.ar\-N.ar 2 C.3\-C.3\-N.ar\-C.
301 \& ar 2 C.3\-C.ar\-C.ar\-C.ar 1 C.3\-C.ar\-N.ar\-C.3 1 C.3\-C.ar\-N.ar\-C.ar 1 ...
302 \&
303 \& FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
304 \& lues;IDsAndValuesPairsString;N21\-None\-None\-None 9 N7\-None\-None\-None 4
305 \& None\-N21\-None\-None 10 None\-N7\-None\-None 3 None\-N7\-None\-O3 1 None\-None\-
306 \& None\-None 44 None\-None\-None\-O3 3 None\-None\-None\-O4 5
307 \&
308 \& FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
309 \& lues;IDsAndValuesPairsString;C_2\-C_3\-C_3\-C_3 1 C_2\-C_3\-C_3\-O_3 1 C_2\-C
310 \& _R\-C_R\-C_3 1 C_2\-C_R\-C_R\-C_R 2 C_2\-C_R\-C_R\-N_R 1 C_2\-N_3\-C_R\-C_R 2 C_3
311 \& \-C_3\-C_2\-O_2 1 C_3\-C_3\-C_2\-O_3 1 C_3\-C_3\-C_3\-C_3 3 C_3\-C_3\-C_3\-N_R 1 C
312 \& _3\-C_3\-C_3\-O_3 3 C_3\-C_3\-C_R\-C_R 2 C_3\-C_3\-C_R\-N_R 2 C_3\-C_3\-N_R\-C_R 2
313 \& C_3\-C_R\-C_R\-C_R 1 C_3\-C_R\-N_R\-C_3 1 C_3\-C_R\-N_R\-C_R 1 C_3\-N_R\-C_R\-...
314 .Ve
315 .SH "OPTIONS"
316 .IX Header "OPTIONS"
317 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
318 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
319 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
320 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
321 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
322 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
323 .Sp
324 The supported aromaticity model names along with model specific control parameters
325 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
326 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
327 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
328 for detecting aromaticity corresponding to a specific model.
329 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
330 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
331 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
332 atoms during calculation of topological atom torsions fingerprints. Possible values in the current
333 release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
334 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
335 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
336 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
337 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
338 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
339 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
340 option. It's a list of comma separated valid atomic invariant atom types.
341 .Sp
342 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,
343 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.
344 .Sp
345 The atomic invariants abbreviations correspond to:
346 .Sp
347 .Vb 1
348 \& AS = Atom symbol corresponding to element symbol
349 \&
350 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
351 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
352 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
353 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
354 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
355 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
356 \& H<n> = Number of implicit and explicit hydrogens for atom
357 \& Ar = Aromatic annotation indicating whether atom is aromatic
358 \& RA = Ring atom annotation indicating whether atom is a ring
359 \& FC<+n/\-n> = Formal charge assigned to atom
360 \& MN<n> = Mass number indicating isotope other than most abundant isotope
361 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
362 \& 3 (triplet)
363 .Ve
364 .Sp
365 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
366 .Sp
367 .Vb 1
368 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
369 .Ve
370 .Sp
371 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
372 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
373 .Sp
374 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
375 are also allowed:
376 .Sp
377 .Vb 12
378 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
379 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
380 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
381 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
382 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
383 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
384 \& H : NumOfImplicitAndExplicitHydrogens
385 \& Ar : Aromatic
386 \& RA : RingAtom
387 \& FC : FormalCharge
388 \& MN : MassNumber
389 \& SM : SpinMultiplicity
390 .Ve
391 .Sp
392 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
393 atom types.
394 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
395 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
396 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
397 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
398 option. It's a list of comma separated valid functional classes.
399 .Sp
400 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.
401 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
402 .Sp
403 The functional class abbreviations correspond to:
404 .Sp
405 .Vb 9
406 \& HBD: HydrogenBondDonor
407 \& HBA: HydrogenBondAcceptor
408 \& PI : PositivelyIonizable
409 \& NI : NegativelyIonizable
410 \& Ar : Aromatic
411 \& Hal : Halogen
412 \& H : Hydrophobic
413 \& RA : RingAtom
414 \& CA : ChainAtom
415 \&
416 \& Functional class atom type specification for an atom corresponds to:
417 \&
418 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
419 .Ve
420 .Sp
421 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
422 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
423 .Sp
424 .Vb 4
425 \& HydrogenBondDonor: NH, NH2, OH
426 \& HydrogenBondAcceptor: N[!H], O
427 \& PositivelyIonizable: +, NH2
428 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
429 .Ve
430 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
431 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
432 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
433 .Sp
434 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
435 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
436 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
437 look like Cmpd<Number>.
438 .Sp
439 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
440 .Sp
441 .Vb 2
442 \& MolID
443 \& ExtReg
444 .Ve
445 .Sp
446 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
447 .Sp
448 .Vb 1
449 \& Compound
450 .Ve
451 .Sp
452 The value specified above generates compound IDs which correspond to Compound<Number>
453 instead of default value of Cmpd<Number>.
454 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
455 .IX Item "--CompoundIDLabel text"
456 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
457 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
458 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
459 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
460 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
461 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
462 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
463 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
464 .Sp
465 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
466 Default value: \fILabelPrefix\fR.
467 .Sp
468 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
469 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
470 values are replaced with sequential compound IDs.
471 .Sp
472 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
473 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
474 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
475 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
476 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
477 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
478 .Sp
479 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
480 .Sp
481 Examples:
482 .Sp
483 .Vb 2
484 \& Extreg
485 \& MolID,CompoundName
486 .Ve
487 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
488 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
489 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
490 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
491 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
492 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
493 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
494 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
495 .IX Item "-f, --Filter Yes | No"
496 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
497 Default value: \fIYes\fR.
498 .Sp
499 By default, compound data is checked before calculating fingerprints and compounds containing
500 atom data corresponding to non-element symbols or no atom data are ignored.
501 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
502 .IX Item "--FingerprintsLabel text"
503 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
504 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalAtomTorsionsFingerprints\fR.
505 .IP "\fB\-h, \-\-help\fR" 4
506 .IX Item "-h, --help"
507 Print this help message.
508 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
509 .IX Item "-k, --KeepLargestComponent Yes | No"
510 Generate fingerprints for only the largest component in molecule. Possible values:
511 \&\fIYes or No\fR. Default value: \fIYes\fR.
512 .Sp
513 For molecules containing multiple connected components, fingerprints can be generated
514 in two different ways: use all connected components or just the largest connected
515 component. By default, all atoms except for the largest connected component are
516 deleted before generation of fingerprints.
517 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
518 .IX Item "--OutDelim comma | tab | semicolon"
519 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
520 Default value: \fIcomma\fR.
521 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
522 .IX Item "--output SD | FP | text | all"
523 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
524 .IP "\fB\-o, \-\-overwrite\fR" 4
525 .IX Item "-o, --overwrite"
526 Overwrite existing files.
527 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
528 .IX Item "-q, --quote Yes | No"
529 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
530 \&\fIYes or No\fR. Default value: \fIYes\fR
531 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
532 .IX Item "-r, --root RootName"
533 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
534 <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The file type determines <Ext> value.
535 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
536 delimited text files, respectively.This option is ignored for multiple input files.
537 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
538 .IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
539 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
540 \&\fB\-\-output\fR option. Possible values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
541 ValuesAndIDsPairsString\fR. Defaultvalue: \fIIDsAndValuesString\fR.
542 .Sp
543 Examples:
544 .Sp
545 .Vb 5
546 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
547 \& 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-
548 \& C.X3.BO4 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 C.X2.BO2.H2\-C.X2.BO
549 \& 2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.BO3.H1\-O...;
550 \& 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
551 \&
552 \& FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
553 \& 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3
554 \& .BO4\-C.X3.BO4 2 C.X1.BO1.H3\-C.X3.BO3.H1\-C.X3.BO4\-N.X3.BO3 2 C.X2.BO2.H
555 \& 2\-C.X2.BO2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-C.X2.BO2.H2\-C.X3.B
556 \& O3.H1\-O.X1.BO1.H1 1 C.X2.BO2.H2\-C.X2.BO2.H2\-N.X3.BO3\-C.X3.BO4 2 C.X2.B
557 \& O2.H2\-C.X3.BO3.H1\-C.X2.BO2.H2\-C.X3.BO3.H1 2 C.X2.BO2.H2\-C.X3.BO3.H1...
558 .Ve
559 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
560 .IX Item "-w, --WorkingDir DirName"
561 Location of working directory. Default value: current directory.
562 .SH "EXAMPLES"
563 .IX Header "EXAMPLES"
564 To generate topological atom torsions fingerprints using atomic invariants atom types in
565 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
566 compound IDs along with fingerprints vector strings data, type:
567 .PP
568 .Vb 1
569 \& % TopologicalAtomTorsionsFingerprints.pl \-r SampleTATFP \-o Sample.sdf
570 .Ve
571 .PP
572 To generate topological atom torsions fingerprints using atomic invariants atom types in
573 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
574 files containing sequential compound IDs in \s-1CSV\s0 file along with fingerprints vector strings
575 data, type:
576 .PP
577 .Vb 2
578 \& % TopologicalAtomTorsionsFingerprints.pl \-\-output all \-r SampleTATFP
579 \& \-o Sample.sdf
580 .Ve
581 .PP
582 To generate topological atom torsions fingerprints using atomic invariants atom types in
583 IDsAndValuesPairsString format and create a SampleTATFP.csv file containing sequential
584 compound IDs along with fingerprints vector strings data, type:
585 .PP
586 .Vb 2
587 \& % TopologicalAtomTorsionsFingerprints.pl \-\-VectorStringFormat
588 \& IDsAndValuesPairsString \-r SampleTATFP \-o Sample.sdf
589 .Ve
590 .PP
591 To generate topological atom torsions fingerprints using \s-1DREIDING\s0 atom types in
592 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
593 compound IDs along with fingerprints vector strings data, type:
594 .PP
595 .Vb 2
596 \& % TopologicalAtomTorsionsFingerprints.pl \-a DREIDINGAtomTypes
597 \& \-r SampleTATFP \-o Sample.sdf
598 .Ve
599 .PP
600 To generate topological atom torsions fingerprints using E\-state atom types in
601 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
602 compound IDs along with fingerprints vector strings data, type:
603 .PP
604 .Vb 2
605 \& % TopologicalAtomTorsionsFingerprints.pl \-a EStateAtomTypes
606 \& \-r SampleTATFP \-o Sample.sdf
607 .Ve
608 .PP
609 To generate topological atom torsions fingerprints using functional class atom types in
610 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
611 compound IDs along with fingerprints vector strings data, type:
612 .PP
613 .Vb 2
614 \& % TopologicalAtomTorsionsFingerprints.pl \-a FunctionalClassAtomTypes
615 \& \-r SampleTATFP \-o Sample.sdf
616 .Ve
617 .PP
618 To generate topological atom torsions fingerprints using \s-1MMFF94\s0 atom types in
619 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
620 compound IDs along with fingerprints vector strings data, type:
621 .PP
622 .Vb 2
623 \& % TopologicalAtomTorsionsFingerprints.pl \-a MMFF94AtomTypes
624 \& \-r SampleTATFP \-o Sample.sdf
625 .Ve
626 .PP
627 To generate topological atom torsions fingerprints using SLogP atom types in
628 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
629 compound IDs along with fingerprints vector strings data, type:
630 .PP
631 .Vb 2
632 \& % TopologicalAtomTorsionsFingerprints.pl \-a SLogPAtomTypes
633 \& \-r SampleTATFP \-o Sample.sdf
634 .Ve
635 .PP
636 To generate topological atom torsions fingerprints using \s-1SYBYL\s0 atom types in
637 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
638 compound IDs along with fingerprints vector strings data, type:
639 .PP
640 .Vb 2
641 \& % TopologicalAtomTorsionsFingerprints.pl \-a SYBYLAtomTypes
642 \& \-r SampleTATFP \-o Sample.sdf
643 .Ve
644 .PP
645 To generate topological atom torsions fingerprints using \s-1TPSA\s0 atom types in
646 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
647 compound IDs along with fingerprints vector strings data, type:
648 .PP
649 .Vb 2
650 \& % TopologicalAtomTorsionsFingerprints.pl \-a TPSAAtomTypes
651 \& \-r SampleTATFP \-o Sample.sdf
652 .Ve
653 .PP
654 To generate topological atom torsions fingerprints using \s-1UFF\s0 atom types in
655 IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
656 compound IDs along with fingerprints vector strings data, type:
657 .PP
658 .Vb 2
659 \& % TopologicalAtomTorsionsFingerprints.pl \-a UFFAtomTypes
660 \& \-r SampleTATFP \-o Sample.sdf
661 .Ve
662 .PP
663 To generate topological atom torsions fingerprints using only \s-1AS\s0,X atomic invariants atom
664 types in IDsAndValuesString format and create a SampleTATFP.csv file containing sequential
665 compound IDs along with fingerprints vector strings data, type:
666 .PP
667 .Vb 2
668 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
669 \& \-\-AtomicInvariantsToUse "AS,X" \-r SampleTATFP \-o Sample.sdf
670 .Ve
671 .PP
672 To generate topological atom torsions fingerprints using atomic invariants atom types in
673 IDsAndValuesString format and create a SampleTATFP.csv file containing compoundID
674 from molecule name line along with fingerprints vector strings, type:
675 .PP
676 .Vb 3
677 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
678 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
679 \& \-r SampleTATFP \-o Sample.sdf
680 .Ve
681 .PP
682 To generate topological atom torsions fingerprints using atomic invariants atom types in
683 IDsAndValuesString format and create a SampleTATFP.csv file containing compound IDs
684 using specified data field along with fingerprints vector strings, type:
685 .PP
686 .Vb 3
687 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
688 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID
689 \& Mol_ID \-r SampleTATFP \-o Sample.sdf
690 .Ve
691 .PP
692 To generate topological atom torsions fingerprints using atomic invariants atom types in
693 IDsAndValuesString format and create a SampleTATFP.csv file containing compound \s-1ID\s0
694 using combination of molecule name line and an explicit compound prefix along with
695 fingerprints vector strings data, type:
696 .PP
697 .Vb 3
698 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
699 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
700 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTATFP \-o Sample.sdf
701 .Ve
702 .PP
703 To generate topological atom torsions fingerprints using atomic invariants atom types in
704 IDsAndValuesString format and create a SampleTATFP.csv file containing specific data
705 fields columns along with fingerprints vector strings, type:
706 .PP
707 .Vb 3
708 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
709 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTATFP
710 \& \-o Sample.sdf
711 .Ve
712 .PP
713 To generate topological atom torsions fingerprints using atomic invariants atom types in
714 IDsAndValuesString format and create a SampleTATFP.csv file containing common
715 data fields columns along with fingerprints vector strings, type:
716 .PP
717 .Vb 2
718 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
719 \& \-\-DataFieldsMode Common \-r SampleTATFP \-o Sample.sdf
720 .Ve
721 .PP
722 To generate topological atom torsions fingerprints using atomic invariants atom types in
723 IDsAndValuesString format and create SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv
724 files containing all data fields columns in \s-1CSV\s0 file along with fingerprints data, type:
725 .PP
726 .Vb 3
727 \& % TopologicalAtomTorsionsFingerprints.pl \-a AtomicInvariantsAtomTypes
728 \& \-\-DataFieldsMode All \-\-output all \-r SampleTATFP
729 \& \-o Sample.sdf
730 .Ve
731 .SH "AUTHOR"
732 .IX Header "AUTHOR"
733 Manish Sud <msud@san.rr.com>
734 .SH "SEE ALSO"
735 .IX Header "SEE ALSO"
736 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
737 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
738 PathLengthFingerprints.pl, TopologicalAtomPairsFingerprints.pl,
739 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
740 .SH "COPYRIGHT"
741 .IX Header "COPYRIGHT"
742 Copyright (C) 2015 Manish Sud. All rights reserved.
743 .PP
744 This file is part of MayaChemTools.
745 .PP
746 MayaChemTools is free software; you can redistribute it and/or modify it under
747 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
748 Software Foundation; either version 3 of the License, or (at your option)
749 any later version.