Sorry to hear about the flooding. As an aside if you want to get they smiles atom output order, it is saved as a property on the molecule after a call to MolToSmiles,
To get to the property, use mol.GetPropsAsDict(True,True) and it will be there with the key named something like "_smilesAtomOutputOrder" We should probably make a helper function for this. ---- Brian Kelley > On Jun 15, 2017, at 6:27 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu> wrote: > >> On 06/15/2017 10:13 AM, Maciek Wójcikowski wrote: >> Hi, >> >> If you really want to rely on the order of atom you can renumber them >> anyhow you like with Chem.RenumberAtoms() >> http://rdkit.org/Python_Docs/rdkit.Chem.rdmolops-module.html#RenumberAtoms >> There is also a function which returns canonical order of atoms for >> you: Chem.CanonicalRankAtoms() As I remember correctly the order may differ >> from the canonical smiles, although that might have changed. > > https://www.nature.com/articles/sdata201773 > > Unfortunately we got flooded day before yesterday and the servers doing > the crunching are currently down. > > -- > Dimitri Maziuk > Programmer/sysadmin > BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu > > ------------------------------------------------------------------------------ > Check out the vibrant tech community on one of the world's most > engaging tech sites, Slashdot.org! http://sdm.link/slashdot > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
