Hi Rocco, Point taken. I don’t think you’d be able to get RDKit to spit such SMILES strings out unless you tortured it pretty hard, however. Dave
On Mon, 18 Nov 2019 at 16:36, Rocco Moretti <rmoretti...@gmail.com> wrote: > Actually, it is possible to get arbitrary orders, if you (ab)use the '.' > component ("zero order bond") directive and the numeric bonding ("ring > closure") directives: > > >>> Chem.MolToSmiles( Chem.MolFromSmiles("O1.Cl2.C12" ) ) > 'OCCl' > > Whether you want to do things that way is another question. > > On Mon, Nov 18, 2019 at 10:24 AM David Cosgrove < > davidacosgrov...@gmail.com> wrote: > >> Hi Rafal, >> It is not always possible to preserve the atom ordering in the SMILES >> string because there is an implied bond between contiguous symbols in the >> SMILES. I think, for example, that the molecule with the SMILES OCCl >> couldn’t have the order in the molecule object O first, Cl second, C third, >> with bonds between 1 and 3 and 2 and 3 and get the SMILES in that order. >> >> I hope that made sense. Please ask again if not. >> >> Best regards, >> Dave >> >> >> On Mon, 18 Nov 2019 at 12:33, Rafal Roszak <rmrmg.c...@gmail.com> wrote: >> >>> Hi all, >>> >>> Is there any way to preserve atom order from Mol object during >>> exporting to smiles? I tried MolToSmiles with rootedAtAtom=0 and >>> canonical=False options but it not always prevent oryginal order. >>> I know I can use _smilesAtomOutputOrder to map old indices to new one >>> in canonical smiles but maybe we have something more handy? >>> >>> Best, >>> >>> Rafał >>> >>> >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> Rdkit-discuss@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> -- >> David Cosgrove >> Freelance computational chemistry and chemoinformatics developer >> http://cozchemix.co.uk >> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > -- David Cosgrove Freelance computational chemistry and chemoinformatics developer http://cozchemix.co.uk
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