On 2016-09-26 18:19, Peter S. Shenkin wrote: > 2D drawing code is tough. The 90/10 rule applies: the last 10% of > I think for the present purposes what we need is something correct, > robust and legible, and of course the example shown does not exhibit > that. (But I don't know what the starting SMILES is, so I don't know > whether the 7-bonded C is due to a bad SMILES, in which case all bets > are off.)
That was actually a "kudos to RDKit" post. I have an application where I need a drawing with all Hs and all atom labels, and molecule description in mmCIF(-ish) format. I use RDKit for the latter because of OpenBabel's stereochemistry "model", and OpenBabel for the drawings because 90% of the time it generates better layouts. THE comment is that RDKit's layout algorithm appears to be more stable: for this molecule OB generated a "better" picture from the original SDF downloaded from PubChem, and that complete mess when we re-ordered the atoms. RDKit generated the same picture in both cases. only one is a mirror image of the other. Dima ------------------------------------------------------------------------------ _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
