All Classes

Class Summary

Class	Description
Atom	Class to enclose Atom level information.
AtomDataset	Wrapper using JavaRDD and Dataset of Atom
AtomSelectObject	Class to make selections of atoms to be considered for inter-atom contacts.
ChainExample	An example of taking a list of PDB IDs, pulling them from the MMTF server and returning a SegmentDataRDD of their calpha chains.
CheckPdbIdExists	Check a given PDB exists in a hadoop sequence file
Contact	A bean to store Atom Atom contact information.
DownloadPdb	Simple example of how to download the PDB.
FlatMapIntList	Converts an Integer into a list of integers.
FragmentExample	An example generating fragments from the whole PDB and then clustering them.
GenerateMoments	Generate the USR moments for a given Point3d array.
GenerateSegments	A mapper from StructureDataInterface to the Point3d[] of the calpha coordinates.
GetData	Create an RDD by pulling data from the MMTF servers.
Group	A basic group representation.
MapToAtoms	Flat map a StructureDataInterface to it's underlying atoms.
MapToGroups	Map a StructureDataInterface to its groups.
MapToPairs	Map the individual numbers to pairs of integers - to do half matrix comparisons.
MmtfStructureData	Class to hold the undecoded MmtfStructure data.
ResultsSet	A convenience wrapper for a Spark results set.
Segment	Simple data structure for segments of proteins, e.g.
SegmentClusters	A class to consider clusters of segmenets.
SegmentDataRDD	A class to hold information and utilities around Segment information.
SparkUtils	A class of Spark utility methods
StringByteToTextByteWriter	Converts a tuple of string and byte array, to a Text and Bytes writeable.
StructureDataRDD	A class to provide functions on a series of StructureDataInterface objects.
TwoWayHashmap<K,V>	A class to have a bi-directional map.
UpdatePdb	An example of how to update the local copy of the PDB