| Name | Description | Type | Package | Framework |
| ClusterDomains | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| Cut | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutDomain | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutSites | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| CutValues | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| Domain | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| GetDistanceMatrix | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| PDPDistanceMatrix | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| PDPDomain | Class | org.biojava.nbio.structure.domain | BioJava | |
| PDPParameters | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| PDPProvider | Decomposes a structure into representative PDP domains. | Interface | org.biojava.nbio.structure.domain | BioJava |
| Segment | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| SegmentComparator | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |
| ShortSegmentRemover | Class | org.biojava.nbio.structure.domain.pdp | BioJava | |