|
1
|
1 NAME
|
|
|
2 ExtendedConnectivityFingerprints
|
|
|
3
|
|
|
4 SYNOPSIS
|
|
|
5 use Fingerprints::ExtendedConnectivityFingerprints;
|
|
|
6
|
|
|
7 use Fingerprints::ExtendedConnectivityFingerprints qw(:all);
|
|
|
8
|
|
|
9 DESCRIPTION
|
|
|
10 ExtendedConnectivityFingerprints [ Ref 48, Ref 52 ] class provides the
|
|
|
11 following methods:
|
|
|
12
|
|
|
13 new, GenerateFingerprints, GetDescription, SetAtomIdentifierType,
|
|
|
14 SetAtomicInvariantsToUse, SetFunctionalClassesToUse,
|
|
|
15 SetNeighborhoodRadius, StringifyExtendedConnectivityFingerprints
|
|
|
16
|
|
|
17 ExtendedConnectivityFingerprints is derived from Fingerprints class
|
|
|
18 which in turn is derived from ObjectProperty base class that provides
|
|
|
19 methods not explicitly defined in ExtendedConnectivityFingerprints,
|
|
|
20 Fingerprints or ObjectProperty classes using Perl's AUTOLOAD
|
|
|
21 functionality. These methods are generated on-the-fly for a specified
|
|
|
22 object property:
|
|
|
23
|
|
|
24 Set<PropertyName>(<PropertyValue>);
|
|
|
25 $PropertyValue = Get<PropertyName>();
|
|
|
26 Delete<PropertyName>();
|
|
|
27
|
|
|
28 The current release of MayaChemTools supports generation of
|
|
|
29 ExtendedConnectivityFingerprints corresponding to following
|
|
|
30 AtomtomIdentifierTypes:
|
|
|
31
|
|
|
32 AtomicInvariantsAtomTypes, DREIDINGAtomTypes, EStateAtomTypes,
|
|
|
33 FunctionalClassAtomTypes, MMFF94AtomTypes, SLogPAtomTypes,
|
|
|
34 SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes
|
|
|
35
|
|
|
36 Based on the values specified for AtomIdentifierType,
|
|
|
37 AtomicInvariantsToUse and FunctionalClassesToUse, initial atom types are
|
|
|
38 assigned to all non-hydrogen atoms in a molecule and these atom types
|
|
|
39 strings are converted into initial atom identifier integers using
|
|
|
40 TextUtil::HashCode function. The duplicate atom identifiers are removed.
|
|
|
41
|
|
|
42 For NeighborhoodRadius value of *0*, the initial set of unique atom
|
|
|
43 identifiers comprises the molecule fingerprints. Otherwise, atom
|
|
|
44 neighborhoods are generated for each non-hydrogen atom up-to specified
|
|
|
45 NeighborhoodRadius value. For each non-hydrogen central atom at a
|
|
|
46 specific radius, its neighbors at next radius level along with their
|
|
|
47 bond orders and previously calculated atom identifiers are collected
|
|
|
48 which in turn are used to generate a new integer atom identifier; the
|
|
|
49 bond orders and atom identifier pairs list is first sorted by bond order
|
|
|
50 followed by atom identifiers to make these values graph invariant.
|
|
|
51
|
|
|
52 After integer atom identifiers have been generated for all non-hydrogen
|
|
|
53 atoms at all specified neighborhood radii, the duplicate integer atom
|
|
|
54 identifiers corresponding to same hash code value generated using
|
|
|
55 TextUtil::HashCode are tracked by keeping the atom identifiers at lower
|
|
|
56 radius. Additionally, all structurally duplicate integer atom
|
|
|
57 identifiers at each specified radius are also tracked by identifying
|
|
|
58 equivalent atom and bonds corresponding to substructures used for
|
|
|
59 generating atom identifier and keeping integer atom identifier with
|
|
|
60 lowest value.
|
|
|
61
|
|
|
62 For *ExtendedConnnectivity* value of fingerprints Type, the duplicate
|
|
|
63 identifiers are removed from the list and the unique atom identifiers
|
|
|
64 constitute the extended connectivity fingerprints of a molecule.
|
|
|
65
|
|
|
66 For *ExtendedConnnectivityCount* value of fingerprints Type, the
|
|
|
67 occurrence of each unique atom identifiers appears is counted and the
|
|
|
68 unique atom identifiers along with their count constitute the extended
|
|
|
69 connectivity fingerprints of a molecule.
|
|
|
70
|
|
|
71 For *ExtendedConnectivityBits* value of fingerprints -m, --mode, the
|
|
|
72 unique atom identifiers are used as a random number seed to generate a
|
|
|
73 random integer value between 0 and --Size which in turn is used to set
|
|
|
74 corresponding bits in the fingerprint bit-vector string.
|
|
|
75
|
|
|
76 The current release of MayaChemTools generates the following types of
|
|
|
77 extended connectivity fingerprints vector strings:
|
|
|
78
|
|
|
79 FingerprintsVector;ExtendedConnectivity:AtomicInvariantsAtomTypes:Radi
|
|
|
80 us2;60;AlphaNumericalValues;ValuesString;73555770 333564680 352413391
|
|
|
81 666191900 1001270906 1371674323 1481469939 1977749791 2006158649 21414
|
|
|
82 08799 49532520 64643108 79385615 96062769 273726379 564565671 85514103
|
|
|
83 5 906706094 988546669 1018231313 1032696425 1197507444 1331250018 1338
|
|
|
84 532734 1455473691 1607485225 1609687129 1631614296 1670251330 17303...
|
|
|
85
|
|
|
86 FingerprintsVector;ExtendedConnectivityCount:AtomicInvariantsAtomTypes
|
|
|
87 :Radius2;60;NumericalValues;IDsAndValuesString;73555770 333564680 3524
|
|
|
88 13391 666191900 1001270906 1371674323 1481469939 1977749791 2006158649
|
|
|
89 2141408799 49532520 64643108 79385615 96062769 273726379 564565671...;
|
|
|
90 3 2 1 1 14 1 2 10 4 3 1 1 1 1 2 1 2 1 1 1 2 3 1 1 2 1 3 3 8 2 2 2 6 2
|
|
|
91 1 2 1 1 2 1 1 1 2 1 1 2 1 2 1 1 1 1 1 1 1 1 1 2 1 1
|
|
|
92
|
|
|
93 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
94 es:Radius2;1024;BinaryString;Ascending;0000000000000000000000000000100
|
|
|
95 0000000001010000000110000011000000000000100000000000000000000000100001
|
|
|
96 1000000110000000000000000000000000010011000000000000000000000000010000
|
|
|
97 0000000000000000000000000010000000000000000001000000000000000000000000
|
|
|
98 0000000000010000100001000000000000101000000000000000100000000000000...
|
|
|
99
|
|
|
100 FingerprintsBitVector;ExtendedConnectivityBits:AtomicInvariantsAtomTyp
|
|
|
101 es:Radius2;1024;HexadecimalString;Ascending;000000010050c0600800000803
|
|
|
102 0300000091000004000000020000100000000124008200020000000040020000000000
|
|
|
103 2080000000820040010020000000008040000000000080001000000000400000000000
|
|
|
104 4040000090000061010000000800200000000000001400000000020080000000000020
|
|
|
105 00008020200000408000
|
|
|
106
|
|
|
107 FingerprintsVector;ExtendedConnectivity:FunctionalClassAtomTypes:Radiu
|
|
|
108 s2;57;AlphaNumericalValues;ValuesString;24769214 508787397 850393286 8
|
|
|
109 62102353 981185303 1231636850 1649386610 1941540674 263599683 32920567
|
|
|
110 1 571109041 639579325 683993318 723853089 810600886 885767127 90326012
|
|
|
111 7 958841485 981022393 1126908698 1152248391 1317567065 1421489994 1455
|
|
|
112 632544 1557272891 1826413669 1983319256 2015750777 2029559552 20404...
|
|
|
113
|
|
|
114 FingerprintsVector;ExtendedConnectivityCount:FunctionalClassAtomTypes:
|
|
|
115 Radius2;57;NumericalValues;IDsAndValuesString;24769214 508787397 85039
|
|
|
116 3286 862102353 981185303 1231636850 1649386610 1941540674 263599683 32
|
|
|
117 9205671 571109041 639579325 683993318 723853089 810600886 885767127...;
|
|
|
118 1 1 1 10 2 22 3 1 3 3 1 1 1 3 2 2 1 2 2 2 3 1 1 1 1 1 14 1 1 1 1 1 1 2
|
|
|
119 1 2 1 1 2 2 1 1 2 1 1 1 2 1 1 2 1 1 1 1 1 1 1
|
|
|
120
|
|
|
121 FingerprintsBitVector;ExtendedConnectivityBits:FunctionalClassAtomType
|
|
|
122 s:Radius2;1024;BinaryString;Ascending;00000000000000000000100000000000
|
|
|
123 0000000001000100000000001000000000000000000000000000000000101000000010
|
|
|
124 0000001000000000010000000000000000000000000000000000000000000000000100
|
|
|
125 0000000000001000000000000001000000000001001000000000000000000000000000
|
|
|
126 0000000000000000100000000000001000000000000000000000000000000000000...
|
|
|
127
|
|
|
128 FingerprintsVector;ExtendedConnectivity:DREIDINGAtomTypes:Radius2;56;A
|
|
|
129 lphaNumericalValues;ValuesString;280305427 357928343 721790579 1151822
|
|
|
130 898 1207111054 1380963747 1568213839 1603445250 4559268 55012922 18094
|
|
|
131 0813 335715751 534801009 684609658 829361048 972945982 999881534 10076
|
|
|
132 55741 1213692591 1222032501 1224517934 1235687794 1244268533 152812070
|
|
|
133 0 1629595024 1856308891 1978806036 2001865095 2096549435 172675415 ...
|
|
|
134
|
|
|
135 FingerprintsVector;ExtendedConnectivity:EStateAtomTypes:Radius2;62;Alp
|
|
|
136 haNumericalValues;ValuesString;25189973 528584866 662581668 671034184
|
|
|
137 926543080 1347067490 1738510057 1759600920 2034425745 2097234755 21450
|
|
|
138 44754 96779665 180364292 341712110 345278822 386540408 387387308 50430
|
|
|
139 1706 617094135 771528807 957666640 997798220 1158349170 1291258082 134
|
|
|
140 1138533 1395329837 1420277211 1479584608 1486476397 1487556246 1566...
|
|
|
141
|
|
|
142 FingerprintsVector;ExtendedConnectivity:MMFF94AtomTypes:Radius2;64;Alp
|
|
|
143 haNumericalValues;ValuesString;224051550 746527773 998750766 103704190
|
|
|
144 2 1239701709 1248384926 1259447756 1521678386 1631549126 1909437580 20
|
|
|
145 37095052 2104274756 2117729376 8770364 31445800 81450228 314289324 344
|
|
|
146 041929 581773587 638555787 692022098 811840536 929651561 936421792 988
|
|
|
147 636432 1048624296 1054288509 1369487579 1454058929 1519352190 17271...
|
|
|
148
|
|
|
149 FingerprintsVector;ExtendedConnectivity:SLogPAtomTypes:Radius2;71;Alph
|
|
|
150 aNumericalValues;ValuesString;78989290 116507218 489454042 888737940 1
|
|
|
151 162561799 1241797255 1251494264 1263717127 1471206899 1538061784 17654
|
|
|
152 07295 1795036542 1809833874 2020454493 2055310842 2117729376 11868981
|
|
|
153 56731842 149505242 184525155 196984339 288181334 481409282 556716568 6
|
|
|
154 41915747 679881756 721736571 794256218 908276640 992898760 10987549...
|
|
|
155
|
|
|
156 FingerprintsVector;ExtendedConnectivity:SYBYLAtomTypes:Radius2;58;Alph
|
|
|
157 aNumericalValues;ValuesString;199957044 313356892 455463968 465982819
|
|
|
158 1225318176 1678585943 1883366064 1963811677 2117729376 113784599 19153
|
|
|
159 8837 196629033 263865277 416380653 477036669 681527491 730724924 90906
|
|
|
160 5537 1021959189 1133014972 1174311016 1359441203 1573452838 1661585138
|
|
|
161 1668649038 1684198062 1812312554 1859266290 1891651106 2072549404 ...
|
|
|
162
|
|
|
163 FingerprintsVector;ExtendedConnectivity:TPSAAtomTypes:Radius2;47;Alpha
|
|
|
164 NumericalValues;ValuesString;20818206 259344053 862102353 1331904542 1
|
|
|
165 700688206 265614156 363161397 681332588 810600886 885767127 950172500
|
|
|
166 951454814 1059668746 1247054493 1382302230 1399502637 1805025917 19189
|
|
|
167 39561 2114677228 2126402271 8130483 17645742 32278373 149975755 160327
|
|
|
168 654 256360355 279492740 291251259 317592700 333763396 972105960 101...
|
|
|
169
|
|
|
170 FingerprintsVector;ExtendedConnectivity:UFFAtomTypes:Radius2;56;AlphaN
|
|
|
171 umericalValues;ValuesString;280305427 357928343 721790579 1151822898 1
|
|
|
172 207111054 1380963747 1568213839 1603445250 4559268 55012922 180940813
|
|
|
173 335715751 534801009 684609658 829361048 972945982 999881534 1007655741
|
|
|
174 1213692591 1222032501 1224517934 1235687794 1244268533 1528120700 162
|
|
|
175 9595024 1856308891 1978806036 2001865095 2096549435 172675415 18344...
|
|
|
176
|
|
|
177 METHODS
|
|
|
178 new
|
|
|
179 $NewExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
180 %NamesAndValues);
|
|
|
181
|
|
|
182 Using specified *ExtendedConnectivityFingerprints* property names
|
|
|
183 and values hash, new method creates a new object and returns a
|
|
|
184 reference to newly created ExtendedConnectivityFingerprints object.
|
|
|
185 By default, the following properties are initialized:
|
|
|
186
|
|
|
187 Molecule = ''
|
|
|
188 Type = 'ExtendedConnectivity'
|
|
|
189 NeighborhoodRadius = 2
|
|
|
190 AtomIdentifierType = ''
|
|
|
191 AtomicInvariantsToUse = ['AS', 'X', 'BO', 'H', 'FC', 'MN']
|
|
|
192 FunctionalClassesToUse = ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal']
|
|
|
193
|
|
|
194 Examples:
|
|
|
195
|
|
|
196 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
197 'Molecule' => $Molecule,
|
|
|
198 'AtomIdentifierType' =>
|
|
|
199 'AtomicInvariantsAtomTypes');
|
|
|
200
|
|
|
201 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
202 'Type' => 'ExtendedConnectivityCount',
|
|
|
203 'Molecule' => $Molecule,
|
|
|
204 'AtomIdentifierType' =>
|
|
|
205 'AtomicInvariantsAtomTypes');
|
|
|
206
|
|
|
207 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
208 'Type' => 'ExtendedConnectivityBits',
|
|
|
209 'Molecule' => $Molecule,
|
|
|
210 'Size' => 1024,
|
|
|
211 'AtomIdentifierType' =>
|
|
|
212 'AtomicInvariantsAtomTypes');
|
|
|
213
|
|
|
214 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
215 'Type' => 'ExtendedConnectivity',
|
|
|
216 'Molecule' => $Molecule,
|
|
|
217 'NeighborhoodRadius' => 2,
|
|
|
218 'AtomIdentifierType' =>
|
|
|
219 'AtomicInvariantsAtomTypes',
|
|
|
220 'AtomicInvariantsToUse' =>
|
|
|
221 ['AS', 'X', 'BO', 'H', 'FC', 'MN'] );
|
|
|
222
|
|
|
223 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
224 'Type' => 'ExtendedConnectivity',
|
|
|
225 'Molecule' => $Molecule,
|
|
|
226 'NeighborhoodRadius' => 2,
|
|
|
227 'AtomIdentifierType' =>
|
|
|
228 'FunctionalClassAtomTypes',
|
|
|
229 'FunctionalClassesToUse' =>
|
|
|
230 ['HBD', 'HBA', 'PI', 'NI', 'Ar', 'Hal'] );
|
|
|
231
|
|
|
232 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
233 'Type' => 'ExtendedConnectivity',
|
|
|
234 'Molecule' => $Molecule,;
|
|
|
235 'AtomIdentifierType' =>
|
|
|
236 'MMFF94AtomTypes');
|
|
|
237
|
|
|
238 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
239 'Type' => 'ExtendedConnectivityCount',
|
|
|
240 'Molecule' => $Molecule,;
|
|
|
241 'AtomIdentifierType' =>
|
|
|
242 'MMFF94AtomTypes');
|
|
|
243
|
|
|
244 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
245 'Type' => 'ExtendedConnectivityCount',
|
|
|
246 'Molecule' => $Molecule,;
|
|
|
247 'AtomIdentifierType' =>
|
|
|
248 'SLogPAtomTypes');
|
|
|
249
|
|
|
250 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
251 'Type' => 'ExtendedConnectivity',
|
|
|
252 'Molecule' => $Molecule,;
|
|
|
253 'AtomIdentifierType' =>
|
|
|
254 'SLogPAtomTypes');
|
|
|
255
|
|
|
256 $ExtendedConnectivityFingerprints = new ExtendedConnectivityFingerprints(
|
|
|
257 'Type' => 'ExtendedConnectivity',
|
|
|
258 'Molecule' => $Molecule,;
|
|
|
259 'AtomIdentifierType' =>
|
|
|
260 'SYBYLAtomTypes');
|
|
|
261
|
|
|
262 $ExtendedConnectivityFingerprints->GenerateFingerprints();
|
|
|
263 print "$ExtendedConnectivityFingerprints\n";
|
|
|
264
|
|
|
265 GenerateFingerprints
|
|
|
266 $ExtendedConnectivityFingerprints->GenerateFingerprints();
|
|
|
267
|
|
|
268 Generates extended connectivity fingerprints and returns
|
|
|
269 *ExtendedConnectivityFingerprints*.
|
|
|
270
|
|
|
271 GetDescription
|
|
|
272 $Description = $ExtendedConnectivityFingerprints->GetDescription();
|
|
|
273
|
|
|
274 Returns a string containing description of extended connectivity
|
|
|
275 fingerprints fingerprints.
|
|
|
276
|
|
|
277 SetAtomIdentifierType
|
|
|
278 $ExtendedConnectivityFingerprints->SetAtomIdentifierType($IdentifierType);
|
|
|
279
|
|
|
280 Sets atom *IdentifierType* to use during extended connectivity
|
|
|
281 fingerprints generation and returns
|
|
|
282 *ExtendedConnectivityFingerprints*.
|
|
|
283
|
|
|
284 Possible values: *AtomicInvariantsAtomTypes, DREIDINGAtomTypes,
|
|
|
285 EStateAtomTypes, FunctionalClassAtomTypes, MMFF94AtomTypes,
|
|
|
286 SLogPAtomTypes, SYBYLAtomTypes, TPSAAtomTypes, UFFAtomTypes*.
|
|
|
287
|
|
|
288 SetAtomicInvariantsToUse
|
|
|
289 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse($ValuesRef);
|
|
|
290 $ExtendedConnectivityFingerprints->SetAtomicInvariantsToUse(@Values);
|
|
|
291
|
|
|
292 Sets atomic invariants to use during *AtomicInvariantsAtomTypes*
|
|
|
293 value of *AtomIdentifierType* for extended connectivity fingerprints
|
|
|
294 generation and returns *ExtendedConnectivityFingerprints*.
|
|
|
295
|
|
|
296 Possible values for atomic invariants are: *AS, X, BO, LBO, SB, DB,
|
|
|
297 TB, H, Ar, RA, FC, MN, SM*. Default value [ Ref 24 ]:
|
|
|
298 *AS,X,BO,H,FC,MN*.
|
|
|
299
|
|
|
300 The atomic invariants abbreviations correspond to:
|
|
|
301
|
|
|
302 AS = Atom symbol corresponding to element symbol
|
|
|
303
|
|
|
304 X<n> = Number of non-hydrogen atom neighbors or heavy atoms
|
|
|
305 BO<n> = Sum of bond orders to non-hydrogen atom neighbors or heavy atoms
|
|
|
306 LBO<n> = Largest bond order of non-hydrogen atom neighbors or heavy atoms
|
|
|
307 SB<n> = Number of single bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
308 DB<n> = Number of double bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
309 TB<n> = Number of triple bonds to non-hydrogen atom neighbors or heavy atoms
|
|
|
310 H<n> = Number of implicit and explicit hydrogens for atom
|
|
|
311 Ar = Aromatic annotation indicating whether atom is aromatic
|
|
|
312 RA = Ring atom annotation indicating whether atom is a ring
|
|
|
313 FC<+n/-n> = Formal charge assigned to atom
|
|
|
314 MN<n> = Mass number indicating isotope other than most abundant isotope
|
|
|
315 SM<n> = Spin multiplicity of atom. Possible values: 1 (singlet), 2 (doublet) or
|
|
|
316 3 (triplet)
|
|
|
317
|
|
|
318 Atom type generated by AtomTypes::AtomicInvariantsAtomTypes class
|
|
|
319 corresponds to:
|
|
|
320
|
|
|
321 AS.X<n>.BO<n>.LBO<n>.<SB><n>.<DB><n>.<TB><n>.H<n>.Ar.RA.FC<+n/-n>.MN<n>.SM<n>
|
|
|
322
|
|
|
323 Except for AS which is a required atomic invariant in atom types,
|
|
|
324 all other atomic invariants are optional. Atom type specification
|
|
|
325 doesn't include atomic invariants with zero or undefined values.
|
|
|
326
|
|
|
327 In addition to usage of abbreviations for specifying atomic
|
|
|
328 invariants, the following descriptive words are also allowed:
|
|
|
329
|
|
|
330 X : NumOfNonHydrogenAtomNeighbors or NumOfHeavyAtomNeighbors
|
|
|
331 BO : SumOfBondOrdersToNonHydrogenAtoms or SumOfBondOrdersToHeavyAtoms
|
|
|
332 LBO : LargestBondOrderToNonHydrogenAtoms or LargestBondOrderToHeavyAtoms
|
|
|
333 SB : NumOfSingleBondsToNonHydrogenAtoms or NumOfSingleBondsToHeavyAtoms
|
|
|
334 DB : NumOfDoubleBondsToNonHydrogenAtoms or NumOfDoubleBondsToHeavyAtoms
|
|
|
335 TB : NumOfTripleBondsToNonHydrogenAtoms or NumOfTripleBondsToHeavyAtoms
|
|
|
336 H : NumOfImplicitAndExplicitHydrogens
|
|
|
337 Ar : Aromatic
|
|
|
338 RA : RingAtom
|
|
|
339 FC : FormalCharge
|
|
|
340 MN : MassNumber
|
|
|
341 SM : SpinMultiplicity
|
|
|
342
|
|
|
343 *AtomTypes::AtomicInvariantsAtomTypes* module is used to assign
|
|
|
344 atomic invariant atom types.
|
|
|
345
|
|
|
346 SetFunctionalClassesToUse
|
|
|
347 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse($ValuesRef);
|
|
|
348 $ExtendedConnectivityFingerprints->SetFunctionalClassesToUse(@Values);
|
|
|
349
|
|
|
350 Sets functional classes invariants to use during
|
|
|
351 *FunctionalClassAtomTypes* value of *AtomIdentifierType* for
|
|
|
352 extended connectivity fingerprints generation and returns
|
|
|
353 *ExtendedConnectivityFingerprints*.
|
|
|
354
|
|
|
355 Possible values for atom functional classes are: *Ar, CA, H, HBA,
|
|
|
356 HBD, Hal, NI, PI, RA*. Default value [ Ref 24 ]:
|
|
|
357 *HBD,HBA,PI,NI,Ar,Hal*.
|
|
|
358
|
|
|
359 The functional class abbreviations correspond to:
|
|
|
360
|
|
|
361 HBD: HydrogenBondDonor
|
|
|
362 HBA: HydrogenBondAcceptor
|
|
|
363 PI : PositivelyIonizable
|
|
|
364 NI : NegativelyIonizable
|
|
|
365 Ar : Aromatic
|
|
|
366 Hal : Halogen
|
|
|
367 H : Hydrophobic
|
|
|
368 RA : RingAtom
|
|
|
369 CA : ChainAtom
|
|
|
370
|
|
|
371 Functional class atom type specification for an atom corresponds to:
|
|
|
372
|
|
|
373 Ar.CA.H.HBA.HBD.Hal.NI.PI.RA or None
|
|
|
374
|
|
|
375 *AtomTypes::FunctionalClassAtomTypes* module is used to assign
|
|
|
376 functional class atom types. It uses following definitions [ Ref
|
|
|
377 60-61, Ref 65-66 ]:
|
|
|
378
|
|
|
379 HydrogenBondDonor: NH, NH2, OH
|
|
|
380 HydrogenBondAcceptor: N[!H], O
|
|
|
381 PositivelyIonizable: +, NH2
|
|
|
382 NegativelyIonizable: -, C(=O)OH, S(=O)OH, P(=O)OH
|
|
|
383
|
|
|
384 SetNeighborhoodRadius
|
|
|
385 $ExtendedConnectivityFingerprints->SetNeighborhoodRadius($Radius);
|
|
|
386
|
|
|
387 Sets neighborhood radius to use during extended connectivity
|
|
|
388 fingerprints generation and returns
|
|
|
389 *ExtendedConnectivityFingerprints*.
|
|
|
390
|
|
|
391 StringifyExtendedConnectivityFingerprints
|
|
|
392 $String = $Fingerprints->StringifyExtendedConnectivityFingerprints();
|
|
|
393
|
|
|
394 Returns a string containing information about
|
|
|
395 *ExtendedConnectivityFingerprints* object.
|
|
|
396
|
|
|
397 AUTHOR
|
|
|
398 Manish Sud <msud@san.rr.com>
|
|
|
399
|
|
|
400 SEE ALSO
|
|
|
401 Fingerprints.pm, FingerprintsStringUtil.pm,
|
|
|
402 AtomNeighborhoodsFingerprints.pm, AtomTypesFingerprints.pm,
|
|
|
403 EStateIndiciesFingerprints.pm, MACCSKeys.pm, PathLengthFingerprints.pm,
|
|
|
404 TopologicalAtomPairsFingerprints.pm,
|
|
|
405 TopologicalAtomTripletsFingerprints.pm,
|
|
|
406 TopologicalAtomTorsionsFingerprints.pm,
|
|
|
407 TopologicalPharmacophoreAtomPairsFingerprints.pm,
|
|
|
408 TopologicalPharmacophoreAtomTripletsFingerprints.pm
|
|
|
409
|
|
|
410 COPYRIGHT
|
|
|
411 Copyright (C) 2015 Manish Sud. All rights reserved.
|
|
|
412
|
|
|
413 This file is part of MayaChemTools.
|
|
|
414
|
|
|
415 MayaChemTools is free software; you can redistribute it and/or modify it
|
|
|
416 under the terms of the GNU Lesser General Public License as published by
|
|
|
417 the Free Software Foundation; either version 3 of the License, or (at
|
|
|
418 your option) any later version.
|
|
|
419
|
