Mercurial > repos > deepakjadmin > mayatool3_test2

comparison docs/scripts/txt/TopologicalAtomTorsionsFingerprints.txt @ 0:4816e4a8ae95 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author deepakjadmin
date Wed, 20 Jan 2016 09:23:18 -0500
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:4816e4a8ae95
1 NAME
2 TopologicalAtomTorsionsFingerprints.pl - Generate topological atom
3 torsions fingerprints for SD files
4
5 SYNOPSIS
6 TopologicalAtomTorsionsFingerprints.pl SDFile(s)...
7
8 TopologicalAtomTorsionsFingerprints.pl [--AromaticityModel
9 *AromaticityModelType*] [-a, --AtomIdentifierType
10 *AtomicInvariantsAtomTypes*] [--AtomicInvariantsToUse
11 *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse
12 *"FunctionalClass1,FunctionalClass2..."*] [--CompoundID *DataFieldName
13 or LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode]
14 [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
15 *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*]
16 [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent
17 *Yes | No*] [--OutDelim *comma | tab | semicolon*] [--output *SD | FP |
18 text | all*] [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root
19 *RootName*] [-v, --VectorStringFormat] [-w, --WorkingDir dirname]
20 SDFile(s)...
21
22 DESCRIPTION
23 Generate topological atom torsions fingerprints [ Ref 58, Ref 72 ] for
24 *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
25 containing fingerprints vector strings corresponding to molecular
26 fingerprints.
27
28 Multiple SDFile names are separated by spaces. The valid file extensions
29 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
30 in a current directory can be specified either by **.sdf* or the current
31 directory name.
32
33 The current release of MayaChemTools supports generation of topological
34 atom torsions fingerprints corresponding to following -a,
35 --AtomIdentifierTypes:
36
37 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
38 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
39 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
40
41 Based on the values specified for -a, --AtomIdentifierType and
42 --AtomicInvariantsToUse, initial atom types are assigned to all
43 non-hydrogen atoms in a molecule. All unique atom torsions are
44 identified and an atom torsion identifier is generated; the format of
45 atom torsion identifier is:
46
47 <AtomType1>-<AtomType2>-<AtomType3>-<AtomType4>
48
49 AtomType1, AtomType2, AtomType3, AtomTyp4: Assigned atom types
50
51 where AtomType1 <= AtomType2 <= AtomType3 <= AtomType4
52
53 The atom torsion identifiers for all unique atom torsions corresponding
54 to non-hydrogen atoms constitute topological atom torsions fingerprints
55 of the molecule.
56
57 Example of *SD* file containing topological atom torsions fingerprints
58 string data:
59
60 ... ...
61 ... ...
62 $$$$
63 ... ...
64 ... ...
65 ... ...
66 41 44 0 0 0 0 0 0 0 0999 V2000
67 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
68 ... ...
69 2 3 1 0 0 0 0
70 ... ...
71 M END
72 > <CmpdID>
73 Cmpd1
74
75 > <TopologicalAtomTorsionsFingerprints>
76 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;33
77 ;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.
78 X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO2.H
79 2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O.X1....;
80 2 2 1 1 2 2 1 1 3 4 4 8 4 2 2 6 2 2 1 2 1 1 2 1 1 2 6 2 4 2 1 3 1
81
82 $$$$
83 ... ...
84 ... ...
85
86 Example of *FP* file containing topological atom torsions fingerprints
87 string data:
88
89 #
90 # Package = MayaChemTools 7.4
91 # Release Date = Oct 21, 2010
92 #
93 # TimeStamp = Fri Mar 11 15:17:20 2011
94 #
95 # FingerprintsStringType = FingerprintsVector
96 #
97 # Description = TopologicalAtomTorsions:AtomicInvariantsAtomTypes
98 # VectorStringFormat = IDsAndValuesString
99 # VectorValuesType = NumericalValues
100 #
101 Cmpd1 33;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-C.X3.BO4...;2 2 1 1 2 2 ...
102 Cmpd2 23;C.X1.BO1.H3-C.X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2...;2 2 1 5 ...
103 ... ...
104 ... ..
105
106 Example of CSV *Text* file containing topological atom torsions
107 fingerprints string data:
108
109 "CompoundID","TopologicalAtomTorsionsFingerprints"
110 "Cmpd1","FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAto
111 mTypes;33;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.
112 X3.BO4-C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C
113 .X2.BO2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3....;
114 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
115 ... ...
116 ... ...
117
118 The current release of MayaChemTools generates the following types of
119 topological atom torsions fingerprints vector strings:
120
121 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
122 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
123 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
124 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
125 ;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
126
127 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
128 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
129 .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
130 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
131 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
132 O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
133
134 FingerprintsVector;TopologicalAtomTorsions:DREIDINGAtomTypes;27;Numeri
135 calValues;IDsAndValuesString;C_2-C_3-C_3-C_3 C_2-C_3-C_3-O_3 C_2-C_R-C
136 _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
137 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_...;
138 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
139
140 FingerprintsVector;TopologicalAtomTorsions:EStateAtomTypes;36;Numerica
141 lValues;IDsAndValuesString;aaCH-aaCH-aaCH-aaCH aaCH-aaCH-aaCH-aasC aaC
142 H-aaCH-aasC-aaCH aaCH-aaCH-aasC-aasC aaCH-aaCH-aasC-sF aaCH-aaCH-aasC-
143 ssNH aaCH-aasC-aasC-aasC aaCH-aasC-aasC-aasN aaCH-aasC-ssNH-dssC a...;
144 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
145
146 FingerprintsVector;TopologicalAtomTorsions:FunctionalClassAtomTypes;26
147 ;NumericalValues;IDsAndValuesString;Ar-Ar-Ar-Ar Ar-Ar-Ar-Ar.HBA Ar-Ar-
148 Ar-HBD Ar-Ar-Ar-Hal Ar-Ar-Ar-None Ar-Ar-Ar.HBA-Ar Ar-Ar-Ar.HBA-None Ar
149 -Ar-HBD-None Ar-Ar-None-HBA Ar-Ar-None-HBD Ar-Ar-None-None Ar-Ar.H...;
150 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
151
152 FingerprintsVector;TopologicalAtomTorsions:MMFF94AtomTypes;43;Numerica
153 lValues;IDsAndValuesString;C5A-C5B-C5B-C5A C5A-C5B-C5B-C=ON C5A-C5B-C5
154 B-CB C5A-C5B-C=ON-NC=O C5A-C5B-C=ON-O=CN C5A-C5B-CB-CB C5A-CB-CB-CB C5
155 A-N5-C5A-C5B C5A-N5-C5A-CB C5A-N5-C5A-CR C5A-N5-CR-CR C5B-C5A-CB-C...;
156 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
157 1 1 2 1 1 3 1 3
158
159 FingerprintsVector;TopologicalAtomTorsions:SLogPAtomTypes;49;Numerical
160 Values;IDsAndValuesPairsString;C1-C10-N11-C20 1 C1-C10-N11-C21 1 C1-C1
161 1-C21-C21 2 C1-C11-C21-N11 2 C1-CS-C1-C10 1 C1-CS-C1-C5 1 C1-CS-C1-CS
162 2 C10-C1-CS-O2 1 C10-N11-C20-C20 2 C10-N11-C21-C11 1 C10-N11-C21-C21 1
163 C11-C21-C21-C20 1 C11-C21-C21-C5 1 C11-C21-N11-C20 1 C14-C18-C18-C20
164 2 C18-C14-C18-C18 2 C18-C18-C14-F 2 C18-C18-C18-C18 4 C18-C18-C18-C...
165
166 FingerprintsVector;TopologicalAtomTorsions:SYBYLAtomTypes;26;Numerical
167 Values;IDsAndValuesPairsString;C.2-C.3-C.3-C.3 1 C.2-C.3-C.3-O.3 1 C.2
168 -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.
169 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
170 -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.
171 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 ...
172
173 FingerprintsVector;TopologicalAtomTorsions:TPSAAtomTypes;8;NumericalVa
174 lues;IDsAndValuesPairsString;N21-None-None-None 9 N7-None-None-None 4
175 None-N21-None-None 10 None-N7-None-None 3 None-N7-None-O3 1 None-None-
176 None-None 44 None-None-None-O3 3 None-None-None-O4 5
177
178 FingerprintsVector;TopologicalAtomTorsions:UFFAtomTypes;27;NumericalVa
179 lues;IDsAndValuesPairsString;C_2-C_3-C_3-C_3 1 C_2-C_3-C_3-O_3 1 C_2-C
180 _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
181 -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
182 _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
183 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-...
184
185 OPTIONS
186 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
187 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
188 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
189 MayaChemToolsAromaticityModel*
190 Specify aromaticity model to use during detection of aromaticity.
191 Possible values in the current release are: *MDLAromaticityModel,
192 TriposAromaticityModel, MMFFAromaticityModel,
193 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
194 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
195 value: *MayaChemToolsAromaticityModel*.
196
197 The supported aromaticity model names along with model specific
198 control parameters are defined in AromaticityModelsData.csv, which
199 is distributed with the current release and is available under
200 lib/data directory. Molecule.pm module retrieves data from this file
201 during class instantiation and makes it available to method
202 DetectAromaticity for detecting aromaticity corresponding to a
203 specific model.
204
205 -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
206 | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
207 SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
208 Specify atom identifier type to use for assignment of initial atom
209 identifier to non-hydrogen atoms during calculation of topological
210 atom torsions fingerprints. Possible values in the current release
211 are: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
212 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
213 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
214 *AtomicInvariantsAtomTypes*.
215
216 --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
217 This value is used during *AtomicInvariantsAtomTypes* value of a,
218 --AtomIdentifierType option. It's a list of comma separated valid
219 atomic invariant atom types.
220
221 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
222 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
223
224 The atomic invariants abbreviations correspond to:
225
226 AS = Atom symbol corresponding to element symbol
227
228 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
229 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
230 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
231 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
232 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
233 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
234 H<n> = Number of implicit and explicit hydrogens for atom
235 Ar = Aromatic annotation indicating whether atom is aromatic
236 RA = Ring atom annotation indicating whether atom is a ring
237 FC<+n/-n> = Formal charge assigned to atom
238 MN<n> = Mass number indicating isotope other than most abundant isotope
239 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
240 3 (triplet)
241
242 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
243 corresponds to:
244
245 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
246
247 Except for AS which is a required atomic invariant in atom types,
248 all other atomic invariants are optional. Atom type specification
249 doesn't include atomic invariants with zero or undefined values.
250
251 In addition to usage of abbreviations for specifying atomic
252 invariants, the following descriptive words are also allowed:
253
254 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
255 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
256 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
257 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
258 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
259 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
260 H : NumOfImplicitAndExplicitHydrogens
261 Ar : Aromatic
262 RA : RingAtom
263 FC : FormalCharge
264 MN : MassNumber
265 SM : SpinMultiplicity
266
267 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
268 atomic invariant atom types.
269
270 --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
271 This value is used during *FunctionalClassAtomTypes* value of a,
272 --AtomIdentifierType option. It's a list of comma separated valid
273 functional classes.
274
275 Possible values for atom functional classes are: *Ar, CA, H, HBA,
276 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
277 *HBD,HBA,PI,NI,Ar,Hal*.
278
279 The functional class abbreviations correspond to:
280
281 HBD: HydrogenBondDonor
282 HBA: HydrogenBondAcceptor
283 PI : PositivelyIonizable
284 NI : NegativelyIonizable
285 Ar : Aromatic
286 Hal : Halogen
287 H : Hydrophobic
288 RA : RingAtom
289 CA : ChainAtom
290
291 Functional class atom type specification for an atom corresponds to:
292
293 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
294
295 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
296 functional class atom types. It uses following definitions [ Ref
297 60-61, Ref 65-66 ]:
298
299 HydrogenBondDonor: NH, NH2, OH
300 HydrogenBondAcceptor: N[!H], O
301 PositivelyIonizable: +, NH2
302 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
303
304 --CompoundID *DataFieldName or LabelPrefixString*
305 This value is --CompoundIDMode specific and indicates how compound
306 ID is generated.
307
308 For *DataField* value of --CompoundIDMode option, it corresponds to
309 datafield label name whose value is used as compound ID; otherwise,
310 it's a prefix string used for generating compound IDs like
311 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
312 IDs which look like Cmpd<Number>.
313
314 Examples for *DataField* value of --CompoundIDMode:
315
316 MolID
317 ExtReg
318
319 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
320 --CompoundIDMode:
321
322 Compound
323
324 The value specified above generates compound IDs which correspond to
325 Compound<Number> instead of default value of Cmpd<Number>.
326
327 --CompoundIDLabel *text*
328 Specify compound ID column label for CSV/TSV text file(s) used
329 during *CompoundID* value of --DataFieldsMode option. Default value:
330 *CompoundID*.
331
332 --CompoundIDMode *DataField | MolName | LabelPrefix |
333 MolNameOrLabelPrefix*
334 Specify how to generate compound IDs and write to FP or CSV/TSV text
335 file(s) along with generated fingerprints for *FP | text | all*
336 values of --output option: use a *SDFile(s)* datafield value; use
337 molname line from *SDFile(s)*; generate a sequential ID with
338 specific prefix; use combination of both MolName and LabelPrefix
339 with usage of LabelPrefix values for empty molname lines.
340
341 Possible values: *DataField | MolName | LabelPrefix |
342 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
343
344 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
345 in *SDFile(s)* takes precedence over sequential compound IDs
346 generated using *LabelPrefix* and only empty molname values are
347 replaced with sequential compound IDs.
348
349 This is only used for *CompoundID* value of --DataFieldsMode option.
350
351 --DataFields *"FieldLabel1,FieldLabel2,..."*
352 Comma delimited list of *SDFiles(s)* data fields to extract and
353 write to CSV/TSV text file(s) along with generated fingerprints for
354 *text | all* values of --output option.
355
356 This is only used for *Specify* value of --DataFieldsMode option.
357
358 Examples:
359
360 Extreg
361 MolID,CompoundName
362
363 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
364 Specify how data fields in *SDFile(s)* are transferred to output
365 CSV/TSV text file(s) along with generated fingerprints for *text |
366 all* values of --output option: transfer all SD data field; transfer
367 SD data files common to all compounds; extract specified data
368 fields; generate a compound ID using molname line, a compound
369 prefix, or a combination of both. Possible values: *All | Common |
370 specify | CompoundID*. Default value: *CompoundID*.
371
372 -f, --Filter *Yes | No*
373 Specify whether to check and filter compound data in SDFile(s).
374 Possible values: *Yes or No*. Default value: *Yes*.
375
376 By default, compound data is checked before calculating fingerprints
377 and compounds containing atom data corresponding to non-element
378 symbols or no atom data are ignored.
379
380 --FingerprintsLabel *text*
381 SD data label or text file column label to use for fingerprints
382 string in output SD or CSV/TSV text file(s) specified by --output.
383 Default value: *TopologicalAtomTorsionsFingerprints*.
384
385 -h, --help
386 Print this help message.
387
388 -k, --KeepLargestComponent *Yes | No*
389 Generate fingerprints for only the largest component in molecule.
390 Possible values: *Yes or No*. Default value: *Yes*.
391
392 For molecules containing multiple connected components, fingerprints
393 can be generated in two different ways: use all connected components
394 or just the largest connected component. By default, all atoms
395 except for the largest connected component are deleted before
396 generation of fingerprints.
397
398 --OutDelim *comma | tab | semicolon*
399 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
400 tab, or semicolon* Default value: *comma*.
401
402 --output *SD | FP | text | all*
403 Type of output files to generate. Possible values: *SD, FP, text, or
404 all*. Default value: *text*.
405
406 -o, --overwrite
407 Overwrite existing files.
408
409 -q, --quote *Yes | No*
410 Put quote around column values in output CSV/TSV text file(s).
411 Possible values: *Yes or No*. Default value: *Yes*
412
413 -r, --root *RootName*
414 New file name is generated using the root: <Root>.<Ext>. Default for
415 new file names: <SDFileName><TopologicalAtomTorsionsFP>.<Ext>. The
416 file type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext>
417 values are used for SD, FP, comma/semicolon, and tab delimited text
418 files, respectively.This option is ignored for multiple input files.
419
420 -v, --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString |
421 ValuesAndIDsString | ValuesAndIDsPairsString*
422 Format of fingerprints vector string data in output SD, FP or
423 CSV/TSV text file(s) specified by --output option. Possible values:
424 *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
425 ValuesAndIDsPairsString*. Defaultvalue: *IDsAndValuesString*.
426
427 Examples:
428
429 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
430 3;NumericalValues;IDsAndValuesString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-
431 C.X3.BO4 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 C.X2.BO2.H2-C.X2.BO
432 2.H2-C.X3.BO3.H1-C.X2.BO2.H2 C.X2.BO2.H2-C.X2.BO2.H2-C.X3.BO3.H1-O...;
433 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
434
435 FingerprintsVector;TopologicalAtomTorsions:AtomicInvariantsAtomTypes;3
436 3;NumericalValues;IDsAndValuesPairsString;C.X1.BO1.H3-C.X3.BO3.H1-C.X3
437 .BO4-C.X3.BO4 2 C.X1.BO1.H3-C.X3.BO3.H1-C.X3.BO4-N.X3.BO3 2 C.X2.BO2.H
438 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
439 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
440 O2.H2-C.X3.BO3.H1-C.X2.BO2.H2-C.X3.BO3.H1 2 C.X2.BO2.H2-C.X3.BO3.H1...
441
442 -w, --WorkingDir *DirName*
443 Location of working directory. Default value: current directory.
444
445 EXAMPLES
446 To generate topological atom torsions fingerprints using atomic
447 invariants atom types in IDsAndValuesString format and create a
448 SampleTATFP.csv file containing sequential compound IDs along with
449 fingerprints vector strings data, type:
450
451 % TopologicalAtomTorsionsFingerprints.pl -r SampleTATFP -o Sample.sdf
452
453 To generate topological atom torsions fingerprints using atomic
454 invariants atom types in IDsAndValuesString format and create
455 SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv files containing
456 sequential compound IDs in CSV file along with fingerprints vector
457 strings data, type:
458
459 % TopologicalAtomTorsionsFingerprints.pl --output all -r SampleTATFP
460 -o Sample.sdf
461
462 To generate topological atom torsions fingerprints using atomic
463 invariants atom types in IDsAndValuesPairsString format and create a
464 SampleTATFP.csv file containing sequential compound IDs along with
465 fingerprints vector strings data, type:
466
467 % TopologicalAtomTorsionsFingerprints.pl --VectorStringFormat
468 IDsAndValuesPairsString -r SampleTATFP -o Sample.sdf
469
470 To generate topological atom torsions fingerprints using DREIDING atom
471 types in IDsAndValuesString format and create a SampleTATFP.csv file
472 containing sequential compound IDs along with fingerprints vector
473 strings data, type:
474
475 % TopologicalAtomTorsionsFingerprints.pl -a DREIDINGAtomTypes
476 -r SampleTATFP -o Sample.sdf
477
478 To generate topological atom torsions fingerprints using E-state atom
479 types in IDsAndValuesString format and create a SampleTATFP.csv file
480 containing sequential compound IDs along with fingerprints vector
481 strings data, type:
482
483 % TopologicalAtomTorsionsFingerprints.pl -a EStateAtomTypes
484 -r SampleTATFP -o Sample.sdf
485
486 To generate topological atom torsions fingerprints using functional
487 class atom types in IDsAndValuesString format and create a
488 SampleTATFP.csv file containing sequential compound IDs along with
489 fingerprints vector strings data, type:
490
491 % TopologicalAtomTorsionsFingerprints.pl -a FunctionalClassAtomTypes
492 -r SampleTATFP -o Sample.sdf
493
494 To generate topological atom torsions fingerprints using MMFF94 atom
495 types in IDsAndValuesString format and create a SampleTATFP.csv file
496 containing sequential compound IDs along with fingerprints vector
497 strings data, type:
498
499 % TopologicalAtomTorsionsFingerprints.pl -a MMFF94AtomTypes
500 -r SampleTATFP -o Sample.sdf
501
502 To generate topological atom torsions fingerprints using SLogP atom
503 types in IDsAndValuesString format and create a SampleTATFP.csv file
504 containing sequential compound IDs along with fingerprints vector
505 strings data, type:
506
507 % TopologicalAtomTorsionsFingerprints.pl -a SLogPAtomTypes
508 -r SampleTATFP -o Sample.sdf
509
510 To generate topological atom torsions fingerprints using SYBYL atom
511 types in IDsAndValuesString format and create a SampleTATFP.csv file
512 containing sequential compound IDs along with fingerprints vector
513 strings data, type:
514
515 % TopologicalAtomTorsionsFingerprints.pl -a SYBYLAtomTypes
516 -r SampleTATFP -o Sample.sdf
517
518 To generate topological atom torsions fingerprints using TPSA atom types
519 in IDsAndValuesString format and create a SampleTATFP.csv file
520 containing sequential compound IDs along with fingerprints vector
521 strings data, type:
522
523 % TopologicalAtomTorsionsFingerprints.pl -a TPSAAtomTypes
524 -r SampleTATFP -o Sample.sdf
525
526 To generate topological atom torsions fingerprints using UFF atom types
527 in IDsAndValuesString format and create a SampleTATFP.csv file
528 containing sequential compound IDs along with fingerprints vector
529 strings data, type:
530
531 % TopologicalAtomTorsionsFingerprints.pl -a UFFAtomTypes
532 -r SampleTATFP -o Sample.sdf
533
534 To generate topological atom torsions fingerprints using only AS,X
535 atomic invariants atom types in IDsAndValuesString format and create a
536 SampleTATFP.csv file containing sequential compound IDs along with
537 fingerprints vector strings data, type:
538
539 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
540 --AtomicInvariantsToUse "AS,X" -r SampleTATFP -o Sample.sdf
541
542 To generate topological atom torsions fingerprints using atomic
543 invariants atom types in IDsAndValuesString format and create a
544 SampleTATFP.csv file containing compoundID from molecule name line along
545 with fingerprints vector strings, type:
546
547 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
548 --DataFieldsMode CompoundID -CompoundIDMode MolName
549 -r SampleTATFP -o Sample.sdf
550
551 To generate topological atom torsions fingerprints using atomic
552 invariants atom types in IDsAndValuesString format and create a
553 SampleTATFP.csv file containing compound IDs using specified data field
554 along with fingerprints vector strings, type:
555
556 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
557 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
558 Mol_ID -r SampleTATFP -o Sample.sdf
559
560 To generate topological atom torsions fingerprints using atomic
561 invariants atom types in IDsAndValuesString format and create a
562 SampleTATFP.csv file containing compound ID using combination of
563 molecule name line and an explicit compound prefix along with
564 fingerprints vector strings data, type:
565
566 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
567 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
568 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTATFP -o Sample.sdf
569
570 To generate topological atom torsions fingerprints using atomic
571 invariants atom types in IDsAndValuesString format and create a
572 SampleTATFP.csv file containing specific data fields columns along with
573 fingerprints vector strings, type:
574
575 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
576 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTATFP
577 -o Sample.sdf
578
579 To generate topological atom torsions fingerprints using atomic
580 invariants atom types in IDsAndValuesString format and create a
581 SampleTATFP.csv file containing common data fields columns along with
582 fingerprints vector strings, type:
583
584 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
585 --DataFieldsMode Common -r SampleTATFP -o Sample.sdf
586
587 To generate topological atom torsions fingerprints using atomic
588 invariants atom types in IDsAndValuesString format and create
589 SampleTATFP.sdf, SampleTATFP.fpf and SampleTATFP.csv files containing
590 all data fields columns in CSV file along with fingerprints data, type:
591
592 % TopologicalAtomTorsionsFingerprints.pl -a AtomicInvariantsAtomTypes
593 --DataFieldsMode All --output all -r SampleTATFP
594 -o Sample.sdf
595
596 AUTHOR
597 Manish Sud <msud@san.rr.com>
598
599 SEE ALSO
600 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
601 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
602 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
603 TopologicalAtomPairsFingerprints.pl,
604 TopologicalPharmacophoreAtomPairsFingerprints.pl,
605 TopologicalPharmacophoreAtomTripletsFingerprints.pl
606
607 COPYRIGHT
608 Copyright (C) 2015 Manish Sud. All rights reserved.
609
610 This file is part of MayaChemTools.
611
612 MayaChemTools is free software; you can redistribute it and/or modify it
613 under the terms of the GNU Lesser General Public License as published by
614 the Free Software Foundation; either version 3 of the License, or (at
615 your option) any later version.
616