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Implementation of the BRICS algorithm from Degen et al. ChemMedChem *3* 1503-7 (2008)
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environs = {'L1': '[C;D3]([#0,#6,#7,#8])(=O)', 'L3': '[O;D2]-;
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reactionDefs = [('1', '3', '-'), ('1', '5', '-'), ('1', '10',
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smartsGps = copy.deepcopy(reactionDefs)
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environMatchers = {}
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bondMatchers = []
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reactions = tuple([[Reactions.ReactionFromSmarts(y) for y in x
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reverseReactions = []
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dummyPattern = Chem.MolFromSmiles('[*]')
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Imports: sys, re, Chem, Reactions, iteritems, iterkeys, next, range, copy, random
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returns the bonds in a molecule that BRICS would cleave >>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(FindBRICSBonds(m)) >>> res [((3, 2), ('3', '4')), ((3, 4), ('3', '4'))] a more complicated case: >>> m = Chem.MolFromSmiles('CCCOCCC(=O)c1ccccc1') >>> res = list(FindBRICSBonds(m)) >>> res [((3, 2), ('3', '4')), ((3, 4), ('3', '4')), ((6, 8), ('6', '16'))] we can also randomize the order of the results: >>> random.seed(23) >>> res = list(FindBRICSBonds(m,randomizeOrder=True)) >>> sorted(res) [((3, 2), ('3', '4')), ((3, 4), ('3', '4')), ((6, 8), ('6', '16'))] Note that this is a generator function : >>> res = FindBRICSBonds(m) >>> res <generator object ...> >>> next(res) ((3, 2), ('3', '4')) >>> m = Chem.MolFromSmiles('CC=CC') >>> res = list(FindBRICSBonds(m)) >>> sorted(res) [((1, 2), ('7', '7'))] make sure we don't match ring bonds: >>> m = Chem.MolFromSmiles('O=C1NCCC1') >>> list(FindBRICSBonds(m)) [] another nice one, make sure environment 8 doesn't match something connected to a ring atom: >>> m = Chem.MolFromSmiles('CC1(C)CCCCC1') >>> list(FindBRICSBonds(m)) [] |
breaks the BRICS bonds in a molecule and returns the results >>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCCOCC') >>> m2=BreakBRICSBonds(m) >>> Chem.MolToSmiles(m2,True) '[3*]O[3*].[4*]CC.[4*]CCC' a more complicated case: >>> m = Chem.MolFromSmiles('CCCOCCC(=O)c1ccccc1') >>> m2=BreakBRICSBonds(m) >>> Chem.MolToSmiles(m2,True) '[16*]c1ccccc1.[3*]O[3*].[4*]CCC.[4*]CCC([6*])=O' can also specify a limited set of bonds to work with: >>> m = Chem.MolFromSmiles('CCCOCC') >>> m2 = BreakBRICSBonds(m,[((3, 2), ('3', '4'))]) >>> Chem.MolToSmiles(m2,True) '[3*]OCC.[4*]CCC' this can be used as an alternate approach for doing a BRICS decomposition by following BreakBRICSBonds with a call to Chem.GetMolFrags: >>> m = Chem.MolFromSmiles('CCCOCC') >>> m2=BreakBRICSBonds(m) >>> frags = Chem.GetMolFrags(m2,asMols=True) >>> [Chem.MolToSmiles(x,True) for x in frags] ['[4*]CCC', '[3*]O[3*]', '[4*]CC'] |
returns the BRICS decomposition for a molecule >>> from rdkit import Chem >>> m = Chem.MolFromSmiles('CCCOCc1cc(c2ncccc2)ccc1') >>> res = list(BRICSDecompose(m)) >>> sorted(res) ['[14*]c1ccccn1', '[16*]c1cccc([16*])c1', '[3*]O[3*]', '[4*]CCC', '[4*]C[8*]'] >>> res = list(BRICSDecompose(m,returnMols=True)) >>> res[0] <rdkit.Chem.rdchem.Mol object ...> >>> smis = [Chem.MolToSmiles(x,True) for x in res] >>> sorted(smis) ['[14*]c1ccccn1', '[16*]c1cccc([16*])c1', '[3*]O[3*]', '[4*]CCC', '[4*]C[8*]'] nexavar, an example from the paper (corrected): >>> m = Chem.MolFromSmiles('CNC(=O)C1=NC=CC(OC2=CC=C(NC(=O)NC3=CC(=C(Cl)C=C3)C(F)(F)F)C=C2)=C1') >>> res = list(BRICSDecompose(m)) >>> sorted(res) ['[1*]C([1*])=O', '[1*]C([6*])=O', '[14*]c1cc([16*])ccn1', '[16*]c1ccc(Cl)c([16*])c1', '[16*]c1ccc([16*])cc1', '[3*]O[3*]', '[5*]NC', '[5*]N[5*]', '[8*]C(F)(F)F'] it's also possible to keep pieces that haven't been fully decomposed: >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True)) >>> sorted(res) ['CCCOCC', '[3*]OCC', '[3*]OCCC', '[3*]O[3*]', '[4*]CC', '[4*]CCC'] >>> m = Chem.MolFromSmiles('CCCOCc1cc(c2ncccc2)ccc1') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True)) >>> sorted(res) ['CCCOCc1cccc(-c2ccccn2)c1', '[14*]c1ccccn1', '[16*]c1cccc(-c2ccccn2)c1', '[16*]c1cccc(COCCC)c1', '[16*]c1cccc([16*])c1', '[3*]OCCC', '[3*]OC[8*]', '[3*]OCc1cccc(-c2ccccn2)c1', '[3*]OCc1cccc([16*])c1', '[3*]O[3*]', '[4*]CCC', '[4*]C[8*]', '[4*]Cc1cccc(-c2ccccn2)c1', '[4*]Cc1cccc([16*])c1', '[8*]COCCC'] or to only do a single pass of decomposition: >>> m = Chem.MolFromSmiles('CCCOCc1cc(c2ncccc2)ccc1') >>> res = list(BRICSDecompose(m,singlePass=True)) >>> sorted(res) ['CCCOCc1cccc(-c2ccccn2)c1', '[14*]c1ccccn1', '[16*]c1cccc(-c2ccccn2)c1', '[16*]c1cccc(COCCC)c1', '[3*]OCCC', '[3*]OCc1cccc(-c2ccccn2)c1', '[4*]CCC', '[4*]Cc1cccc(-c2ccccn2)c1', '[8*]COCCC'] setting a minimum size for the fragments: >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True,minFragmentSize=2)) >>> sorted(res) ['CCCOCC', '[3*]OCC', '[3*]OCCC', '[4*]CC', '[4*]CCC'] >>> m = Chem.MolFromSmiles('CCCOCC') >>> res = list(BRICSDecompose(m,keepNonLeafNodes=True,minFragmentSize=3)) >>> sorted(res) ['CCCOCC', '[3*]OCC', '[4*]CCC'] >>> res = list(BRICSDecompose(m,minFragmentSize=2)) >>> sorted(res) ['[3*]OCC', '[3*]OCCC', '[4*]CC', '[4*]CCC'] |
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environs
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reactionDefs
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reactions
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