On 2013-11-17 12:34, Geoffrey Hutchison wrote:

> It doesn't take a cheminformatics specialist to realize these strings are 
> different:

Well, as I understand it, one of the problems with smiles is you can 
start your graph at any atom. Which gives you any number of different 
smiles string for the same molecule. For all I know they're all 
different descriptions of the exact same graph.

...
> Now, if I take the 3D SDF version from the website, Open Babel gives a 
> similar SMILES to CACTVS:
> C(=O)([C@@H]1CCCCN1C(=O)C(=O)C(CC)(C)C)O[C@H](CCc1ccccc1)c1ccccc1

Well, sorry, it does take a cheminformatics specialist to know that is 
"more similar" to
"CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)O[C@H](CCc2ccccc2)c3ccccc3"
than
"CCC(C)(C)C(=O)C(=O)N1CCCC[C@H]1C(=O)OC(CCc2ccccc2)c3ccccc3"

> And.. I get the same SMILES from the PDB file on that webpage. So I
guess we're confused where the problem is in Open Babel?

I don't think the problem is in OpenBabel, but I can't tell. RCSB says 
they're all describing the same molecule. OpenBabel says they aren't. 
Who should I trust and why? So I asked.

Dima


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