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RMSD Conformer List Filter

StreamableVernalis PMI-extension for KNIME Workbench version 1.28.2.v202101281353 by Vernalis (R&D), UK

This node filters conformers according to an RMSD threshold. All conformers of a molecule must be in a List cell in a single row.

Filtering is performed by calculating the RMSD for each conformer against all kept so far for the current molecule, and only keeping those which have a minimum RMSD to a previously kept conformer greater than the threshold value

Other non-molecule format List columns can be selected and filtered according to whether the corresponding conformer was kept or removed. If a list cell has a different number of members than the conformers cell, it will not be filtered (it will either be kept unchanged, or replaced with a missing cell according to the node configuration), and the row will be added to the warning message at the end of the node execution

Options

Conformers
The input molecule column containing the conformers. Accepted formats are Lists of MOL, SDF and RDKit
Conformer Properties Columns
Lists of properties associated with the conformers to be filtered
Replace unfilterable list cells with missing values
If this option is selected, list cells which cannot be filtered by virtue of having a different number of members to the incoming conformer column will be replaced with a missing value cell rather than being passed through unchanged
RMSD Filter Threshold (Å)
The cut-off threshold for keeping conformers
Ignore H's
Hydrogen atoms are ignored. Significant performance increases can be obtained selecting this option.

Input Ports

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Conformers for processing

Output Ports

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Filtered input table

Best Friends (Incoming)

Best Friends (Outgoing)

Installation

To use this node in KNIME, install Vernalis KNIME Nodes from the following update site:

KNIME 4.3

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

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