| 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 |
| 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 |
| IFinalMapping | Interface for mappings. | Interface | org.openscience.cdk.smsd.interfaces | CDK |
| IMCSBase | Interface that holds basic core interface for all MCS algorithm. | Interface | org.openscience.cdk.smsd.interfaces | CDK |