Hi RDKitters, I'm sure this must of been covered somewhere else but I can't find it in the forum or the source.
I am manipulating SMILES strings and wonder whether I can use RDKit as a
shortcut, so my question is does the order of occurrence in a SMILES string of
an atom match the atom index that is given by RDKit. It seems to me that it
does but I'd like to know for all cases. For example
>>> from rdkit import Chem
>>> mol=Chem.MolFromSmiles('CSNOC')
>>> for atom in mol.GetAtoms(): print atom.GetAtomicNum(),atom.GetIdx()
...
6 0
16 1
7 2
8 3
6 4
This is what I would expect, but is there a case when this order might not be
conserved?
If the order isn't always conserved, how does the indexing cope with RDKit
canonical smiles?
Thanks in advance.
Best,
Nick
Nicholas C. Firth | PhD Student | Cancer Therapeutics
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