Package org.biojava.nbio.structure.contact

Class AtomContactSet

java.lang.Object

org.biojava.nbio.structure.contact.AtomContactSet

All Implemented Interfaces:

Serializable, Iterable<AtomContact>

public class AtomContactSet
extends Object
implements Serializable, Iterable<AtomContact>

A set of atom-atom contacts to hold the results of intra and inter-chain contact calculations

Author:

duarte_j

See Also:

• Serialized Form

Constructor Summary

Constructors

Constructor	Description
AtomContactSet(double cutoff)

Method Summary

Modifier and Type	Method	Description
void	add(AtomContact contact)
void	addAll(Collection<AtomContact> list)
AtomContact	getContact(Atom atom1, Atom atom2)	Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms
List<AtomContact>	getContactsWithinDistance(double distance)	Returns the list of contacts from this set that are within the given distance.
boolean	hasContact(Atom atom1, Atom atom2)
boolean	hasContact(AtomIdentifier atomId1, AtomIdentifier atomId2)
boolean	hasContactsWithinDistance(double distance)	Returns true if at least 1 contact from this set is within the given distance.
Iterator<AtomContact>	iterator()
int	size()

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Details

AtomContactSet

public AtomContactSet(double cutoff)

Method Details

add

public void add(AtomContact contact)

addAll

public void addAll(Collection<AtomContact> list)

hasContact

public boolean hasContact(Atom atom1,
 Atom atom2)

hasContact

public boolean hasContact(AtomIdentifier atomId1,
 AtomIdentifier atomId2)

getContact

public AtomContact getContact(Atom atom1,
 Atom atom2)

Returns the corresponding AtomContact or null if no contact exists between the 2 given atoms

Parameters:

atom1 -

atom2 -

Returns:

size

public int size()

iterator

public Iterator<AtomContact> iterator()

Specified by:

iterator in interface Iterable<AtomContact>

hasContactsWithinDistance

public boolean hasContactsWithinDistance(double distance)

Returns true if at least 1 contact from this set is within the given distance. Note that if the distance given is larger than the distance cutoff used to calculate the contacts then nothing will be found.

Parameters:

distance -

Returns:

Throws:

IllegalArgumentException - if given distance is larger than distance cutoff used for calculation of contacts

getContactsWithinDistance

public List<AtomContact> getContactsWithinDistance(double distance)

Returns the list of contacts from this set that are within the given distance.

Parameters:

distance -

Returns:

Throws:

IllegalArgumentException - if given distance is larger than distance cutoff used for calculation of contacts