Re: [Jmol-users] PubChem SDF

[Robert H. <ha...@st...>]

I think it's OK, Angel. These a "user-defined data" --- data that could be
of any format whatsoever. We could consider reading it.

On Tue, Jan 18, 2011 at 10:19 AM, Otis Rothenberger
<osr...@ch...>wrote:

> 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" <ang...@ua...>
> *Sent*: Tuesday, January 18, 2011 5:18 AM
> *To*: osr...@ch..., jmo...@li...
> *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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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
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phone: 507-786-3107


If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900