All Classes

Class Summary

Class	Description
AlignmentTools	Class to calculate the TM Score between two Atom arrays.
AtomContactRDD	Class to hold AtomContact data in an JavaRDD
AtomDataRDD	A wrapper around JavaRDD and Dataset of atoms.
BiojavaSparkUtils	A class of Biojava related Spark utility methods.
BuildUndirectedGraph	Created by ap3 on 09/05/2016.
CalculateContacts	Class to calculate all interatomic distances between charged atoms.
CalculateFrequency	A class to calculate the frequency of a given atom defined in a AtomSelectObject object.
CanonNames	A class of static methods to find the canonical names of AtomContact interactions.
ChainAligner	Demo code of clustering C-alpha chains.
ChainDataRDD	The class to provide functions on chains using the JavaPairRDD of Chain.
CountContacts	An example reading the PDB and finding the mean C-alpha to C-alpha distance between Proline and Lysine.
CountElements	An example reading the PDB and finding the mean frequency of every element in the PDB.
EntryPoint	An entry point using Python to access Spark functions.
FlatMapCluster	Created by ap3 on 09/05/2016.
FragmentAndGroup	Generate fragments and group them by their sequence.
GetAverageCalphaDist	Example of mapping the PDB to chains of just C-alpha coords.
GetSubsetOfSequences	Created by ap3 on 06/05/2016.
GroupDataRDD	An RDD to comprise Group level data.
MapperUtils	A class to preserve the log if the functions in mappers.
PairwiseSequenceComparison	Performs a pairwise alignment and returns a Tuple5.
PairwiseSequenceComparison	Performs a pairwise alignment and returns a Tuple5.
PdbIdToMmtf	Generate the internal data structure (using biojava) from a PDB code.
PrintClusterInfo	Created by ap3 on 10/05/2016.
RandomKeyAssigner	Maps a key to a randomly generated key.
ReadFromMmcif	Demo function to read Structure data interface from MMCIF
ShowGraph	A class to render a Graph given a list of label names
ShowGraph.MyEdge
SimpleExample	A very simple example reading the PDB and finding the number of entries in the PDB with resolution better than 3.0 Angstrom and R-free better than 0.3.
StringByteToTextByteWriter	Converts a tuple of string and byte array, to a Text and Bytes writeable.
WeightedGraph