[N-]=[N+]=NC(=O)N1C(=O)N([N+]([O-])=O)C2(C13C4=C56)C4=C5C2=C36 [N-]=[N+]=NC(=O)N(C(=O)N1[N+]([O-])=O)C(c23)(c4c56)C16c3c5c24
rdkit canonicalizes the two to the following, respectively: [N-]=[N+]=NC(=O)N1C(=O)N([N+](=O)[O-])C23c4c5c2c2c-5c4C213 [N-]=[N+]=NC(=O)N1C(=O)N([N+](=O)[O-])C23c4c5c6c(c2c4=6)C513 I believe these represent the same structure, with the following caveat: It is not impossible that the two SMILES actually code for different structures in some subtle way. I've tried visualizing them in several packages, however, and I've not been able to find a difference. Some packages canonicalize them to the same structure and others do not. The actual structure is chiral, but I've been looking at this from the point of view of SMILES without stereochemical information. The two original SMILES come from a different package. That package puts them out as SMILES which are dependent on the atom numbering in the input structure file. The originating package does canonicalize these to the same structure, however. I don't think it is correct to consider the double-bonded atoms aromatic, which the originating package does in one case. However, FWIW, RDKit canonicalizes them as aromatic in both cases. But the main issue is that RDKit canonicalizes them differently. It's kind of a grotty molecule, so it's possible I'm missing something. If so, I'd appreciate being set right. ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
