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RDKit Molecule Highlighting

StreamableRDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

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.

Input Ports

Icon
Table with an RDKit Molecules and list(s) of atoms and/or bonds to be highlighted.

Output Ports

Icon
The input table with an additional column that shows the highlighted atoms and bonds in an SVG molecule graphic.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install RDKit KNIME JUnit Test from the following update site:

KNIME 4.2

A zipped version of the software site can be downloaded here.

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