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A

AlignmentTools - Class in org.biojava.spark.function

Class to calculate the TM Score between two Atom arrays.

AlignmentTools() - Constructor for class org.biojava.spark.function.AlignmentTools

AtomContactRDD - Class in org.biojava.spark.data

Class to hold AtomContact data in an JavaRDD

AtomContactRDD(JavaRDD<AtomContact>) - Constructor for class org.biojava.spark.data.AtomContactRDD

Construct an AtomContactRDD from a JavaRDD AtomContact.

AtomDataRDD - Class in org.biojava.spark.data

A wrapper around JavaRDD and Dataset of atoms.

AtomDataRDD(JavaRDD<Atom>) - Constructor for class org.biojava.spark.data.AtomDataRDD

Construct from an JavaRDD

AtomDataRDD(Dataset<Atom>) - Constructor for class org.biojava.spark.data.AtomDataRDD

Construct from a Dataset

B

BiojavaSparkUtils - Class in org.biojava.spark.utils

A class of Biojava related Spark utility methods.

BiojavaSparkUtils() - Constructor for class org.biojava.spark.utils.BiojavaSparkUtils

build(List<Tuple3<Integer, Integer, Double>>) - Static method in class org.biojava.spark.graph.WeightedGraph

Builds a simple weighted graph

buildGraph(double, boolean) - Static method in class org.biojava.spark.graph.ShowGraph

BuildUndirectedGraph - Class in org.biojava.spark.function

Created by ap3 on 09/05/2016.

BuildUndirectedGraph(Graph) - Constructor for class org.biojava.spark.function.BuildUndirectedGraph

byteArrToBiojavaStruct(String, byte[]) - Static method in class org.biojava.spark.mappers.MapperUtils

Converts a byte array of the messagepack (mmtf) to a Biojava structure.

C

cacheData() - Method in class org.biojava.spark.data.AtomContactRDD

Cache the data - for multi-processing.

cacheData() - Method in class org.biojava.spark.data.AtomDataRDD

Cache the data - for multi-processing.

cacheData() - Method in class org.biojava.spark.data.GroupDataRDD

Cache the data - for multi-processing.

CalculateContacts - Class in org.biojava.spark.mappers

Class to calculate all interatomic distances between charged atoms.

CalculateContacts(AtomSelectObject, AtomSelectObject, double) - Constructor for class org.biojava.spark.mappers.CalculateContacts

CalculateContacts(AtomSelectObject, AtomSelectObject, double, boolean) - Constructor for class org.biojava.spark.mappers.CalculateContacts

CalculateFrequency - Class in org.biojava.spark.mappers

A class to calculate the frequency of a given atom defined in a AtomSelectObject object.

CalculateFrequency(AtomSelectObject) - Constructor for class org.biojava.spark.mappers.CalculateFrequency

Constructor for the CalculateFrequency class.

call(Iterable<String>) - Method in class org.biojava.spark.function.FlatMapCluster

call(String) - Method in class org.biojava.spark.function.RandomKeyAssigner

call(String) - Method in class org.biojava.spark.mappers.PdbIdToMmtf

call(Tuple2<String, byte[]>) - Method in class org.biojava.spark.mappers.StringByteToTextByteWriter

call(Tuple2<String, String>) - Method in class org.biojava.spark.function.BuildUndirectedGraph

call(Tuple2<String, String>) - Method in class org.biojava.spark.function.GetSubsetOfSequences

call(Tuple2<String, String>) - Method in class org.biojava.spark.function.PrintClusterInfo

call(Tuple2<String, StructureDataInterface>) - Method in class org.biojava.spark.mappers.CalculateContacts

call(Tuple2<String, StructureDataInterface>) - Method in class org.biojava.spark.mappers.CalculateFrequency

call(Tuple2<Tuple2<String, String>, Tuple2<String, String>>) - Method in class org.biojava.spark.function.PairwiseSequenceComparison

call(Tuple2<Tuple2<String, String>, Tuple2<String, String>>) - Method in class org.biojava.spark.mappers.PairwiseSequenceComparison

CanonNames - Class in org.biojava.spark.utils

A class of static methods to find the canonical names of AtomContact interactions.

CanonNames() - Constructor for class org.biojava.spark.utils.CanonNames

ChainAligner - Class in demo

Demo code of clustering C-alpha chains.

ChainAligner() - Constructor for class demo.ChainAligner

ChainDataRDD - Class in org.biojava.spark.data

The class to provide functions on chains using the JavaPairRDD of Chain.

ChainDataRDD(JavaPairRDD<String, Chain>) - Constructor for class org.biojava.spark.data.ChainDataRDD

The constructore of the ChainDataRDD using a JavaPairRDD of type Chain.

convertToStructDataInt(Structure) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get a StructureDataInterface from a Biojava Structure.

countByAtomName() - Method in class org.biojava.spark.data.AtomDataRDD

Count the number of times each atom name appears.

countByElement() - Method in class org.biojava.spark.data.AtomDataRDD

Count the number of times each element appears.

countByGroupAtomName() - Method in class org.biojava.spark.data.AtomDataRDD

Get the unique group atom name combinations in this.

countByGroupName() - Method in class org.biojava.spark.data.GroupDataRDD

Count the number of times each group name appears.

CountContacts - Class in demo

An example reading the PDB and finding the mean C-alpha to C-alpha distance between Proline and Lysine.

CountContacts() - Constructor for class demo.CountContacts

CountElements - Class in demo

An example reading the PDB and finding the mean frequency of every element in the PDB.

CountElements() - Constructor for class demo.CountElements

countInterAtomContacts(String, String) - Method in class org.biojava.spark.data.AtomContactRDD

Get the number of inter-atom name contacts for a given pair of atoms names.

countInterElementContacts(String, String) - Method in class org.biojava.spark.data.AtomContactRDD

Get the number of inter-element contacts for a given pair of element names.

countInterGroupContacts(String, String) - Method in class org.biojava.spark.data.AtomContactRDD

Get the number of inter-group contacts for a given pair of group names.

D

demo - package demo

E

EntryPoint - Class in org.biojava.spark.utils

An entry point using Python to access Spark functions.

EntryPoint() - Constructor for class org.biojava.spark.utils.EntryPoint

Constructor initialises the SparkUtils class.

F

filterDistance(double) - Method in class org.biojava.spark.data.AtomContactRDD

Filter all contacts greater than a certain distance.

filterElementElementContacts(String, String) - Method in class org.biojava.spark.data.AtomContactRDD

Filter an AtomContactRDD based on two elements being in contact.

filterElementGroupContacts(String, String) - Method in class org.biojava.spark.data.AtomContactRDD

Filter an AtomContactRDD based on two elements being in contact.

filterSequenceSimilar(SegmentDataRDD, String, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Filter the SegmentDataRDD based on minimum sequence similarity to a reference sequence.

findAtoms(StructureDataRDD) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Find all the atoms in the RDD.

findAtoms(StructureDataRDD, AtomSelectObject) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Find the given type of atoms for each structure in the PDB.

findCalphaCalphaContacts() - Static method in class demo.CountContacts

Example of finding C-alpha C-alpha contacts.

findContacts(StructureDataRDD, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Find the contacts for each structure in the PDB.

findContacts(StructureDataRDD, AtomSelectObject, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Find the contacts for each structure in the PDB.

findContacts(StructureDataRDD, AtomSelectObject, AtomSelectObject, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Find the contacts for each structure in the PDB.

findFeHisContacts() - Static method in class demo.CountContacts

Example of finding Fe His contacts.

findNOChargedContacts() - Static method in class demo.CountContacts

Example of finding N O charged contacts.

FlatMapCluster - Class in org.biojava.spark.function

Created by ap3 on 09/05/2016.

FlatMapCluster() - Constructor for class org.biojava.spark.function.FlatMapCluster

FragmentAndGroup - Class in demo

Generate fragments and group them by their sequence.

FragmentAndGroup() - Constructor for class demo.FragmentAndGroup

G

generateRdd(List<String>, String) - Static method in class org.biojava.spark.mappers.MapperUtils

PDB RDD generator.

getAllInterAtomElementContacts() - Method in class org.biojava.spark.data.AtomContactRDD

Get a map counting the number of interactions between atom element names.

getAllInterAtomNameContacts() - Method in class org.biojava.spark.data.AtomContactRDD

Get a map counting the number of interactions between atom names.

getAllInterGroupContacts() - Method in class org.biojava.spark.data.AtomContactRDD

Get a map counting the number of interactions between groups.

getAtomContactRDD() - Method in class org.biojava.spark.data.AtomContactRDD

Get the JavaRDD of AtomContact objects.

getAtomContacts(List<Atom>, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get all the atom contacts in a list of atoms.

getAtomContacts(List<Atom>, List<Atom>, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get the contacts between two lists of atoms

getAtomContactsSlow(List<Atom>, List<Atom>, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get the contacts between two lists of atoms using iteration and not grids

getAtoms() - Method in class org.biojava.spark.data.AtomContactRDD

Get the contacts as an AtomDataRDD

getAtoms() - Method in class org.biojava.spark.data.GroupDataRDD

Get the atoms from the groups.

getAtoms(StructureDataInterface) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get all the atoms in the structure using a StructureDataInterface.

getAtoms(StructureDataInterface, AtomSelectObject) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get all the atoms of a given name or in a given group in the structure using a StructureDataInterface.

GetAverageCalphaDist - Class in demo

Example of mapping the PDB to chains of just C-alpha coords.

GetAverageCalphaDist() - Constructor for class demo.GetAverageCalphaDist

getBiojavaAlignment(Atom[], Atom[], String) - Static method in class org.biojava.spark.function.AlignmentTools

Performs an alignment and returns the AFPChain scores between two C-alpha Atom arrays.

getBiojavaRdd(String) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get an JavaPairRDD of String Structure from a file path.

getBiojavaSparkUtils() - Method in class org.biojava.spark.utils.EntryPoint

Ability to get the BiojavaSparkUtils .

getByteArray(String) - Static method in class org.biojava.spark.mappers.MapperUtils

Get the available data as a byte array from an input PDB id.

getByteArray(String, String) - Static method in class org.biojava.spark.mappers.MapperUtils

Get the available data as a byte array from an input PDB id.

getCaAtoms(Segment) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Gets the C-alpha Atom for the given input Segment.

getCanonAtomNames(AtomContact) - Static method in class org.biojava.spark.utils.CanonNames

Canonically represent atom name pairs as strings.

getCanonChains(AtomContact) - Static method in class org.biojava.spark.utils.CanonNames

Get the canonical names of two chains from an AtomContact

getCanonElementNames(AtomContact) - Static method in class org.biojava.spark.utils.CanonNames

Canonically represent element name pairs as strings.

getCanonGroups(AtomContact) - Static method in class org.biojava.spark.utils.CanonNames

Canonically represent group pairs as strings.

getCanonResidueNumbers(AtomContact) - Static method in class org.biojava.spark.utils.CanonNames

Get the canonical names of two residues from an AtomContact

getChainRDD(String, int, double) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.

getChainRDD(List<String>) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.

getChainRDD(List<String>, int) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.

getChainRDD(StructureDataRDD, int) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.

getDistanceDistOfAtomInts(String, String) - Method in class org.biojava.spark.data.AtomContactRDD

Get the distance distributions for all of the atom types.

getFromList(File[]) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Generate a JavaPairRDD of String Structure from a list of PDB files.

getGraph() - Static method in class org.biojava.spark.graph.ShowGraph

getGroupAtomName(Atom) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get a conjoined group atom name from an atom.

getGroupIds() - Method in class org.biojava.spark.data.AtomContactRDD

Get the associate group ids

getGroupRdd() - Method in class org.biojava.spark.data.GroupDataRDD

Get the JavaPairRDD of Group data.

getGroups() - Method in class org.biojava.spark.data.ChainDataRDD

Get the Group objects as an GroupDataRDD.

getMinimumSpanningTree(Graph<Integer, DefaultWeightedEdge>) - Static method in class org.biojava.spark.graph.WeightedGraph

Builds a graph that contains a Minimum Spanning Tree

getNames() - Method in class org.biojava.spark.graph.ShowGraph

getNonPolymerChains() - Method in class org.biojava.spark.data.ChainDataRDD

Get only the non-polymer chains.

getPairs() - Method in class org.biojava.spark.data.AtomContactRDD

Get the assoicated pairs of atoms found in this

getPdbIds() - Method in class org.biojava.spark.data.AtomContactRDD

Get the associated PDB ids as a list of Strings

getPolymerChains() - Method in class org.biojava.spark.data.ChainDataRDD

Get only the polymer chains.

getRdd() - Method in class org.biojava.spark.data.AtomDataRDD

Get the underlying JavaRDD for this AtomDataRDD.

getRDD() - Method in class org.biojava.spark.data.ChainDataRDD

Get the JavaPairRDD of the Chain objects.

getSparkUtils() - Method in class org.biojava.spark.utils.EntryPoint

Ability to get the SparkUtils.

getStructureRDDFromMmcif(String) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Function (for benchmarking) to get a StructureDataRDD from a Hadoop file of mmCIF data.

GetSubsetOfSequences - Class in org.biojava.spark.function

Created by ap3 on 06/05/2016.

GetSubsetOfSequences(Broadcast<List<String>>) - Constructor for class org.biojava.spark.function.GetSubsetOfSequences

getTypeFromChainId(StructureDataInterface, int) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Get the type of a given chain index - SHOULD BE MOVED INTO ENCODER UTILS

getWaterChains() - Method in class org.biojava.spark.data.ChainDataRDD

Get only the water chains.

GroupDataRDD - Class in org.biojava.spark.data

An RDD to comprise Group level data.

GroupDataRDD(JavaPairRDD<String, Group>) - Constructor for class org.biojava.spark.data.GroupDataRDD

Constructor of the RDD from a JavaPairRDD of Group

M

main(String[]) - Static method in class demo.ChainAligner

Cluster the C-alpha chains of a set of PDB ids.

main(String[]) - Static method in class demo.CountContacts

An example reading the PDB and finding the mean C-alpha to C-alpha distance between Proline and Lysine.

main(String[]) - Static method in class demo.CountElements

An example reading the PDB and finding the mean frequency of every element in the PDB.

main(String[]) - Static method in class demo.FragmentAndGroup

Function to fragment and group those fragments based on sequence identity.

main(String[]) - Static method in class demo.GetAverageCalphaDist

Example of mapping the PDB to chains of just C-alpha coords.

main(String[]) - Static method in class demo.ReadFromMmcif

Load the data and print the number of entries.

main(String[]) - Static method in class demo.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.

main(String[]) - Static method in class org.biojava.spark.utils.EntryPoint

Function to set up the gateway server and get it going.

MapperUtils - Class in org.biojava.spark.mappers

A class to preserve the log if the functions in mappers.

MapperUtils() - Constructor for class org.biojava.spark.mappers.MapperUtils

MyEdge() - Constructor for class org.biojava.spark.graph.ShowGraph.MyEdge

O

org.biojava.spark.data - package org.biojava.spark.data

org.biojava.spark.function - package org.biojava.spark.function

org.biojava.spark.graph - package org.biojava.spark.graph

org.biojava.spark.mappers - package org.biojava.spark.mappers

org.biojava.spark.utils - package org.biojava.spark.utils

P

PairwiseSequenceComparison - Class in org.biojava.spark.function

Performs a pairwise alignment and returns a Tuple5.

PairwiseSequenceComparison - Class in org.biojava.spark.mappers

Performs a pairwise alignment and returns a Tuple5.

PairwiseSequenceComparison() - Constructor for class org.biojava.spark.function.PairwiseSequenceComparison

PairwiseSequenceComparison(List<Tuple2<String, String>>, float, float) - Constructor for class org.biojava.spark.mappers.PairwiseSequenceComparison

PdbIdToMmtf - Class in org.biojava.spark.mappers

Generate the internal data structure (using biojava) from a PDB code.

PdbIdToMmtf(String) - Constructor for class org.biojava.spark.mappers.PdbIdToMmtf

Constructor to provide the producer.

PrintClusterInfo - Class in org.biojava.spark.function

Created by ap3 on 10/05/2016.

PrintClusterInfo(List<Tuple2<String, Iterable<String>>>) - Constructor for class org.biojava.spark.function.PrintClusterInfo

R

RandomKeyAssigner - Class in org.biojava.spark.function

Maps a key to a randomly generated key.

RandomKeyAssigner(int) - Constructor for class org.biojava.spark.function.RandomKeyAssigner

ReadFromMmcif - Class in demo

Demo function to read Structure data interface from MMCIF

ReadFromMmcif() - Constructor for class demo.ReadFromMmcif

S

setGraph(Graph<Integer, DefaultWeightedEdge>) - Static method in class org.biojava.spark.graph.ShowGraph

setNames(String[]) - Method in class org.biojava.spark.graph.ShowGraph

setUpBioJava() - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Set up the configuration parameters for BioJava.

setUpBioJava(String) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Set up the configuration parameters for BioJava.

showGraph(double, boolean) - Method in class org.biojava.spark.graph.ShowGraph

ShowGraph - Class in org.biojava.spark.graph

A class to render a Graph given a list of label names

ShowGraph(Graph<Integer, DefaultWeightedEdge>, String[]) - Constructor for class org.biojava.spark.graph.ShowGraph

Constructor requires the graph and the labels of the vertices.

ShowGraph.MyEdge - Class in org.biojava.spark.graph

SimpleExample - Class in demo

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.

SimpleExample() - Constructor for class demo.SimpleExample

StringByteToTextByteWriter - Class in org.biojava.spark.mappers

Converts a tuple of string and byte array, to a Text and Bytes writeable.

StringByteToTextByteWriter() - Constructor for class org.biojava.spark.mappers.StringByteToTextByteWriter

T

toString() - Method in class org.biojava.spark.graph.ShowGraph.MyEdge

traverse(Graph<Integer, DefaultWeightedEdge>) - Static method in class org.biojava.spark.graph.WeightedGraph

Builds a path (root and branches) to traverse a graph

W

WeightedGraph - Class in org.biojava.spark.graph

WeightedGraph() - Constructor for class org.biojava.spark.graph.WeightedGraph

writeToFile(List<String>, String, String) - Static method in class org.biojava.spark.utils.BiojavaSparkUtils

Write a list of PDB ids to a hadoop sequence file in MMTF format.

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