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Markush Composer

StreamableChemAxon/Infocom JChem Extensions version 4.3.0.v202000 by Infocom Corporation

Automatically generate Markush structures based on a set of compounds.

Options

Structure column
The structure column.
Enable nested R-groups
If you want to generate single level Markush structures, uncheck the Enable nested R-groups check box.
Merge duplicated R-groups
If you don't want to reuse any R-group definition, uncheck the Merge duplicated R-groups check box.
Enable position variation
If you don't want to generate position variation bonds, uncheck the Enable position variation check box.
Enable atom lists
If you don't want to generate atom lists, uncheck the Enable atom lists check box.
Scaffold options
You can choose between Automatic detection of scaffold or User-defined scaffold.
Calculation mode
For processing a very large set of compounds, you can choose a fast search mode instead of normal in Search mode. With fast search mode, the precision of the common substructure finding algorithm is lower, which can cause suboptimal result in some cases.
Minimum scaffold size
If the largest common part of the set of compounds is lower than the Minimum scaffold size, the composer generates more than one Markush structures with larger scaffolds.
Minimum common size of nesting R-groups
If some of the R-group fragments in an R-group definition have larger common parts than the Minimum common size of nesting R-groups, the algorithm generates a new nested R-group.

Input Ports

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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format.
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Input table that contains structure in Structure(Mrv, Sdf, Smiles, etc.) format.

Output Ports

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Output table that contains Markush structure.

Best Friends (Incoming)

Best Friends (Outgoing)

Workflows

Installation

To use this node in KNIME, install ChemAxon/Infocom JChem Extensions Feature from the following update site:

KNIME 4.3

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Developers

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