| Name | Description | Type | Package | Framework |
| AFP | A class to represent a FATCAT AFPAuthor:Andreas PrlicSee Also:Serialized Form | Class | org.biojava.nbio.structure.align.model | BioJava |
| AFPChain | A bean to contain the core of a structure alignment. | Class | org.biojava.nbio.structure.align.model | BioJava |
| AfpChainWriter | A class to convert the data in an AfpChain object to various String outputs. | Class | org.biojava.nbio.structure.align.model | BioJava |