exception on molecule for HBDAPlugin

Dear Support,





An exception occurs when I want to calculate the molecule mol_error.mol (attached)

Quote:

java.lang.ArrayIndexOutOfBoundsException: -1 at chemaxon.marvin.modules.Parity.putToTheTop(Parity.java:1997) at chemaxon.marvin.modules.Parity.setupStereoBonds(Parity.java:736) at chemaxon.marvin.modules.Parity.setParity2D(Parity.java:476) at chemaxon.marvin.modules.Parity.setParity(Parity.java:381) at chemaxon.marvin.modules.Parity.modfunc(Parity.java:175) at chemaxon.struc.MoleculeGraph.setParity(MoleculeGraph.java:1214) at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:237) at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:47) at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:438) at chemaxon.struc.MoleculeGraph.implicitizeHydrogens(MoleculeGraph.java:414) at chemaxon.calculations.Interaction.implicitize(Interaction.java:67) at chemaxon.calculations.Interaction.initHBond(Interaction.java:248) at chemaxon.calculations.Interaction.calcAcceptorDonorCount(Interaction.java:137) at chemaxon.marvin.calculations.HBDAPlugin.run(HBDAPlugin.java:358)

I use the code as follow

Code:

HBDAPlugin hbda = new HBDAPlugin(); 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.setMolecule(m); hbda.run(); System.out.println(hbda.getDonorAtomCount()); System.out.println(hbda.getAcceptorAtomCount());

Is there a bug or the molecule is not in a good MDL format?





Thank you for your help


Kind Regards ;)


Jacques

I could reproduce this only with the latest released Marvin 3.5.7 and Marvin 3.5.6 versions, but it does not exist with either the earlier Marvin 3.5.5 or the current CVS version which will come out as Marvin 4.0.





Thanks for the report.


You can either downgrade to Marvin 3.5.5 to get rid of this bug or wait for Marvin 4.0.


I hope this is acceptable for you -

oh.. sorry, I forgot to tell you that I'm using JChem API 3.0.12


Thank you for your answer.

JChem API 3.0.12 includes the latest Marvin release 3.5.7.


If the correction is important and urgent then we can release a JChem 3.0.13 with Marvin 3.5.8, in which we correct this bug. Otherwise it will be automatically fixed in the next major JChem 3.1 (including Marvin 4.0) release.


Please let us know if you need the urgent bugfix release.

It's okay.. I will use JChem 3.0.10 which includes Marvin 3.5.5.


I look forward to see the new improvement in JChem 3.1


Thank you for your help.


Regards,


Jacques

Now we have the correction:





in the latest bugfix release JChem3.0.13 at


www.jchem.com


(jchem3.0.13.tar.gz or jchem3.0.13.zip):





http://www.chemaxon.com/download.php?d=/data/download/jchem/jchem3.0.13.tar.gz


or


http://www.chemaxon.com/download.php?d=/data/download/jchem/jchem3.0.13.zip





and we also have an alpha pre-release of the next major JChem3.1 at


http://www.chemaxon.com/download.php?dl=&d=/data/download/jchem/test/


(jchemTEST_2005_06_30.tar.gz or jchemTEST_2005_06_30.zip):





http://www.chemaxon.com/download.php?dl=&d=/data/download/jchem/test/jchemTEST_2005_06_30.tar.gz&sid=f247d3b0dabb4cb4934f6efbd27cc577


or


http://www.chemaxon.com/download.php?dl=&d=/data/download/jchem/test/jchemTEST_2005_06_30.zip&sid=f247d3b0dabb4cb4934f6efbd27cc577

thank you very much.