org.biojava.spark.mappers

Class CalculateContacts

java.lang.Object

org.biojava.spark.mappers.CalculateContacts

All Implemented Interfaces:

Serializable, org.apache.spark.api.java.function.FlatMapFunction<scala.Tuple2<String,org.rcsb.mmtf.api.StructureDataInterface>,org.biojava.nbio.structure.contact.AtomContact>

public class CalculateContacts
extends Object
implements org.apache.spark.api.java.function.FlatMapFunction<scala.Tuple2<String,org.rcsb.mmtf.api.StructureDataInterface>,org.biojava.nbio.structure.contact.AtomContact>

Class to calculate all interatomic distances between charged atoms. Tuple2StringStructureDataInterface is the entry type. String is the return type. Flatmap means that the return from call must be an interable of String and Float (stored in Tuple2). String and Float can be changed to any type (including custom data objects).

Author:

Anthony Bradley

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
CalculateContacts(org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne, org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectTwo, double cutoff)
CalculateContacts(org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne, org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectTwo, double cutoff, boolean fast)

Method Summary

Modifier and Type	Method and Description
Iterator<org.biojava.nbio.structure.contact.AtomContact>	call(scala.Tuple2<String,org.rcsb.mmtf.api.StructureDataInterface> t)

Methods inherited from class java.lang.Object

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

Constructor Detail

CalculateContacts

public CalculateContacts(org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne,
                         org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectTwo,
                         double cutoff)

Parameters:

selectObjectOne -

selectObjectTwo -

cutoff -

CalculateContacts

public CalculateContacts(org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectOne,
                         org.rcsb.mmtf.spark.data.AtomSelectObject selectObjectTwo,
                         double cutoff,
                         boolean fast)

Parameters:

selectObjectOne -

selectObjectTwo -

cutoff -

fast -

Method Detail

call

public Iterator<org.biojava.nbio.structure.contact.AtomContact> call(scala.Tuple2<String,org.rcsb.mmtf.api.StructureDataInterface> t)
                                                              throws Exception

Specified by:

call in interface org.apache.spark.api.java.function.FlatMapFunction<scala.Tuple2<String,org.rcsb.mmtf.api.StructureDataInterface>,org.biojava.nbio.structure.contact.AtomContact>

Throws:

Exception