| Name | Description | Type | Package | Framework |
| CountProgressListener | Class | org.biojava.nbio.structure.align.client | BioJava | |
| FarmJobParameters | Class | org.biojava.nbio.structure.align.client | BioJava | |
| FarmJobRunnable | Contains the single thread for a job that can run multiple alignments. | Class | org.biojava.nbio.structure.align.client | BioJava |
| JFatCatClient | Class | org.biojava.nbio.structure.align.client | BioJava | |
| JobKillException | Class | org.biojava.nbio.structure.align.client | BioJava | |
| PdbPair | A pair for structure alignmentAuthor:Andreas Prlic | Class | org.biojava.nbio.structure.align.client | BioJava |
| StructureName | A utility class that makes working with names of structures, domains and ranges easier. | Class | org.biojava.nbio.structure.align.client | BioJava |
| StructureName .Source | Class | org.biojava.nbio.structure.align.client | BioJava | |