On 01/13/2016 07:37 PM, Eric Martz wrote:
> Dear Angel (and everyone),
>
> For years I have wanted a way to find out (in javascript or in JSmol)
> the number of atoms (or molecular weight) of a PDB entry before
> attempting to load it into JSmol. But I have not known how to do this.
>
> If you know, please send me a sample of the code.
>
> When the size exceeds a threshold, I would load only alpha carbons.
>
Eric, as you might have expected, you could do it by using the PDBE API
that Angel used within his question.
The following function needs as a parameter the PDB code (lower-case!)
and would return the combined molecular weight of all molecules.
It will only work for asymmetric units. (If you would build up a
biological unit within Jmol more information would be needed.)
------- Jmol function ------------------------------
function getPdbEntryWeight(pdbId) {
var weight = 0;
if (pdbId != "") {
var queryUrl = "http://www.ebi.ac.uk/pdbe/api/pdb/entry/molecules/";
+ pdbId;
var info = eval(load(queryUrl));
if (info.type == "hash") {
for (var entity in info[pdbId]) {
var currentWeight = entity..weight;
if (currentWeight != "") {
weight = weight + currentWeight;
}
}
}
}
return weight;
}
----- Example code ---------------
weight = getPdbEntry("1deh");
print weight;
------Example output -------------
40749.875
----------------------------------
--
Rolf Huehne
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