|
1
|
1 NAME
|
|
|
2 TopologicalAtomPairsFingerprints.pl - Generate topological atom pairs
|
|
|
3 fingerprints for SD files
|
|
|
4
|
|
|
5 SYNOPSIS
|
|
|
6 TopologicalAtomPairsFingerprints.pl SDFile(s)...
|
|
|
7
|
|
|
8 TopologicalAtomPairsFingerprints.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*] [--MinDistance *number*] [--MaxDistance *number*]
|
|
|
18 [--OutDelim *comma | tab | semicolon*] [--output *SD | FP | text | all*]
|
|
|
19 [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root *RootName*] [-v,
|
|
|
20 --VectorStringFormat *ValuesString, IDsAndValuesString |
|
|
|
21 IDsAndValuesPairsString | ValuesAndIDsString | ValuesAndIDsPairsString*]
|
|
|
22 [-w, --WorkingDir dirname] SDFile(s)...
|
|
|
23
|
|
|
24 DESCRIPTION
|
|
|
25 Generate topological atom pairs fingerprints [ Ref 57, Ref 59, Ref 72 ]
|
|
|
26 for *SDFile(s)* and create appropriate SD, FP or CSV/TSV text file(s)
|
|
|
27 containing fingerprints vector strings corresponding to molecular
|
|
|
28 fingerprints.
|
|
|
29
|
|
|
30 Multiple SDFile names are separated by spaces. The valid file extensions
|
|
|
31 are *.sdf* and *.sd*. All other file names are ignored. All the SD files
|
|
|
32 in a current directory can be specified either by **.sdf* or the current
|
|
|
33 directory name.
|
|
|
34
|
|
|
35 The current release of MayaChemTools supports generation of topological
|
|
|
36 atom pairs corresponding to following -a, --AtomIdentifierTypes:
|
|
|
37
|
|
|
38 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
39 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
40 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
41
|
|
|
42 Based on the values specified for -a, --AtomIdentifierType and
|
|
|
43 --AtomicInvariantsToUse, initial atom types are assigned to all
|
|
|
44 non-hydrogen atoms in a molecule. Using the distance matrix for the
|
|
|
45 molecule and initial atom types assigned to non-hydrogen atoms, all
|
|
|
46 unique atom pairs within --MinDistance and --MaxDistance are identified
|
|
|
47 and counted. An atom pair identifier is generated for each unique atom
|
|
|
48 pair; the format of the atom pair identifier is:
|
|
|
49
|
|
|
50 <AtomType1>-D<n>-<AtomType2>
|
|
|
51
|
|
|
52 AtomType1, AtomType2: Atom types assigned to atom1 and atom2
|
|
|
53 D: Distance between atom1 and atom2
|
|
|
54
|
|
|
55 where AtomType1 <= AtomType2
|
|
|
56
|
|
|
57 The atom pair identifiers for all unique atom pairs corresponding to
|
|
|
58 non-hydrogen atoms constitute topological atom pairs fingerprints of the
|
|
|
59 molecule.
|
|
|
60
|
|
|
61 Example of *SD* file containing topological atom pairs fingerprints
|
|
|
62 string data:
|
|
|
63
|
|
|
64 ... ...
|
|
|
65 ... ...
|
|
|
66 $$$$
|
|
|
67 ... ...
|
|
|
68 ... ...
|
|
|
69 ... ...
|
|
|
70 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
71 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
72 ... ...
|
|
|
73 2 3 1 0 0 0 0
|
|
|
74 ... ...
|
|
|
75 M END
|
|
|
76 > <CmpdID>
|
|
|
77 Cmpd1
|
|
|
78
|
|
|
79 > <TopologicalAtomPairsFingerprints>
|
|
|
80 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi
|
|
|
81 stance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1.H
|
|
|
82 3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.H1
|
|
|
83 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-C.X2...;
|
|
|
84 2 1 4 1 1 10 8 1 2 6 1 2 2 1 2 1 2 2 1 2 1 5 1 10 12 2 2 1 2 1 9 1 3 1
|
|
|
85 1 1 2 2 1 3 6 1 6 14 2 2 2 3 1 3 1 8 2 2 1 3 2 6 1 2 2 5 1 3 1 23 1 ...
|
|
|
86
|
|
|
87 $$$$
|
|
|
88 ... ...
|
|
|
89 ... ...
|
|
|
90
|
|
|
91 Example of *FP* file containing topological atom pairs fingerprints
|
|
|
92 string data:
|
|
|
93
|
|
|
94 #
|
|
|
95 # Package = MayaChemTools 7.4
|
|
|
96 # Release Date = Oct 21, 2010
|
|
|
97 #
|
|
|
98 # TimeStamp = Fri Mar 11 15:04:36 2011
|
|
|
99 #
|
|
|
100 # FingerprintsStringType = FingerprintsVector
|
|
|
101 #
|
|
|
102 # Description = TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinDi...
|
|
|
103 # VectorStringFormat = IDsAndValuesString
|
|
|
104 # VectorValuesType = NumericalValues
|
|
|
105 #
|
|
|
106 Cmpd1 223;C.X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2...;1 1...
|
|
|
107 Cmpd2 128;C.X1.BO1.H3-D1-C.X2.BO2.H2 C.X1.BO1.H3-D1-C.X3.BO4...;1 1...
|
|
|
108 ... ...
|
|
|
109 ... ..
|
|
|
110
|
|
|
111 Example of CSV *Text* file containing topological atom pairs
|
|
|
112 fingerprints string data:
|
|
|
113
|
|
|
114 "CompoundID","TopologicalAtomPairsFingerprints"
|
|
|
115 "Cmpd1","FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTy
|
|
|
116 pes:MinDistance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C
|
|
|
117 .X1.BO1.H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X
|
|
|
118 3.BO3.H1C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1...;
|
|
|
119 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
|
|
|
120 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 ...
|
|
|
121 ... ...
|
|
|
122 ... ...
|
|
|
123
|
|
|
124 The current release of MayaChemTools generates the following types of
|
|
|
125 topological atom pairs fingerprints vector strings:
|
|
|
126
|
|
|
127 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
128 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
129 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
130 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
131 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
|
|
|
132 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...
|
|
|
133
|
|
|
134 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
135 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
|
|
|
136 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
|
|
|
137 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
|
|
|
138 .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
|
|
|
139 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...
|
|
|
140
|
|
|
141 FingerprintsVector;TopologicalAtomPairs:DREIDINGAtomTypes:MinDistance1
|
|
|
142 :MaxDistance10;157;NumericalValues;IDsAndValuesString;C_2-D1-C_3 C_2-D
|
|
|
143 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_
|
|
|
144 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
|
|
|
145 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
|
|
|
146 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...
|
|
|
147
|
|
|
148 FingerprintsVector;TopologicalAtomPairs:EStateAtomTypes:MinDistance1:M
|
|
|
149 axDistance10;251;NumericalValues;IDsAndValuesString;aaCH-D1-aaCH aaCH-
|
|
|
150 D1-aasC aasC-D1-aasC aasC-D1-aasN aasC-D1-dssC aasC-D1-sF aasC-D1-ssNH
|
|
|
151 aasC-D1-sssCH aasN-D1-ssCH2 dO-D1-dssC dssC-D1-sOH dssC-D1-ssCH2 d...;
|
|
|
152 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
|
|
|
153 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...
|
|
|
154
|
|
|
155 FingerprintsVector;TopologicalAtomPairs:FunctionalClassAtomTypes:MinDi
|
|
|
156 stance1:MaxDistance10;144;NumericalValues;IDsAndValuesString;Ar-D1-Ar
|
|
|
157 Ar-D1-Ar.HBA Ar-D1-HBD Ar-D1-Hal Ar-D1-None Ar.HBA-D1-None HBA-D1-NI H
|
|
|
158 BA-D1-None HBA.HBD-D1-NI HBA.HBD-D1-None HBD-D1-None NI-D1-None No...;
|
|
|
159 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
|
|
|
160 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 ...
|
|
|
161
|
|
|
162 FingerprintsVector;TopologicalAtomPairs:MMFF94AtomTypes:MinDistance1:M
|
|
|
163 axDistance10;227;NumericalValues;IDsAndValuesPairsString;C5A-D1-C5B 2
|
|
|
164 C5A-D1-CB 1 C5A-D1-CR 1 C5A-D1-N5 2 C5B-D1-C5B 1 C5B-D1-C=ON 1 C5B-D1-
|
|
|
165 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
|
|
|
166 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
|
|
|
167 2 C5A-D2-C5A 1 C5A-D2-C5B 2 C5A-D2-C=ON 1 C5A-D2-CB 3 C5A-D2-CR 4 ...
|
|
|
168
|
|
|
169 FingerprintsVector;TopologicalAtomPairs:SLogPAtomTypes:MinDistance1:Ma
|
|
|
170 xDistance10;329;NumericalValues;IDsAndValuesPairsString;C1-D1-C10 1 C1
|
|
|
171 -D1-C11 2 C1-D1-C5 1 C1-D1-CS 4 C10-D1-N11 1 C11-D1-C21 1 C14-D1-C18 2
|
|
|
172 C14-D1-F 1 C18-D1-C18 10 C18-D1-C20 4 C18-D1-C22 2 C20-D1-C20 3 C20-D
|
|
|
173 1-C21 1 C20-D1-N11 1 C21-D1-C21 1 C21-D1-C5 1 C21-D1-N11 1 C22-D1-N4 1
|
|
|
174 C5-D1-N4 1 C5-D1-O10 1 C5-D1-O2 1 C5-D1-O9 1 CS-D1-O2 2 C1-D2-C1 3...
|
|
|
175
|
|
|
176 FingerprintsVector;TopologicalAtomPairs:SYBYLAtomTypes:MinDistance1:Ma
|
|
|
177 xDistance10;159;NumericalValues;IDsAndValuesPairsString;C.2-D1-C.3 1 C
|
|
|
178 .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.
|
|
|
179 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
|
|
|
180 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
|
|
|
181 -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...
|
|
|
182
|
|
|
183 FingerprintsVector;TopologicalAtomPairs:TPSAAtomTypes:MinDistance1:Max
|
|
|
184 Distance10;64;NumericalValues;IDsAndValuesPairsString;N21-D1-None 3 N7
|
|
|
185 -D1-None 2 None-D1-None 34 None-D1-O3 2 None-D1-O4 3 N21-D2-None 5 N7-
|
|
|
186 D2-None 3 N7-D2-O3 1 None-D2-None 44 None-D2-O3 2 None-D2-O4 5 O3-D2-O
|
|
|
187 4 1 N21-D3-None 7 N7-D3-None 4 None-D3-None 45 None-D3-O3 4 None-D3-O4
|
|
|
188 5 N21-D4-N7 1 N21-D4-None 5 N21-D4-O3 1 N21-D4-O4 1 N7-D4-None 4 N...
|
|
|
189
|
|
|
190 FingerprintsVector;TopologicalAtomPairs:UFFAtomTypes:MinDistance1:MaxD
|
|
|
191 istance10;157;NumericalValues;IDsAndValuesPairsString;C_2-D1-C_3 1 C_2
|
|
|
192 -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
|
|
|
193 _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
|
|
|
194 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
|
|
|
195 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-...
|
|
|
196
|
|
|
197 OPTIONS
|
|
|
198 --AromaticityModel *MDLAromaticityModel | TriposAromaticityModel |
|
|
|
199 MMFFAromaticityModel | ChemAxonBasicAromaticityModel |
|
|
|
200 ChemAxonGeneralAromaticityModel | DaylightAromaticityModel |
|
|
|
201 MayaChemToolsAromaticityModel*
|
|
|
202 Specify aromaticity model to use during detection of aromaticity.
|
|
|
203 Possible values in the current release are: *MDLAromaticityModel,
|
|
|
204 TriposAromaticityModel, MMFFAromaticityModel,
|
|
|
205 ChemAxonBasicAromaticityModel, ChemAxonGeneralAromaticityModel,
|
|
|
206 DaylightAromaticityModel or MayaChemToolsAromaticityModel*. Default
|
|
|
207 value: *MayaChemToolsAromaticityModel*.
|
|
|
208
|
|
|
209 The supported aromaticity model names along with model specific
|
|
|
210 control parameters are defined in AromaticityModelsData.csv, which
|
|
|
211 is distributed with the current release and is available under
|
|
|
212 lib/data directory. Molecule.pm module retrieves data from this file
|
|
|
213 during class instantiation and makes it available to method
|
|
|
214 DetectAromaticity for detecting aromaticity corresponding to a
|
|
|
215 specific model.
|
|
|
216
|
|
|
217 -a, --AtomIdentifierType *AtomicInvariantsAtomTypes | DREIDINGAtomTypes
|
|
|
218 | EStateAtomTypes | FunctionalClassAtomTypes | MMFF94AtomTypes |
|
|
|
219 SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes | UFFAtomTypes*
|
|
|
220 Specify atom identifier type to use for assignment of initial atom
|
|
|
221 identifier to non-hydrogen atoms during calculation of topological
|
|
|
222 atom pairs fingerprints. Possible values in the current release are:
|
|
|
223 *AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
224 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
225 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*. Default value:
|
|
|
226 *AtomicInvariantsAtomTypes*.
|
|
|
227
|
|
|
228 --AtomicInvariantsToUse *"AtomicInvariant,AtomicInvariant..."*
|
|
|
229 This value is used during *AtomicInvariantsAtomTypes* value of a,
|
|
|
230 --AtomIdentifierType option. It's a list of comma separated valid
|
|
|
231 atomic invariant atom types.
|
|
|
232
|
|
|
233 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
|
|
|
234 TB, H, Ar, RA, FC, MN, SM*. Default value: *AS,X,BO,H,FC*.
|
|
|
235
|
|
|
236 The atomic invariants abbreviations correspond to:
|
|
|
237
|
|
|
238 AS = Atom symbol corresponding to element symbol
|
|
|
239
|
|
|
240 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
241 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
242 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
243 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
244 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
245 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
246 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
247 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
248 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
249 FC<+n/-n> = Formal charge assigned to atom
|
|
|
250 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
251 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
252 3 (triplet)
|
|
|
253
|
|
|
254 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
|
|
|
255 corresponds to:
|
|
|
256
|
|
|
257 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
258
|
|
|
259 Except for AS which is a required atomic invariant in atom types,
|
|
|
260 all other atomic invariants are optional. Atom type specification
|
|
|
261 doesn't include atomic invariants with zero or undefined values.
|
|
|
262
|
|
|
263 In addition to usage of abbreviations for specifying atomic
|
|
|
264 invariants, the following descriptive words are also allowed:
|
|
|
265
|
|
|
266 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
267 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
268 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
269 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
270 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
271 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
272 H : NumOfImplicitAndExplicitHydrogens
|
|
|
273 Ar : Aromatic
|
|
|
274 RA : RingAtom
|
|
|
275 FC : FormalCharge
|
|
|
276 MN : MassNumber
|
|
|
277 SM : SpinMultiplicity
|
|
|
278
|
|
|
279 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
|
|
|
280 atomic invariant atom types.
|
|
|
281
|
|
|
282 --FunctionalClassesToUse *"FunctionalClass1,FunctionalClass2..."*
|
|
|
283 This value is used during *FunctionalClassAtomTypes* value of a,
|
|
|
284 --AtomIdentifierType option. It's a list of comma separated valid
|
|
|
285 functional classes.
|
|
|
286
|
|
|
287 Possible values for atom functional classes are: *Ar, CA, H, HBA,
|
|
|
288 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
|
|
|
289 *HBD,HBA,PI,NI,Ar,Hal*.
|
|
|
290
|
|
|
291 The functional class abbreviations correspond to:
|
|
|
292
|
|
|
293 HBD: HydrogenBondDonor
|
|
|
294 HBA: HydrogenBondAcceptor
|
|
|
295 PI : PositivelyIonizable
|
|
|
296 NI : NegativelyIonizable
|
|
|
297 Ar : Aromatic
|
|
|
298 Hal : Halogen
|
|
|
299 H : Hydrophobic
|
|
|
300 RA : RingAtom
|
|
|
301 CA : ChainAtom
|
|
|
302
|
|
|
303 Functional class atom type specification for an atom corresponds to:
|
|
|
304
|
|
|
305 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA
|
|
|
306
|
|
|
307 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
|
|
|
308 functional class atom types. It uses following definitions [ Ref
|
|
|
309 60-61, Ref 65-66 ]:
|
|
|
310
|
|
|
311 HydrogenBondDonor: NH, NH2, OH
|
|
|
312 HydrogenBondAcceptor: N[!H], O
|
|
|
313 PositivelyIonizable: +, NH2
|
|
|
314 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
315
|
|
|
316 --CompoundID *DataFieldName or LabelPrefixString*
|
|
|
317 This value is --CompoundIDMode specific and indicates how compound
|
|
|
318 ID is generated.
|
|
|
319
|
|
|
320 For *DataField* value of --CompoundIDMode option, it corresponds to
|
|
|
321 datafield label name whose value is used as compound ID; otherwise,
|
|
|
322 it's a prefix string used for generating compound IDs like
|
|
|
323 LabelPrefixString<Number>. Default value, *Cmpd*, generates compound
|
|
|
324 IDs which look like Cmpd<Number>.
|
|
|
325
|
|
|
326 Examples for *DataField* value of --CompoundIDMode:
|
|
|
327
|
|
|
328 MolID
|
|
|
329 ExtReg
|
|
|
330
|
|
|
331 Examples for *LabelPrefix* or *MolNameOrLabelPrefix* value of
|
|
|
332 --CompoundIDMode:
|
|
|
333
|
|
|
334 Compound
|
|
|
335
|
|
|
336 The value specified above generates compound IDs which correspond to
|
|
|
337 Compound<Number> instead of default value of Cmpd<Number>.
|
|
|
338
|
|
|
339 --CompoundIDLabel *text*
|
|
|
340 Specify compound ID column label for CSV/TSV text file(s) used
|
|
|
341 during *CompoundID* value of --DataFieldsMode option. Default value:
|
|
|
342 *CompoundID*.
|
|
|
343
|
|
|
344 --CompoundIDMode *DataField | MolName | LabelPrefix |
|
|
|
345 MolNameOrLabelPrefix*
|
|
|
346 Specify how to generate compound IDs and write to FP or CSV/TSV text
|
|
|
347 file(s) along with generated fingerprints for *FP | text | all*
|
|
|
348 values of --output option: use a *SDFile(s)* datafield value; use
|
|
|
349 molname line from *SDFile(s)*; generate a sequential ID with
|
|
|
350 specific prefix; use combination of both MolName and LabelPrefix
|
|
|
351 with usage of LabelPrefix values for empty molname lines.
|
|
|
352
|
|
|
353 Possible values: *DataField | MolName | LabelPrefix |
|
|
|
354 MolNameOrLabelPrefix*. Default value: *LabelPrefix*.
|
|
|
355
|
|
|
356 For *MolNameAndLabelPrefix* value of --CompoundIDMode, molname line
|
|
|
357 in *SDFile(s)* takes precedence over sequential compound IDs
|
|
|
358 generated using *LabelPrefix* and only empty molname values are
|
|
|
359 replaced with sequential compound IDs.
|
|
|
360
|
|
|
361 This is only used for *CompoundID* value of --DataFieldsMode option.
|
|
|
362
|
|
|
363 --DataFields *"FieldLabel1,FieldLabel2,..."*
|
|
|
364 Comma delimited list of *SDFiles(s)* data fields to extract and
|
|
|
365 write to CSV/TSV text file(s) along with generated fingerprints for
|
|
|
366 *text | both* values of --output option.
|
|
|
367
|
|
|
368 This is only used for *Specify* value of --DataFieldsMode option.
|
|
|
369
|
|
|
370 Examples:
|
|
|
371
|
|
|
372 Extreg
|
|
|
373 MolID,CompoundName
|
|
|
374
|
|
|
375 -d, --DataFieldsMode *All | Common | Specify | CompoundID*
|
|
|
376 Specify how data fields in *SDFile(s)* are transferred to output
|
|
|
377 CSV/TSV text file(s) along with generated fingerprints for *text |
|
|
|
378 both* values of --output option: transfer all SD data field;
|
|
|
379 transfer SD data files common to all compounds; extract specified
|
|
|
380 data fields; generate a compound ID using molname line, a compound
|
|
|
381 prefix, or a combination of both. Possible values: *All | Common |
|
|
|
382 specify | CompoundID*. Default value: *CompoundID*.
|
|
|
383
|
|
|
384 -f, --Filter *Yes | No*
|
|
|
385 Specify whether to check and filter compound data in SDFile(s).
|
|
|
386 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
387
|
|
|
388 By default, compound data is checked before calculating fingerprints
|
|
|
389 and compounds containing atom data corresponding to non-element
|
|
|
390 symbols or no atom data are ignored.
|
|
|
391
|
|
|
392 --FingerprintsLabel *text*
|
|
|
393 SD data label or text file column label to use for fingerprints
|
|
|
394 string in output SD or CSV/TSV text file(s) specified by --output.
|
|
|
395 Default value: *TopologicalAtomPairsFingerprints*.
|
|
|
396
|
|
|
397 -h, --help
|
|
|
398 Print this help message.
|
|
|
399
|
|
|
400 -k, --KeepLargestComponent *Yes | No*
|
|
|
401 Generate fingerprints for only the largest component in molecule.
|
|
|
402 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
403
|
|
|
404 For molecules containing multiple connected components, fingerprints
|
|
|
405 can be generated in two different ways: use all connected components
|
|
|
406 or just the largest connected component. By default, all atoms
|
|
|
407 except for the largest connected component are deleted before
|
|
|
408 generation of fingerprints.
|
|
|
409
|
|
|
410 --MinDistance *number*
|
|
|
411 Minimum bond distance between atom pairs for generating topological
|
|
|
412 atom pairs. Default value: *1*. Valid values: positive integers and
|
|
|
413 less than --MaxDistance.
|
|
|
414
|
|
|
415 --MaxDistance *number*
|
|
|
416 Maximum bond distance between atom pairs for generating topological
|
|
|
417 atom pairs. Default value: *10*. Valid values: positive integers and
|
|
|
418 greater than --MinDistance.
|
|
|
419
|
|
|
420 --OutDelim *comma | tab | semicolon*
|
|
|
421 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
|
|
422 tab, or semicolon* Default value: *comma*
|
|
|
423
|
|
|
424 --output *SD | FP | text | all*
|
|
|
425 Type of output files to generate. Possible values: *SD, FP, text, or
|
|
|
426 all*. Default value: *text*.
|
|
|
427
|
|
|
428 -o, --overwrite
|
|
|
429 Overwrite existing files.
|
|
|
430
|
|
|
431 -q, --quote *Yes | No*
|
|
|
432 Put quote around column values in output CSV/TSV text file(s).
|
|
|
433 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
434
|
|
|
435 -r, --root *RootName*
|
|
|
436 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
437 new file names: <SDFileName><TopologicalAtomPairsFP>.<Ext>. The file
|
|
|
438 type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values
|
|
|
439 are used for SD, FP, comma/semicolon, and tab delimited text files,
|
|
|
440 respectively.This option is ignored for multiple input files.
|
|
|
441
|
|
|
442 -v, --VectorStringFormat *IDsAndValuesString | IDsAndValuesPairsString |
|
|
|
443 ValuesAndIDsString | ValuesAndIDsPairsString*
|
|
|
444 Format of fingerprints vector string data in output SD, FP or
|
|
|
445 CSV/TSV text file(s) specified by --output option. Possible values:
|
|
|
446 *IDsAndValuesString | IDsAndValuesPairsString | ValuesAndIDsString |
|
|
|
447 ValuesAndIDsPairsString*. Default value: *IDsAndValuesString*.
|
|
|
448
|
|
|
449 Examples:
|
|
|
450
|
|
|
451 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
452 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesString;C.X1.BO1
|
|
|
453 .H3-D1-C.X3.BO3.H1 C.X2.BO2.H2-D1-C.X2.BO2.H2 C.X2.BO2.H2-D1-C.X3.BO3.
|
|
|
454 H1 C.X2.BO2.H2-D1-C.X3.BO4 C.X2.BO2.H2-D1-N.X3.BO3 C.X2.BO3.H1-D1-...;
|
|
|
455 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
|
|
|
456 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...
|
|
|
457
|
|
|
458 FingerprintsVector;TopologicalAtomPairs:AtomicInvariantsAtomTypes:MinD
|
|
|
459 istance1:MaxDistance10;223;NumericalValues;IDsAndValuesPairsString;C.X
|
|
|
460 1.BO1.H3-D1-C.X3.BO3.H1 2 C.X2.BO2.H2-D1-C.X2.BO2.H2 1 C.X2.BO2.H2-D1-
|
|
|
461 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
|
|
|
462 .BO3.H1-D1-C.X2.BO3.H1 10 C.X2.BO3.H1-D1-C.X3.BO4 8 C.X3.BO3.H1-D1-C.X
|
|
|
463 3.BO4 1 C.X3.BO3.H1-D1-O.X1.BO1.H1 2 C.X3.BO4-D1-C.X3.BO4 6 C.X3.BO...
|
|
|
464
|
|
|
465 -w, --WorkingDir *DirName*
|
|
|
466 Location of working directory. Default value: current directory.
|
|
|
467
|
|
|
468 EXAMPLES
|
|
|
469 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
470 distances from 1 through 10 using atomic invariants atom types in
|
|
|
471 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
472 sequential compound IDs along with fingerprints vector strings data,
|
|
|
473 type:
|
|
|
474
|
|
|
475 % TopologicalAtomPairsFingerprints.pl -r SampleTAPFP -o Sample.sdf
|
|
|
476
|
|
|
477 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
478 distances from 1 through 10 using atomic invariants atom types in
|
|
|
479 IDsAndValuesString format and create SampleTAPFP.sdf, SampleTAPFP.fpf
|
|
|
480 and SampleTAPFP.csv files containing sequential compound IDs in CSV file
|
|
|
481 along with fingerprints vector strings data, type:
|
|
|
482
|
|
|
483 % TopologicalAtomPairsFingerprints.pl --output all -r SampleTAPFP
|
|
|
484 -o Sample.sdf
|
|
|
485
|
|
|
486 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
487 distances from 1 through 10 using DREIDING atom types in
|
|
|
488 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
489 sequential compound IDs along with fingerprints vector strings data,
|
|
|
490 type:
|
|
|
491
|
|
|
492 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
493 -r SampleTAPFP -o Sample.sdf
|
|
|
494
|
|
|
495 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
496 distances from 1 through 10 using E-state types in IDsAndValuesString
|
|
|
497 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
498 IDs along with fingerprints vector strings data, type:
|
|
|
499
|
|
|
500 % TopologicalAtomPairsFingerprints.pl -a EStateAtomTypes
|
|
|
501 -r SampleTAPFP -o Sample.sdf
|
|
|
502
|
|
|
503 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
504 distances from 1 through 10 using DREIDING atom types in
|
|
|
505 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
506 sequential compound IDs along with fingerprints vector strings data,
|
|
|
507 type:
|
|
|
508
|
|
|
509 % TopologicalAtomPairsFingerprints.pl -a DREIDINGAtomTypes
|
|
|
510 -r SampleTAPFP -o Sample.sdf
|
|
|
511
|
|
|
512 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
513 distances from 1 through 10 using functional class atom types in
|
|
|
514 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
515 sequential compound IDs along with fingerprints vector strings data,
|
|
|
516 type:
|
|
|
517
|
|
|
518 % TopologicalAtomPairsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
519 -r SampleTAPFP -o Sample.sdf
|
|
|
520
|
|
|
521 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
522 distances from 1 through 10 using MMFF94 atom types in
|
|
|
523 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
524 sequential compound IDs along with fingerprints vector strings data,
|
|
|
525 type:
|
|
|
526
|
|
|
527 % TopologicalAtomPairsFingerprints.pl -a MMFF94AtomTypes
|
|
|
528 -r SampleTAPFP -o Sample.sdf
|
|
|
529
|
|
|
530 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
531 distances from 1 through 10 using SLogP atom types in IDsAndValuesString
|
|
|
532 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
533 IDs along with fingerprints vector strings data, type:
|
|
|
534
|
|
|
535 % TopologicalAtomPairsFingerprints.pl -a SLogPAtomTypes
|
|
|
536 -r SampleTAPFP -o Sample.sdf
|
|
|
537
|
|
|
538 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
539 distances from 1 through 10 using SYBYL atom types in IDsAndValuesString
|
|
|
540 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
541 IDs along with fingerprints vector strings data, type:
|
|
|
542
|
|
|
543 % TopologicalAtomPairsFingerprints.pl -a SYBYLAtomTypes
|
|
|
544 -r SampleTAPFP -o Sample.sdf
|
|
|
545
|
|
|
546 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
547 distances from 1 through 10 using TPSA atom types in IDsAndValuesString
|
|
|
548 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
549 IDs along with fingerprints vector strings data, type:
|
|
|
550
|
|
|
551 % TopologicalAtomPairsFingerprints.pl -a TPSAAtomTypes
|
|
|
552 -r SampleTAPFP -o Sample.sdf
|
|
|
553
|
|
|
554 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
555 distances from 1 through 10 using UFF atom types in IDsAndValuesString
|
|
|
556 format and create a SampleTAPFP.csv file containing sequential compound
|
|
|
557 IDs along with fingerprints vector strings data, type:
|
|
|
558
|
|
|
559 % TopologicalAtomPairsFingerprints.pl -a UFFAtomTypes
|
|
|
560 -r SampleTAPFP -o Sample.sdf
|
|
|
561
|
|
|
562 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
563 distances from 1 through 10 using atomic invariants atom types in
|
|
|
564 IDsAndValuesPairsString format and create a SampleTAPFP.csv file
|
|
|
565 containing sequential compound IDs along with fingerprints vector
|
|
|
566 strings data, type:
|
|
|
567
|
|
|
568 % TopologicalAtomPairsFingerprints.pl --VectorStringFormat
|
|
|
569 IDsAndValuesPairsString -r SampleTAPFP -o Sample.sdf
|
|
|
570
|
|
|
571 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
572 distances from 1 through 6 using atomic invariants atom types in
|
|
|
573 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
574 sequential compound IDs along with fingerprints vector strings data,
|
|
|
575 type:
|
|
|
576
|
|
|
577 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
578 --MinDistance 1 --MaxDistance 6 -r SampleTAPFP -o Sample.sdf
|
|
|
579
|
|
|
580 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
581 distances from 1 through 10 using only AS,X atomic invariants atom types
|
|
|
582 in IDsAndValuesString format and create a SampleTAPFP.csv file
|
|
|
583 containing sequential compound IDs along with fingerprints vector
|
|
|
584 strings data, type:
|
|
|
585
|
|
|
586 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
587 --AtomicInvariantsToUse "AS,X" --MinDistance 1 --MaxDistance 6
|
|
|
588 -r SampleTAPFP -o Sample.sdf
|
|
|
589
|
|
|
590 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
591 distances from 1 through 10 using atomic invariants atom types in
|
|
|
592 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
593 compound ID from molecule name line along with fingerprints vector
|
|
|
594 strings data, type:
|
|
|
595
|
|
|
596 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
597 --DataFieldsMode CompoundID -CompoundIDMode MolName
|
|
|
598 -r SampleTAPFP -o Sample.sdf
|
|
|
599
|
|
|
600 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
601 distances from 1 through 10 using atomic invariants atom types in
|
|
|
602 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
603 compound IDs using specified data field along with fingerprints vector
|
|
|
604 strings data, type:
|
|
|
605
|
|
|
606 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
607 --DataFieldsMode CompoundID -CompoundIDMode DataField --CompoundID
|
|
|
608 Mol_ID -r SampleTAPFP -o Sample.sdf
|
|
|
609
|
|
|
610 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
611 distances from 1 through 10 using atomic invariants atom types in
|
|
|
612 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
613 compound ID using combination of molecule name line and an explicit
|
|
|
614 compound prefix along with fingerprints vector strings data, type:
|
|
|
615
|
|
|
616 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
617 --DataFieldsMode CompoundID -CompoundIDMode MolnameOrLabelPrefix
|
|
|
618 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleTAPFP -o Sample.sdf
|
|
|
619
|
|
|
620 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
621 distances from 1 through 10 using atomic invariants atom types in
|
|
|
622 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
623 specific data fields columns along with fingerprints vector strings
|
|
|
624 data, type:
|
|
|
625
|
|
|
626 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
627 --DataFieldsMode Specify --DataFields Mol_ID -r SampleTAPFP
|
|
|
628 -o Sample.sdf
|
|
|
629
|
|
|
630 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
631 distances from 1 through 10 using atomic invariants atom types in
|
|
|
632 IDsAndValuesString format and create a SampleTAPFP.csv file containing
|
|
|
633 common data fields columns along with fingerprints vector strings data,
|
|
|
634 type:
|
|
|
635
|
|
|
636 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
637 --DataFieldsMode Common -r SampleTAPFP -o Sample.sdf
|
|
|
638
|
|
|
639 To generate topological atom pairs fingerprints corresponding to bond
|
|
|
640 distances from 1 through 10 using atomic invariants atom types in
|
|
|
641 IDsAndValuesString format and create SampleTAPFP.sdf, SampleTAPFP.fpf
|
|
|
642 and SampleTAPFP.csv files containing all data fields columns in CSV file
|
|
|
643 along with fingerprints data, type:
|
|
|
644
|
|
|
645 % TopologicalAtomPairsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
646 --DataFieldsMode All --output all -r SampleTAPFP
|
|
|
647 -o Sample.sdf
|
|
|
648
|
|
|
649 AUTHOR
|
|
|
650 Manish Sud <msud@san.rr.com>
|
|
|
651
|
|
|
652 SEE ALSO
|
|
|
653 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
|
|
|
654 AtomNeighborhoodsFingerprints.pl, ExtendedConnectivityFingerprints.pl,
|
|
|
655 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
656 TopologicalAtomTorsionsFingerprints.pl,
|
|
|
657 TopologicalPharmacophoreAtomPairsFingerprints.pl,
|
|
|
658 TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
659
|
|
|
660 COPYRIGHT
|
|
|
661 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
662
|
|
|
663 This file is part of MayaChemTools.
|
|
|
664
|
|
|
665 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
666 under the terms of the GNU Lesser General Public License as published by
|
|
|
667 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
668 your option) any later version.
|
|
|
669
|
