Hi all, Is it possible to get stereochemical atom order around chiral center?
To be more verbose: in smiles/smarts chirality (@ or @@) is determined by atom order which is not exactly the same as atom idxes in mol. The difference may appear in ring-containing compounds, according to https://www.daylight.com/dayhtml/doc/theory/theory.smiles.html: """The chiral order of the ring closure bond is implied by the lexical order that the ring closure digit appears on the chiral atom (not in the lexical order of the "substituent" atom).""" For example all smileses below represent the same molecule: C1CN[C@@H](C)OC1 --chiralOrder-> N,C,O --smiOrder-> N,C,O O1CCCN[C@H]1C --chiralOrder-> N,O,C --smiOrder-> O,N,C C[C@@H]1NCCCO1 --chiralOrder-> C,O,N --smiOrder-> C,N,O only in first example chiral order is the same as atom order in mol object. So is it possible to get chiral order? Best, Rafał _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
