| Name | Description | Type | Package | Framework |
| BondEnergies | Class that stores bond breaking/formation energy between two atoms. | Class | org.openscience.cdk.smsd.tools | CDK |
| ExtAtomContainerManipulator | Class that handles some customised features for SMSD atom containers. | Class | org.openscience.cdk.smsd.tools | CDK |
| MoleculeSanityCheck | Class that cleans a molecule before MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| MolHandler | Class that handles molecules for MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |
| TimeManager | Class that handles execution time of the MCS search. | Class | org.openscience.cdk.smsd.tools | CDK |