org.biojava.spark.data

Class AtomContactRDD

java.lang.Object

org.biojava.spark.data.AtomContactRDD

All Implemented Interfaces:

Serializable

public class AtomContactRDD
extends Object
implements Serializable

Class to hold AtomContact data in an JavaRDD

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
AtomContactRDD(org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.contact.AtomContact> atomContactRdd) Construct an AtomContactRDD from a JavaRDD AtomContact.

Method Summary

Modifier and Type	Method and Description
void	cacheData() Cache the data - for multi-processing.
Long	countInterAtomContacts(String atomNameOne, String atomNameTwo) Get the number of inter-atom name contacts for a given pair of atoms names.
Long	countInterElementContacts(String elementOne, String elementTwo) Get the number of inter-element contacts for a given pair of element names.
Long	countInterGroupContacts(String groupNameOne, String groupNameTwo) Get the number of inter-group contacts for a given pair of group names.
AtomContactRDD	filterDistance(double cutoff) Filter all contacts greater than a certain distance.
AtomContactRDD	filterElementElementContacts(String elementNameOne, String elementNameTwo) Filter an AtomContactRDD based on two elements being in contact.
AtomContactRDD	filterElementGroupContacts(String groupName, String elementName) Filter an AtomContactRDD based on two elements being in contact.
Map<String,Long>	getAllInterAtomElementContacts() Get a map counting the number of interactions between atom element names.
Map<String,Long>	getAllInterAtomNameContacts() Get a map counting the number of interactions between atom names.
Map<String,Long>	getAllInterGroupContacts() Get a map counting the number of interactions between groups.
org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.contact.AtomContact>	getAtomContactRDD() Get the JavaRDD of AtomContact objects.
AtomData	getAtoms() Get the contacts as an AtomDataRDD
org.apache.spark.api.java.JavaDoubleRDD	getDistanceDistOfAtomInts(String atomName, String otherAtomName) Get the distance distributions for all of the atom types.
List<String>	getGroupIds() Get the associate group ids
org.apache.spark.api.java.JavaPairRDD<org.biojava.nbio.structure.Atom,org.biojava.nbio.structure.Atom>	getPairs() Get the assoicated pairs of atoms found in this
List<String>	getPdbIds() Get the associated PDB ids as a list of Strings

Methods inherited from class java.lang.Object

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

Constructor Detail

AtomContactRDD

public AtomContactRDD(org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.contact.AtomContact> atomContactRdd)

Construct an AtomContactRDD from a JavaRDD AtomContact.

Parameters:

atomContactRdd - the input JavaRDD of AtomContact

Method Detail

cacheData

public void cacheData()

Cache the data - for multi-processing.

getAtomContactRDD

public org.apache.spark.api.java.JavaRDD<org.biojava.nbio.structure.contact.AtomContact> getAtomContactRDD()

Get the JavaRDD of AtomContact objects.

Returns:

the JavaRDD of AtomContact objects

filterDistance

public AtomContactRDD filterDistance(double cutoff)

Filter all contacts greater than a certain distance.

Returns:

the AtomContactRDD after filtering

getDistanceDistOfAtomInts

public org.apache.spark.api.java.JavaDoubleRDD getDistanceDistOfAtomInts(String atomName,
                                                                         String otherAtomName)

Get the distance distributions for all of the atom types.

Parameters:

atomName - the original atom name

otherAtomName - the other atom name

Returns:

the map of atom contact types and the distances

getAllInterGroupContacts

public Map<String,Long> getAllInterGroupContacts()

Get a map counting the number of interactions between groups. e.g. "LYS_PRO" is the number of lysine-proline interactions.

Returns:

a map of strings to counts of interactions

countInterGroupContacts

public Long countInterGroupContacts(String groupNameOne,
                                    String groupNameTwo)

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

Parameters:

groupNameOne - the name of the first groups

groupNameTwo - the name of the second group

Returns:

the number of contacts between these two groups

countInterElementContacts

public Long countInterElementContacts(String elementOne,
                                      String elementTwo)

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

Parameters:

elementOne - the name of the first element (e.g. Ca for Calcium)

elementTwo - the name of the second element (e.g. Ca for Calcium)

Returns:

the number of contacts between these two groups

countInterAtomContacts

public Long countInterAtomContacts(String atomNameOne,
                                   String atomNameTwo)

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

Parameters:

atomNameOne - the name of the first atom name (e.g. CA for C-alpha)

atomNameTwo - the name of the second atom name (e.g. CA for C-alpha)

Returns:

the number of contacts between these two groups

getAllInterAtomNameContacts

public Map<String,Long> getAllInterAtomNameContacts()

Get a map counting the number of interactions between atom names. e.g. "CA_CA" is the C-alpha to C-alpha (and Calcium to calcium) interactions.

Returns:

a map of strings to counts of interactions

getAllInterAtomElementContacts

public Map<String,Long> getAllInterAtomElementContacts()

Get a map counting the number of interactions between atom element names. e.g. "C_N" is the C to N interactions.

Returns:

a map of strings to counts of interactions

filterElementGroupContacts

public AtomContactRDD filterElementGroupContacts(String groupName,
                                                 String elementName)

Filter an AtomContactRDD based on two elements being in contact.

Parameters:

groupName - the group name, e.g. HIS for histidine

elementName - the element name (IUPAC) e.g. Ca for calcium

Returns:

the filtered AtomContactRDD

filterElementElementContacts

public AtomContactRDD filterElementElementContacts(String elementNameOne,
                                                   String elementNameTwo)

Filter an AtomContactRDD based on two elements being in contact.

Parameters:

elementNameOne - the second element name (IUPAC) e.g. Ca for calcium

elementNameOne - the second element name (IUPAC) e.g. Ca for calcium

Returns:

the filtered AtomContactRDD

getPdbIds

public List<String> getPdbIds()

Get the associated PDB ids as a list of Strings

Returns:

a list of PDB ids for related entries

getGroupIds

public List<String> getGroupIds()

Get the associate group ids

Returns:

the list of assicated group ids

getPairs

public org.apache.spark.api.java.JavaPairRDD<org.biojava.nbio.structure.Atom,org.biojava.nbio.structure.Atom> getPairs()

Get the assoicated pairs of atoms found in this

Returns:

the pairs of atoms as an RDD

getAtoms

public AtomData getAtoms()

Get the contacts as an AtomDataRDD

Returns:

an AtomDataRDD of all the atoms found in these contacts