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Markush Enumeration

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

The Markush enumeration node can be used to generate a whole or a subset of the library of a generic Markush structure. It is also capable of calculating the total number of specific structures present in a Markush library.

Options

Markush library size
The size of the Markush library can be calculated by arbitrary precision.
Sequential enumeration
Enumerates members of the Markush library in a sequential manner (by substituting the first definition of the first variable, etc).
Random enumeration
This mode generates a random subset of the Markush library to give a quick sampling. It is especially helpful for huge libraries, where full enumeration is impossible. In random mode variable parts are chosen randomly, and the substitution probability of each definition is proportionate with the fragment library size that the given definition generates. This ensures the generation of a representative random subset over the Markush library space.
Homology group enumeration
Homology groups are R-groups, represented as pseudo atoms - with the names covering a set of R-groups either built-in or user-defined.
Valence filter
If the Markush structure is not properly (or too generally) formulated, it is possible that it describes structures with valence errors. In this case, the valence filter setting is useful to filter out the offending result structures. The default value is off (no filtering).
Scaffold alignment and coloring
Coloring the scaffold (part of the structure containing no Markush features) and/or the R-groups in enumerated structures can help visual recognition of parts of the molecules. Differentiation of the structures is aided by alignment of all structures to the original scaffold. These options are available in sequential and random enumeration.
Generate Markush code
Sets scaffold ID to be used in Markush code generation.
Structure column
The structure column.

Input Ports

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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 enumerated 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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