MCS

The MCS the maximum common substructure (MCS) of two molecules. More precisely, these algorithms find the maximum common edge subgraph (MCES) of the input structures. The provided MCS algorithms are powerful heuristic methods, which typically find large common substructures in a short time. However, note that they do not always provide the exact optimal result due to the complexity of the MCS problem (especially for large molecules). Furthermore, as the algorithms perform randomized search, different results might be obtained for equivalent molecule representations. Query and target structures basically play the same role in MCS search except for query features: a query molecule may contain generic query atoms (A, Q, M, X, list atom, not list atom, etc.) and query bonds (any, single or double, etc.), but query properties (e.g. valence, hydrogen count) are ignored. If exact query atom/bond matching is set to true, then query atoms/bonds are allowed in both the query and the target, but they are not evaluated (only exact matching is accepted).

Options

Query structure column

The query structure column.

Target structure column

The target structure column.

MCS Algorithm

Maximum clique algorithm: Heuristic MCS algorithm based on a maximum clique algorithm.
Build-Up algorithm: Algorithm for the Maximal Common Induced Subgraph problem based on the Build-Up Algorithm of Takeshi Kawabata.

Minimum Fragments Size

Sets the minimum required size of the fragments of MCS.

MCES Search Mode

Sets search mode.

Atom type

Matching atom type.

Exact query atom

Sets whether query atoms should be matched only to query atoms of exactly the same type.

Bond type

Matching bond type.

Exact query bond

Sets whether query bonds should be matched only to query bonds of exactly the same type.

Charge

Matching charge.

Isotopes

Matching isotopes.

Radical

Matching radical.

Atom map number

Matching atom map number.

Connected Mode

Sets whether the common substructures should be connected.

Ring Handling Mode

Sets how rings should be handled during the search.

Maximum Rings Size

Sets the maximum size of rings considered for ring matching purposes.

Input Ports

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

Output Ports

: Output table that contains maximum common substructures.

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Installation

To use this node in KNIME, install the extension ChemAxon/Infocom JChem Extensions Feature from the below update site following our NodePit Product and Node Installation Guide:

v5.3

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

Plugin provider: Infocom Corporation

Plugin version: 4.7.0.v240300

On NodePit since: 2024-07-09

Last update: 2024-11-21

KNIME versions: v5.3, v5.2, v5.1, v4.7, v4.6, v4.5, v4.4, v4.3, v4.2, v4.1, v4.0

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MCS