toFormat("smiles:u,a") exception

User e7455c8684

23-10-2009 17:37:06

[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


 


 

ChemAxon 25dcd765a3

26-10-2009 08:35:17

Hi,


 


Could you please attach the problematic molecule?


thank you


Andras

User e7455c8684

26-10-2009 12:58:48

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?


 

ChemAxon 25dcd765a3

27-10-2009 14:14:52

Hi,


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


We try to look after it.


Andras

User e7455c8684

27-10-2009 14:17:03










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.

ChemAxon 8b644e6bf4

29-10-2009 14:49:12

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

User e7455c8684

29-10-2009 17:14:46










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?


 


 

ChemAxon 8b644e6bf4

02-11-2009 04:27:37

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