I guess I’ll pursue Phil’s question one philosophical step further. We have to
remember that we (3d model twiddlers) found them - the cheminformatics guys who
created these tools. For the most part, these folks are not 3d model twiddlers
like us. They are engaged in the systematic organization (and curation) of
chemical information. InChI, SMILES, IUPAC, SDF (2D and 3D), etc are all unique
chemical identifiers in their world. Indeed, some of them not only identify,
but they are also searchable for data in their own right (e.g. SDF). Check the
addendum info in 2D and 3D PubChem SDF’s. The stored data is not the same in 2d
and 3d. That some of these identifiers are useful to model twiddlers like us is
almost incidental.
All of this was driven home to me once again within the past year (Markus was
my original teacher on this point). A PubChem staff member was very patiently
helping me deal with PubChem JSONP. I naively thought that 3d SDF’s existed in
stored entities on PubChem servers - i.e. Jmol was just grabbing an intact SDF
right from the sever. The staff member pointed out that this was more like what
was actually on the server:
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/439570/record/JSON/?record_type=3d&response_type=display
<https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/439570/record/JSON/?record_type=3d&response_type=display>
He volunteered to show me how to pull the 3d coordinates out of the above, but
I declined. I was just happy that he explained how to pull the data that I
wanted from the “SDF’s” - 2d and 3d.
Bottom Line: in addition to being useful to model twiddlers like us, SDF’s
store data, and at PubChem 2d SDF’s store different data than 3d SDF’s. Well
that’s not quite right! All the info is stored more like the data in the 3d
“SDF” above: (-)-carvone by the way! Here’s the 2D “SDF"
https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/439570/record/JSON/?record_type=2d&response_type=display
<https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/439570/record/JSON/?record_type=2d&response_type=display>
Otis
--
Otis Rothenberger
o...@chemagic.org
http://chemagic.org
> On Apr 30, 2016, at 6:35 PM, J. Bays <pb...@saintmarys.edu> wrote:
>
> I have been trying to look at the structures of various cancer drugs. Most
> download like taxol, as flat structures. I realize that I can do a
> minimization in Jmol to improve that, but it is slow on my computers. I
> have been exporting them as mol files and then minimizing them Student
> Spartan which is very fast. I then reload the resultant .mol file into
> jmol.
>
> The questions I keep asking myself are of what use are these flat structures
> and why are they in the databases in that form? Anybody know?
>
>
>
> J. Philip Bays
> Emeritus Professor of Chemistry
> Department of Chemistry and Physics
> Saint Mary's College
> Notre Dame, IN 46556
> pb...@saintmarys.edu
>
>
>
>
>
>
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