| Name | Description | Type | Package | Framework |
| AminoAcidComposition | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| AminoAcidCompositionTable | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| CaseFreeAminoAcidCompoundSet | Set of proteinogenic amino acids. | Class | org.biojava.nbio.aaproperties.xml | BioJava |
| CommandPrompt | Class | org.biojava.nbio.aaproperties | BioJava | |
| CommandPrompt .PropertyName | Class | org.biojava.nbio.aaproperties | BioJava | |
| Constraints | This class is used to support the implementation of properties stated in IPeptideProperties. | Class | org.biojava.nbio.aaproperties | BioJava |
| Convert2Charge | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2Hydrophobicity | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2NormalizedVanDerWaalsVolume | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2Polarity | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2Polarizability | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2SecondaryStructure | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convert2SolventAccessibility | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Convertor | Class | org.biojava.nbio.aaproperties.profeat.convertor | BioJava | |
| Element | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| ElementTable | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| IPeptideProperties | An interface to generate some basic physico-chemical properties of protein sequences. | Interface | org.biojava.nbio.aaproperties | BioJava |
| IProfeatProperties | Interface | org.biojava.nbio.aaproperties.profeat | BioJava | |
| IProfeatProperties .ATTRIBUTE | Class | org.biojava.nbio.aaproperties.profeat | BioJava | |
| IProfeatProperties .DISTRIBUTION | Class | org.biojava.nbio.aaproperties.profeat | BioJava | |
| IProfeatProperties .GROUPING | Class | org.biojava.nbio.aaproperties.profeat | BioJava | |
| IProfeatProperties .TRANSITION | Class | org.biojava.nbio.aaproperties.profeat | BioJava | |
| Isotope | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| ModifiedAminoAcidCompoundSet | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| MyValidationEventHandler | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| Name2Count | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| PeptideProperties | This is an adaptor class which enable the ease of generating protein properties. | Class | org.biojava.nbio.aaproperties | BioJava |
| PeptideProperties .SingleLetterAACode | Class | org.biojava.nbio.aaproperties | BioJava | |
| PeptidePropertiesImpl | This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use. | Class | org.biojava.nbio.aaproperties | BioJava |
| ProfeatProperties | This is an adaptor class which enable the ease of generating profeat properties. | Class | org.biojava.nbio.aaproperties.profeat | BioJava |
| ProfeatPropertiesImpl | Class | org.biojava.nbio.aaproperties.profeat | BioJava | |
| SchemaGenerator | Class | org.biojava.nbio.aaproperties.xml | BioJava | |
| Utils | This is a utility class that contains utility methods which will facilitates the coding of other methodsSince:3. | Class | org.biojava.nbio.aaproperties | BioJava |