RDKit RMSD Filter

Calculates the best RMSD value for different conformers of the same RDKit molecules and filters them based on a threshold value. To know which conformers belong together a reference column is used. It must contain unique keys for each conformer molecule group. Otherwise the result is undefined.

Options

RDKit Mol column with conformers: The name of the column with RDKit molecules, each with exactly one conformer. If the molecule has more than one conformer embedded, only the first one will be used for the calculation.
Reference column (e.g. an ID): The name of the column that defines which conformers belong to each other.
Ignore Hs (increases performance): Set this option to remove any existing hydrogens before performing the calculation. (Default is false)

Input Ports

: Input table with Conformers and Reference Data (e.g. ID)

Output Ports

: Conformers with RMSD >= Threshold
: Conformers with RMSD < Threshold

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Installation

To use this node in KNIME, install the extension RDKit Nodes Tests Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.9

Plugin provider: Novartis

Plugin version: 5.2.1.v202507231837

On NodePit since: 2025-12-12

Last update: 2026-01-21

KNIME versions: v5.9, v5.8, v5.7, v5.6, v5.5, v5.4, v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0, v3.7, v3.6

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