RDKit Adjust Query Properties

This node allows common adjustments to the matching behavior of molecules that are intended to be used as queries. Structure searches based on queries molecules are not always leading to the desired results. Often some fine tuning of the query structure helps to increase the search results. RDKit offers query properties that can be set explicitly for query molecules to influence a search. This node lets the user define the properties to be adjusted.

Options

RDKit Mol column

The input column with molecules to be used as queries.

New column name

The name of the new column which will contain the tuned queries as RDKit Molecules.

Remove source column

Set to true to remove the specified source column from the result table.

Adjust degree

Enable so that modified atoms have an explicit-degree query added based on their degree in the query.

Adjust degree flag

Control which atoms have a degree query added.

Adjust ring count

Enable so that modified atoms have a ring-count query added based on their ring count in the query.

Adjust ring count flag

Control which atoms have a ring-count query added.

Make atoms generic

Convert atoms to any-atom queries.

Make atoms generic flag

Control which atoms are converted to any-atom queries.

Make bonds generic

Convert bonds to any-bond queries.

Make bonds generic flag

Control which bonds are converted to any-bond queries.

Make dummies queries

Enable so that dummy atoms that do not have a specified isotope are converted to any-atom queries.

Aromatize if possible

Perceive and set aromaticity.

Adjust conjugated 5 rings

Sets bond queries in conjugated five-rings to SINGLE|DOUBLE|AROMATIC.

Set MDL 5 ring aromaticity

Uses the 5-ring aromaticity behavior of the (former) MDL software as documented in the Chemical Representation Guide.

Adjust single bonds to degree 1 neighbors

Sets single bonds between aromatic atoms and degree one neighbors to SINGLE|AROMATIC.

Adjust single bonds between aromatic atoms

Sets non-ring single bonds between two aromatic atoms to SINGLE|AROMATIC.

Use stereo care for bonds

Remove stereochemistry info from double bonds that do not have the stereoCare property set.

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Workflows

• DDU-TA_isosteric_replacement_suggestionsKNIME Hub
• WCAIR_isosteric_replacement_suggestions_table_builderKNIME Hub

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