problem with HBDA calculation

Dear support,








I have a problem to calculate descriptors of the attached molecule. This is the error:

Code:

at chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin.getMainMolecule(MajorMicrospeciesAccessorPlugin.java:144)    at chemaxon.marvin.plugin.CalculatorPlugin.createStandardizedMolecule(CalculatorPlugin.java:775)    at chemaxon.marvin.calculations.MajorMicrospeciesAccessorPlugin.createStandardizedMolecule(MajorMicrospeciesAccessorPlugin.java:126)    at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:694)    at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:673)    at chemaxon.marvin.plugin.CalculatorPlugin.setMolecule(CalculatorPlugin.java:656)

I copied this structure into marvin sketch and I used it to calculate the descriptor HBDA and it worked well.





Have you got any idea of what happens with this structure?


I am using jchem 3.15





best regards,


Severine

Dear Severine,





I can not reproduce the error. How do you calculate the HBDA descriptor?





Do you use


- API (HBDAPlugin),


- cxcalc command line tool,


- or evaluate command line tool + Chemical Terms expression?





If you use API, then please send the part of your code that throws this exception.


If you use one of our command line tools, then please send the exact command line call you use.





Best regards,


Zsolt

Excuse me Zsolt, I was not precise enough.





I am using the API





This the code:

Code:

hbda.validate(licenceHBDAPlugin); Properties params = new Properties(); params.put("type", "don,acc,donsitecount,accsitecount,donorcount,acceptorcount,msdon,msacc"); params.put("lower", "2.0"); params.put("upper", "12.0"); params.put("step", "2.0"); hbda.setParameters(params); hbda.setpH(7.4); hbda.setMolecule(mol); hbda.run(); System.out.println(hbda.getAcceptorAtomCount()); System.out.println(hbda.getDonorAtomCount());

Hi Severine,





The problem is caused by the major microspecies calculation, it throws an exception when tries to calculate the protonation form of your input molecule at pH 7.4.





If you comment out this line:

Code:

hbda.setpH(7.4);

then major microspecies will not be calculated and it will work.





From Marvin 4.1.4 and JChem 3.2.2 this kind of problem is handled, and it will work without commenting out this line.





Best regards,


Zsolt

Thank you Zsolt for your help.





The same problem occured with the Polarizability Plugin and commenting the same line resolved it.





Best regards,


Severine