On 01/13/2016 08:22 PM, Rolf Huehne wrote:
> 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
> ----------------------------------
>
Sorry, I forgot the 'Weight' in the example function call':
weight = getPdbEntryWeight("1deh");
Regards,
Rolf
--
Rolf Huehne
Postdoc
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