Hi, hope you are enjoying your holidays too :) There is no specific "RDKit SDF Writer" node in Knime. Not to worry - the Knime "SDF Writer" node is all you need.
You may need to convert from Knime molecule to RDKit molecule types (and back again) to get things to work. Also, have you set your output SDF filename correctly in the SDF Writer node ? I have put together an example Knime workflow which is attached. The attached .knar file contains a workflow, and a CSV file (ChEMBL-25 pharmaceuticals that were withdrawn from the market). [image: Screenshot 2019-12-30 at 09.38.22.png] You can import this workflow and the associated CSV file by selecting "Import Knime Workflow..." from the File menu within Knime. Make sure all files are imported. You'll need to point the "CSV Reader" node to the CSV file which will be in your Knime workspace / RDKit-Mol-To-SDF folder. You'll then need to configure the "SDF Writer" node to save the output file somewhere appropriate on your system. To configure each of these nodes, double-click on them and set the file locations. Note the RDKit from Molecule and RDKit to Molecule conversion nodes. Another way you can get Knime and RDKit-Knime help is to post on the Knime Community Forum, at https://forum.knime.com/ I recommend you create an account and have a look around if you haven't already :) Best, Drew On Sun, 29 Dec 2019 at 20:34, Mak Kit Kay <kitkay...@imu.edu.my> wrote: > Hi all, > > Hope everyone is enjoying their holidays! > > I wanted to know if: > 1) there an RDKit SDF writer node on KNIME? I looked, but I can only see > one from 'Chemistry' > 2) anyone is familiar with the SDF writer from Chemistry, when I write the > file, it appeared as an unknown file without the .sdf extension - which I > then have to manually add the extension by renaming my files on my folder > explorer. Not sure if I am missing a step on KNIME. > > Thank you, greatly appreciate it! > > Best wishes, > > > > * Kit-Kay Mak MSc (Med Chem), BSc (Pharm Chem), MRSC, > MRSB Lecturer, Department of Pharmaceutical Chemistry School of Pharmacy > International Medical University* > *No. 126, Jln Jalil Perkasa 19, Bukit Jalil, 57000 * > *Kuala Lumpur, Malaysia* > Website: http://www.imu.edu.my > > Office: +603-2731 7061 | Fax:+603-8656 7229 | E-mail: > kitkay...@imu.edu.my > LinkedIn <https://www.linkedin.com/in/kit-kay-mak/> . ResearchGate > <https://www.researchgate.net/profile/Kit_Kay_Mak> . Google Scholar > <https://scholar.google.com/citations?user=dGoJ3BwAAAAJ&hl=en> . > <http://www.imu.edu.my/ipops>6th IPOPS Organising Chair > <http://imu.edu.my/ipops/committee/> > > > > > > Interested in studying at IMU? Don’t miss our January Open Day! > Gain insight into your dream career in healthcare. > Find out more at http://www.imu.edu.my/openday > > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
RDKit-Mol-To-SDF.knar
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