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.

RMSD threshold

The RMSD threshold used by the node to split the input table into two output tables. Conformers with an RMSD value above or equal to the threshold go to the first output table, those below go to the second.

Ignore Hs (increases performance)

Set this option to remove any existing hydrogens before performing the calculation. (Default is false)

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Workflows

• Conf_RMSD_Cleaner_Multi_setsKNIME Hub
• Low energy conformers and PMIKNIME Forum
• PMI Plotting ExampleKNIME Hub
• PMI Plotting ExampleKNIME Hub

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Developers