|
1
|
1 NAME
|
|
|
2 AtomNeighborhoodsFingerprints.pl - Generate atom neighborhoods
|
|
|
3 fingerprints for SD files
|
|
|
4
|
|
|
5 SYNOPSIS
|
|
|
6 AtomNeighborhoodsFingerprints.pl SDFile(s)...
|
|
|
7
|
|
|
8 AtomNeighborhoodsFingerprints.pl [--AromaticityModel
|
|
|
9 *AromaticityModelType*] [-a, --AtomIdentifierType
|
|
|
10 *AtomicInvariantsAtomTypes | DREIDINGAtomTypes | EStateAtomTypes |
|
|
|
11 MMFF94AtomTypes | SLogPAtomTypes | SYBYLAtomTypes | TPSAAtomTypes |
|
|
|
12 UFFAtomTypes*] [--AtomicInvariantsToUse
|
|
|
13 *"AtomicInvariant,AtomicInvariant..."*] [--FunctionalClassesToUse
|
|
|
14 *"FunctionalClass1,FunctionalClass2..."*] [--CompoundID *DataFieldName
|
|
|
15 or LabelPrefixString*] [--CompoundIDLabel *text*] [--CompoundIDMode]
|
|
|
16 [--DataFields *"FieldLabel1,FieldLabel2,..."*] [-d, --DataFieldsMode
|
|
|
17 *All | Common | Specify | CompoundID*] [-f, --Filter *Yes | No*]
|
|
|
18 [--FingerprintsLabel *text*] [-h, --help] [-k, --KeepLargestComponent
|
|
|
19 *Yes | No*] [--MinNeighborhoodRadius *number*] [--MaxNeighborhoodRadius
|
|
|
20 *number*] [--OutDelim *comma | tab | semicolon*] [--output *SD | FP |
|
|
|
21 text | all*] [-o, --overwrite] [-q, --quote *Yes | No*] [-r, --root
|
|
|
22 *RootName*] [-w, --WorkingDir dirname] SDFile(s)...
|
|
|
23
|
|
|
24 DESCRIPTION
|
|
|
25 Generate atom neighborhoods fingerprints [ Ref 53-56, Ref 73 ] for
|
|
|
26 *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 atom
|
|
|
36 neighborhoods fingerprints corresponding to following -a,
|
|
|
37 --AtomIdentifierTypes:
|
|
|
38
|
|
|
39 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
40 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
41 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
42
|
|
|
43 Based on the values specified for -a, --AtomIdentifierType and
|
|
|
44 --AtomicInvariantsToUse, initial atom types are assigned to all
|
|
|
45 non-hydrogen atoms in a molecule. Using atom neighborhoods around each
|
|
|
46 non-hydrogen central atom corresponding to radii between specified
|
|
|
47 values --MinNeighborhoodRadius and --MaxNeighborhoodRadius, unique atom
|
|
|
48 types at each radii level are counted and an atom neighborhood
|
|
|
49 identifier is generated.
|
|
|
50
|
|
|
51 The format of an atom neighborhood identifier around a central
|
|
|
52 non-hydrogen atom at a specific radius is:
|
|
|
53
|
|
|
54 NR<n>-<AtomType>-ATC<n>
|
|
|
55
|
|
|
56 NR: Neighborhood radius
|
|
|
57 AtomType: Assigned atom type
|
|
|
58 ATC: Atom type count
|
|
|
59
|
|
|
60 The atom neighborhood identifier for a non-hydrogen central atom
|
|
|
61 corresponding to all specified radii is generated by concatenating
|
|
|
62 neighborhood identifiers at each radii by colon as a delimiter:
|
|
|
63
|
|
|
64 NR<n>-<AtomType>-ATC<n>:NR<n>-<AtomType>-ATC<n>:...
|
|
|
65
|
|
|
66 The atom neighborhood identifiers for all non-hydrogen central atoms at
|
|
|
67 all specified radii are concatenated using space as a delimiter and
|
|
|
68 constitute atom neighborhood fingerprint of the molecule.
|
|
|
69
|
|
|
70 Example of *SD* file containing atom neighborhood fingerprints string
|
|
|
71 data:
|
|
|
72
|
|
|
73 ... ...
|
|
|
74 ... ...
|
|
|
75 $$$$
|
|
|
76 ... ...
|
|
|
77 ... ...
|
|
|
78 ... ...
|
|
|
79 41 44 0 0 0 0 0 0 0 0999 V2000
|
|
|
80 -3.3652 1.4499 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
|
|
|
81 ... ...
|
|
|
82 2 3 1 0 0 0 0
|
|
|
83 ... ...
|
|
|
84 M END
|
|
|
85 > <CmpdID>
|
|
|
86 Cmpd1
|
|
|
87
|
|
|
88 > <AtomNeighborhoodsFingerprints>
|
|
|
89 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu
|
|
|
90 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-ATC1
|
|
|
91 :NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X1.B
|
|
|
92 O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
|
|
|
93 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C...
|
|
|
94
|
|
|
95 $$$$
|
|
|
96 ... ...
|
|
|
97 ... ...
|
|
|
98
|
|
|
99 Example of *FP* file containing atom neighborhood fingerprints string
|
|
|
100 data:
|
|
|
101
|
|
|
102 #
|
|
|
103 # Package = MayaChemTools 7.4
|
|
|
104 # Release Date = Oct 21, 2010
|
|
|
105 #
|
|
|
106 # TimeStamp = Fri Mar 11 14:15:27 2011
|
|
|
107 #
|
|
|
108 # FingerprintsStringType = FingerprintsVector
|
|
|
109 #
|
|
|
110 # Description = AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadiu...
|
|
|
111 # VectorStringFormat = ValuesString
|
|
|
112 # VectorValuesType = AlphaNumericalValues
|
|
|
113 #
|
|
|
114 Cmpd1 41;NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-A...
|
|
|
115 Cmpd2 23;NR0-C.X1.BO1.H3-ATC1:NR1-C.X2.BO2.H2-ATC1:NR2-C.X3.BO3.H1-A...
|
|
|
116 ... ...
|
|
|
117 ... ..
|
|
|
118
|
|
|
119 Example of CSV *Text* file containing atom neighborhood fingerprints
|
|
|
120 string data:
|
|
|
121
|
|
|
122 "CompoundID","AtomNeighborhoodsFingerprints"
|
|
|
123 "Cmpd1","FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes
|
|
|
124 :MinRadius0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.B
|
|
|
125 O1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1
|
|
|
126 NR0-C.X1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3
|
|
|
127 .BO4-ATC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1..."
|
|
|
128 ... ...
|
|
|
129 ... ...
|
|
|
130
|
|
|
131 The current release of MayaChemTools generates the following types of
|
|
|
132 atom neighborhoods fingerprints vector strings:
|
|
|
133
|
|
|
134 FingerprintsVector;AtomNeighborhoods:AtomicInvariantsAtomTypes:MinRadi
|
|
|
135 us0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-C.X1.BO1.H3-AT
|
|
|
136 C1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-ATC1 NR0-C.X
|
|
|
137 1.BO1.H3-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2-C.X1.BO1.H3-ATC1:NR2-C.X3.BO4-A
|
|
|
138 TC1 NR0-C.X2.BO2.H2-ATC1:NR1-C.X2.BO2.H2-ATC1:NR1-C.X3.BO3.H1-ATC1:NR2
|
|
|
139 -C.X2.BO2.H2-ATC1:NR2-N.X3.BO3-ATC1:NR2-O.X1.BO1.H1-ATC1 NR0-C.X2.B...
|
|
|
140
|
|
|
141 FingerprintsVector;AtomNeighborhoods:DREIDINGAtomTypes:MinRadius0:MaxR
|
|
|
142 adius2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:
|
|
|
143 NR1-O_2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N
|
|
|
144 _3-ATC1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-AT
|
|
|
145 C1:NR2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR
|
|
|
146 1-N_R-ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-...
|
|
|
147
|
|
|
148 FingerprintsVector;AtomNeighborhoods:EStateAtomTypes:MinRadius0:MaxRad
|
|
|
149 ius2;41;AlphaNumericalValues;ValuesString;NR0-aaCH-ATC1:NR1-aaCH-ATC1:
|
|
|
150 NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-aaCH-ATC1:NR
|
|
|
151 1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC1:NR2-sF-ATC1 NR0-
|
|
|
152 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 NR0-
|
|
|
153 aaCH-ATC1:NR1-aaCH-ATC1:NR1-aasC-ATC1:NR2-aaCH-ATC1:NR2-aasC-ATC2 N...
|
|
|
154
|
|
|
155 FingerprintsVector;AtomNeighborhoods:FunctionalClassAtomTypes:MinRadiu
|
|
|
156 s0:MaxRadius2;41;AlphaNumericalValues;ValuesString;NR0-Ar-ATC1:NR1-Ar-
|
|
|
157 ATC1:NR1-Ar.HBA-ATC1:NR1-None-ATC1:NR2-Ar-ATC2:NR2-None-ATC4 NR0-Ar-AT
|
|
|
158 C1:NR1-Ar-ATC2:NR1-Ar.HBA-ATC1:NR2-Ar-ATC5:NR2-None-ATC1 NR0-Ar-ATC1:N
|
|
|
159 R1-Ar-ATC2:NR1-HBD-ATC1:NR2-Ar-ATC2:NR2-None-ATC1 NR0-Ar-ATC1:NR1-Ar-A
|
|
|
160 TC2:NR1-Hal-ATC1:NR2-Ar-ATC2 NR0-Ar-ATC1:NR1-Ar-ATC2:NR1-None-ATC1:...
|
|
|
161
|
|
|
162 FingerprintsVector;AtomNeighborhoods:MMFF94AtomTypes:MinRadius0:MaxRad
|
|
|
163 ius2;41;AlphaNumericalValues;ValuesString;NR0-C5A-ATC1:NR1-C5B-ATC1:NR
|
|
|
164 1-CB-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C5B-ATC1:NR2-CB-ATC3:NR2-CR-ATC
|
|
|
165 1 NR0-C5A-ATC1:NR1-C5B-ATC1:NR1-CR-ATC1:NR1-N5-ATC1:NR2-C5A-ATC1:NR2-C
|
|
|
166 5B-ATC1:NR2-C=ON-ATC1:NR2-CR-ATC3 NR0-C5B-ATC1:NR1-C5A-ATC1:NR1-C5B-AT
|
|
|
167 C1:NR1-C=ON-ATC1:NR2-C5A-ATC1:NR2-CB-ATC1:NR2-CR-ATC1:NR2-N5-ATC1:N...
|
|
|
168
|
|
|
169 FingerprintsVector;AtomNeighborhoods:SLogPAtomTypes:MinRadius0:MaxRadi
|
|
|
170 us2;41;AlphaNumericalValues;ValuesString;NR0-C1-ATC1:NR1-C10-ATC1:NR1-
|
|
|
171 CS-ATC1:NR2-C1-ATC1:NR2-N11-ATC1:NR2-O2-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:
|
|
|
172 NR2-C1-ATC1:NR2-C21-ATC1 NR0-C1-ATC1:NR1-C11-ATC1:NR2-C1-ATC1:NR2-C21-
|
|
|
173 ATC1 NR0-C1-ATC1:NR1-C5-ATC1:NR1-CS-ATC1:NR2-C1-ATC1:NR2-O2-ATC2:NR2-O
|
|
|
174 9-ATC1 NR0-C1-ATC1:NR1-CS-ATC2:NR2-C1-ATC2:NR2-O2-ATC2 NR0-C10-ATC1...
|
|
|
175
|
|
|
176 FingerprintsVector;AtomNeighborhoods:SYBYLAtomTypes:MinRadius0:MaxRadi
|
|
|
177 us2;41;AlphaNumericalValues;ValuesString;NR0-C.2-ATC1:NR1-C.3-ATC1:NR1
|
|
|
178 -O.co2-ATC2:NR2-C.3-ATC1 NR0-C.2-ATC1:NR1-C.ar-ATC1:NR1-N.am-ATC1:NR1-
|
|
|
179 O.2-ATC1:NR2-C.ar-ATC3 NR0-C.3-ATC1:NR1-C.2-ATC1:NR1-C.3-ATC1:NR2-C.3-
|
|
|
180 ATC1:NR2-O.3-ATC1:NR2-O.co2-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR1-N.ar-AT
|
|
|
181 C1:NR2-C.3-ATC1:NR2-C.ar-ATC2 NR0-C.3-ATC1:NR1-C.3-ATC1:NR2-C.3-ATC...
|
|
|
182
|
|
|
183 FingerprintsVector;AtomNeighborhoods:TPSAAtomTypes:MinRadius0:MaxRadiu
|
|
|
184 s2;41;AlphaNumericalValues;ValuesString;NR0-N21-ATC1:NR1-None-ATC3:NR2
|
|
|
185 -None-ATC5 NR0-N7-ATC1:NR1-None-ATC2:NR2-None-ATC3:NR2-O3-ATC1 NR0-Non
|
|
|
186 e-ATC1:NR1-N21-ATC1:NR1-None-ATC1:NR2-None-ATC3 NR0-None-ATC1:NR1-N21-
|
|
|
187 ATC1:NR1-None-ATC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N21-ATC1:NR1-None-A
|
|
|
188 TC2:NR2-None-ATC6 NR0-None-ATC1:NR1-N7-ATC1:NR1-None-ATC1:NR1-O3-AT...
|
|
|
189
|
|
|
190 FingerprintsVector;AtomNeighborhoods:UFFAtomTypes:MinRadius0:MaxRadius
|
|
|
191 2;41;AlphaNumericalValues;ValuesString;NR0-C_2-ATC1:NR1-C_3-ATC1:NR1-O
|
|
|
192 _2-ATC1:NR1-O_3-ATC1:NR2-C_3-ATC1 NR0-C_2-ATC1:NR1-C_R-ATC1:NR1-N_3-AT
|
|
|
193 C1:NR1-O_2-ATC1:NR2-C_R-ATC3 NR0-C_3-ATC1:NR1-C_2-ATC1:NR1-C_3-ATC1:NR
|
|
|
194 2-C_3-ATC1:NR2-O_2-ATC1:NR2-O_3-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR1-N_R
|
|
|
195 -ATC1:NR2-C_3-ATC1:NR2-C_R-ATC2 NR0-C_3-ATC1:NR1-C_3-ATC1:NR2-C_3-A...
|
|
|
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 atom
|
|
|
222 neighborhoods fingerprints. Possible values in the current release
|
|
|
223 are: *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 FP or CSV/TSV text file(s) used
|
|
|
341 during *CompoundID* value of --DataFieldsMode option. Default:
|
|
|
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: *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 | all* 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 all* values of --output option: transfer all SD data field; transfer
|
|
|
379 SD data files common to all compounds; extract specified data
|
|
|
380 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: *AtomNeighborhoodsFingerprints*.
|
|
|
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 --MinNeighborhoodRadius *number*
|
|
|
411 Minimum atom neighborhood radius for generating atom neighborhoods.
|
|
|
412 Default value: *0*. Valid values: positive integers and less than
|
|
|
413 --MaxNeighborhoodRadius. Neighborhood radius of zero corresponds to
|
|
|
414 list of non-hydrogen atoms.
|
|
|
415
|
|
|
416 --MaxNeighborhoodRadius *number*
|
|
|
417 Maximum atom neighborhood radius for generating atom neighborhoods.
|
|
|
418 Default value: *2*. Valid values: positive integers and greater than
|
|
|
419 --MineighborhoodRadius.
|
|
|
420
|
|
|
421 --OutDelim *comma | tab | semicolon*
|
|
|
422 Delimiter for output CSV/TSV text file(s). Possible values: *comma,
|
|
|
423 tab, or semicolon* Default value: *comma*.
|
|
|
424
|
|
|
425 --output *SD | FP | text | all*
|
|
|
426 Type of output files to generate. Possible values: *SD, FP, text, or
|
|
|
427 all*. Default value: *text*.
|
|
|
428
|
|
|
429 -o, --overwrite
|
|
|
430 Overwrite existing files.
|
|
|
431
|
|
|
432 -q, --quote *Yes | No*
|
|
|
433 Put quote around column values in output CSV/TSV text file(s).
|
|
|
434 Possible values: *Yes or No*. Default value: *Yes*.
|
|
|
435
|
|
|
436 -r, --root *RootName*
|
|
|
437 New file name is generated using the root: <Root>.<Ext>. Default for
|
|
|
438 new file names: <SDFileName><AtomNeighborhoodsFP>.<Ext>. The file
|
|
|
439 type determines <Ext> value. The sdf, fpf, csv, and tsv <Ext> values
|
|
|
440 are used for SD, comma/semicolon, and tab delimited text files,
|
|
|
441 respectively.This option is ignored for multiple input files.
|
|
|
442
|
|
|
443 -w, --WorkingDir *DirName*
|
|
|
444 Location of working directory. Default: current directory.
|
|
|
445
|
|
|
446 EXAMPLES
|
|
|
447 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
448 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
449 vector string format and create a SampleANFP.csv file containing
|
|
|
450 sequential compound IDs along with fingerprints vector strings data,
|
|
|
451 type:
|
|
|
452
|
|
|
453 % AtomNeighborhoodsFingerprints.pl -r SampleANFP -o Sample.sdf
|
|
|
454
|
|
|
455 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
456 neighborhood radii from 0 to 2 using DREIDING atom types in vector
|
|
|
457 string format and create a SampleANFP.csv file containing sequential
|
|
|
458 compound IDs along with fingerprints vector strings data, type:
|
|
|
459
|
|
|
460 % AtomNeighborhoodsFingerprints.pl -a DREIDINGAtomTypes -r SampleANFP
|
|
|
461 -o Sample.sdf
|
|
|
462
|
|
|
463 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
464 neighborhood radii from 0 to 2 using EStateAtomTypes types in vector
|
|
|
465 string format and create a SampleANFP.csv file containing sequential
|
|
|
466 compound IDs along with fingerprints vector strings data, type:
|
|
|
467
|
|
|
468 % AtomNeighborhoodsFingerprints.pl -a EStateAtomTypes -r SampleANFP
|
|
|
469 -o Sample.sdf
|
|
|
470
|
|
|
471 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
472 neighborhood radii from 0 to 2 using SYBYL atom types in vector string
|
|
|
473 format and create a SampleANFP.csv file containing sequential compound
|
|
|
474 IDs along with fingerprints vector strings data, type:
|
|
|
475
|
|
|
476 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
477 -o Sample.sdf
|
|
|
478
|
|
|
479 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
480 neighborhood radii from 0 to 2 using FunctionalClass atom types in
|
|
|
481 vector string format and create a SampleANFP.csv file containing
|
|
|
482 sequential compound IDs along with fingerprints vector strings data,
|
|
|
483 type:
|
|
|
484
|
|
|
485 % AtomNeighborhoodsFingerprints.pl -a FunctionalClassAtomTypes
|
|
|
486 -r SampleANFP -o Sample.sdf
|
|
|
487
|
|
|
488 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
489 neighborhood radii from 0 to 2 using MMFF94 atom types in vector string
|
|
|
490 format and create a SampleANFP.csv file containing sequential compound
|
|
|
491 IDs along with fingerprints vector strings data, type:
|
|
|
492
|
|
|
493 % AtomNeighborhoodsFingerprints.pl -a MMFF94AtomTypes -r SampleANFP
|
|
|
494 -o Sample.sdf
|
|
|
495
|
|
|
496 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
497 neighborhood radii from 0 to 2 using SLogP atom types in vector string
|
|
|
498 format and create a SampleANFP.csv file containing sequential compound
|
|
|
499 IDs along with fingerprints vector strings data, type:
|
|
|
500
|
|
|
501 % AtomNeighborhoodsFingerprints.pl -a SLogPAtomTypes -r SampleANFP
|
|
|
502 -o Sample.sdf
|
|
|
503
|
|
|
504 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
505 neighborhood radii from 0 to 2 using SYBYL atom types in vector string
|
|
|
506 format and create a SampleANFP.csv file containing sequential compound
|
|
|
507 IDs along with fingerprints vector strings data, type:
|
|
|
508
|
|
|
509 % AtomNeighborhoodsFingerprints.pl -a SYBYLAtomTypes -r SampleANFP
|
|
|
510 -o Sample.sdf
|
|
|
511
|
|
|
512 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
513 neighborhood radii from 0 to 2 using TPSA atom types in vector string
|
|
|
514 format and create a SampleANFP.csv file containing sequential compound
|
|
|
515 IDs along with fingerprints vector strings data, type:
|
|
|
516
|
|
|
517 % AtomNeighborhoodsFingerprints.pl -a TPSAAtomTypes -r SampleANFP
|
|
|
518 -o Sample.sdf
|
|
|
519
|
|
|
520 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
521 neighborhood radii from 0 to 2 using UFF atom types in vector string
|
|
|
522 format and create a SampleANFP.csv file containing sequential compound
|
|
|
523 IDs along with fingerprints vector strings data, type:
|
|
|
524
|
|
|
525 % AtomNeighborhoodsFingerprints.pl -a UFFAtomTypes -r SampleANFP
|
|
|
526 -o Sample.sdf
|
|
|
527
|
|
|
528 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
529 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
530 vector string format and create SampleANFP.sdf, SampleANFP.fpf and
|
|
|
531 SampleANFP.csv files containing sequential compound IDs in CSV file
|
|
|
532 along with fingerprints vector strings data, type:
|
|
|
533
|
|
|
534 % AtomNeighborhoodsFingerprints.pl --output all -r SampleANFP
|
|
|
535 -o Sample.sdf
|
|
|
536
|
|
|
537 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
538 neighborhood radii from 1 to 3 using atomic invariants atom types in
|
|
|
539 vector string format and create a SampleANFP.csv file containing
|
|
|
540 sequential compound IDs along with fingerprints vector strings data,
|
|
|
541 type:
|
|
|
542
|
|
|
543 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
544 --MinNeighborhoodRadius 1 --MaxNeighborhoodRadius 3 -r SampleANFP
|
|
|
545 -o Sample.sdf
|
|
|
546
|
|
|
547 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
548 neighborhood radii from 0 to 2 using only AS,X atomic invariants atom
|
|
|
549 types in vector string format and create a SampleANFP.csv file
|
|
|
550 containing sequential compound IDs along with fingerprints vector
|
|
|
551 strings data, type:
|
|
|
552
|
|
|
553 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
554 --AtomicInvariantsToUse "AS,X" --MinNeighborhoodRadius 0
|
|
|
555 --MaxNeighborhoodRadius 3 -r SampleANFP -o Sample.sdf
|
|
|
556
|
|
|
557 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
558 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
559 vector string format and create a SampleANFP.csv file containing
|
|
|
560 compound ID from molecule name line along with fingerprints vector
|
|
|
561 strings data, type:
|
|
|
562
|
|
|
563 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
564 --DataFieldsMode CompoundID --CompoundIDMode MolName
|
|
|
565 -r SampleANFP -o Sample.sdf
|
|
|
566
|
|
|
567 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
568 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
569 vector string format and create a SampleANFP.csv file containing
|
|
|
570 compound IDs using specified data field along with fingerprints vector
|
|
|
571 strings data, type:
|
|
|
572
|
|
|
573 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
574 --DataFieldsMode CompoundID --CompoundIDMode DataField --CompoundID
|
|
|
575 Mol_ID -r SampleANFP -o Sample.sdf
|
|
|
576
|
|
|
577 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
578 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
579 vector string format and create a SampleANFP.csv file containing
|
|
|
580 compound ID using combination of molecule name line and an explicit
|
|
|
581 compound prefix along with fingerprints vector strings data, type:
|
|
|
582
|
|
|
583 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
584 --DataFieldsMode CompoundID --CompoundIDMode MolnameOrLabelPrefix
|
|
|
585 --CompoundID Cmpd --CompoundIDLabel MolID -r SampleANFP -o Sample.sdf
|
|
|
586
|
|
|
587 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
588 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
589 vector string format and create a SampleANFP.csv file containing
|
|
|
590 specific data fields columns along with fingerprints vector strings
|
|
|
591 data, type:
|
|
|
592
|
|
|
593 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
594 --DataFieldsMode Specify --DataFields Mol_ID -r SampleANFP
|
|
|
595 -o Sample.sdf
|
|
|
596
|
|
|
597 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
598 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
599 vector string format and create a SampleANFP.csv file containing common
|
|
|
600 data fields columns along with fingerprints vector strings data, type:
|
|
|
601
|
|
|
602 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
603 --DataFieldsMode Common -r SampleANFP -o Sample.sdf
|
|
|
604
|
|
|
605 To generate atom neighborhoods fingerprints corresponding to atom
|
|
|
606 neighborhood radii from 0 to 2 using atomic invariants atom types in
|
|
|
607 vector string format and create SampleANFP.sdf, SampleANFP.fpf and
|
|
|
608 SampleANFP.csv files containing all data fields columns in CSV file
|
|
|
609 along with fingerprints data, type:
|
|
|
610
|
|
|
611 % AtomNeighborhoodsFingerprints.pl -a AtomicInvariantsAtomTypes
|
|
|
612 --DataFieldsMode All --output all -r SampleANFP
|
|
|
613 -o Sample.sdf
|
|
|
614
|
|
|
615 AUTHOR
|
|
|
616 Manish Sud <msud@san.rr.com>
|
|
|
617
|
|
|
618 SEE ALSO
|
|
|
619 InfoFingerprintsFiles.pl, SimilarityMatricesFingerprints.pl,
|
|
|
620 SimilaritySearchingFingerprints.pl, ExtendedConnectivityFingerprints.pl,
|
|
|
621 MACCSKeysFingerprints.pl, PathLengthFingerprints.pl,
|
|
|
622 TopologicalAtomPairsFingerprints.pl,
|
|
|
623 TopologicalAtomTorsionsFingerprints.pl,
|
|
|
624 TopologicalPharmacophoreAtomPairsFingerprints.pl,
|
|
|
625 TopologicalPharmacophoreAtomTripletsFingerprints.pl
|
|
|
626
|
|
|
627 COPYRIGHT
|
|
|
628 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
629
|
|
|
630 This file is part of MayaChemTools.
|
|
|
631
|
|
|
632 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
633 under the terms of the GNU Lesser General Public License as published by
|
|
|
634 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
635 your option) any later version.
|
|
|
636
|
