rdkit.Chem.BRICS module

rdkit.Chem.BRICS.BRICSBuild(fragments, onlyCompleteMols=True, seeds=None, uniquify=True, scrambleReagents=True, maxDepth=3)

rdkit.Chem.BRICS.BRICSDecompose(mol, allNodes=None, minFragmentSize=1, onlyUseReactions=None, silent=True, keepNonLeafNodes=False, singlePass=False, returnMols=False)

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']

rdkit.Chem.BRICS.BreakBRICSBonds(mol, bonds=None, sanitize=True, silent=True)

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']

rdkit.Chem.BRICS.FindBRICSBonds(mol, randomizeOrder=False, silent=True)

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))
[]