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RDKit MCS

RDKit Nodes for Knime version 4.0.1.v202006261025 by NIBR

This node is used to find the Maximum Common Substructure (MCS) of a set of compounds using the RDKit MCS code. Such a calculation can be a long running process. Therefore, a timeout must be specified as part of the options. The MCS of an empty list of molecules is undefined and results in empty result cells. The MCS of a single molecule is the molecule itself (as SMARTS value). All other MCS calculations are based on the specified parameters.

Options

RDKit molecule column
Select here the RDKit Molecule column to be used as input.
Threshold
Fraction of molecules that the MCS must cover. Defaults to 1.0. 0.0 < threshold ≤ 1.0.
Ring matches ring only
Determines whether ring bonds only match other ring bonds. Default is unchecked.
Complete rings only
Determines whether only complete rings are included in the MCS. Default is unchecked.
Match valences
Determines whether atom valences are used in the comparison. Default is unchecked.
Atom comparison
Specify here how atoms shall be compared: Compare Any, Compare Elements, Compare Isotopes.
Bond comparison
Specify here how bonds shall be compared: Compare Any, Compare Order, Compare Exact Order.
Timeout (in seconds)
Specify here how long the MCS calculation shall run at a maximum. Default is 300 seconds. There is currently no way to interrupt a long-running MCS calculation. Even if you cancel an executing node the calculation will continue in the background and will occupy system resources until it is either done or the specified timeout occurs. Use longer timeouts with care!

Input Ports

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Input table with RDKit Molecules

Output Ports

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Table containing a single row with the MCS as a SMARTS value and additional information (atom count, bond count and if calculation timed out).

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

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

KNIME 4.2

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

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Developers

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