• AlignmentTools
• AtomContactRDD
• AtomDataRDD
• BiojavaSparkUtils
• BuildUndirectedGraph
• CalculateContacts
• CalculateFrequency
• CanonNames
• ChainAligner
• ChainDataRDD
• CountContacts
• CountElements
• EntryPoint
• FlatMapCluster
• FragmentAndGroup
• GetAverageCalphaDist
• GetSubsetOfSequences
• GroupDataRDD
• MapperUtils
• PairwiseSequenceComparison
• PairwiseSequenceComparison
• PdbIdToMmtf
• PrintClusterInfo
• RandomKeyAssigner
• ReadFromMmcif
• ShowGraph
• ShowGraph.MyEdge
• SimpleExample
• StringByteToTextByteWriter
• WeightedGraph