IconRDKit RMSD Filter0 ×

RDKit Nodes for Knime version 3.3.1.v201712181039 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.

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

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Update Site

To use this node in KNIME, install RDKit Nodes for Knime from the following update site:

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