Correctness of SDF created

We are converting data in csv files to sd files.
How to check the correct ness of the sd file generated through Knime nodes?
The suspected error is  SD blocks are not generated correctly for some rows causing 
shift in data between differerent datasets.How to rectify this issue?

Thanks and regards


Mon, 10/15/2012 - 09:35

Hi ebio2,

Can you tell us which nodes your workflow consists of? I guess that you use some kind of reader node, then if the molecules are stored as SMILES in the csv file, some kind of converter node and finally a sd writer, right?

Without the information about which nodes you use it's hard to tell which node might expose an incorrect behaviour. A quick test to check is to open the csv file in a text editor, scroll down to the bottom and compare the last line with the produced sdf. But that's only a quick and dirty qualitative test.



Mon, 10/15/2012 - 09:48

hi Guido,

Thanks for quick reply.

We are having Inchls in csv file.We use File Reader node to read csv file ,then Open Babel for conversion of Inchls to SD blocks and finally write the sd file using SDF Writer node.

We tried direct writing of the generated SDF file to csv file,so we can see the rows.

Used SDf reader node and CSV writer node here.

Inchls which are having more than 1640 characters are seen broken and data for that row is spread out in the sheet

Thanks and regards


Mon, 10/15/2012 - 03:29


I'm not sure why you need to write to a csv file? Why don't you output as an SDF and then browse the file in notepad (or notepad++ if the file is large). 

This way you can view the contents of the file without potentially corrupting the information by using an incorect format. 

However I believe there is an issue with converting the inchi format in OpenBabel which causes it to not generate coordinates. A simple fix for this is to generate the SDF from inchi using openbabel and then using the MolConverter node from the ChemAxon/Infocom Marvin nodes. 

You can also copy and paste the text content of and SDF cell into notepad from a KNIME table. 






Fri, 10/19/2012 - 10:27

Hi  ,

Thanks for giving tips.

I tried viewing sdf files  using notepad,still it shows broken strings.Also tried generating sdf from Inchls using Openbabel and then used Molconvertor node(sdf-MDL mol format),then write the sd file.But sdf generated here  is not having any data.

We are having large amount of data in excel format and is in the process of converting that in to sd files,  and structure data is available as Inchls  .

Is this issue due to Open babel ?

One more point we need help is,

How can we create a  workflow to convert png images to sd blocks using knime nodes.Is that possible?

Thanks and regards