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124 .\" ========================================================================
125 .\"
126 .IX Title "TOPOLOGICALATOMPAIRSFINGERPRINTS 1"
127 .TH TOPOLOGICALATOMPAIRSFINGERPRINTS 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 TopologicalAtomPairsFingerprints.pl \- Generate topological atom pairs fingerprints for SD files
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 TopologicalAtomPairsFingerprints.pl SDFile(s)...
137 .PP
138 TopologicalAtomPairsFingerprints.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\-\-MinDistance\fR \fInumber\fR] [\fB\-\-MaxDistance\fR \fInumber\fR]
147 [\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR] [\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR] [\fB\-o, \-\-overwrite\fR]
148 [\fB\-q, \-\-quote\fR \fIYes | No\fR] [\fB\-r, \-\-root\fR \fIRootName\fR]
149 [\fB\-v, \-\-VectorStringFormat\fR \fIValuesString, IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR]
150 [\fB\-w, \-\-WorkingDir\fR dirname] SDFile(s)...
151 .SH "DESCRIPTION"
152 .IX Header "DESCRIPTION"
153 Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ] for \fISDFile(s)\fR and create
154 appropriate \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) containing fingerprints vector strings corresponding to
155 molecular fingerprints.
156 .PP
157 Multiple SDFile names are separated by spaces. The valid file extensions are \fI.sdf\fR
158 and \fI.sd\fR. All other file names are ignored. All the \s-1SD\s0 files in a current directory
159 can be specified either by \fI*.sdf\fR or the current directory name.
160 .PP
161 The current release of MayaChemTools supports generation of topological atom pairs
162 corresponding to following \fB\-a, \-\-AtomIdentifierTypes\fR:
163 .PP
164 .Vb 3
165 \& AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
166 \& FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
167 \& SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
168 .Ve
169 .PP
170 Based on the values specified for \fB\-a, \-\-AtomIdentifierType\fR and \fB\-\-AtomicInvariantsToUse\fR,
171 initial atom types are assigned to all non-hydrogen atoms in a molecule. Using the distance
172 matrix for the molecule and initial atom types assigned to non-hydrogen atoms, all unique atom
173 pairs within \fB\-\-MinDistance\fR and \fB\-\-MaxDistance\fR are identified and counted. An atom pair
174 identifier is generated for each unique atom pair; the format of the atom pair identifier is:
175 .PP
176 .Vb 1
177 \& <AtomType1>\-D<n>\-<AtomType2>
178 \&
179 \& AtomType1, AtomType2: Atom types assigned to atom1 and atom2
180 \& D: Distance between atom1 and atom2
181 \&
182 \& where AtomType1 <= AtomType2
183 .Ve
184 .PP
185 The atom pair identifiers for all unique atom pairs corresponding to non-hydrogen atoms constitute
186 topological atom pairs fingerprints of the molecule.
187 .PP
188 Example of \fI\s-1SD\s0\fR file containing topological atom pairs fingerprints string data:
189 .PP
190 .Vb 10
191 \& ... ...
192 \& ... ...
193 \& $$$$
194 \& ... ...
195 \& ... ...
196 \& ... ...
197 \& 41 44 0 0 0 0 0 0 0 0999 V2000
198 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
199 \& ... ...
200 \& 2 3 1 0 0 0 0
201 \& ... ...
202 \& M END
203 \& > <CmpdID>
204 \& Cmpd1
205 \&
206 \& > <TopologicalAtomPairsFingerprints>
207 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi
208 \& stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H
209 \& 3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.H1
210 \& C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-C.X2...;
211 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
212 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
213 \&
214 \& $$$$
215 \& ... ...
216 \& ... ...
217 .Ve
218 .PP
219 Example of \fI\s-1FP\s0\fR file containing topological atom pairs fingerprints string data:
220 .PP
221 .Vb 10
222 \& #
223 \& # Package = MayaChemTools 7.4
224 \& # Release Date = Oct 21, 2010
225 \& #
226 \& # TimeStamp = Fri Mar 11 15:04:36 2011
227 \& #
228 \& # FingerprintsStringType = FingerprintsVector
229 \& #
230 \& # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi...
231 \& # VectorStringFormat = IDsAndValuesString
232 \& # VectorValuesType = NumericalValues
233 \& #
234 \& Cmpd1 223;C.X1.BO1.H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2...;1 1...
235 \& Cmpd2 128;C.X1.BO1.H3\-D1\-C.X2.BO2.H2 C.X1.BO1.H3\-D1\-C.X3.BO4...;1 1...
236 \& ... ...
237 \& ... ..
238 .Ve
239 .PP
240 Example of \s-1CSV\s0 \fIText\fR file containing topological atom pairs fingerprints string data:
241 .PP
242 .Vb 9
243 \& "CompoundID","TopologicalAtomPairsFingerprints"
244 \& "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy
245 \& pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C
246 \& .X1.BO1.H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X
247 \& 3.BO3.H1C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1...;
248 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
249 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
250 \& ... ...
251 \& ... ...
252 .Ve
253 .PP
254 The current release of MayaChemTools generates the following types of topological atom pairs
255 fingerprints vector strings:
256 .PP
257 .Vb 6
258 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
259 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
260 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
261 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
262 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
263 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
264 \&
265 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
266 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
267 \& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\-
268 \& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2
269 \& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X
270 \& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO...
271 \&
272 \& FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
273 \& :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2\-D1\-C_3 C_2\-D
274 \& 1\-C_R C_2\-D1\-N_3 C_2\-D1\-O_2 C_2\-D1\-O_3 C_3\-D1\-C_3 C_3\-D1\-C_R C_3\-D1\-N_
275 \& R C_3\-D1\-O_3 C_R\-D1\-C_R C_R\-D1\-F_ C_R\-D1\-N_3 C_R\-D1\-N_R C_2\-D2\-C_3 C_2
276 \& 1 1 1 2 1 7 1 1 2 23 1 1 2 1 3 5 5 2 1 5 28 2 3 3 1 1 1 2 4 1 1 4 9 3
277 \& 1 4 24 2 4 3 3 4 5 5 14 1 1 2 3 22 1 3 4 4 1 1 1 1 2 2 5 1 4 21 3 1...
278 \&
279 \& FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
280 \& axDistance10;251;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH aaCH\-
281 \& D1\-aasC aasC\-D1\-aasC aasC\-D1\-aasN aasC\-D1\-dssC aasC\-D1\-sF aasC\-D1\-ssNH
282 \& aasC\-D1\-sssCH aasN\-D1\-ssCH2 dO\-D1\-dssC dssC\-D1\-sOH dssC\-D1\-ssCH2 d...;
283 \& 10 8 5 2 1 1 1 1 1 2 1 1 1 2 2 1 4 10 12 2 2 6 3 1 3 2 2 1 1 1 1 1 1 1
284 \& 1 1 5 2 1 1 6 12 2 2 2 2 6 1 3 2 2 5 2 2 1 2 1 1 1 1 1 1 3 1 3 19 2...
285 \&
286 \& FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
287 \& stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar\-D1\-Ar
288 \& Ar\-D1\-Ar.HBA Ar\-D1\-HBD Ar\-D1\-Hal Ar\-D1\-None Ar.HBA\-D1\-None HBA\-D1\-NI H
289 \& BA\-D1\-None HBA.HBD\-D1\-NI HBA.HBD\-D1\-None HBD\-D1\-None NI\-D1\-None No...;
290 \& 23 2 1 1 2 1 1 1 1 2 1 1 7 28 3 1 3 2 8 2 1 1 1 5 1 5 24 3 3 4 2 13 4
291 \& 1 1 4 1 5 22 4 4 3 1 19 1 1 1 1 1 2 2 3 1 1 8 25 4 5 2 3 1 26 1 4 1 ...
292 \&
293 \& FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
294 \& axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A\-D1\-C5B 2
295 \& C5A\-D1\-CB 1 C5A\-D1\-CR 1 C5A\-D1\-N5 2 C5B\-D1\-C5B 1 C5B\-D1\-C=ON 1 C5B\-D1\-
296 \& CB 1 C=ON\-D1\-NC=O 1 C=ON\-D1\-O=CN 1 CB\-D1\-CB 18 CB\-D1\-F 1 CB\-D1\-NC=O 1
297 \& COO\-D1\-CR 1 COO\-D1\-O=CO 1 COO\-D1\-OC=O 1 CR\-D1\-CR 7 CR\-D1\-N5 1 CR\-D1\-OR
298 \& 2 C5A\-D2\-C5A 1 C5A\-D2\-C5B 2 C5A\-D2\-C=ON 1 C5A\-D2\-CB 3 C5A\-D2\-CR 4 ...
299 \&
300 \& FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
301 \& xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1\-D1\-C10 1 C1
302 \& \-D1\-C11 2 C1\-D1\-C5 1 C1\-D1\-CS 4 C10\-D1\-N11 1 C11\-D1\-C21 1 C14\-D1\-C18 2
303 \& C14\-D1\-F 1 C18\-D1\-C18 10 C18\-D1\-C20 4 C18\-D1\-C22 2 C20\-D1\-C20 3 C20\-D
304 \& 1\-C21 1 C20\-D1\-N11 1 C21\-D1\-C21 1 C21\-D1\-C5 1 C21\-D1\-N11 1 C22\-D1\-N4 1
305 \& C5\-D1\-N4 1 C5\-D1\-O10 1 C5\-D1\-O2 1 C5\-D1\-O9 1 CS\-D1\-O2 2 C1\-D2\-C1 3...
306 \&
307 \& FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
308 \& xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2\-D1\-C.3 1 C
309 \& .2\-D1\-C.ar 1 C.2\-D1\-N.am 1 C.2\-D1\-O.2 1 C.2\-D1\-O.co2 2 C.3\-D1\-C.3 7 C.
310 \& 3\-D1\-C.ar 1 C.3\-D1\-N.ar 1 C.3\-D1\-O.3 2 C.ar\-D1\-C.ar 23 C.ar\-D1\-F 1 C.a
311 \& r\-D1\-N.am 1 C.ar\-D1\-N.ar 2 C.2\-D2\-C.3 1 C.2\-D2\-C.ar 3 C.3\-D2\-C.3 5 C.3
312 \& \-D2\-C.ar 5 C.3\-D2\-N.ar 2 C.3\-D2\-O.3 4 C.3\-D2\-O.co2 2 C.ar\-D2\-C.ar 2...
313 \&
314 \& FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
315 \& Distance10;64;NumericalValues;IDsAndValuesPairsString;N21\-D1\-None 3 N7
316 \& \-D1\-None 2 None\-D1\-None 34 None\-D1\-O3 2 None\-D1\-O4 3 N21\-D2\-None 5 N7\-
317 \& D2\-None 3 N7\-D2\-O3 1 None\-D2\-None 44 None\-D2\-O3 2 None\-D2\-O4 5 O3\-D2\-O
318 \& 4 1 N21\-D3\-None 7 N7\-D3\-None 4 None\-D3\-None 45 None\-D3\-O3 4 None\-D3\-O4
319 \& 5 N21\-D4\-N7 1 N21\-D4\-None 5 N21\-D4\-O3 1 N21\-D4\-O4 1 N7\-D4\-None 4 N...
320 \&
321 \& FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
322 \& istance10;157;NumericalValues;IDsAndValuesPairsString;C_2\-D1\-C_3 1 C_2
323 \& \-D1\-C_R 1 C_2\-D1\-N_3 1 C_2\-D1\-O_2 2 C_2\-D1\-O_3 1 C_3\-D1\-C_3 7 C_3\-D1\-C
324 \& _R 1 C_3\-D1\-N_R 1 C_3\-D1\-O_3 2 C_R\-D1\-C_R 23 C_R\-D1\-F_ 1 C_R\-D1\-N_3 1
325 \& C_R\-D1\-N_R 2 C_2\-D2\-C_3 1 C_2\-D2\-C_R 3 C_3\-D2\-C_3 5 C_3\-D2\-C_R 5 C_3\-D
326 \& 2\-N_R 2 C_3\-D2\-O_2 1 C_3\-D2\-O_3 5 C_R\-D2\-C_R 28 C_R\-D2\-F_ 2 C_R\-D2\-...
327 .Ve
328 .SH "OPTIONS"
329 .IX Header "OPTIONS"
330 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
331 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
332 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
333 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
334 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
335 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
336 .Sp
337 The supported aromaticity model names along with model specific control parameters
338 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
339 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
340 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
341 for detecting aromaticity corresponding to a specific model.
342 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
343 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
344 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
345 atoms during calculation of topological atom pairs fingerprints. Possible values in the current
346 release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
347 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
348 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
349 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
350 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
351 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
352 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
353 option. It's a list of comma separated valid atomic invariant atom types.
354 .Sp
355 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,
356 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.
357 .Sp
358 The atomic invariants abbreviations correspond to:
359 .Sp
360 .Vb 1
361 \& AS = Atom symbol corresponding to element symbol
362 \&
363 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
364 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
365 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
366 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
367 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
368 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
369 \& H<n> = Number of implicit and explicit hydrogens for atom
370 \& Ar = Aromatic annotation indicating whether atom is aromatic
371 \& RA = Ring atom annotation indicating whether atom is a ring
372 \& FC<+n/\-n> = Formal charge assigned to atom
373 \& MN<n> = Mass number indicating isotope other than most abundant isotope
374 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
375 \& 3 (triplet)
376 .Ve
377 .Sp
378 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
379 .Sp
380 .Vb 1
381 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
382 .Ve
383 .Sp
384 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
385 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
386 .Sp
387 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
388 are also allowed:
389 .Sp
390 .Vb 12
391 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
392 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
393 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
394 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
395 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
396 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
397 \& H : NumOfImplicitAndExplicitHydrogens
398 \& Ar : Aromatic
399 \& RA : RingAtom
400 \& FC : FormalCharge
401 \& MN : MassNumber
402 \& SM : SpinMultiplicity
403 .Ve
404 .Sp
405 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
406 atom types.
407 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
408 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
409 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
410 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
411 option. It's a list of comma separated valid functional classes.
412 .Sp
413 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.
414 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
415 .Sp
416 The functional class abbreviations correspond to:
417 .Sp
418 .Vb 9
419 \& HBD: HydrogenBondDonor
420 \& HBA: HydrogenBondAcceptor
421 \& PI : PositivelyIonizable
422 \& NI : NegativelyIonizable
423 \& Ar : Aromatic
424 \& Hal : Halogen
425 \& H : Hydrophobic
426 \& RA : RingAtom
427 \& CA : ChainAtom
428 \&
429 \& Functional class atom type specification for an atom corresponds to:
430 \&
431 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
432 .Ve
433 .Sp
434 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
435 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
436 .Sp
437 .Vb 4
438 \& HydrogenBondDonor: NH, NH2, OH
439 \& HydrogenBondAcceptor: N[!H], O
440 \& PositivelyIonizable: +, NH2
441 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
442 .Ve
443 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
444 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
445 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
446 .Sp
447 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
448 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
449 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
450 look like Cmpd<Number>.
451 .Sp
452 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
453 .Sp
454 .Vb 2
455 \& MolID
456 \& ExtReg
457 .Ve
458 .Sp
459 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
460 .Sp
461 .Vb 1
462 \& Compound
463 .Ve
464 .Sp
465 The value specified above generates compound IDs which correspond to Compound<Number>
466 instead of default value of Cmpd<Number>.
467 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
468 .IX Item "--CompoundIDLabel text"
469 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
470 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
471 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
472 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
473 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
474 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
475 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
476 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
477 .Sp
478 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
479 Default value: \fILabelPrefix\fR.
480 .Sp
481 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
482 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
483 values are replaced with sequential compound IDs.
484 .Sp
485 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
486 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
487 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
488 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
489 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
490 with generated fingerprints for \fItext | both\fR values of \fB\-\-output\fR option.
491 .Sp
492 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
493 .Sp
494 Examples:
495 .Sp
496 .Vb 2
497 \& Extreg
498 \& MolID,CompoundName
499 .Ve
500 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
501 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
502 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
503 with generated fingerprints for \fItext | both\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
504 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
505 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
506 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
507 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
508 .IX Item "-f, --Filter Yes | No"
509 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
510 Default value: \fIYes\fR.
511 .Sp
512 By default, compound data is checked before calculating fingerprints and compounds containing
513 atom data corresponding to non-element symbols or no atom data are ignored.
514 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
515 .IX Item "--FingerprintsLabel text"
516 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
517 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalAtomPairsFingerprints\fR.
518 .IP "\fB\-h, \-\-help\fR" 4
519 .IX Item "-h, --help"
520 Print this help message.
521 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
522 .IX Item "-k, --KeepLargestComponent Yes | No"
523 Generate fingerprints for only the largest component in molecule. Possible values:
524 \&\fIYes or No\fR. Default value: \fIYes\fR.
525 .Sp
526 For molecules containing multiple connected components, fingerprints can be generated
527 in two different ways: use all connected components or just the largest connected
528 component. By default, all atoms except for the largest connected component are
529 deleted before generation of fingerprints.
530 .IP "\fB\-\-MinDistance\fR \fInumber\fR" 4
531 .IX Item "--MinDistance number"
532 Minimum bond distance between atom pairs for generating topological atom pairs. Default value:
533 \&\fI1\fR. Valid values: positive integers and less than \fB\-\-MaxDistance\fR.
534 .IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4
535 .IX Item "--MaxDistance number"
536 Maximum bond distance between atom pairs for generating topological atom pairs. Default value:
537 \&\fI10\fR. Valid values: positive integers and greater than \fB\-\-MinDistance\fR.
538 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
539 .IX Item "--OutDelim comma | tab | semicolon"
540 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
541 Default value: \fIcomma\fR
542 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
543 .IX Item "--output SD | FP | text | all"
544 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
545 .IP "\fB\-o, \-\-overwrite\fR" 4
546 .IX Item "-o, --overwrite"
547 Overwrite existing files.
548 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
549 .IX Item "-q, --quote Yes | No"
550 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
551 \&\fIYes or No\fR. Default value: \fIYes\fR.
552 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
553 .IX Item "-r, --root RootName"
554 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
555 <SDFileName><TopologicalAtomPairsFP>.<Ext>. The file type determines <Ext> value.
556 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
557 delimited text files, respectively.This option is ignored for multiple input files.
558 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
559 .IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
560 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
561 \&\fB\-\-output\fR option. Possible values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
562 ValuesAndIDsPairsString\fR. Default value: \fIIDsAndValuesString\fR.
563 .Sp
564 Examples:
565 .Sp
566 .Vb 6
567 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
568 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
569 \& .H3\-D1\-C.X3.BO3.H1 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 C.X2.BO2.H2\-D1\-C.X3.BO3.
570 \& H1 C.X2.BO2.H2\-D1\-C.X3.BO4 C.X2.BO2.H2\-D1\-N.X3.BO3 C.X2.BO3.H1\-D1\-...;
571 \& 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
572 \& 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1...
573 \&
574 \& FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
575 \& istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
576 \& 1.BO1.H3\-D1\-C.X3.BO3.H1 2 C.X2.BO2.H2\-D1\-C.X2.BO2.H2 1 C.X2.BO2.H2\-D1\-
577 \& C.X3.BO3.H1 4 C.X2.BO2.H2\-D1\-C.X3.BO4 1 C.X2.BO2.H2\-D1\-N.X3.BO3 1 C.X2
578 \& .BO3.H1\-D1\-C.X2.BO3.H1 10 C.X2.BO3.H1\-D1\-C.X3.BO4 8 C.X3.BO3.H1\-D1\-C.X
579 \& 3.BO4 1 C.X3.BO3.H1\-D1\-O.X1.BO1.H1 2 C.X3.BO4\-D1\-C.X3.BO4 6 C.X3.BO...
580 .Ve
581 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
582 .IX Item "-w, --WorkingDir DirName"
583 Location of working directory. Default value: current directory.
584 .SH "EXAMPLES"
585 .IX Header "EXAMPLES"
586 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
587 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
588 file containing sequential compound IDs along with fingerprints vector strings data, type:
589 .PP
590 .Vb 1
591 \& % TopologicalAtomPairsFingerprints.pl \-r SampleTAPFP \-o Sample.sdf
592 .Ve
593 .PP
594 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
595 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
596 SampleTAPFP.fpf and SampleTAPFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along
597 with fingerprints vector strings data, type:
598 .PP
599 .Vb 2
600 \& % TopologicalAtomPairsFingerprints.pl \-\-output all \-r SampleTAPFP
601 \& \-o Sample.sdf
602 .Ve
603 .PP
604 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
605 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
606 file containing sequential compound IDs along with fingerprints vector strings data, type:
607 .PP
608 .Vb 2
609 \& % TopologicalAtomPairsFingerprints.pl \-a DREIDINGAtomTypes
610 \& \-r SampleTAPFP \-o Sample.sdf
611 .Ve
612 .PP
613 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
614 10 using E\-state types in IDsAndValuesString format and create a SampleTAPFP.csv
615 file containing sequential compound IDs along with fingerprints vector strings data, type:
616 .PP
617 .Vb 2
618 \& % TopologicalAtomPairsFingerprints.pl \-a EStateAtomTypes
619 \& \-r SampleTAPFP \-o Sample.sdf
620 .Ve
621 .PP
622 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
623 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
624 file containing sequential compound IDs along with fingerprints vector strings data, type:
625 .PP
626 .Vb 2
627 \& % TopologicalAtomPairsFingerprints.pl \-a DREIDINGAtomTypes
628 \& \-r SampleTAPFP \-o Sample.sdf
629 .Ve
630 .PP
631 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
632 10 using functional class atom types in IDsAndValuesString format and create a SampleTAPFP.csv
633 file containing sequential compound IDs along with fingerprints vector strings data, type:
634 .PP
635 .Vb 2
636 \& % TopologicalAtomPairsFingerprints.pl \-a FunctionalClassAtomTypes
637 \& \-r SampleTAPFP \-o Sample.sdf
638 .Ve
639 .PP
640 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
641 10 using \s-1MMFF94\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
642 file containing sequential compound IDs along with fingerprints vector strings data, type:
643 .PP
644 .Vb 2
645 \& % TopologicalAtomPairsFingerprints.pl \-a MMFF94AtomTypes
646 \& \-r SampleTAPFP \-o Sample.sdf
647 .Ve
648 .PP
649 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
650 10 using SLogP atom types in IDsAndValuesString format and create a SampleTAPFP.csv
651 file containing sequential compound IDs along with fingerprints vector strings data, type:
652 .PP
653 .Vb 2
654 \& % TopologicalAtomPairsFingerprints.pl \-a SLogPAtomTypes
655 \& \-r SampleTAPFP \-o Sample.sdf
656 .Ve
657 .PP
658 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
659 10 using \s-1SYBYL\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
660 file containing sequential compound IDs along with fingerprints vector strings data, type:
661 .PP
662 .Vb 2
663 \& % TopologicalAtomPairsFingerprints.pl \-a SYBYLAtomTypes
664 \& \-r SampleTAPFP \-o Sample.sdf
665 .Ve
666 .PP
667 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
668 10 using \s-1TPSA\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
669 file containing sequential compound IDs along with fingerprints vector strings data, type:
670 .PP
671 .Vb 2
672 \& % TopologicalAtomPairsFingerprints.pl \-a TPSAAtomTypes
673 \& \-r SampleTAPFP \-o Sample.sdf
674 .Ve
675 .PP
676 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
677 10 using \s-1UFF\s0 atom types in IDsAndValuesString format and create a SampleTAPFP.csv
678 file containing sequential compound IDs along with fingerprints vector strings data, type:
679 .PP
680 .Vb 2
681 \& % TopologicalAtomPairsFingerprints.pl \-a UFFAtomTypes
682 \& \-r SampleTAPFP \-o Sample.sdf
683 .Ve
684 .PP
685 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
686 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTAPFP.csv
687 file containing sequential compound IDs along with fingerprints vector strings data, type:
688 .PP
689 .Vb 2
690 \& % TopologicalAtomPairsFingerprints.pl \-\-VectorStringFormat
691 \& IDsAndValuesPairsString \-r SampleTAPFP \-o Sample.sdf
692 .Ve
693 .PP
694 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
695 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
696 file containing sequential compound IDs along with fingerprints vector strings data, type:
697 .PP
698 .Vb 2
699 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
700 \& \-\-MinDistance 1 \-\-MaxDistance 6 \-r SampleTAPFP \-o Sample.sdf
701 .Ve
702 .PP
703 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
704 10 using only \s-1AS\s0,X atomic invariants atom types in IDsAndValuesString format and create a
705 SampleTAPFP.csv file containing sequential compound IDs along with fingerprints vector strings
706 data, type:
707 .PP
708 .Vb 3
709 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
710 \& \-\-AtomicInvariantsToUse "AS,X" \-\-MinDistance 1 \-\-MaxDistance 6
711 \& \-r SampleTAPFP \-o Sample.sdf
712 .Ve
713 .PP
714 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
715 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
716 file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings
717 data, type:
718 .PP
719 .Vb 3
720 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
721 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
722 \& \-r SampleTAPFP \-o Sample.sdf
723 .Ve
724 .PP
725 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
726 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
727 file containing compound IDs using specified data field along with fingerprints vector strings
728 data, type:
729 .PP
730 .Vb 3
731 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
732 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID
733 \& Mol_ID \-r SampleTAPFP \-o Sample.sdf
734 .Ve
735 .PP
736 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
737 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
738 file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
739 prefix along with fingerprints vector strings data, type:
740 .PP
741 .Vb 3
742 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
743 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
744 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTAPFP \-o Sample.sdf
745 .Ve
746 .PP
747 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
748 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
749 file containing specific data fields columns along with fingerprints vector strings
750 data, type:
751 .PP
752 .Vb 3
753 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
754 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTAPFP
755 \& \-o Sample.sdf
756 .Ve
757 .PP
758 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
759 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTAPFP.csv
760 file containing common data fields columns along with fingerprints vector strings
761 data, type:
762 .PP
763 .Vb 2
764 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
765 \& \-\-DataFieldsMode Common \-r SampleTAPFP \-o Sample.sdf
766 .Ve
767 .PP
768 To generate topological atom pairs fingerprints corresponding to bond distances from 1 through
769 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTAPFP.sdf,
770 SampleTAPFP.fpf and SampleTAPFP.csv files containing all data fields columns in \s-1CSV\s0 file along
771 with fingerprints data, type:
772 .PP
773 .Vb 3
774 \& % TopologicalAtomPairsFingerprints.pl \-a AtomicInvariantsAtomTypes
775 \& \-\-DataFieldsMode All \-\-output all \-r SampleTAPFP
776 \& \-o Sample.sdf
777 .Ve
778 .SH "AUTHOR"
779 .IX Header "AUTHOR"
780 Manish Sud <msud@san.rr.com>
781 .SH "SEE ALSO"
782 .IX Header "SEE ALSO"
783 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
784 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
785 PathLengthFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
786 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
787 .SH "COPYRIGHT"
788 .IX Header "COPYRIGHT"
789 Copyright (C) 2015 Manish Sud. All rights reserved.
790 .PP
791 This file is part of MayaChemTools.
792 .PP
793 MayaChemTools is free software; you can redistribute it and/or modify it under
794 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
795 Software Foundation; either version 3 of the License, or (at your option)
796 any later version.