org.biojava.nbio.structure.contact

Class GroupContactSet

java.lang.Object

org.biojava.nbio.structure.contact.GroupContactSet

All Implemented Interfaces:

Serializable, Iterable<GroupContact>

public class GroupContactSet
extends Object
implements Serializable, Iterable<GroupContact>

A set of residue-residue contacts. Relies on residue indices (based on SEQRES and starting with 1) to store the pairs and thus to match contacts.

Author:

duarte_j

See Also:

ResidueIdentifier, Serialized Form

Constructor Summary

Constructors

Constructor and Description
GroupContactSet()
GroupContactSet(AtomContactSet atomContacts) Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.

Method Summary

Methods

Modifier and Type	Method and Description
void	add(GroupContact groupContact)
GroupContact	getContact(Group group1, Group group2) Returns the corresponding GroupContact or null if no contact exists between the 2 given groups
boolean	hasContact(Group group1, Group group2) Tell whether the given group pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
boolean	hasContact(org.biojava.nbio.structure.contact.ResidueIdentifier resId1, org.biojava.nbio.structure.contact.ResidueIdentifier resId2) Tell whether the given pair is a contact in this GroupContactSet, in a chain-identifier independent way: contacts happening between different copies of the same Compound(Entity) will be considered equal as long as they have the same residue numbers.
boolean	hasContact(ResidueNumber resNumber1, ResidueNumber resNumber2) Tell whether the given pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers
Iterator<GroupContact>	iterator()
int	size()

Methods inherited from class java.lang.Object

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

Constructor Detail

GroupContactSet

public GroupContactSet()

GroupContactSet

public GroupContactSet(AtomContactSet atomContacts)

Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.

Parameters:

atomContacts -

Method Detail

add

public void add(GroupContact groupContact)

hasContact

public boolean hasContact(Group group1,
                 Group group2)

Tell whether the given group pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers

Parameters:

group1 -

group2 -

Returns:

hasContact

public boolean hasContact(ResidueNumber resNumber1,
                 ResidueNumber resNumber2)

Tell whether the given pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers

Parameters:

resNumber1 -

resNumber2 -

Returns:

hasContact

public boolean hasContact(org.biojava.nbio.structure.contact.ResidueIdentifier resId1,
                 org.biojava.nbio.structure.contact.ResidueIdentifier resId2)

Tell whether the given pair is a contact in this GroupContactSet, in a chain-identifier independent way: contacts happening between different copies of the same Compound(Entity) will be considered equal as long as they have the same residue numbers.

Parameters:

resId1 -

resId2 -

Returns:

getContact

public GroupContact getContact(Group group1,
                      Group group2)

Returns the corresponding GroupContact or null if no contact exists between the 2 given groups

Parameters:

group1 -

group2 -

Returns:

size

public int size()

iterator

public Iterator<GroupContact> iterator()

Specified by:

iterator in interface Iterable<GroupContact>