generatemd java.lang.NullPointerException

Hello,


I'm trying to generate pharmacophore fingerprints with a specified xml configuration file.


So if I use the function


generatemd c test.sdf -k PF -g -D -v -o test.pfp


I obtain the pfp


But if I precise the .xml file :


generatemd c test.sdf -k PF -c pharma-frag.xml -g -D -v -o test.pfp


I obtain only the following message :


java.lang.NullPointerException


at chemaxon.pharmacophore.PFParameters.processDocument(PFParameters.java:943)


at chemaxon.descriptors.MDParameters.readFromXmlFile(MDParameters.java:856)


at chemaxon.pharmacophore.PFParameters.<init>(PFParameters.java:281)


at chemaxon.descriptors.GenerateMD.processDescriptorTypeSpecificOptions(GenerateMD.java:1706)


at chemaxon.descriptors.GenerateMD.processDescriptorOptions(GenerateMD.java:1691)


at chemaxon.descriptors.GenerateMD.processCmdLineOptions(GenerateMD.java:1512)


at chemaxon.descriptors.GenerateMD.main(GenerateMD.java:1410)


Do you know what is the problem?


Thanks


Best Regards and sorry for this stupid question!

Hi Varin,





Our colleague who develops Screen is on holiday at the moment, but he will investigate the problem when he is back. Sorry for the inconvenience.





Szabolcs

Hi,





is pharma-frag.xml located in your working directory? If not, then you need to specify its location, or change the working directory.


Are you familiar with these command line related concepts?





Regards,


MIklos

Yes the pharma-frag.xml file is in the working directory. And when I use the pmapper fonction, it works (pmapper c test.sdf -c pharma-frag.xml)!!!


The first time the problem appears was when we have change our Jchem version (3.2.7 to 3.2.8). I've tryed with exactly the same command line, in the same conditions... and this message appears.


Please...... help me!!!


Thank you


Regards


Tibo

Oh, I see.


An unfortunate incompatibility problem was introduced recently, this may cause the problem.





Please check the third line of your xml configuration file, it should begin with "<PharmacophoreFingerprintConfiguration ".


The new release should contain the right xml file in examples/config directory.





Apologies for the inconvenience this caused.





Regards,


Miklos

mvargyas wrote:

Oh, I see. An unfortunate incompatibility problem was introduced recently, this may cause the problem. Please check the third line of your xml configuration file, it should begin with "<PharmacophoreFingerprintConfiguration ". The new release should contain the right xml file in examples/config directory. Apologies for the inconvenience this caused. Regards, Miklos

Hi, ok that works!


For the other users, I precise we need also change the last line of the xml file.


Bye, thank you very much


Regards


Tibo

For the other users, I precise we need also change the last line of the xml file.





That's correct, indeed. Thank you!





Miklos