Hi
I have come across a difference in behaviour with the BRICS algorithms
depending on how the molecule is fragmented when using non-canonical smiles
input.
RDKIT 2015_03, Python 2.7.10
BRICSDecompose gives back the starting chirality
>>> smi='C1CCOC[C@H]1NC'
>>> mol=Chem.MolFromSmiles(smi)
>>> cansmi=Chem.MolToSmiles(mol,1)
>>> cansmi
'CN[C@H]1CCCOC1'
>>> frags=BRICS.BRICSDecompose(mol,returnMols=True)
>>> bm=list(BRICS.BRICSBuild(frags))
>>> [Chem.MolToSmiles(m,1) for m in bm]
['CN[C@H]1CCCOC1']
BreakBRICSBonds inverts the centre.
>>> frags=Chem.GetMolFrags(BRICS.BreakBRICSBonds(mol),asMols=True)
>>> bm=list(BRICS.BRICSBuild(frags))
>>> [Chem.MolToSmiles(m,1) for m in bm]
['CN[C@@H]1CCCOC1']
Starting from the canonical smiles works fine
>>> smi='CN[C@H]1CCCOC1'
>>> mol=Chem.MolFromSmiles(smi)
>>> frags=Chem.GetMolFrags(BRICS.BreakBRICSBonds(mol),asMols=True)
>>> bm=list(BRICS.BRICSBuild(frags))
>>> [Chem.MolToSmiles(m,1) for m in bm]
['CN[C@H]1CCCOC1']
The inversion happens in BreakBRICSBonds
>>> smi='C1CCOC[C@H]1NC'
>>> mol=Chem.MolFromSmiles(smi)
>>> Chem.MolToSmiles(BRICS.BreakBRICSBonds(mol),1)
'[15*][C@@H]1CCCOC1.[5*]NC'
Using the pre canonicalised SMILES is clearly the way to go, but thought that
this might be indicative of an issue somewhere.
Regards
Stephen
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