Cannot generate SVG with "cannot expand invisible group" err

Hi,

We use JChem 5.6.0.2 on Oracle Database 10.2.0.5 x86_64.

We have som structures for which we cannot generate SVG.

One of them is attached to post.

We use some such SQL to generate SVG:

update chem_structs set svg = jc_molconvert(structure, 'svg:H_off') where unit_id = -2129476396;

and We've got:

SQL Error: ORA-29532: Java call terminated by uncaught Java exception: java.rmi.ServerException: RemoteException occurred in server thread; nested exception is: 


	java.rmi.RemoteException: cannot expand invisible group


ORA-06512: at "JCHEM.JCHEM_CLOB_PKG", line 187


ORA-06512: at "JCHEM.MOLCONVERTC_FUNCC", line 23

 

Thanks,

Pavel.

Hi Pavel,

I have moved this topic to the visualization forum as the problem can be reproduced with the molconvert command-line tool as well:

C:\Users\pkovacs\chemaxon\packages\jchem-5.6.0.2\cartridge>..\bin\molconvert svg C:\Users\pkovacs\Downloads\_misc\Sunday\-2129476396.mol

C:\Users\pkovacs\Downloads\_misc\Sunday\-2129476396.mol: error: cannot expand invisible group

java.lang.IllegalArgumentException: cannot expand invisible group

        at chemaxon.struc.sgroup.SuperatomSgroup.expand(SuperatomSgroup.java:539)

        at chemaxon.marvin.io.formats.cml.MrvExport.writeSuperatomSgroup(MrvExport.java:1157)

        at chemaxon.marvin.io.formats.cml.MrvExport.appendSgroup(MrvExport.java:906)

        at chemaxon.marvin.io.formats.cml.MrvExport.appendSgroup(MrvExport.java:932)

        at chemaxon.marvin.io.formats.cml.MrvExport.appendSgroup(MrvExport.java:932)

        at chemaxon.marvin.io.formats.cml.MrvExport.sgroupExtension(MrvExport.java:853)

        at chemaxon.marvin.io.formats.cml.CMLExport.appendMolecule0(CMLExport.java:367)

        at chemaxon.marvin.io.formats.cml.CMLExport.appendMolecule0(CMLExport.java:336)

        at chemaxon.marvin.io.formats.cml.CMLExport.appendMolecule(CMLExport.java:191)

        at chemaxon.marvin.io.formats.cml.MrvExport.appendChemicalStruct(MrvExport.java:458)

        at chemaxon.marvin.io.formats.cml.MrvExport.convert0(MrvExport.java:255)

        at chemaxon.marvin.io.formats.cml.MrvExport.convert(MrvExport.java:223)

        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1627)

        at chemaxon.struc.Molecule.exportToObject(Molecule.java:1592)

        at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1441)

        at chemaxon.struc.Molecule.toFormat(Molecule.java:1419)

        at chemaxon.marvin.io.image.exporter.ImageExport.preconvert(ImageExport.java:649)

        at chemaxon.marvin.io.formats.vectgraphics.SvgExport.convert(SvgExport.java:101)

        at chemaxon.formats.MolExporter.write(MolExporter.java:756)

        at chemaxon.formats.MolConverter.write(MolConverter.java:1209)

        at chemaxon.formats.MolConverter.convert0(MolConverter.java:1082)

        at chemaxon.formats.MolConverter.convert(MolConverter.java:935)

        at chemaxon.formats.MolConverter.main(MolConverter.java:2013)

 

Thanks

Peter

Thanks, Peter.

Maybe source mol has errors? Is it possible?

P.S. Do you sleep ever and have a holidays? You are always answering on my a lot of questions.

Hi Pavel,

i think it is some S-group handling problem inside
Marvin. I moved the topic forward to Structure representation forum since this issue relates to S-group representation, and I/O.

It
needs a bit more examination i think, but the professionals of this area have their own forum for few days ago, and the question belongs to them.

Regards,

Istvan

Thanks, Istvan.

Hi Pavel,

We examine the exception.

Hi Pavel,

thank you for your report, the exception is caused by wrong handling of abbreviations (superatoms) embedded into each other. Embedding of expandable S-groups (abbreviations and multiple S-groups) is not supported yet, this functionality is disabled in our Sketcher too. The documentation about this is missing, we will make it up in the near future.

However, we will fix  the MRV import/export of some specific cases of superatom S-groups embedded into each other (if they are all contracted or all expanded ) in release 5.8. This will solve the problem with your molecule too (there all abbreviations are contracted). We will notify you as soon as the fix is available.

Just a remark: please, check the mol file, because it seems chemically strange. Three embedded abbreviations have the name "COOH" and do not contain a carboxylic group, the group NH2 does not contain the Nitrogen (it is contained in another group), only the Hydrogen. 

Best regards,

Zsuzsa

Thanks, Zsuzsa.

Our chemists will check these mols.

Pavel

Hi Pavel,

I just would like to inform yout that version 5.8 containing the mentioned fix of embedded S-groups has been released .

Regards,

Zsuzsa