| Name | Description | Type | Package | Framework |
| BinaryTree | Class to construct a Binary tree for McGregor search. | Class | org.openscience.cdk.smsd.helper | CDK |
| BondEnergy | Helper class defining the energy for a bond type. | Class | org.openscience.cdk.smsd.helper | CDK |
| FinalMappings | Class that stores raw mapping(s) after each algorithm is executed. | Class | org.openscience.cdk.smsd.helper | CDK |
| LabelContainer | Class that handles atoms and assignes an integer lable to them. | Class | org.openscience.cdk.smsd.helper | CDK |