Creating Image

Hi

When I try to create a image from the chemaxon applets mrv output I'm getting no image and no error or execption.

I'm using Chemaxon 5.2.0.6.

Here is the process I'm using;

The chemaxon applet loads and chemical structure using File/Open and the file is 'methyl ether.cdx'. This file is an output from ChemDraw application.

The applet loads the chemical structure. The issue is when I call the java to convert the mrv xml to an image it fails. The jar I'm using to convert to the image is called convert2image.jar.

The java doesnt throw an exception but still doesnt convert it to an image.

I'm passing the jar the following parmaters

java test.images.Convert2Image jpeg:w500,h500 C:/OPENTEXT/dev971/Temp/~LL10001000194954

 

This usually works for other chemical structures and type, but not for cdx files.

 

Is there extra logging I can enable to see whats happening in the MarvinBeans.jar classes.

 

I have attached the sample files in the files.zip. I didnt include the marvinbeans.jar because its over 11,694,080 bytes.

 

If further information is required, please ask,

Kind Regards

Karl

 

 

 

Indeed, MolImporter.read(mol) return with false. Since structure import was unsuccessful, there is no output file.

Although MolConverter can read the given cdx file.

We will check why it does not work in the attached example.

We are still investigating the issue.

The problem occurs only when the cdx contains a reaction and it's read into a Molecule.

If it's possible try to use RxnMolecule as a workaround for files that contains a reaction until we find the solution.

Apologies for not responding any sooner.

Hi Nolan,

Is the workaround satisfactory for you?

Best regards,

Akos

Hi,

The image is now being created.

Since the java code changed was not tested and verified by Chemaxon I need
to passed it on to QA here because they have the final say.

I will update the post when I hear back from QA,

Kind Regards

Karl

Hi Akos, the image is now being created.

I'm now having a problem now when I try to show the mrv structure in the applet. The structure saves fine and the image seems correct too, but when I try to reload the structure if falls over.

I have included ChemaxonError.zip which outlines exactly the issue I'm having.

If you require further information please ask,

Kind Regards

Karl

Hi Nolan,

Thanks for the information. We are investigating the issue and we will respond soon.

Best regards,

Peter

Hi Nolan,

We could not reproduce the problem. What does "try to reload the chemical strucure" mean after the image creation?

Kind regards,

Peter

'Hi Peter,

When I say 'When I try to reload the chemical structure I’m getting the error'

 

I mean that when I save the chemical structure and try to show it again (after getting it back from the database) I get the error.

 

Do you get the two marvin tags when you retrieve it from the database? Is this normal?

Where do I go from here??? is there more information that you require??

 

Cheers

Karl

Hi Nolan,

I seems that you store the reactions in RXN format (in your Chemical Error.doc file in the html source), but for some reason the RXN file is cut after the first molecule (the RXN shows "14 2" in its 4th line, which means there should be 14 reactants and 2 products, but only one molecule is defined in the reactant block).

So I think somewhere in your reaction storing procedure the other 15 molecules are lost.

Best regards,

Akos

Hi Akos,

 

We eventually got it working by escaping the response from the database because our application wasnt processing some of the characters.

 

Thanks again for all you time on this,

 

Kind Regards

Karl