rdkit.Chem.BRICS module — The RDKit 2016.09.1 documentation

# rdkit.Chem.BRICS module

Implementation of the BRICS algorithm from Degen et al. ChemMedChem 3 1503-7 (2008)

`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)) []