Export to SDF doesn't include empty molecule properties

Hi,

I have an SDF file that contains properties that do not have values. I can successfully import the molecules from the SDF file using MolImporter. The imported molecules contain properties such as purity whose values are an empty string. 

When I try to export the imported molecules back to an SDF file using MolExporter the export file does not contain all the molecule's properties. Specifically, it does not contain properties whose imported value is the empty string.

Is there anyway to force all molecule properties to be exported to the SDF file?

This is on JChem 5.6.

Thanks,

Tyler

Hi Tyler,

We do not export empty properties to SDF files. This is a known issue for us which has already been reported before, thus we will consider exporting empty properties too. Still, we would like to suggest you a workaround, so could you let us know us where does it cause problems to you? Why do you need to export empty properties? Your answer would also help us to decide whether to implement this feature.

Best regards,

Zsuzsa

Hi Zsuzsa,

I'm experiencing this issue when exporting molecules to an error file.  What follows is the process being executed:

1. Molecules are imported from a SDF file (the original SDF file)


2. The imported molecules are written to a database


3. If an error occurs while writing a molecule to the database, write the molecule to the error SDF file

What I want is for the molecules that are added to the error SDF file to be identical to the molecules in the original SDF file.  The purpose of having the molecules in both files be identical is that the user can then use the error SDF file as the input to step 1 above.

This can be advantageous because the original SDF file could contain thousands of molecules while the error file may only contain the few molecules that failed to import but if the molecules in the error file are different then the molecules in the original file, the user's data has been subtly altered.

The reason I want to have the empty properties is that empty properties may have meaning - like an assay was run but could not get a result. 

Thanks,

Tyler

 

 

 

Hi Tyler,

thank you for the detailed answer. We have decided to add the possibility to export empty properties to SDF file format. We will inform you when it will be available.

I have checked that we do export empty properties to MRV format already, maybe as a workaround it would be a solution for you to create the error file in MRV format then the molecules reimported from the MRV format error file would not differ from the original molecules.

I hope that could help.

Best regards,

Zsuzsa