RDKit Molecule Highlighting

Creates an SVG column showing a molecule with highlighted atoms and bonds based on information in the input table. A molecule column as well as column(s) with a list of the atom and/or bond indexes to be highlighted needs to be provided. The node lets the user define colors to be applied for the highlighting. If highlighting definitions overlap (e.g. atom indexes in definition 1 is 1,2,3 and in definition 2 is 3,4,5) the highlighting of the first definition will be applied (e.g to atom 3) with the color it defined.

Options

RDKit mol column

The input column with RDKit molecules.

Column name for molecule with highlighting

The name of the new column, which will contain the result.

Highlighting definitions

Each entry defines a set of atoms or bonds to highlight with an optional color.

• Highlighting: Activates the highlighting definition. Inactive definitions are ignored and not applied to the molecule.
• Type: Determines whether the indexes refer to atoms or bonds.
• Column with indexes: Select the column that contains atom or bond indexes (integer or long collection).
• Color: Hex color for highlighting (e.g. #FF0000). Leave blank to use the RDKit default color.
• Include neighborhood: Flag to also highlight bonds between two highlighted atoms or atoms around a highlighted bond.

Views

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Workflows

• 01_Clustering_and_Interactive_Compound_SelectionKNIME Hub
• 01_Hitlist_FilterKNIME Hub
• 01_Hitlist_Filter v2KNIME Hub
• 01. Flow VariableKNIME Hub
• 01. Flow VariableKNIME Hub
• Show all 81 workflows

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Developers