RDKit Substructure Filter

Applies a substructure filter to an input RDKit Mol column. The substructure query is given as a single SMARTS pattern. Molecules that match the pattern appear in the first output table, molecules that don't match appear in the second output table.

Options

RDKit Mol column

The column containing the molecules

SMARTS query

A SMARTS string describing the query.

Do exact match

If this is set, only molecules containing the same number of atoms as the substructure query can match. This isn't exactly equivalent to an exact structure match, because query features in the query molecule can still be used, but it's close.

Match handling

Specify here, if an additional column with details about the match shall be added. It is possible to add the Atom List of the First Match or of all matches (overlaps possible).

Column name for matching atom list

The column name of the for the atom list column, if enabled.

Input Ports

Table with RDKit molecules

Output Ports

Molecules matching the substructure query

Molecules not matching the substructure query

Best Friends (Incoming)

• RDKit From Molecule (16 %) 
• RDKit Substructure Filter (6 %) 
• SDF Reader (6 %) 
• Column Filter (5 %) Streamable
• Row Filter (5 %) Streamable
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Best Friends (Outgoing)

• RDKit Substructure Filter (7 %) 
• SDF Writer (6 %) 
• RDKit Molecule Highlighting (6 %) Streamable
• Loop End (6 %) 
• RDKit Molecule Substructure Filter (5 %) 
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Workflows

• _​01_​ChemicalLibraryEnumeration (KNIME Hub) 
• 01_​Hitlist_​Filter (KNIME Hub) 
• 02_​Bioactivity_​Prediction_​Transform (KNIME Hub) 
• 05_​ChEBI_​ontology_​explorer (KNIME Hub) 
• 06_​Find_​Scaffolds_​And_​Sidechains (KNIME Hub) 
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Installation

To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

Developers

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