How to open/read sdf

Groups BioInformatics
1

Hello
Any idea how I can open and read the sdf after using the csv reader-openbabel-sdf writer workflow in knime?
Thank you in advance

2

Hi @Razanknime_123 , there’s an SDF Reader node

Does that work?

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3

Thank you!
But what I’m looking for is a way to export the sdf which i converted from csv using “csv reader- openbabel-sdf writer”, how can i save an sdf and open it on my pc (after obtaining it from knime).
also, the input I gave for the sdf writer is an excel sheet, how can I make and choose an sdf instead, to feed it to this node? (What file should i open on my pc to feed it to the sdf writer node and then be able to read it)

4

There’s also an SDF Writer that allows you to export as an SDF.

How you open the sdf on your PC depends on quite a few factors, namely what software you have that can read the sdf.

For example, for a csv file, you can open it via any text editor/viewer or Excel. So it really depends on what you have, and what’s your preference to use. Same thing for the sdf file.

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5

Before you use the SDF Writer node, you can use the RDKit Interactive Table node to view the contents:

And after you export the data with the SDF Writer node, well an SD File is just text. So if you want to view the structures, grab something like DataWarrior https://datawarrior.org (Free) that was designed around molecule viewing.

(the other) Simon

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