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123 .rm #[ #] #H #V #F C
124 .\" ========================================================================
125 .\"
126 .IX Title "TOPOLOGICALATOMTRIPLETSFINGERPRINTS 1"
127 .TH TOPOLOGICALATOMTRIPLETSFINGERPRINTS 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 TopologicalAtomTripletsFingerprints.pl \- Generate topological atom triplets fingerprints for SD files
134 .SH "SYNOPSIS"
135 .IX Header "SYNOPSIS"
136 TopologicalAtomTripletsFingerprints.pl SDFile(s)...
137 .PP
138 TopologicalAtomTripletsFingerprints.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] [\fB\-u, \-\-UseTriangleInequality\fR \fIYes | No\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 triplets fingerprints 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 triplets
162 fingerprints 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 triplet
174 identifier is generated for each unique atom triplet; the format of the atom triplet identifier is:
175 .PP
176 .Vb 1
177 \& <ATx>\-Dyz\-<ATy>\-Dxz\-<ATz>\-Dxy
178 \&
179 \& ATx, ATy, ATz: Atom types assigned to atom x, atom y, and atom z
180 \& Dxy: Distance between atom x and atom y
181 \& Dxz: Distance between atom x and atom z
182 \& Dyz: Distance between atom y and atom z
183 \&
184 \& where <AT1>\-D23 <= <AT2>\-D13 <= <AT3>\-D12
185 .Ve
186 .PP
187 The atom triplet identifiers for all unique atom triplets corresponding to non-hydrogen atoms constitute
188 topological atom triplets fingerprints of the molecule.
189 .PP
190 Example of \fI\s-1SD\s0\fR file containing topological atom triplets fingerprints string data:
191 .PP
192 .Vb 10
193 \& ... ...
194 \& ... ...
195 \& $$$$
196 \& ... ...
197 \& ... ...
198 \& ... ...
199 \& 41 44 0 0 0 0 0 0 0 0999 V2000
200 \& \-3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
201 \& ... ...
202 \& 2 3 1 0 0 0 0
203 \& ... ...
204 \& M END
205 \& > <CmpdID>
206 \& Cmpd1
207 \&
208 \& > <TopologicalAtomTripletsFingerprints>
209 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi
210 \& nDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1.B
211 \& O1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D10\-C
212 \& .X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1...;
213 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
214 \& 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
215 \&
216 \& $$$$
217 \& ... ...
218 \& ... ...
219 .Ve
220 .PP
221 Example of \fI\s-1FP\s0\fR file containing topological atom triplets fingerprints string data:
222 .PP
223 .Vb 10
224 \& #
225 \& # Package = MayaChemTools 7.4
226 \& # Release Date = Oct 21, 2010
227 \& #
228 \& # TimeStamp = Fri Mar 11 15:24:01 2011
229 \& #
230 \& # FingerprintsStringType = FingerprintsVector
231 \& #
232 \& # Description = TopologicalAtomTriplets:AtomicInvariantsAtomTypes:Mi...
233 \& # VectorStringFormat = IDsAndValuesString
234 \& # VectorValuesType = NumericalValues
235 \& #
236 \& Cmpd1 3096;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2...;1 2 2 2 2...
237 \& Cmpd2 1093;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D3\-C.X2.BO2.H2\-D4...;2 2 2 2 2...
238 \& ... ...
239 \& ... ..
240 .Ve
241 .PP
242 Example of \s-1CSV\s0 \fIText\fR file containing topological atom triplets fingerprints string data:
243 .PP
244 .Vb 9
245 \& "CompoundID","TopologicalAtomTripletsFingerprints"
246 \& "Cmpd1","FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAto
247 \& mTypes:MinDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesStri
248 \& ng;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2
249 \& .H2\-D10\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1....;
250 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2 2
251 \& 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8 8 ...
252 \& ... ...
253 \& ... ...
254 .Ve
255 .PP
256 The current release of MayaChemTools generates the following types of topological atom triplets
257 fingerprints vector strings:
258 .PP
259 .Vb 7
260 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
261 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
262 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
263 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
264 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
265 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
266 \& 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
267 \&
268 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
269 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
270 \& ;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 1 C.X1.BO1.H3\-D1\-C.X2.BO
271 \& 2.H2\-D10\-C.X3.BO4\-D9 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 2 C.X
272 \& 1.BO1.H3\-D1\-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2
273 \& \-D6\-C.X3.BO3.H1\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3.BO3.H1\-D7 2...
274 \&
275 \& FingerprintsVector;TopologicalAtomTriplets:DREIDINGAtomTypes:MinDistan
276 \& ce1:MaxDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D
277 \& 9\-C_3\-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_
278 \& 3\-D9 C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_
279 \& 2\-D1\-C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D...;
280 \& 1 1 1 2 1 1 3 1 1 2 2 1 1 1 1 1 1 1 1 2 1 3 4 5 1 1 6 4 2 2 3 1 1 1 2
281 \& 2 1 2 1 1 2 2 2 1 2 1 2 1 1 3 3 2 6 4 2 1 1 1 2 2 1 1 1 1 1 1 1 1 1...
282 \&
283 \& FingerprintsVector;TopologicalAtomTriplets:EStateAtomTypes:MinDistance
284 \& 1:MaxDistance10;3298;NumericalValues;IDsAndValuesString;aaCH\-D1\-aaCH\-D
285 \& 1\-aaCH\-D2 aaCH\-D1\-aaCH\-D1\-aasC\-D2 aaCH\-D1\-aaCH\-D10\-aaCH\-D9 aaCH\-D1\-aaC
286 \& H\-D10\-aasC\-D9 aaCH\-D1\-aaCH\-D2\-aaCH\-D3 aaCH\-D1\-aaCH\-D2\-aasC\-D1 aaCH\-D1\-
287 \& aaCH\-D2\-aasC\-D3 aaCH\-D1\-aaCH\-D3\-aasC\-D2 aaCH\-D1\-aaCH\-D4\-aasC\-D5 aa...;
288 \& 6 4 24 4 16 8 8 4 8 8 8 12 10 14 4 16 24 4 12 2 2 4 1 10 2 2 15 2 2 2
289 \& 2 2 2 14 4 2 2 2 2 1 2 10 2 2 4 1 2 4 8 3 3 3 4 6 4 2 2 3 3 1 1 1 2 1
290 \& 2 2 4 2 3 2 1 2 4 5 3 2 2 1 2 4 3 2 8 12 6 2 2 4 4 7 1 4 2 4 2 2 2 ...
291 \&
292 \& FingerprintsVector;TopologicalAtomTriplets:FunctionalClassAtomTypes:Mi
293 \& nDistance1:MaxDistance10;2182;NumericalValues;IDsAndValuesString;Ar\-D1
294 \& \-Ar\-D1\-Ar\-D2 Ar\-D1\-Ar\-D1\-Ar.HBA\-D2 Ar\-D1\-Ar\-D10\-Ar\-D9 Ar\-D1\-Ar\-D10\-Hal
295 \& \-D9 Ar\-D1\-Ar\-D2\-Ar\-D2 Ar\-D1\-Ar\-D2\-Ar\-D3 Ar\-D1\-Ar\-D2\-Ar.HBA\-D1 Ar\-D1\-Ar
296 \& \-D2\-Ar.HBA\-D2 Ar\-D1\-Ar\-D2\-Ar.HBA\-D3 Ar\-D1\-Ar\-D2\-HBD\-D1 Ar\-D1\-Ar\-D2...;
297 \& 27 1 32 2 2 63 3 2 1 2 1 2 3 1 1 40 3 1 2 2 2 2 4 2 2 47 4 2 2 1 2 1 5
298 \& 2 2 51 4 3 1 3 1 9 1 1 50 3 3 4 1 9 50 2 2 3 3 5 45 1 1 1 2 1 2 2 3 3
299 \& 4 4 3 2 1 1 3 4 5 5 3 1 2 3 2 3 5 7 2 7 3 7 1 1 2 2 2 2 3 1 4 3 1 2...
300 \&
301 \& FingerprintsVector;TopologicalAtomTriplets:MMFF94AtomTypes:MinDistance
302 \& 1:MaxDistance10;2966;NumericalValues;IDsAndValuesString;C5A\-D1\-C5A\-D1\-
303 \& N5\-D2 C5A\-D1\-C5A\-D2\-C5B\-D2 C5A\-D1\-C5A\-D3\-CB\-D2 C5A\-D1\-C5A\-D3\-CR\-D2 C5A
304 \& \-D1\-C5B\-D1\-C5B\-D2 C5A\-D1\-C5B\-D2\-C=ON\-D1 C5A\-D1\-C5B\-D2\-CB\-D1 C5A\-D1\-C5B
305 \& \-D3\-C=ON\-D2 C5A\-D1\-C5B\-D3\-CB\-D2 C5A\-D1\-C=ON\-D3\-NC=O\-D2 C5A\-D1\-C=ON\-D3\-
306 \& O=CN\-D2 C5A\-D1\-C=ON\-D4\-NC=O\-D3 C5A\-D1\-C=ON\-D4\-O=CN\-D3 C5A\-D1\-CB\-D1\-...
307 \&
308 \& FingerprintsVector;TopologicalAtomTriplets:SLogPAtomTypes:MinDistance1
309 \& :MaxDistance10;3710;NumericalValues;IDsAndValuesString;C1\-D1\-C1\-D1\-C11
310 \& \-D2 C1\-D1\-C1\-D1\-CS\-D2 C1\-D1\-C1\-D10\-C5\-D9 C1\-D1\-C1\-D3\-C10\-D2 C1\-D1\-C1\-D
311 \& 3\-C5\-D2 C1\-D1\-C1\-D3\-CS\-D2 C1\-D1\-C1\-D3\-CS\-D4 C1\-D1\-C1\-D4\-C10\-D5 C1\-D1\-C
312 \& 1\-D4\-C11\-D5 C1\-D1\-C1\-D5\-C10\-D4 C1\-D1\-C1\-D5\-C5\-D4 C1\-D1\-C1\-D6\-C11\-D7 C1
313 \& \-D1\-C1\-D6\-CS\-D5 C1\-D1\-C1\-D6\-CS\-D7 C1\-D1\-C1\-D8\-C11\-D9 C1\-D1\-C1\-D8\-CS...
314 \&
315 \& FingerprintsVector;TopologicalAtomTriplets:SYBYLAtomTypes:MinDistance1
316 \& :MaxDistance10;2332;NumericalValues;IDsAndValuesString;C.2\-D1\-C.2\-D9\-C
317 \& .3\-D10 C.2\-D1\-C.2\-D9\-C.ar\-D10 C.2\-D1\-C.3\-D1\-C.3\-D2 C.2\-D1\-C.3\-D10\-C.3\-
318 \& D9 C.2\-D1\-C.3\-D2\-C.3\-D3 C.2\-D1\-C.3\-D2\-C.ar\-D3 C.2\-D1\-C.3\-D3\-C.3\-D4 C.2
319 \& \-D1\-C.3\-D3\-N.ar\-D4 C.2\-D1\-C.3\-D3\-O.3\-D2 C.2\-D1\-C.3\-D4\-C.3\-D5 C.2\-D1\-C.
320 \& 3\-D5\-C.3\-D6 C.2\-D1\-C.3\-D5\-O.3\-D4 C.2\-D1\-C.3\-D6\-C.3\-D7 C.2\-D1\-C.3\-D7...
321 \&
322 \& FingerprintsVector;TopologicalAtomTriplets:TPSAAtomTypes:MinDistance1:
323 \& MaxDistance10;1007;NumericalValues;IDsAndValuesString;N21\-D1\-N7\-D3\-Non
324 \& e\-D4 N21\-D1\-N7\-D5\-None\-D4 N21\-D1\-None\-D1\-None\-D2 N21\-D1\-None\-D2\-None\-D
325 \& 2 N21\-D1\-None\-D2\-None\-D3 N21\-D1\-None\-D3\-None\-D4 N21\-D1\-None\-D4\-None\-D5
326 \& N21\-D1\-None\-D4\-O3\-D3 N21\-D1\-None\-D4\-O4\-D3 N21\-D1\-None\-D5\-None\-D6 N21\-
327 \& D1\-None\-D6\-None\-D7 N21\-D1\-None\-D6\-O4\-D5 N21\-D1\-None\-D7\-None\-D8 N21\-...
328 \&
329 \& FingerprintsVector;TopologicalAtomTriplets:UFFAtomTypes:MinDistance1:M
330 \& axDistance10;2377;NumericalValues;IDsAndValuesString;C_2\-D1\-C_2\-D9\-C_3
331 \& \-D10 C_2\-D1\-C_2\-D9\-C_R\-D10 C_2\-D1\-C_3\-D1\-C_3\-D2 C_2\-D1\-C_3\-D10\-C_3\-D9
332 \& C_2\-D1\-C_3\-D2\-C_3\-D3 C_2\-D1\-C_3\-D2\-C_R\-D3 C_2\-D1\-C_3\-D3\-C_3\-D4 C_2\-D1\-
333 \& C_3\-D3\-N_R\-D4 C_2\-D1\-C_3\-D3\-O_3\-D2 C_2\-D1\-C_3\-D4\-C_3\-D5 C_2\-D1\-C_3\-D5\-
334 \& C_3\-D6 C_2\-D1\-C_3\-D5\-O_3\-D4 C_2\-D1\-C_3\-D6\-C_3\-D7 C_2\-D1\-C_3\-D7\-C_3\-...
335 .Ve
336 .SH "OPTIONS"
337 .IX Header "OPTIONS"
338 .IP "\fB\-\-AromaticityModel\fR \fIMDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel\fR" 4
339 .IX Item "--AromaticityModel MDLAromaticityModel | TriposAromaticityModel | MMFFAromaticityModel | ChemAxonBasicAromaticityModel | ChemAxonGeneralAromaticityModel | DaylightAromaticityModel | MayaChemToolsAromaticityModel"
340 Specify aromaticity model to use during detection of aromaticity. Possible values in the current
341 release are: \fIMDLAromaticityModel, TriposAromaticityModel, MMFFAromaticityModel,
342 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel, DaylightAromaticityModel
343 or MayaChemToolsAromaticityModel\fR. Default value: \fIMayaChemToolsAromaticityModel\fR.
344 .Sp
345 The supported aromaticity model names along with model specific control parameters
346 are defined in \fBAromaticityModelsData.csv\fR, which is distributed with the current release
347 and is available under \fBlib/data\fR directory. \fBMolecule.pm\fR module retrieves data from
348 this file during class instantiation and makes it available to method \fBDetectAromaticity\fR
349 for detecting aromaticity corresponding to a specific model.
350 .IP "\fB\-a, \-\-AtomIdentifierType\fR \fIAtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes\fR" 4
351 .IX Item "-a, --AtomIdentifierType AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes"
352 Specify atom identifier type to use for assignment of initial atom identifier to non-hydrogen
353 atoms during calculation of topological atom triplets fingerprints. Possible values in the current
354 release are: \fIAtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
355 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes, SYBYLAtomTypes,
356 TPSAAtomTypes, UFFAtomTypes\fR. Default value: \fIAtomicInvariantsAtomTypes\fR.
357 .ie n .IP "\fB\-\-AtomicInvariantsToUse\fR \fI""AtomicInvariant,AtomicInvariant...""\fR" 4
358 .el .IP "\fB\-\-AtomicInvariantsToUse\fR \fI``AtomicInvariant,AtomicInvariant...''\fR" 4
359 .IX Item "--AtomicInvariantsToUse AtomicInvariant,AtomicInvariant..."
360 This value is used during \fIAtomicInvariantsAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
361 option. It's a list of comma separated valid atomic invariant atom types.
362 .Sp
363 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,
364 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.
365 .Sp
366 The atomic invariants abbreviations correspond to:
367 .Sp
368 .Vb 1
369 \& AS = Atom symbol corresponding to element symbol
370 \&
371 \& X<n> = Number of non\-hydrogen atom neighbors or heavy atoms
372 \& BO<n> = Sum of bond orders to non\-hydrogen atom neighbors or heavy atoms
373 \& LBO<n> = Largest bond order of non\-hydrogen atom neighbors or heavy atoms
374 \& SB<n> = Number of single bonds to non\-hydrogen atom neighbors or heavy atoms
375 \& DB<n> = Number of double bonds to non\-hydrogen atom neighbors or heavy atoms
376 \& TB<n> = Number of triple bonds to non\-hydrogen atom neighbors or heavy atoms
377 \& H<n> = Number of implicit and explicit hydrogens for atom
378 \& Ar = Aromatic annotation indicating whether atom is aromatic
379 \& RA = Ring atom annotation indicating whether atom is a ring
380 \& FC<+n/\-n> = Formal charge assigned to atom
381 \& MN<n> = Mass number indicating isotope other than most abundant isotope
382 \& SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
383 \& 3 (triplet)
384 .Ve
385 .Sp
386 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class corresponds to:
387 .Sp
388 .Vb 1
389 \& AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/\-n>.MN<n>.SM<n>
390 .Ve
391 .Sp
392 Except for \s-1AS\s0 which is a required atomic invariant in atom types, all other atomic invariants are
393 optional. Atom type specification doesn't include atomic invariants with zero or undefined values.
394 .Sp
395 In addition to usage of abbreviations for specifying atomic invariants, the following descriptive words
396 are also allowed:
397 .Sp
398 .Vb 12
399 \& X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
400 \& BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
401 \& LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
402 \& SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
403 \& DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
404 \& TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
405 \& H : NumOfImplicitAndExplicitHydrogens
406 \& Ar : Aromatic
407 \& RA : RingAtom
408 \& FC : FormalCharge
409 \& MN : MassNumber
410 \& SM : SpinMultiplicity
411 .Ve
412 .Sp
413 \&\fIAtomTypes::AtomicInvariantsAtomTypes\fR module is used to assign atomic invariant
414 atom types.
415 .ie n .IP "\fB\-\-FunctionalClassesToUse\fR \fI""FunctionalClass1,FunctionalClass2...""\fR" 4
416 .el .IP "\fB\-\-FunctionalClassesToUse\fR \fI``FunctionalClass1,FunctionalClass2...''\fR" 4
417 .IX Item "--FunctionalClassesToUse FunctionalClass1,FunctionalClass2..."
418 This value is used during \fIFunctionalClassAtomTypes\fR value of \fBa, \-\-AtomIdentifierType\fR
419 option. It's a list of comma separated valid functional classes.
420 .Sp
421 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.
422 Default value [ Ref 24 ]: \fI\s-1HBD\s0,HBA,PI,NI,Ar,Hal\fR.
423 .Sp
424 The functional class abbreviations correspond to:
425 .Sp
426 .Vb 9
427 \& HBD: HydrogenBondDonor
428 \& HBA: HydrogenBondAcceptor
429 \& PI : PositivelyIonizable
430 \& NI : NegativelyIonizable
431 \& Ar : Aromatic
432 \& Hal : Halogen
433 \& H : Hydrophobic
434 \& RA : RingAtom
435 \& CA : ChainAtom
436 \&
437 \& Functional class atom type specification for an atom corresponds to:
438 \&
439 \& Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
440 .Ve
441 .Sp
442 \&\fIAtomTypes::FunctionalClassAtomTypes\fR module is used to assign functional class atom
443 types. It uses following definitions [ Ref 60\-61, Ref 65\-66 ]:
444 .Sp
445 .Vb 4
446 \& HydrogenBondDonor: NH, NH2, OH
447 \& HydrogenBondAcceptor: N[!H], O
448 \& PositivelyIonizable: +, NH2
449 \& NegativelyIonizable: \-, C(=O)OH, S(=O)OH, P(=O)OH
450 .Ve
451 .IP "\fB\-\-CompoundID\fR \fIDataFieldName or LabelPrefixString\fR" 4
452 .IX Item "--CompoundID DataFieldName or LabelPrefixString"
453 This value is \fB\-\-CompoundIDMode\fR specific and indicates how compound \s-1ID\s0 is generated.
454 .Sp
455 For \fIDataField\fR value of \fB\-\-CompoundIDMode\fR option, it corresponds to datafield label name
456 whose value is used as compound \s-1ID\s0; otherwise, it's a prefix string used for generating compound
457 IDs like LabelPrefixString<Number>. Default value, \fICmpd\fR, generates compound IDs which
458 look like Cmpd<Number>.
459 .Sp
460 Examples for \fIDataField\fR value of \fB\-\-CompoundIDMode\fR:
461 .Sp
462 .Vb 2
463 \& MolID
464 \& ExtReg
465 .Ve
466 .Sp
467 Examples for \fILabelPrefix\fR or \fIMolNameOrLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR:
468 .Sp
469 .Vb 1
470 \& Compound
471 .Ve
472 .Sp
473 The value specified above generates compound IDs which correspond to Compound<Number>
474 instead of default value of Cmpd<Number>.
475 .IP "\fB\-\-CompoundIDLabel\fR \fItext\fR" 4
476 .IX Item "--CompoundIDLabel text"
477 Specify compound \s-1ID\s0 column label for \s-1CSV/TSV\s0 text file(s) used during \fICompoundID\fR value
478 of \fB\-\-DataFieldsMode\fR option. Default value: \fICompoundID\fR.
479 .IP "\fB\-\-CompoundIDMode\fR \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR" 4
480 .IX Item "--CompoundIDMode DataField | MolName | LabelPrefix | MolNameOrLabelPrefix"
481 Specify how to generate compound IDs and write to \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) along with generated
482 fingerprints for \fI\s-1FP\s0 | text | all\fR values of \fB\-\-output\fR option: use a \fISDFile(s)\fR datafield value;
483 use molname line from \fISDFile(s)\fR; generate a sequential \s-1ID\s0 with specific prefix; use combination
484 of both MolName and LabelPrefix with usage of LabelPrefix values for empty molname lines.
485 .Sp
486 Possible values: \fIDataField | MolName | LabelPrefix | MolNameOrLabelPrefix\fR.
487 Default value: \fILabelPrefix\fR.
488 .Sp
489 For \fIMolNameAndLabelPrefix\fR value of \fB\-\-CompoundIDMode\fR, molname line in \fISDFile(s)\fR takes
490 precedence over sequential compound IDs generated using \fILabelPrefix\fR and only empty molname
491 values are replaced with sequential compound IDs.
492 .Sp
493 This is only used for \fICompoundID\fR value of \fB\-\-DataFieldsMode\fR option.
494 .ie n .IP "\fB\-\-DataFields\fR \fI""FieldLabel1,FieldLabel2,...""\fR" 4
495 .el .IP "\fB\-\-DataFields\fR \fI``FieldLabel1,FieldLabel2,...''\fR" 4
496 .IX Item "--DataFields FieldLabel1,FieldLabel2,..."
497 Comma delimited list of \fISDFiles(s)\fR data fields to extract and write to \s-1CSV/TSV\s0 text file(s) along
498 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option.
499 .Sp
500 This is only used for \fISpecify\fR value of \fB\-\-DataFieldsMode\fR option.
501 .Sp
502 Examples:
503 .Sp
504 .Vb 2
505 \& Extreg
506 \& MolID,CompoundName
507 .Ve
508 .IP "\fB\-d, \-\-DataFieldsMode\fR \fIAll | Common | Specify | CompoundID\fR" 4
509 .IX Item "-d, --DataFieldsMode All | Common | Specify | CompoundID"
510 Specify how data fields in \fISDFile(s)\fR are transferred to output \s-1CSV/TSV\s0 text file(s) along
511 with generated fingerprints for \fItext | all\fR values of \fB\-\-output\fR option: transfer all \s-1SD\s0
512 data field; transfer \s-1SD\s0 data files common to all compounds; extract specified data fields;
513 generate a compound \s-1ID\s0 using molname line, a compound prefix, or a combination of both.
514 Possible values: \fIAll | Common | specify | CompoundID\fR. Default value: \fICompoundID\fR.
515 .IP "\fB\-f, \-\-Filter\fR \fIYes | No\fR" 4
516 .IX Item "-f, --Filter Yes | No"
517 Specify whether to check and filter compound data in SDFile(s). Possible values: \fIYes or No\fR.
518 Default value: \fIYes\fR.
519 .Sp
520 By default, compound data is checked before calculating fingerprints and compounds containing
521 atom data corresponding to non-element symbols or no atom data are ignored.
522 .IP "\fB\-\-FingerprintsLabel\fR \fItext\fR" 4
523 .IX Item "--FingerprintsLabel text"
524 \&\s-1SD\s0 data label or text file column label to use for fingerprints string in output \s-1SD\s0 or
525 \&\s-1CSV/TSV\s0 text file(s) specified by \fB\-\-output\fR. Default value: \fITopologicalAtomTripletsFingerprints\fR.
526 .IP "\fB\-h, \-\-help\fR" 4
527 .IX Item "-h, --help"
528 Print this help message.
529 .IP "\fB\-k, \-\-KeepLargestComponent\fR \fIYes | No\fR" 4
530 .IX Item "-k, --KeepLargestComponent Yes | No"
531 Generate fingerprints for only the largest component in molecule. Possible values:
532 \&\fIYes or No\fR. Default value: \fIYes\fR.
533 .Sp
534 For molecules containing multiple connected components, fingerprints can be generated
535 in two different ways: use all connected components or just the largest connected
536 component. By default, all atoms except for the largest connected component are
537 deleted before generation of fingerprints.
538 .IP "\fB\-\-MinDistance\fR \fInumber\fR" 4
539 .IX Item "--MinDistance number"
540 Minimum bond distance between atom triplets for generating topological atom triplets. Default value:
541 \&\fI1\fR. Valid values: positive integers and less than \fB\-\-MaxDistance\fR.
542 .IP "\fB\-\-MaxDistance\fR \fInumber\fR" 4
543 .IX Item "--MaxDistance number"
544 Maximum bond distance between atom triplets for generating topological atom triplets. Default value:
545 \&\fI10\fR. Valid values: positive integers and greater than \fB\-\-MinDistance\fR.
546 .IP "\fB\-\-OutDelim\fR \fIcomma | tab | semicolon\fR" 4
547 .IX Item "--OutDelim comma | tab | semicolon"
548 Delimiter for output \s-1CSV/TSV\s0 text file(s). Possible values: \fIcomma, tab, or semicolon\fR
549 Default value: \fIcomma\fR
550 .IP "\fB\-\-output\fR \fI\s-1SD\s0 | \s-1FP\s0 | text | all\fR" 4
551 .IX Item "--output SD | FP | text | all"
552 Type of output files to generate. Possible values: \fI\s-1SD\s0, \s-1FP\s0, text, or all\fR. Default value: \fItext\fR.
553 .IP "\fB\-o, \-\-overwrite\fR" 4
554 .IX Item "-o, --overwrite"
555 Overwrite existing files.
556 .IP "\fB\-q, \-\-quote\fR \fIYes | No\fR" 4
557 .IX Item "-q, --quote Yes | No"
558 Put quote around column values in output \s-1CSV/TSV\s0 text file(s). Possible values:
559 \&\fIYes or No\fR. Default value: \fIYes\fR.
560 .IP "\fB\-r, \-\-root\fR \fIRootName\fR" 4
561 .IX Item "-r, --root RootName"
562 New file name is generated using the root: <Root>.<Ext>. Default for new file names:
563 <SDFileName><TopologicalAtomTripletsFP>.<Ext>. The file type determines <Ext> value.
564 The sdf, fpf, csv, and tsv <Ext> values are used for \s-1SD\s0, \s-1FP\s0, comma/semicolon, and tab
565 delimited text files, respectively.This option is ignored for multiple input files.
566 .IP "\fB\-u, \-\-UseTriangleInequality\fR \fIYes | No\fR" 4
567 .IX Item "-u, --UseTriangleInequality Yes | No"
568 Specify whether to imply triangle distance inequality test to distances between atom pairs in
569 atom triplets during generation of atom triplets generation. Possible values: \fIYes or No\fR.
570 Default value: \fINo\fR.
571 .Sp
572 Triangle distance inequality test implies that distance or binned distance between any two atom
573 pairs in an atom triplet must be less than the sum of distances or binned distances between other
574 two atoms pairs and greater than the difference of their distances.
575 .Sp
576 .Vb 1
577 \& For atom triplet ATx\-Dyz\-ATy\-Dxz\-ATz\-Dxy to satisfy triangle inequality:
578 \&
579 \& Dyz > |Dxz \- Dxy| and Dyz < Dxz + Dxy
580 \& Dxz > |Dyz \- Dxy| and Dyz < Dyz + Dxy
581 \& Dxy > |Dyz \- Dxz| and Dxy < Dyz + Dxz
582 .Ve
583 .IP "\fB\-v, \-\-VectorStringFormat\fR \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString\fR" 4
584 .IX Item "-v, --VectorStringFormat IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString"
585 Format of fingerprints vector string data in output \s-1SD\s0, \s-1FP\s0 or \s-1CSV/TSV\s0 text file(s) specified by
586 \&\fB\-\-output\fR option. Possible values: \fIIDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
587 ValuesAndIDsPairsString\fR. Default value: \fIIDsAndValuesString\fR.
588 .Sp
589 Examples:
590 .Sp
591 .Vb 7
592 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
593 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesString;C.X1
594 \& .BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D1
595 \& 0\-C.X3.BO4\-D9 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 C.X1.BO1.H3\-D1
596 \& \-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3....;
597 \& 1 2 2 2 2 2 2 2 8 8 4 8 4 4 2 2 2 2 4 2 2 2 4 2 2 2 2 1 2 2 4 4 4 2 2
598 \& 2 4 4 4 8 4 4 2 4 4 4 2 4 4 2 2 2 2 2 2 2 2 1 2 2 2 2 2 2 2 2 2 2 8...
599 \&
600 \& FingerprintsVector;TopologicalAtomTriplets:AtomicInvariantsAtomTypes:M
601 \& inDistance1:MaxDistance10;3096;NumericalValues;IDsAndValuesPairsString
602 \& ;C.X1.BO1.H3\-D1\-C.X1.BO1.H3\-D1\-C.X3.BO3.H1\-D2 1 C.X1.BO1.H3\-D1\-C.X2.BO
603 \& 2.H2\-D10\-C.X3.BO4\-D9 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D3\-N.X3.BO3\-D4 2 C.X
604 \& 1.BO1.H3\-D1\-C.X2.BO2.H2\-D4\-C.X2.BO2.H2\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2
605 \& \-D6\-C.X3.BO3.H1\-D5 2 C.X1.BO1.H3\-D1\-C.X2.BO2.H2\-D6\-C.X3.BO3.H1\-D7 2...
606 .Ve
607 .IP "\fB\-w, \-\-WorkingDir\fR \fIDirName\fR" 4
608 .IX Item "-w, --WorkingDir DirName"
609 Location of working directory. Default value: current directory.
610 .SH "EXAMPLES"
611 .IX Header "EXAMPLES"
612 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
613 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
614 file containing sequential compound IDs along with fingerprints vector strings data, type:
615 .PP
616 .Vb 1
617 \& % TopologicalAtomTripletsFingerprints.pl \-r SampleTATFP \-o Sample.sdf
618 .Ve
619 .PP
620 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
621 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
622 SampleTATFP.fpf and SampleTATFP.csv files containing sequential compound IDs in \s-1CSV\s0 file along
623 with fingerprints vector strings data, type:
624 .PP
625 .Vb 2
626 \& % TopologicalAtomTripletsFingerprints.pl \-\-output all \-r SampleTATFP
627 \& \-o Sample.sdf
628 .Ve
629 .PP
630 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
631 10 using atomic invariants atom types in IDsAndValuesPairsString format and create a SampleTATFP.csv
632 file containing sequential compound IDs along with fingerprints vector strings data, type:
633 .PP
634 .Vb 2
635 \& % TopologicalAtomTripletsFingerprints.pl \-\-VectorStringFormat
636 \& IDsAndValuesPairsString \-r SampleTATFP \-o Sample.sdf
637 .Ve
638 .PP
639 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
640 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
641 file containing sequential compound IDs along with fingerprints vector strings data, type:
642 .PP
643 .Vb 2
644 \& % TopologicalAtomTripletsFingerprints.pl \-a DREIDINGAtomTypes
645 \& \-r SampleTATFP \-o Sample.sdf
646 .Ve
647 .PP
648 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
649 10 using E\-state atom types in IDsAndValuesString format and create a SampleTATFP.csv
650 file containing sequential compound IDs along with fingerprints vector strings data, type:
651 .PP
652 .Vb 2
653 \& % TopologicalAtomTripletsFingerprints.pl \-a EStateAtomTypes
654 \& \-r SampleTATFP \-o Sample.sdf
655 .Ve
656 .PP
657 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
658 10 using functional class atom types in IDsAndValuesString format and create a SampleTATFP.csv
659 file containing sequential compound IDs along with fingerprints vector strings data, type:
660 .PP
661 .Vb 2
662 \& % TopologicalAtomTripletsFingerprints.pl \-a FunctionalClassAtomTypes
663 \& \-r SampleTATFP \-o Sample.sdf
664 .Ve
665 .PP
666 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
667 10 using \s-1DREIDING\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
668 file containing sequential compound IDs along with fingerprints vector strings data, type:
669 .PP
670 .Vb 2
671 \& % TopologicalAtomTripletsFingerprints.pl \-a DREIDINGAtomTypes
672 \& \-r SampleTATFP \-o Sample.sdf
673 .Ve
674 .PP
675 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
676 10 using \s-1MM94\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
677 file containing sequential compound IDs along with fingerprints vector strings data, type:
678 .PP
679 .Vb 2
680 \& % TopologicalAtomTripletsFingerprints.pl \-a MMFF94AtomTypes
681 \& \-r SampleTATFP \-o Sample.sdf
682 .Ve
683 .PP
684 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
685 10 using SLogP atom types in IDsAndValuesString format and create a SampleTATFP.csv
686 file containing sequential compound IDs along with fingerprints vector strings data, type:
687 .PP
688 .Vb 2
689 \& % TopologicalAtomTripletsFingerprints.pl \-a SLogPAtomTypes
690 \& \-r SampleTATFP \-o Sample.sdf
691 .Ve
692 .PP
693 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
694 10 using \s-1SYBYL\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
695 file containing sequential compound IDs along with fingerprints vector strings data, type:
696 .PP
697 .Vb 2
698 \& % TopologicalAtomTripletsFingerprints.pl \-a SYBYLAtomTypes
699 \& \-r SampleTATFP \-o Sample.sdf
700 .Ve
701 .PP
702 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
703 10 using \s-1TPSA\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
704 file containing sequential compound IDs along with fingerprints vector strings data, type:
705 .PP
706 .Vb 2
707 \& % TopologicalAtomTripletsFingerprints.pl \-a TPSAAtomTypes
708 \& \-r SampleTATFP \-o Sample.sdf
709 .Ve
710 .PP
711 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
712 10 using \s-1UFF\s0 atom types in IDsAndValuesString format and create a SampleTATFP.csv
713 file containing sequential compound IDs along with fingerprints vector strings data, type:
714 .PP
715 .Vb 2
716 \& % TopologicalAtomTripletsFingerprints.pl \-a UFFAtomTypes
717 \& \-r SampleTATFP \-o Sample.sdf
718 .Ve
719 .PP
720 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
721 6 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
722 file containing sequential compound IDs along with fingerprints vector strings data, type:
723 .PP
724 .Vb 2
725 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
726 \& \-\-MinDistance 1 \-\-MaxDistance 6 \-r SampleTATFP \-o Sample.sdf
727 .Ve
728 .PP
729 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
730 10 using only \s-1AS\s0,X atomic invariants atom types in IDsAndValuesString format and create a
731 SampleTATFP.csv file containing sequential compound IDs along with fingerprints vector strings
732 data, type:
733 .PP
734 .Vb 3
735 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
736 \& \-\-AtomicInvariantsToUse "AS,X" \-\-MinDistance 1 \-\-MaxDistance 6
737 \& \-r SampleTATFP \-o Sample.sdf
738 .Ve
739 .PP
740 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
741 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
742 file containing compound \s-1ID\s0 from molecule name line along with fingerprints vector strings
743 data, type:
744 .PP
745 .Vb 3
746 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
747 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolName
748 \& \-r SampleTATFP \-o Sample.sdf
749 .Ve
750 .PP
751 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
752 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
753 file containing compound IDs using specified data field along with fingerprints vector strings
754 data, type:
755 .PP
756 .Vb 3
757 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
758 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode DataField \-\-CompoundID
759 \& Mol_ID \-r SampleTATFP \-o Sample.sdf
760 .Ve
761 .PP
762 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
763 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
764 file containing compound \s-1ID\s0 using combination of molecule name line and an explicit compound
765 prefix along with fingerprints vector strings data, type:
766 .PP
767 .Vb 3
768 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
769 \& \-\-DataFieldsMode CompoundID \-CompoundIDMode MolnameOrLabelPrefix
770 \& \-\-CompoundID Cmpd \-\-CompoundIDLabel MolID \-r SampleTATFP \-o Sample.sdf
771 .Ve
772 .PP
773 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
774 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
775 file containing specific data fields columns along with fingerprints vector strings
776 data, type:
777 .PP
778 .Vb 3
779 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
780 \& \-\-DataFieldsMode Specify \-\-DataFields Mol_ID \-r SampleTATFP
781 \& \-o Sample.sdf
782 .Ve
783 .PP
784 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
785 10 using atomic invariants atom types in IDsAndValuesString format and create a SampleTATFP.csv
786 file containing common data fields columns along with fingerprints vector strings
787 data, type:
788 .PP
789 .Vb 2
790 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
791 \& \-\-DataFieldsMode Common \-r SampleTATFP \-o Sample.sdf
792 .Ve
793 .PP
794 To generate topological atom triplets fingerprints corresponding to bond distances from 1 through
795 10 using atomic invariants atom types in IDsAndValuesString format and create SampleTATFP.sdf,
796 SampleTATFP.fpf and SampleTATFP.csv files containing all data fields columns in \s-1CSV\s0 file along with
797 fingerprints data, type:
798 .PP
799 .Vb 3
800 \& % TopologicalAtomTripletsFingerprints.pl \-a AtomicInvariantsAtomTypes
801 \& \-\-DataFieldsMode All \-\-output all \-r SampleTATFP
802 \& \-o Sample.sdf
803 .Ve
804 .SH "AUTHOR"
805 .IX Header "AUTHOR"
806 Manish Sud <msud@san.rr.com>
807 .SH "SEE ALSO"
808 .IX Header "SEE ALSO"
809 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl, AtomNeighborhoodsFingerprints.pl,
810 ExtendedConnectivityFingerprints.pl, MACCSKeysFingerprints.pl,
811 PathLengthFingerprints.pl, TopologicalAtomTorsionsFingerprints.pl,
812 TopologicalPharmacophoreAtomPairsFingerprints.pl, TopologicalPharmacophoreAtomTripletsFingerprints.pl
813 .SH "COPYRIGHT"
814 .IX Header "COPYRIGHT"
815 Copyright (C) 2015 Manish Sud. All rights reserved.
816 .PP
817 This file is part of MayaChemTools.
818 .PP
819 MayaChemTools is free software; you can redistribute it and/or modify it under
820 the terms of the \s-1GNU\s0 Lesser General Public License as published by the Free
821 Software Foundation; either version 3 of the License, or (at your option)
822 any later version.