Merge MajorMicrospeciesPlugin and pKaPlugin!

Hi - This profound insight was happily hanging somewhere down the axon of my tired neuron for some time, but today I had a sudden and almost religious revelation of how weird the stuff is: Why do we need a MajorMicrospeciesPlugin? Why can't getMajorMicrospecies be used in connection to a pKaPlugin?





I tried to write some code where one could choose whether to enumerate all µspecies, or stick to the most stable one, or forget it and stick to the read molecule... After defining a pKaPlugin pkaplug, I said well, if (enumerate_ms) {do the loop over all of them with pkplug.get MsMolecule(running_index)} else if (use_major_ms) {damn the loop and do pkplug.getMajorMicrospecies()} - fatal error! The pKaPlugin has no getMajorMicrospecies! If one defines a MajorMicrospeciesPlugin instead, then one looses the access to the getSingleMsDistribution and for some reason, getSortedMSDistribution() does not work! It told me "chemaxon.marvin.plugin.PluginException: Microspecies distribution calculation is not available in chemaxon.marvin.calculations.MajorMicrospeciesPlugin"





Well, of course there is an easy workarond with the pKaPlugin, it's enough to loop over the getSingleMsDistributions and pick the largest but... we have TWO plugins instead of one and we still need a workaround! Is plugin unemployment such a burning issue in the EU that we need to create artificial jobs for them?

Hi Dragos,





First of all sorry for the late answer.





We have two plugins (MajorMicrospeciesPlugin and pKaPlugin) with partially overlapping functionality because we think it is easier to use these plugins for most of our users in such way.

Quote:

The pKaPlugin has no getMajorMicrospecies! If one defines a MajorMicrospeciesPlugin instead, then one looses the access to the getSingleMsDistribution and for some reason, getSortedMSDistribution() does not work! It told me "chemaxon.marvin.plugin.PluginException: Microspecies distribution calculation is not available in chemaxon.marvin.calculations.MajorMicrospeciesPlugin"

I will check why getSortedMSDistribution() does not work in this case. Can you attach the non-working part of your code?

Quote:

Is plugin unemployment such a burning issue in the EU that we need to create artificial jobs for them?

:) No. pKaPlugin is one of our most complex plugin, and if we put the functionality of the MajorMicrospecies plugin into it too, than its complexity would be hard to handle. We have to provide the functionality of our calculator plugins through Marvin GUI, cxcalc batch processing tool and through API!





Best regards,


Zsolt