Thanks for the reply Angel.
I
suspect PubChem is pretty much married to this system. Between
JavaScript and Jmol script, I think I can import and the partial charge
information.
The PubChem SDF's are "GET-able" with a PubChem CID,
so these files will import directly into Jmol. Jmol reads the
coordinates OK. I'll just grab the charge data and add it via scripting.
The
catch in this whole plan is the PubChem CID. You need it before you can
do a direct GET. Fortunately, there's a whole blog cottage industry
that deals with accessing PubChem data directly, so I think I can set
this all up. I have three potential plans at this point, including a
PubChem API that turns a POST into an appropriate GET query.
In
answer to your question on other software, the only thing I've seen is
academic chemometric discussion lists that discuss converting the
PubChem data to mol2 for their own systems.
Otis
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Angel Herráez" <[email protected]>
Sent: Tuesday, January 18, 2011 5:18 AM
To: [email protected], [email protected]
Subject: Re: [Jmol-users] PubChem SDF
Just my 2 cents:
> Evidently, a fair number of PubChem's sdf's have partial charge data.
I see aproblem here. The format shown in your example is not
according to SDF spec (I think it does not suppor partial charge,
only formal charge). They shouldbe using a different format, like
MOL2.
So if Jmol is made to support reading that, it is not really SDF
import. That should be made clear.
What other software reads those PubChem SDF files?
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