toFormat("smiles:u,a") exception

[javaWrapper] Exception in thread "AWT-EventQueue-0" java.lang.ClassCastException: chemaxon.struc.prop.MStringProp
[javaWrapper]     at chemaxon.marvin.modules.Hydrogenize.implicitizeHydrogens(Hydrogenize.java:351)
[javaWrapper]     at chemaxon.marvin.modules.Hydrogenize.callback(Hydrogenize.java:98)
[javaWrapper]     at chemaxon.struc.Molecule.callHydrogenize(Molecule.java:3294)
[javaWrapper]     at chemaxon.struc.MoleculeGraph.callHydrogenize(MoleculeGraph.java:881)
[javaWrapper]     at chemaxon.struc.MoleculeGraph.hydrogenize(MoleculeGraph.java:782)
[javaWrapper]     at chemaxon.marvin.io.MolExportModule.preconvert(MolExportModule.java:608)
[javaWrapper]     at chemaxon.marvin.io.formats.smiles.SmilesExport.preconvert(SmilesExport.java:627)
[javaWrapper]     at chemaxon.marvin.io.formats.smiles.SmilesExport.toSMILES(SmilesExport.java:690)
[javaWrapper]     at chemaxon.marvin.io.formats.smiles.SmilesExport.convert(SmilesExport.java:578)
[javaWrapper]     at chemaxon.struc.Molecule.exportToObject(Molecule.java:1493)
[javaWrapper]     at chemaxon.struc.Molecule.exportToObject(Molecule.java:1458)
[javaWrapper]     at chemaxon.struc.Molecule.exportToFormat(Molecule.java:1307)
[javaWrapper]     at chemaxon.struc.Molecule.toFormat(Molecule.java:1285)

What might be the cause of this problem? I'm using jchem5.2.04p2

 

 

Hi,

 

Could you please attach the problematic molecule?

thank you

Andras

This problem is very elusive, I kept getting this error the other day, but today I tried a few and they works fine. I was thinking it might be related to the data field associated with the molecule but not the molecule itself. Any clue from the stack trace?

 

Hi,

Did you use 3D coordinates with hydrogen addition before trying to export it to SMILES?

We try to look after it.

Andras

volfi wrote:

Hi, Did you use 3D coordinates with hydrogen addition before trying to export it to SMILES? We try to look after it. Andras

Very likely, I think.

Hi,

A property with name "mrv_H_3d_coordinates" created when explicit hydrogenes on a 3D structure made implicit. If the contents of this property is modified a similar exception seems to be thrown.

Is it possible that your application modified this property?

Regards

Gabor

gimre wrote:

Hi, A property with name "mrv_H_3d_coordinates" created when explicit hydrogenes on a 3D structure made implicit. If the contents of this property is modified a similar exception seems to be thrown. Is it possible that your application modified this property? Regards Gabor

it got to be the reason, although I swear I never used that property depite the coodinartes might be changed during the process. Anyway, after I called mol.clearProperties(), the exception is gone, but why 3D Hydrogen coordinates is required when converting to the smiles?

 

 

Hi,

SMILES export makes explicit hydrogens implicit (dehydrigenize); the property (if present) is processed during this.  It seems that in your case its value was damaged somehow. 

Throwing this exception in this case can certainly considered to be a buggy behavior; we will fix it in the future.

We are sorry for the inconvenience this bug caused,

Regards,

Gabor