Filtered out columns still being written

Community Groups Cheminformatics
#1

Hi Guys,

 

I have a very strange problem when dealing with SD files.

I read an SD file containing various properties, either with the SDF Reader node, or the Infocom MolImporter (to an SDFCell). I do some processing on the different columns, then discard some columns I don't need (Using the Column Filter), and finally write the SD file back (either with the Infocom MolExporter or the SDF Writer node. After the Column Filter, the discarded columns do not appear anymore when I look at the output, but when I open the resulting SD file, the discarded columns are back.

If I read the SD file to a Marvin Cell type, the problem does not occur.

Is there anything I don't understand in the way data are stored in an SDFCell? Or is this a bug?

Thank you for your help

#2

The SDF Cell is the whole SDF record for a structure so it includes all the tags! If you just want the structure you should select MolCell. 

You can remove these tags using the SDF Stripper (or along those lines). Or when reading in the SDF I think you can probably chose not to import the tags, but I'm not sure I always use MolCell. 

I believe I've read in the past that the conversion of SDF to MrvCell strips out the SD Tags to save space.