Package chemaxon.clustering
Class LibraryMCS
java.lang.Object
chemaxon.clustering.libmcs.LibraryMcs
chemaxon.clustering.LibraryMCS
- All Implemented Interfaces:
chemaxon.license.Licensable
@SubjectToRemoval(date=JAN_01_2025)
@Deprecated(forRemoval=true)
@PublicApi
public class LibraryMCS
extends LibraryMcs
Deprecated, for removal: This API element is subject to removal in a future version.
The
It is not one subgraph common to all or to the majority of input molecules that the algorithm determines but the set of the most frequently occurring common substructures. The more diverse the set to be analysed is the larger the number of the frequent common substructures is, while in case of a more focused set with limited structural diversity, the number of frequent common substructures is smaller.
The algorithm is capable of going one or more level further in this kind of scaffold analysis by finding the MCS of the frequent common substructures - and so on in a hierarchical manner.
Practically speaking structures are clustered based on their MCSs (not on their similarities etc.) in a hierarchical clustering procedure.
This class implements the
This class also provides a simple command line interface for batch processing of MCS search for a set of structures, as well as a simple graphical user interface for easy navigation through clusters of structures.
LibraryMCS class computes the maximum common substructure (MCS)
of a set of compounds. It can suggest scaffolds of a library, in particular VHTS hit sets.
Typical size of such input structure set is a few thousand molecules, but LibraryMCS can cope with 10,000s of
molecules.
It is not one subgraph common to all or to the majority of input molecules that the algorithm determines but the set of the most frequently occurring common substructures. The more diverse the set to be analysed is the larger the number of the frequent common substructures is, while in case of a more focused set with limited structural diversity, the number of frequent common substructures is smaller.
The algorithm is capable of going one or more level further in this kind of scaffold analysis by finding the MCS of the frequent common substructures - and so on in a hierarchical manner.
Practically speaking structures are clustered based on their MCSs (not on their similarities etc.) in a hierarchical clustering procedure.
This class implements the
ClusterEnumberator class which
allows clients to retieve the hierarchy. The tree of clusters as well as
data associated with nodes in this tree can be accessed along with various code values
that help reconstruct the hierarchy in custom applications.
This class also provides a simple command line interface for batch processing of MCS search for a set of structures, as well as a simple graphical user interface for easy navigation through clusters of structures.
- Since:
- JChem 3.2
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Nested Class Summary
Nested classes/interfaces inherited from class chemaxon.clustering.libmcs.LibraryMcs
LibraryMcs.ClusterEnumerator -
Field Summary
Fields inherited from class chemaxon.clustering.libmcs.LibraryMcs
ATOM_COUNT_UPPER_BOUND, DEFAULT_ALLOWED_LEVEL_COUNT, DEFAULT_ATOM_TYPE_MATCH, DEFAULT_BOND_TYPE_MATCH, DEFAULT_CHARGE_MATCH, DEFAULT_ISOTOPE_MATCH, DEFAULT_KEEP_RINGS_MODE, DEFAULT_MCS_MODE, DEFAULT_MIN_MCS_SIZE, DEFAULT_RADICAL_MATCH, DEFAULT_REQUIRED_CLUSTER_COUNT, MAX_LEVEL_COUNT, TERMINATION_CANCEL, TERMINATION_CLUSTER_COUNT, TERMINATION_ERROR, TERMINATION_LEVEL_COUNT, TERMINATION_MCS_SIZE_LIMIT, TERMINATION_SAME_PARAMETERS, TERMINATION_STEP_NOT_ALLOWED, TERMINATION_UNKNOWN -
Constructor Summary
ConstructorsConstructorDescriptionDeprecated, for removal: This API element is subject to removal in a future version. -
Method Summary
Methods inherited from class chemaxon.clustering.libmcs.LibraryMcs
addMolecule, getClusterEnumerator, getClusterEnumerator, getInputStructureCount, getLevelCount, getStopCause, getStopCauseExplanation, getTopLevelClusterCount, getTotalClusterCount, isLicensed, main, reset, search, setAllowedLevelCount, setAtomCountUpperBound, setAtomTypeMatch, setBondTypeMatch, setChargeMatch, setIsotopeMatch, setKeepRings, setLicenseEnvironment, setMCSMode, setMinimumMCSSize, setRadicalMatch, setRequiredClusterCount, step
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Constructor Details
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LibraryMCS
public LibraryMCS()Deprecated, for removal: This API element is subject to removal in a future version.
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LibraryMcs.