Hello Violeta,thank you very much for your answer - it helped me a lot but I have 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 bad molecule choice - with the molecule ( attachment )I had choosen, 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: nullI tried only few molecules so far but the attached one is the only one producing this problem.
Have a nice weekend ;) Alex Quoting Violeta Labarta <[EMAIL PROTECTED]>:
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 --- [EMAIL PROTECTED] 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 = new MMFF94BasedParameterSetReader(); PR.readParameterSets(); EF = 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 atorg.openscience.cdk.modeling.forcefield.BondStretching.setMMFF94BondStretchingParameters(BondStretching.java:103)atorg.openscience.cdk.modeling.forcefield.MMFF94EnergyFunction.<init>(MMFF94EnergyFunction.java:46)attest.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-------------------------------------------------------------------------This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Cdk-user mailing list [email protected]https://lists.sourceforge.net/lists/listinfo/cdk-user___________________________________________________________ Yahoo! Answers - Got a question? Someone out there knows the answer. Try it now. http://uk.answers.yahoo.com/ ------------------------------------------------------------------------- This SF.net email is sponsored by: Splunk Inc. Still grepping through log files to find problems? Stop. Now Search log events and configuration files using AJAX and a browser. Download your FREE copy of Splunk now >> http://get.splunk.com/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
cdk_test.mol
Description: MOL mdl chemical test
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