RDKit Molecule Substructure Filter

Applies a substructure filter to an input RDKit Mol column. The patterns are given as SMARTS, SMILES, SDF or RDKit molecules in the second input table. You can choose either a minimum number of patterns to match or to require that all match.

Options

RDKit Mol column

Select the column from the first input table that contains the RDKit molecules

Query Mol column

Select the column from the second input table that contains the query molecules. Acceptable types are SMARTS, SMILES, SDF and RDKit Mol.

Use chirality

If this is set, information about stereochemistry will be used in the substructure search.

Use enhanced stereochemistry

If this is set, information about enhanced stereochemistry will be used in the substructure search.

Matches

Select the minimum number of patterns that must match for each molecule so that it is included in the first output table

New column name for matching substructures

Enter here the name of the new column that will contain a list of all matching substructure row indices

Advanced

Fingerprint screening threshold

Substructure search performance can be improved using fingerprints. This makes sense when there are many different query molecules and a lot of input molecules. In this case the node can pre-calculate fingerprints once for all input and query molecules and do some pre-screening for substructure matching. The fingerprint screening threshold value defines the number of query molecules (table 2) that must be present in order to enable fingerprint calculation and pre-screening. Set it to 0 to disable fingerprint screening completely for this node. Set it to -1 to always use the RDKit Nodes default behavior (the standard setting).

Use row keys as substructure match information

The column for matching substructure indices contained (for historic reasons) the row index, which turned out not to be too useful. Click this flag to use row keys instead, which is today the default for new nodes.

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Workflows

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• 05_ChEBI_ontology_explorerKNIME Hub
• 20220718 Pikairos How to Optimize Parallelized Substructure FilteringKNIME Hub
• 3.1_DruglikeFilterKNIME Hub
• 3.4_Similarity_SubstructureKNIME Hub
• Show all 29 workflows

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