Re: [Cdk-user] forcefields - computing energy of given moelcule

[<Kl...@bi...>]

Hello Violeta,

thank you very much for your answer - it helped me a lot but I have =20
another problem now.

Since you have written the ForceFieldTest class maybe you can help again.

When first trying to use the ForceField package I accidentally made a =20
bad molecule choice - with the molecule ( attachment )I had choosen, =20
even your test classes fail.

Is it a known issue of the Forcefield package that some molecules won't work=
?

Plus I don't get the reason why it fails, the exception thrown is just: null

I tried only few molecules so far but the attached one is the only one =20
  producing this problem.

Have a nice weekend ;)

Alex






Quoting Violeta Labarta <vla...@ya...>:

> Dear Alex,
>
> In ForceFieldTest you can find a method with name
> testGetMMFF94EnergyOfAMolecule, that, I think does the
> same what you want. I would try it.
>
> Best regards,
>
> Violeta
>
> --- Kl...@bi... wrote:
>
>> Hello,
>>
>> I am trying to get the actual energy of a given
>> Molecule using MMFF94.
>> Is this  possible at all? Just to avoid
>> missunderstandings: I don't
>> want to minimize the energy.
>>
>> What I have been trying to do so far is the
>> following:
>>
> ____________________________________________________________
>>
>> public class EnergyCalculations {
>>
>>      MMFF94BasedParameterSetReader PR;
>>      MMFF94EnergyFunction EF;
>>
>>      public EnergyCalculations() {
>>
>>      }
>>
>>    public double getMoleculeEnergy(Molecule mol)
>> throws Exception {
>>
>>          PR =3D new MMFF94BasedParameterSetReader();
>>          PR.readParameterSets();
>>          EF =3D new MMFF94EnergyFunction(mol,
>> PR.getParamterSet());
>>          return EF.energy();
>> }
>>
>>
> _____________________________________________________________
>>
>> I am not sure if this really is what i want, but
>> however it doesnt
>> work. I get a NullPointerException and I'm not sure
>> why...?
>>
>> In detail:
>>
>> Exception in thread "Main
>> java.lang.NullPointerException
>>          at
>>
> org.openscience.cdk.modeling.forcefield.BondStretching.setMMFF94BondStretc=
hingParameters(BondStretching.java:103)
>>          at
>>
> org.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction.<init>(MMFF94=
EnergyFunction.java:46)
>>          at
>>
> test.EnergyCalculations.getMoleculeEnergy(EnergyCalculations.java:62)
>>          at test.Main.<init>(Main.java:107)
>>          at test.Main.main(Main.java:252)
>>
>> Maybe someone who already worked with the
>> implemented ForceFields can
>> share some of his experienence with me or tell me
>> what i am doing
>> wrong here.
>>
>> Thank you for any help &
>>
>> best regards
>>
>> Alex Klenner
>>
>>
>>
>>
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