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RDKit RMSD Filter

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

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.


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

Best Friends (Incoming)

Best Friends (Outgoing)



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


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

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