Hi Peter, to the best of my knowledge: for a given SMILES string, you should always end up with the same molecule object.
On the other hand, generation of (canonical / unique) SMILES often reorders atoms and bonds (to ensure that the SMILES is unique for a given structure). A conversion Molecule -> SMILES -> Molecule could thus lead to a different ordering of atoms and bonds and you will have to canonicalize your structure before you generate your index. [Or make sure that you use non-canonical SMILES.] Best, Nils Am 02.10.2018 um 22:32 schrieb Peter St. John: > If I store a molecule as a SMILES string, along with relevant > information about different bonds, is it safe to annotate those bond > entries by bond index? > > I.e., if I create a new rdkit Molecule with > rdkit.Chem.MolFromSmiles(xxx), will the bond ordering always be the > same? If not, does anyone know a a robust way of specifying a bond > within a molecule as a string-based representation? > > Thanks for the help! > -- Peter > _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
