coordinates change for MOL V3000 MolImporter/MolExporter

Hello

I am using JChem 16.7.4.0. I have noticed that coordinates are changed for MOL V3000 when processing. I have written very short Jython script to investigate it further:

Reading:

importer = MolImporter(inputFile)

Writing for V2000:

while True:
        mol = importer.read()
        if not mol: break
        output.write("%s"%MolExporter.exportToFormat(mol, "sdf"))

Writing for V3000:

while True:
        mol = importer.read()
        if not mol: break
        output.write("%s"%MolExporter.exportToFormat(mol, "sdf:V3"))

Basically it reads MOL file, creates Molecule object and writes it back. I have created V2000 mol file from V3000 mol file and additionally rotated this V2000 file to avoid any default JChem coordinates. Both files have z coordinates set to 0.0.

Read/write operation returns exactly the same coordinates for V2000 MOL file, but changes coordinates in output V3000 file when input V3000 file is used. I don't understand why coordinates are different for V3000 MOL if I don't call any functions which could change the coordinates of the molecule.

Is there a problem with the library or I am missing something?

Thanks

Mieczyslaw

Hi,

Can you attach the original file and the changed one?

Janos

Unfortunately, the structures are confidential. However, I suppose it may be the case for any V3000 file.

Dear Mieczyslaw,

I created a ticket in our issue tracking system. Thank you for the report, we will inform you as soon as the problem is fixed.

Regards,
István