This really isn’t breaking my promise. It’s just interesting! I looks like
PubChem will return proper file for these URL’s with ANY legal SMILES. There’s
probably a size limit, but it worked for some pretty large molecules:
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/SDF?smiles=C([C@@H](C)Cl)[C@@H](C)Br
<http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C(%5BC@@H%5D(C)Cl)%5BC@@H%5D(C)Br>
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/JSON?smiles=C([C@@H](C)Cl)[C@@H](C)Br
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C([C@@H](C)Cl)[C@@H](C)Br
<http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C(%5BC@@H%5D(C)Cl)%5BC@@H%5D(C)Br>
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/XML?smiles=C([C@@H](C)Cl)[C@@H](C)Br
Here’s one that’s NOT in PubChem:
http://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/smiles/PNG?smiles=C/C(C)=C/C(C%5BC@@H%5D(C)%5BC@%5D4(%5BH%5D)%5BC@%5D3(C)%5BC@%5D(%5BH%5D)(%5BC@@%5D1(%5BH%5D)%5BC@@%5D(%5BH%5D)(%5BC@%5D2(C)C(=CC1)C%5BC@@H%5D(O)CC2)CC3)CC4)C(C)C
The SDF is 2D. SDF, XML, and JSON return 2d coordinates, bond annotations
(stereo), Standard InChI, and OpenEye SMILES, which I think is canonical within
PubChem. Of course, if the compound is in PubChem, then the full record is
returned. I mentioned before that to pull data from the JSON you have to go
through an iteration process. Clearly, the structure of these files can vary
from compound to compound.
By the way, I purposely put an undeclared chiral carbon in the above structure
to help me scope out the bond annotations. I think an undeclared stereo bond is
marked with a 3.
Note that this means that PubChem can be used as an InChI resolver and source
of canonical SMILES within PubChem.
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
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