org.biojava.spark.utils

Class BiojavaSparkUtils

java.lang.Object

org.biojava.spark.utils.BiojavaSparkUtils

public class BiojavaSparkUtils
extends Object

A class of Biojava related Spark utility methods. These extend SparkUtils.

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor and Description
BiojavaSparkUtils()

Method Summary

Modifier and Type	Method and Description
static org.rcsb.mmtf.api.StructureDataInterface	convertToStructDataInt(org.biojava.nbio.structure.Structure structure) Get a StructureDataInterface from a Biojava Structure.
static org.rcsb.mmtf.spark.data.SegmentDataRDD	filterSequenceSimilar(org.rcsb.mmtf.spark.data.SegmentDataRDD segmentDataRDD, String inputSequence, double minSimilarity) Filter the SegmentDataRDD based on minimum sequence similarity to a reference sequence.
static AtomData	findAtoms(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD) Find all the atoms in the RDD.
static AtomData	findAtoms(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD, org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne) Find the given type of atoms for each structure in the PDB.
static AtomContactRDD	findContacts(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD, org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne, org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectTwo, double cutoff) Find the contacts for each structure in the PDB.
static AtomContactRDD	findContacts(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD, org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne, double cutoff) Find the contacts for each structure in the PDB.
static AtomContactRDD	findContacts(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD, double cutoff) Find the contacts for each structure in the PDB.
static org.biojava.nbio.structure.contact.AtomContactSet	getAtomContacts(List<org.biojava.nbio.structure.Atom> atoms, double cutoff) Get all the atom contacts in a list of atoms.
static org.biojava.nbio.structure.contact.AtomContactSet	getAtomContacts(List<org.biojava.nbio.structure.Atom> atomListOne, List<org.biojava.nbio.structure.Atom> atomListTwo, double cutoff) Get the contacts between two lists of atoms
static org.biojava.nbio.structure.contact.AtomContactSet	getAtomContactsSlow(List<org.biojava.nbio.structure.Atom> atomListOne, List<org.biojava.nbio.structure.Atom> atomListTwo, double cutoff) Get the contacts between two lists of atoms using iteration and not grids
static List<org.biojava.nbio.structure.Atom>	getAtoms(org.rcsb.mmtf.api.StructureDataInterface structure) Get all the atoms in the structure using a StructureDataInterface.
static List<org.biojava.nbio.structure.Atom>	getAtoms(org.rcsb.mmtf.api.StructureDataInterface structure, org.rcsb.mmtf.spark.data.AtomSelectObject atomSelectObject) Get all the atoms of a given name or in a given group in the structure using a StructureDataInterface.
static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Structure>	getBiojavaRdd(String filePath) Get an JavaPairRDD of String Structure from a file path.
static org.biojava.nbio.structure.Atom[]	getCaAtoms(org.rcsb.mmtf.spark.data.Segment segment) Gets the C-alpha Atom for the given input Segment.
static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]>	getChainRDD(List<String> pdbIdList) Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.
static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]>	getChainRDD(List<String> pdbIdList, int minLength) Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.
static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]>	getChainRDD(String filePath, int minLength, double sample) Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.
static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]>	getChainRDD(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD, int minLength) Get the JavaPairRDD of Key: PDBID.CHAINID and Value: Atom array of the C-alpha coordinates.
static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Structure>	getFromList(File[] pdbIdList) Generate a JavaPairRDD of String Structure from a list of PDB files.
static String	getGroupAtomName(org.biojava.nbio.structure.Atom atom) Get a conjoined group atom name from an atom.
static org.rcsb.mmtf.spark.data.StructureDataRDD	getStructureRDDFromMmcif(String filePath) Function (for benchmarking) to get a StructureDataRDD from a Hadoop file of mmCIF data.
static String	getTypeFromChainId(org.rcsb.mmtf.api.StructureDataInterface structureDataInterface, int chainInd) Get the type of a given chain index - SHOULD BE MOVED INTO ENCODER UTILS

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

BiojavaSparkUtils

public BiojavaSparkUtils()

Method Detail

getCaAtoms

public static org.biojava.nbio.structure.Atom[] getCaAtoms(org.rcsb.mmtf.spark.data.Segment segment)

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

Parameters:

segment - the input Segment object

Returns:

the C-alpha array of Atom objects

findContacts

public static AtomContactRDD findContacts(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD,
                                          org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne,
                                          org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectTwo,
                                          double cutoff)

Find the contacts for each structure in the PDB.

Parameters:

selectObjectOne - the first type of atoms

selectObjectTwo - the second type of atoms

cutoff - the cutoff distance (max) in Angstrom

Returns:

the JavaPairRDD of AtomContact objects

findContacts

public static AtomContactRDD findContacts(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD,
                                          org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne,
                                          double cutoff)

Find the contacts for each structure in the PDB.

Parameters:

selectObjectOne - the type of atoms

cutoff - the cutoff distance (max) in Angstrom

Returns:

the JavaPairRDD of AtomContact objects

findContacts

public static AtomContactRDD findContacts(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD,
                                          double cutoff)

Find the contacts for each structure in the PDB.

Parameters:

cutoff - the cutoff distance (max) in Angstrom

Returns:

the JavaPairRDD of AtomContact objects

findAtoms

public static AtomData findAtoms(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD,
                                 org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne)

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

Parameters:

selectObjectOne - the type of atom to find

Returns:

the JavaRDD of Atom objects

findAtoms

public static AtomData findAtoms(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD)

Find all the atoms in the RDD.

Returns:

the JavaRDD of Atom objects

getBiojavaRdd

public static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Structure> getBiojavaRdd(String filePath)

Get an JavaPairRDD of String Structure from a file path.

Parameters:

filePath - the input path to the hadoop sequence file

Returns:

the JavaPairRDD of String Structure

getAtoms

public static List<org.biojava.nbio.structure.Atom> getAtoms(org.rcsb.mmtf.api.StructureDataInterface structure,
                                                             org.rcsb.mmtf.spark.data.AtomSelectObject atomSelectObject)

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

Parameters:

structure - the input StructureDataInterface

Returns:

the list of atoms fitting the given criteria

getAtomContacts

public static org.biojava.nbio.structure.contact.AtomContactSet getAtomContacts(List<org.biojava.nbio.structure.Atom> atoms,
                                                                                double cutoff)

Get all the atom contacts in a list of atoms.

Parameters:

atoms - the list of Atoms

cutoff - the cutoff distance

Returns:

the AtomContactSet of the contacts

getAtomContacts

public static org.biojava.nbio.structure.contact.AtomContactSet getAtomContacts(List<org.biojava.nbio.structure.Atom> atomListOne,
                                                                                List<org.biojava.nbio.structure.Atom> atomListTwo,
                                                                                double cutoff)

Get the contacts between two lists of atoms

Parameters:

atomListOne - the first list of Atoms

atomListTwo - the second list of Atoms

cutoff - the cutoff to define a contact

Returns:

the AtomContactSet of the contacts

getAtomContactsSlow

public static org.biojava.nbio.structure.contact.AtomContactSet getAtomContactsSlow(List<org.biojava.nbio.structure.Atom> atomListOne,
                                                                                    List<org.biojava.nbio.structure.Atom> atomListTwo,
                                                                                    double cutoff)

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

Parameters:

atomListOne - the first list of Atoms

atomListTwo - the second list of Atoms

cutoff - the cutoff to define a contact

Returns:

the AtomContactSet of the contacts

getChainRDD

public static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]> getChainRDD(List<String> pdbIdList,
                                                                                                          int minLength)
                                                                                                   throws IOException

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

Parameters:

pdbIdList - the input list of PDB ids

minLength - the minimum length of each chain

Returns:

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

Throws:

IOException - due to an error reading the input file

getChainRDD

public static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]> getChainRDD(String filePath,
                                                                                                          int minLength,
                                                                                                          double sample)
                                                                                                   throws IOException

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

Parameters:

filePath - the Haddoop file to read from

minLength - the minimum length of each chain

sample - the sample of this file to take

Returns:

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

Throws:

IOException - due to an error reading the input file

getChainRDD

public static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]> getChainRDD(List<String> pdbIdList)
                                                                                                   throws IOException

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

Parameters:

pdbIdList - the input list of PDB ids

Returns:

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

Throws:

IOException - due to an error reading the input file

getChainRDD

public static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Atom[]> getChainRDD(org.rcsb.mmtf.spark.data.StructureDataRDD structureDataRDD,
                                                                                                          int minLength)
                                                                                                   throws IOException

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

Parameters:

structureDataRDD - the input StructureDataRDD

minLength - the minimum length of each chain

Returns:

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

Throws:

IOException - due to an error reading the input file

getAtoms

public static List<org.biojava.nbio.structure.Atom> getAtoms(org.rcsb.mmtf.api.StructureDataInterface structure)

Get all the atoms in the structure using a StructureDataInterface.

Parameters:

structure - the input StructureDataInterface

Returns:

the list of atoms

filterSequenceSimilar

public static org.rcsb.mmtf.spark.data.SegmentDataRDD filterSequenceSimilar(org.rcsb.mmtf.spark.data.SegmentDataRDD segmentDataRDD,
                                                                            String inputSequence,
                                                                            double minSimilarity)
                                                                     throws org.biojava.nbio.core.exceptions.CompoundNotFoundException

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

Parameters:

inputSequence - the reference sequence to compare

minSimilarity - the minimum similarity (as a double between 0.00 and 1.00)

Returns:

the SegmentDataRDD after being filtered

Throws:

org.biojava.nbio.core.exceptions.CompoundNotFoundException - if Biojava cannot accurately convert the String sequence to a ProteinSequence

getGroupAtomName

public static String getGroupAtomName(org.biojava.nbio.structure.Atom atom)

Get a conjoined group atom name from an atom.

Parameters:

atom - the input atom

Returns:

the String describing the conjoined group atom name.

getStructureRDDFromMmcif

public static org.rcsb.mmtf.spark.data.StructureDataRDD getStructureRDDFromMmcif(String filePath)

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

Parameters:

filePath - the path of the Hadoop sequnece file

Returns:

the StructureDataRDD generated

convertToStructDataInt

public static org.rcsb.mmtf.api.StructureDataInterface convertToStructDataInt(org.biojava.nbio.structure.Structure structure)

Get a StructureDataInterface from a Biojava Structure.

Parameters:

structure - the input structure to covnert

Returns:

the StructureDataInterface of the Biojava Structure

getFromList

public static org.apache.spark.api.java.JavaPairRDD<String,org.biojava.nbio.structure.Structure> getFromList(File[] pdbIdList)

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

Parameters:

pdbIdList - the input list of PDB files

Returns:

the JavaPairRDD of String Structure

getTypeFromChainId

public static String getTypeFromChainId(org.rcsb.mmtf.api.StructureDataInterface structureDataInterface,
                                        int chainInd)

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

Parameters:

structureDataInterface - the input StructureDataInterface

chainInd - the index of the relevant chain

Returns:

the String describing the chain