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).
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