Package 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:

  • Constructor Summary

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

  • Method Summary

    Modifier and Type
    Method
    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(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(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(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

    Methods inherited from interface java.lang.Iterable

    forEach, spliterator

  • Constructor Details

    • 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 Details

    • 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>