HI Phuong, The CIPRank property is the rank of the atom for the assignment of stereochemistry. It's not *exactly* the CIP ranking, but it's reasonably close.
If you just want to have a canonical ordering/ranking of the atoms in the molecule, I would recommend using Chem.CanonicalRankAtoms(): http://rdkit.org/docs/source/rdkit.Chem.rdmolfiles.html#rdkit.Chem.rdmolfiles.CanonicalRankAtoms -greg On Mon, Apr 15, 2019 at 9:50 PM Phuong Chau <pc...@smith.edu> wrote: > Dear all, > > I am quite new to chirality. I read definition of CIP ranking. However, > some sources said that the stereocenter has to has 4 different atoms or > groups. I wonder how atom.GetProp('_CIPRank') works when it can not find > which stereocenter in the molecule is. > For example, > mol=Chem.MolFromSmiles('CCCC') > Atoms=[a for a in mol.GetAtoms() if a.HasProp('_CIPRank")] > AtomNums=[a.GetIdx()+1 for a in Atoms] > print(AtomNums) > [1,2,3,4] > > My purpose is to assign a constant priority score to each of the atom in > the molecule. Is there any ways that I can work on except the CIPRank? > If CIPRank is one, could you please explain how the CIPRank works? > > Phuong Chau > Smith College '20 > Engineering and Data Science Major > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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