0 ×

Activity Cliffs Viewer

Erlwood Knime Open Source Cheminformatics version 4.0.0.qualifier by Erlwood

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

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

Output Ports

Icon
Import 0 is copied here.

Views

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

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Erlwood Knime Open Source Cheminformatics from the following update site:

KNIME 4.2
Wait a sec! You want to explore and install nodes even faster? We highly recommend our NodePit for KNIME extension for your KNIME Analytics Platform.

Developers

You want to see the source code for this node? Click the following button and we’ll use our super-powers to find it for you.