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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