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All Classes Interface Summary Class Summary Enum Summary Class Description AminoAcidComposition AminoAcidCompositionTable AminoAcidProperties This class provides the protein properties at the level of individual amino acids.BioJavaAADemo Created by andreas on 8/9/14.CaseFreeAminoAcidCompoundSet Set of proteinogenic amino acids.CommandPrompt CommandPrompt.PropertyName Constraints This class is used to support the implementation of properties stated in IPeptideProperties.Convert2Charge Convert2Hydrophobicity Convert2NormalizedVanDerWaalsVolume Convert2Polarity Convert2Polarizability Convert2SecondaryStructure Convert2SolventAccessibility Convertor Element One way to model the elementsElementTable IPeptideProperties An interface to generate some basic physico-chemical properties of protein sequences.
The following properties could be generated:IProfeatProperties IProfeatProperties.ATTRIBUTE Enumeration of the seven different attributesIProfeatProperties.DISTRIBUTION Enumeration of the distribution for the first, first 25%, first 50%, first 75% and 100% of the groupingIProfeatProperties.GROUPING Enumeration of the three different groupings for each attributesIProfeatProperties.TRANSITION Enumeration of the transition between groupA and groupBIsotope ModifiedAminoAcidCompoundSet MyValidationEventHandler Name2Count PeptideProperties This is an adaptor class which enable the ease of generating protein properties.PeptideProperties.SingleLetterAACode Enumeration of 20 standard amino acid codePeptidePropertiesImpl This class contains the actual implementation of IPeptideProperties and is wrapped around by PeptideProperties for ease of use.ProfeatProperties This is an adaptor class which enable the ease of generating profeat properties.ProfeatPropertiesImpl SchemaGenerator Utils This is a utility class that contains utility methods which will facilitates the coding of other methods