Markush Enumeration

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.

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Workflows

• Markush_from_documentKNIME Hub
• Markush_from_documentKNIME Hub

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