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3D RMSD

KNIME CDK Integration version 1.5.700.v201907251211 by KNIME GmbH, Konstanz and EMBL-EBI, Cambridge

Creates a new columns containing the RMSD distances between different conformers (required 3D coordinates). The computations are based of the CDK toolkit. At the moment two types of RMSD calculations are possible. One based on the alignment using the Kabsch algorithm and the other based on the isomorphic alignment of the molecular structure and using the global geometry.

Options

Column with molecules
Select the column containing the molecular structure with 3D coordinates
Alignment algorithm
Select the type of alignment to be used for the RMSD calculation

Input Ports

Table containing molecular 3D geometries based on which the RMSD should be calculated

Output Ports

Additional column containing the RMSD distances between conformers

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install KNIME-CDK from the following update site:

KNIME 4.1
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