Hi Maxim, The KNIME node "RDKit Molecule Fragmenter" is indeed quite useful. Since what it does for you in KNIME is based on RDKit functionality, you can do the same also outside of KNIME. Usually, there is not a single method to call, rather a code block that performs multiple operations, also partly based on certain parameters that one can configure in a KNIME node, but all is not that complicated when you are familiar with the RDKit and its classes, types and functionalities.
Since the RDKit Nodes for KNIME are open source you can find the source code of the RDKit Molecule Fragmenter implementation in Github: https://github.com/rdkit/knime-rdkit/blob/master/org.rdkit.knime.nodes/src/org/rdkit/knime/nodes/molfragmenter/RDKitMolFragmenterNodeModel.java (lines 285-356 is the core algorithm) This is Java code, but as the Java API of RDKit is a subset of what is available in C, you will be able to rewrite the same logic also in Python or C. Best regards, Mit freundlichen Grüssen, Meilleures salutations, Manuel Schwarze Senior Principal Software Engineer (KNIME, IJC, CSF, CIx) T: +41 61 3245330 M: +41 79 7470324 manuel.schwa...@novartis.com Novartis Pharma AG NIBR Informatics (NX) - IS SIGMA Novartis Campus, WSJ-310.5.18 CH-4002 Basel Switzerland -----Original Message----- From: rdkit-discuss-requ...@lists.sourceforge.net [mailto:rdkit-discuss-requ...@lists.sourceforge.net] Sent: Dienstag, 6. Juni 2017 14:15 To: rdkit-discuss@lists.sourceforge.net Subject: Rdkit-discuss Digest, Vol 116, Issue 14 Send Rdkit-discuss mailing list submissions to rdkit-discuss@lists.sourceforge.net To subscribe or unsubscribe via the World Wide Web, visit https://lists.sourceforge.net/lists/listinfo/rdkit-discuss or, via email, send a message with subject or body 'help' to rdkit-discuss-requ...@lists.sourceforge.net You can reach the person managing the list at rdkit-discuss-ow...@lists.sourceforge.net When replying, please edit your Subject line so it is more specific than "Re: Contents of Rdkit-discuss digest..." Today's Topics: 1. RDkit Molecule Fragmenter (Popov, Maxim (Ext)) ---------------------------------------------------------------------- Message: 1 Date: Tue, 6 Jun 2017 11:43:08 +0000 From: "Popov, Maxim (Ext)" <maxim.po...@novartis.com> To: "rdkit-discuss@lists.sourceforge.net" <rdkit-discuss@lists.sourceforge.net> Subject: [Rdkit-discuss] RDkit Molecule Fragmenter Message-ID: <ed0c0e94bab14c0e860e6ac0012a6...@db4pr6204mb0192.023d.mgd.msft.net> Content-Type: text/plain; charset="us-ascii" Dear All, I have discovered a very usefule tool in Knime, Molecule Fragmenter by RDKit, but can't find a corresponding class or function outside of Knime. Can I use the Fragmenter without Knime? Thanks! Maxim -------------- next part -------------- An HTML attachment was scrubbed... ------------------------------ ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot ------------------------------ Subject: Digest Footer _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss ------------------------------ End of Rdkit-discuss Digest, Vol 116, Issue 14 ********************************************** ------------------------------------------------------------------------------ Check out the vibrant tech community on one of the world's most engaging tech sites, Slashdot.org! http://sdm.link/slashdot _______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
