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On Jul 9, 2008, at 3:30 PM, Rajarshi Guha wrote:
>
>
> Thanks for the info. However something seems to be wrong. I'm
> generating an IAtomContainer from c1ccccc1CN and then doing
>
> CDKHueckelAromaticityDetector.detectAromaticity(mol1);
> addExplicitHydrogens(mol1);
> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(mol1);
> lpcheck.saturate(mol1);
>
> GasteigerPEPEPartialCharges pepe = new GasteigerPEPEPartialCharges();
> pepe.calculateCharges(mol1);
>
> However, when I print the charge on each atom via atom.getCharge()
> all of them have 0
Digging into the code of GasteigerPEPEPartialCharges I see that there
are two exit points from the method assignGasteigerPiPartialCharges()
It seems that when using c1ccccc1CN the method is exiting at line 237
- - and at this point no charges have been set. Furthermore, exiting at
this point results in the sigma partial charges not even being
calculated.
Unfortunately I don't know more of the details of the implementation
to be able to fix this
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Rajarshi Guha <[EMAIL PROTECTED]>
GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84
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A computer lets you make more mistakes faster than any other invention,
with the possible exceptions of handguns and Tequilla.
-- Mitch Ratcliffe
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