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 stereochemistry

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

Use enhanced stereochemistry when matching

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.

Minimum number of matches

The minimum number of patterns that must match when 'At least' is selected.

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.

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. Enter here the minimum number of query molecules that must be present to enable fingerprint screening. A value of 0 disables fingerprint screening. A value of -1 uses the current default threshold.

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.

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Workflows

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