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).


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.
Matching charge.
Matching isotopes.
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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