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

Active

Flag to activate the highlighting defined in the table row.

Type

Determines, if the indexes are atoms or bonds.

Column with indexes

Select the column here that contains atom or bond indexes.

Color

Pick a special color for highlighting. Use the default color to let RDKit decide.

Neighborhood

Flag to tell if bonds between two highlighted atoms or atoms around a highlighted bond shall also be highlighted with the same color. This is mainly interesting when highlighting substructures based on atom lists.

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 58 workflows

Links

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Developers