Adding hydrogen based on given PH value

Is there a way of adding hydrogens based on the PH value in solution not just when PH=7.4?





Thanks.

Yes. Use the major microspecies plugin first and then add explicit hydrogens to the result.





Best regards,


Szabolcs

Thanks for the answer, but I got another exception:


chemaxon.marvin.plugin.PluginException: Microspecies distribution calculation is not available in chemaxon.marvin.calculations.MajorMicrospeciesPlugin


at chemaxon.marvin.calculations.MajorMicrospeciesPlugin.getSortedMicrospecies(MajorMicrospeciesPlugin.java:209)





I wonder which plugin I should use.





Jun

Hi,





How did you get this error message? Which Marvin/JChem version do you use?





Best regards,


Zsolt

I'm using jchem.3.1.6.





the code is pretty simple:





plugin.setMolecule(...)


plugin.run()


...


plugin.getSortedMicrospecies(i) //plugin.getMcrospecies(i) works!!

Hi, I would like to know whether this problem is reproducible or not, so I know whether I did something wrong even you cannot provide a solution.





thanks.

Hi,





Yes, it is reproducible. I have attached MajorMicrospeciesPluginTest.java, which shows how you can call this method. I will ask my colleague (main author of the calculation) why is so difficult to call this method.





Best regards,


Zsolt





Edit: updated the attachment

If you want to get only the major microspecies on a given pH, then use getMajorMicrospecies() method.





See: http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/calculations/MajorMicrospeciesPlugin.html for documentation and example.





Regards,


Zsolt