Hi Aziz,
What I could see that on my computer with the given SMILES that it takes
about 1.5 minutes to run in Eclipse, so a lot shorter than 15 minutes.
The main bottleneck seems to be this bit:
/*processing for which bonds which are not in resonance*/
for(int number = 0; number < ac.getBondCount() ; number++){
IAtomContainer aa = setAntiFlags(container,ac, number,true);
if(aa != null){
IMoleculeSet ab = gR2.getStructures((IMolecule) aa);
For each bond, setAntiFlags is called and StructureResonanceGenerator's
method getStructures is called. Each call can take seconds, and that
adds up to more than a minute and a half.
I can't be of much more help, perhaps Miguel Rojas would have some
pointers how to possibly speed things up.
cheers,
Mark
> Dear Mark,
>
> > Could you send the source code that runs for 15 minutes to the list? It
> > should be relatively easy to debug it, to find out where things stall.
>
> Thank you for lookng at this issue. here is the jython code I am using
> to calculate partial charge for an atom.
>
>
> sp = smilesParser()
>
> smi =
> /"COC1=CC=C(c...@h]2n(C)C(=O)[...@h](C)NC(=O)[C@@H](C)NC(=O)[...@h]3cc4=cc=c(O)C(OC5=CC=C(C=C5)C(O)[...@h](N(C)C(=O)[...@h](C)NC2=O)C(=O)N3C)=C4)C=C1"/
>
> mol = sp.parseSimles(smi)
>
> mol = reader.next()
>
> desc = PartialTChargePEOEDescriptor ()
>
> atoms = mol.atoms().iterator()
>
> firstAtom = atoms.next()
>
> pcharge = desc.calculate(firstAtom, mol).getValue().doubleValue()
>
>
>
>
>
> I also went through the code of of the one of the java object that is
> instanced by PartialTChargePEOEDescriptor and one of its methods that
> is called to calculate the partial charges, I found out some bizare code
> I paste here:
>
>
>
> public class GasteigerMarsiliPartialCharges implements IChargeCalculator {
>
> …
>
> public IAtomContainer
> assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean
> setCharge) throws Exception {
>
> ….
>
> double[] q_old = new double[ac.getAtomCount()];
>
> for(int i = 0 ; i < q_old.length ; i++)
>
> q_old[*0*] = 20.0; ////// STRANGE
>
> ….
>
> the index should "i" not "0" if I understand this part of the code.
>
>
> thanks ,
>
>
> AYASRI
>
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