Package org.rcsb.mmtf.spark.data

Class StructureDataRDD

java.lang.Object

org.rcsb.mmtf.spark.data.StructureDataRDD

public class StructureDataRDD
extends java.lang.Object

A class to provide functions on a series of StructureDataInterface objects.

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor	Description
StructureDataRDD()	Empty constructor reads the sample data if SparkUtils has not been set with a path.
StructureDataRDD(java.lang.String inputPath)	Constructor from a file.
StructureDataRDD(java.lang.String[] pdbIdArray)	Construtor from an array of PDB ids.
StructureDataRDD(java.util.List<java.lang.String> pdbIdList)	Constructor from a list of PDB ids.
StructureDataRDD(org.apache.spark.api.java.JavaPairRDD<java.lang.String,org.rcsb.mmtf.api.StructureDataInterface> javaPairRDD)	Constructor from a JavaPairRDD of String and StructureDataInterface.

Method Summary

Modifier and Type	Method	Description
StructureDataRDD	cache()	Cache the underlying RDD.
StructureDataRDD	filterResolution(double maxRes)	Filter the StructureDataRDD based on resolution.
StructureDataRDD	filterResolution(double maxRes, double minRes)	Filter the StructureDataRDD based on resolution.
StructureDataRDD	filterRfree(double maxRFree)	Filter the StructureDataRDD based on R-free.
StructureDataRDD	filterRfree(double maxRFree, double minRFree)	Filter the StructureDataRDD based on R-free.
AtomDataset	getAtoms()	Get the atoms in the StructureDataRDD as an AtomDataset.
SegmentDataRDD	getCalpha()	Get the Point3d of the C-alpha co-ordinate data as lightweight point 3d objects.
SegmentDataRDD	getFragments(int fragSize)	Get the Point3d of the C-alpha co-ordinate data as lightweight point 3d objects.
org.apache.spark.api.java.JavaPairRDD<java.lang.String,org.rcsb.mmtf.api.StructureDataInterface>	getJavaRdd()	Get the JavaPairRDD of String StructureDataInterface for this instance
StructureDataRDD	getReduced()	Covert the StructureDataRDD to the reduced format.
StructureDataRDD	sample(double fraction)	Allow the user to sample the data.
void	saveToFile(java.lang.String filePath)	Save the data as a Hadoop sequence file.
java.lang.Long	size()	Get the number of entries in the RDD.

Methods inherited from class java.lang.Object

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

Constructor Detail

StructureDataRDD

public StructureDataRDD()

Empty constructor reads the sample data if SparkUtils has not been set with a path.

StructureDataRDD

public StructureDataRDD(java.lang.String inputPath)

Constructor from a file.

Parameters:

inputPath - the input path of the Hadoop sequence file to read

StructureDataRDD

public StructureDataRDD(org.apache.spark.api.java.JavaPairRDD<java.lang.String,org.rcsb.mmtf.api.StructureDataInterface> javaPairRDD)

Constructor from a JavaPairRDD of String and StructureDataInterface.

Parameters:

javaPairRDD - the input JavaPairRDD of String StructureDataInterface

StructureDataRDD

public StructureDataRDD(java.util.List<java.lang.String> pdbIdList)
                 throws java.io.IOException

Constructor from a list of PDB ids.

Parameters:

pdbIdList - the input list of PDB ids

Throws:

java.io.IOException - due to reading from the URL

StructureDataRDD

public StructureDataRDD(java.lang.String[] pdbIdArray)
                 throws java.io.IOException

Construtor from an array of PDB ids.

Parameters:

pdbIdArray - the input array of PDB ids

Throws:

java.io.IOException - due to reading from the URL

Method Detail

getJavaRdd

public org.apache.spark.api.java.JavaPairRDD<java.lang.String,org.rcsb.mmtf.api.StructureDataInterface> getJavaRdd()

Get the JavaPairRDD of String StructureDataInterface for this instance

Returns:

the JavaPairRDD of String StructureDataInterface

filterRfree

public StructureDataRDD filterRfree(double maxRFree)

Filter the StructureDataRDD based on R-free.

Parameters:

maxRFree - the maximum allowed R-free

Returns:

the filtered StructureDataRDD

filterRfree

public StructureDataRDD filterRfree(double maxRFree,
                                    double minRFree)

Filter the StructureDataRDD based on R-free.

Parameters:

maxRFree - the maximum allowed R-free

minRFree - the minimum allowed R-free

Returns:

the filtered StructureDataRDD

filterResolution

public StructureDataRDD filterResolution(double maxRes)

Filter the StructureDataRDD based on resolution.

Parameters:

maxRes - the maximum allowed resolution (in Angstrom)

Returns:

the filtered StructureDataRDD

filterResolution

public StructureDataRDD filterResolution(double maxRes,
                                         double minRes)

Filter the StructureDataRDD based on resolution.

Parameters:

maxRes - the maximum allowed resolution (in Angstrom)

minRes - the minimum allowed resolution (in Angstrom)

Returns:

the filtered StructureDataRDD

getCalpha

public SegmentDataRDD getCalpha()

Get the Point3d of the C-alpha co-ordinate data as lightweight point 3d objects.

Returns:

the segment data array

getReduced

public StructureDataRDD getReduced()

Covert the StructureDataRDD to the reduced format.

Returns:

the StructureDataRDD of the reduced format

getFragments

public SegmentDataRDD getFragments(int fragSize)

Get the Point3d of the C-alpha co-ordinate data as lightweight point 3d objects. Fragmented based on size. The fragments are continuous and overlapping.

Parameters:

fragSize - the size of every fragment

Returns:

the fragments as an RDD

getAtoms

public AtomDataset getAtoms()

Get the atoms in the StructureDataRDD as an AtomDataset.

Returns:

the AtomDataset generated.

size

public java.lang.Long size()

Get the number of entries in the RDD.

Returns:

the Long number of entries

saveToFile

public void saveToFile(java.lang.String filePath)

Save the data as a Hadoop sequence file.

Parameters:

filePath - the path to save the data to

sample

public StructureDataRDD sample(double fraction)

Allow the user to sample the data.

Parameters:

fraction - the fraction of data to be used (e.g. 0.1 retains 10%)

Returns:

the SegmentDataRDD updated

cache

public StructureDataRDD cache()

Cache the underlying RDD.

Returns:

the cached StructureDataRDD