- AminoAcidComposition
- AminoAcidCompositionTable
- AminoAcidProperties
- BioJavaAADemo
- CaseFreeAminoAcidCompoundSet
- CommandPrompt
- CommandPrompt.PropertyName
- Constraints
- Convert2Charge
- Convert2Hydrophobicity
- Convert2NormalizedVanDerWaalsVolume
- Convert2Polarity
- Convert2Polarizability
- Convert2SecondaryStructure
- Convert2SolventAccessibility
- Convertor
- Element
- ElementTable
- IPeptideProperties
- IProfeatProperties
- IProfeatProperties.ATTRIBUTE
- IProfeatProperties.DISTRIBUTION
- IProfeatProperties.GROUPING
- IProfeatProperties.TRANSITION
- Isotope
- ModifiedAminoAcidCompoundSet
- MyValidationEventHandler
- Name2Count
- PeptideProperties
- PeptideProperties.SingleLetterAACode
- PeptidePropertiesImpl
- ProfeatProperties
- ProfeatPropertiesImpl
- SchemaGenerator
- Utils