Search Java Classes and Packages
#Org.openscience.cdk.smsd Classes and Interfaces - 80 results found.
| Name | Description | Type | Package | Framework |
| AbstractMCS | Interface for all MCS algorithms. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| AbstractMCSAlgorithm | Interface for MCS search algorithm. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| AbstractReactionLabeller | Class | org.openscience.cdk.smsd.labelling | CDK | |
| AbstractSubGraph | Interface class for reporting only substructure searches. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| Algorithm | This class represents various algorithm type supported by SMSD. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| AtomContainerAtomPermutor | Class | org.openscience.cdk.smsd.labelling | CDK | |
| AtomContainerPrinter | Class | org.openscience.cdk.smsd.labelling | CDK | |
| AtomMatcher | Interface for the AtomMatcher (atoms) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| BinaryTree | Class to construct a Binary tree for McGregor search. | Class | org.openscience.cdk.smsd.helper | CDK |
| BKKCKCF | This class implements Bron-Kerbosch clique detection algorithm as it is described in [F. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| BondEnergies | Class that stores bond breaking/formation energy between two atoms. | Class | org.openscience.cdk.smsd.tools | CDK |
| BondEnergy | Helper class defining the energy for a bond type. | Class | org.openscience.cdk.smsd.helper | CDK |
| BondMatcher | Interface for the BondMatcher (bonds) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| CanonicalLabellingAdaptor | Class | org.openscience.cdk.smsd.labelling | CDK | |
| CDKMCSHandler | This class acts as a handler class for CDKMCS algorithm. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKRGraph | This class implements the Resolution Graph (CDKRGraph). | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKRMap | An CDKRMap implements the association between an edge (bond) in G1 and an edge (bond) in G2, G1 and G2 being the compared graphs in a RGraph context. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKRMapHandler | This algorithm derives from the algorithm described in [Tonnelier, C. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKRNode | Node of the resolution graphe (RGraph) An CDKRNode represents an association betwwen two edges of the source graphs G1 and G2 that are compared. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| CDKSubGraphHandler | This class acts as a handler class for CDKMCS algorithm. | Class | org.openscience.cdk.smsd.algorithm.rgraph | CDK |
| ChemicalFilters | Class that ranks MCS final solution according to the chemical rules. | Class | org.openscience.cdk.smsd.filters | CDK |
| DefaultBondMatcher | Checks if a bond is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultMCSPlusAtomMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultRGraphAtomMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultVFAtomMatcher | Checks if atom is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| DefaultVFBondMatcher | Checks if a bond is matching between query and target molecules. | Class | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| EdgeBuilder | Class for building/storing edges (bonds) in the graph with bond query capabilities. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| ExactMapping | This class handles MCS between two identical molecules. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| ExtAtomContainerManipulator | Class that handles some customised features for SMSD atom containers. | Class | org.openscience.cdk.smsd.tools | CDK |
| FinalMappings | Class that stores raw mapping(s) after each algorithm is executed. | Class | org.openscience.cdk.smsd.helper | CDK |
| GenerateCompatibilityGraph | This class generates compatibility graph between query and target molecule. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| HanserRingFinder | Finds the Set of all Rings. | Class | org.openscience.cdk.smsd.ring | CDK |
| ICanonicalMoleculeLabeller | Interface | org.openscience.cdk.smsd.labelling | CDK | |
| ICanonicalReactionLabeller | Interface | org.openscience.cdk.smsd.labelling | CDK | |
| IEdge | Interface for the Edges (bonds) in graph. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IFinalMapping | Interface for mappings. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| IMapper | Interface for the mappings (mapped objects). | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IMCSBase | Interface that holds basic core interface for all MCS algorithm. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| INode | Interface for the Node (atomss) in graph. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IQuery | Interface for the query molecule/graph. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| IQueryCompiler | Interface for the query graph generator. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| Isomorphism | This class implements the Isomorphism- a multipurpose structure comparison tool. | Class | org.openscience.cdk.smsd | CDK |
| IState | Interface for the storing the states of the mapping in the VF algorithm. | Interface | org.openscience.cdk.smsd.algorithm.vflib.interfaces | CDK |
| LabelContainer | Class that handles atoms and assignes an integer lable to them. | Class | org.openscience.cdk.smsd.helper | CDK |
| Match | Holds matching query and target nodes. | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |
| McGregor | Class which reports MCS solutions based on the McGregor algorithm The SMSD algorithm is described in this paper. | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK |
| McGregorChecks | Class to perform check/methods for McGregor class. | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK |
| McgregorHelper | Helper Class for McGregor algorithm. | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK |
| MCSPlus | This class handles MCS plus algorithm which is a combination of c-clique algorithm and McGregor algorithm. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| MCSPlusHandler | This class acts as a handler class for MCSPlus algorithm. | Class | org.openscience.cdk.smsd.algorithm.mcsplus | CDK |
| MoleculeSanityCheck | Class that cleans a molecule before MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| MoleculeSignatureLabellingAdaptor | Class | org.openscience.cdk.smsd.labelling | CDK | |
| MolHandler | Class that handles molecules for MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| NodeBuilder | Class for building/storing nodes (atoms) in the graph with atom query capabilities. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| PathEdge | Class | org.openscience.cdk.smsd.ring | CDK | |
| PathGraph | Class | org.openscience.cdk.smsd.ring | CDK | |
| Permutor | General permutation generator, that uses orderly generation by ranking and unranking. | Class | org.openscience.cdk.smsd.labelling | CDK |
| PostFilter | Class that cleans redundant mappings from the solution set. | Class | org.openscience.cdk.smsd.filters | CDK |
| QueryCompiler | This class creates an template for MCS/substructure query. | Class | org.openscience.cdk.smsd.algorithm.vflib.query | CDK |
| QueryProcessor | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK | |
| RingFilter | Class | org.openscience.cdk.smsd.ring | CDK | |
| RingFinder | Interface | org.openscience.cdk.smsd.ring | CDK | |
| SignatureReactionCanoniser | Class | org.openscience.cdk.smsd.labelling | CDK | |
| SingleMapping | This class handles single atom mapping. | Class | org.openscience.cdk.smsd.algorithm.single | CDK |
| SingleMappingHandler | This is a handler class for single atom mappingAuthor:Syed Asad Rahman | Class | org.openscience.cdk.smsd.algorithm.single | CDK |
| SmilesReactionCanoniser | Class | org.openscience.cdk.smsd.labelling | CDK | |
| TargetProcessor | Class | org.openscience.cdk.smsd.algorithm.mcgregor | CDK | |
| TargetProperties | Class for building/storing nodes (atoms) in the graph with atom query capabilities. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| TimeManager | Class that handles execution time of the MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| TimeOut | Class that manages MCS timeout. | Class | org.openscience.cdk.smsd.global | CDK |
| VFAtomMatcher | Interface for the AtomMatcher (atoms) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| VFBondMatcher | Interface for the BondMatcher (bonds) in graph. | Interface | org.openscience.cdk.smsd.algorithm.matchers | CDK |
| VFlibMCSHandler | This class should be used to find MCS between query graph and target graph. | Class | org.openscience.cdk.smsd.algorithm.vflib | CDK |
| VFlibSubStructureHandler | This is an ultra fast method to report if query is a substructure for target molecule. | Class | org.openscience.cdk.smsd.algorithm.vflib | CDK |
| VFlibTurboHandler | This is an ultra fast method to report if query is a substructure for target molecule. | Class | org.openscience.cdk.smsd.algorithm.vflib | CDK |
| VFMapper | This class finds MCS between query and target molecules using VF2 algorithm. | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |
| VFMCSMapper | This class finds MCS between query and target molecules using VF2 algorithm. | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |
| VFQueryBuilder | Class for parsing and generating query graph. | Class | org.openscience.cdk.smsd.algorithm.vflib.builder | CDK |
| VFState | This class finds mapping states between query and targetAuthor:Syed Asad Rahman | Class | org.openscience.cdk.smsd.algorithm.vflib.map | CDK |