| Name | Description | Type | Package | Framework |
| ExhaustiveFragmenter | Generate fragments exhaustively. | Class | org.openscience.cdk.fragment | CDK |
| FragmentAtom | Class to represent an IPseudoAtom which embeds an IAtomContainer. | Class | org.openscience.cdk | CDK |
| FragmentUtils | Helper methods for fragmentation algorithms. | Class | org.openscience.cdk.fragment | CDK |
| IFragmenter | An interface for classes implementing fragmentation algorithms. | Interface | org.openscience.cdk.fragment | CDK |
| MurckoFragmenter | An implementation of the Murcko fragmenation method . | Class | org.openscience.cdk.fragment | CDK |