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Activity Cliffs Viewer

Structures and activities of molecules is best viewed in the context of chemical neighbourhood. In the network view, molecules are represented by nodes coloured according to chosen property. A pair of nodes is connected based on an edge similarity cutoff provided in options. The edge is coloured in green if the ratio of activity difference to chemical distance is higher than the "cliff" cutoff set in options.

Options

PropertColunm: Choose the (double) column to take the molecular property/activity from.
SmilesColunm: Choose the column containing smiles strings of the molecules.
MolNameColunm: Choose the column containing names of molecules, such as LSN.
EdgeCutoff: Edges will be drawn for pairs of molecules closer in chemical space than this cutoff.
CliffCutoff: Edges will be coloured green if this edge is a cliff, i.e. has a high difference in property as compared to chemistry.

Input Ports

: Smiles, names and properties of molecules should be provided here.
: NxN matrix of pairwise molecular distances should be provided here, say as output by MolPairDist node.

Output Ports

: Import 0 is copied here.

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Views

Network View: The network view uses prefuse Java 2D library and Marvin beans.

Workflows

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Developers

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Installation

To use this node in KNIME, install the extension Erlwood Knime Open Source Cheminformatics from the below update site following our NodePit Product and Node Installation Guide:

v4.2

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

Plugin provider: Erlwood

Plugin version: 4.0.0.qualifier

On NodePit since: 2020-07-13

Last update: 2026-01-09

KNIME versions: From v3.6 to v4.2

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