Bob,
I'm not sure how stable it is, but the JS function below works. I'm also
not sure how cross browser (platform) friendly it is. My Mac buddy is OOO
for six weeks.
If a PubChem molfile with partial chages is pasted into our model kit
script field on the Molecular Editor screen and then run, the PubChem model
will load with partial charges:
http://chemagic.com/web_molecules/script_page_large.aspx
In the function, I display the MEP on load because that seems to light-up
the Jmol menu's Surfaces/MEP selection, but this light-up is erratic.
Nevertheless, Jmols script will display the MEP. Here are three PubChem SDF
links for getting cut/paste files for testing:
cholesterol
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5997&disopt=3DDispla
ySDF
benzoquinone
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=4650&disopt=3DDispla
ySDF
And a pretty one Aspirin
http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=2244&disopt=3DDispla
ySDF
In some cases the charges are pretty primitive, but the MEP's get the point
across. As you can see above, direct loading of the file requires the
PubChem CID. By finagling, I think these can be pulled from a PubChem
InChiKey query via Resolver. More to the point, I'm going to write to
Markus about the possibility of Resolver returning PubChem CID's directly
on a SMILES query. I'm betting these are already in Resolver's many
database connections.
Even if this does not work out, the PubChem SDF's are available via a name
search and two clicks at the PubChem site. This puts MEP display for lots
of models within reach of high school chemistry classes. What I'm really
after, however is:
1) Draw a simple structure in JME
2) Load it into Jmol
3) Click a link that takes you to PubChem for this Model
We have it to this point. The last is within reach.
4) Load the MEP of the model that started in JME directly from PubChem
data.
The JS function, in my usual verbose and chaotic style, follows.
Otis
function pcpc() {
var mf = document.getElementById("script").value;
if (mf.toUpperCase().indexOf("PUBCHEM_MMFF94_PARTIAL_CHARGES") < 0) {
return; }
mf = mf.replace(/(\r\n|\n|\r)/gm, "|");
var scpt1 = ""; var scpt2 = "";
var re = /PARTIAL_CHARGES>\|(.*?)\|\|/;
var chgis;
var chgDs = mf.match(re);
var chgs = chgDs[1].split("|");
for (var x = 1; x <= chgs[0]; x++) {
chgis = chgs[x].split(" ");
scpt1 += "{atomno=" + chgis[0] + "}.partialCharge=" + chgis[1] +
";"
}
scpt2 = "{*}.partialCharge = 0;" + scpt1 + "isosurface vdw 80% map mep
translucent;";
jmolScript(scpt2);
}
--
Otis Rothenberger
Department of Chemistry
Illinois State University
Normal, IL 61790-4160
http://chemagic.org
----------------------------------------
From: "Robert Hanson" <[email protected]>
Sent: Tuesday, January 18, 2011 6:55 PM
To: [email protected], [email protected]
Subject: Re: [Jmol-users] PubChem SDF
Of course, Otis is so good at JavaScript, he could easily write a little
JavaScript parser for this....;)
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