| Name | Description | Type | Package | Framework |
| PDBAtom | Represents the idea of an atom as used in PDB files. | Class | org.openscience.cdk.protein.data | CDK |
| PDBMonomer | Represents the idea of an monomer as used in PDB files. | Class | org.openscience.cdk.protein.data | CDK |
| PDBPolymer | An entry in the PDB database. | Class | org.openscience.cdk.protein.data | CDK |
| PDBStrand | An entry in the PDB database. | Class | org.openscience.cdk.protein.data | CDK |
| PDBStructure | Holder for secundary protein structure elements. | Class | org.openscience.cdk.protein.data | CDK |
| ProteinPocketFinder | The detection of pocket and cavities in a bioPolymer is done similar to the program TODO: Optimisation of the cubic grid placement | Class | org.openscience.cdk.protein | CDK |