Hi there @OpenBabel and Greg I am using OpenBabel 2.3.0 and RDKit 201009 release and trying to get them if not work together at least live peacefully :)
So I have a mol file coming from the pdb Astex Diverse Set (1hww.mol). I convert this to a smiles string using Openbabel babel -xn 1hww.mol 1hww.smiles (since I do not want to generate the name). I get the attached smiles file - [...@h]1(O)[...@h]2[n@H](CCC1)C[C@@H](O)[...@h]2o When I try to load this using RDKit (i.e. AllChem.MolFromSmiles(smiles)) I get [19:04:57] Explicit valence for atom # 3 N, 4, is greater than permitted If I copy the isomeric smiles (openeye) c1...@h]([C@@H]2[C@@H]([C@@H](c...@]2c1)O)O)O in the file instead of the openbabel generated smiles RDKit works fine... This is probably a simple chemistry problem, but I am a CS guy so please bear with me. Now my question is: Who is the culprit? (select one) a) No-one - The mol file is incorrect (but then again, why does Openbabel read it with an error message? Still I can read this directly through RDKit) b) Openbabel - it is generating an incorrect smiles string (and ideally this is now fixed and available in 2.3.1 :) ) c) RDkit - The smiles is perfectly fine, please redirect your query elsewhere d) None of the above, the OS/hardware is playing tricks on you I appreciate any help and any light you can shed. Cheers JP PS These two frameworks are really great!! well done everyone!!
1hww.mol
Description: Binary data
1hww.smiles
Description: Binary data
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