MolPrinter orientation dependent display issue

Hello,

 

Using MarvinSketch v5.9.1, I drew the acetamide structure in two different orientations (see attached). When I render the structures with MolPrinter, in one of the orietations the hetero atoms display properly, but not in the other. I have tried switching between MolPrinter and MolPainter, and the behavior is the same regardless of the renderer. Could someone please help take a look?

 

Thanks,

Ning Yu

UPDATE: it turns out the second line of test4.sdf (with hetero atoms missing) is as follows:

 

Mrv0541 06031310363D

 

Notice the last two characters indicate the structure is in 3D, which is why MolPrinter does not display the hetero atoms. Now the follow on question: is there a setting I can change to force MolPrinter to render it as a 2D structure?

Unfortunately, there is not any setting to force MolPrinter to render it as a 2D. However, you can clean your molecule in 2D before painting and it gives you the same results.

You can find the related documentation here,

http://www.chemaxon.com/marvin/help/developer/beans/api/chemaxon/calculations/clean/Cleaner.html.

Best regards,

Efi