| Name | Description | Type | Package | Framework |
| ChargeGroup | A ChargeGroup (CG) is a numbered collection of atoms in an MDMolecule. | Class | org.openscience.cdk.libio.md | CDK |
| MDMolecule | Class | org.openscience.cdk.libio.md | CDK | |
| Residue | A residue is a named, numbered collection of atoms in an MDMolecule. | Class | org.openscience.cdk.libio.md | CDK |