Class GroupContactSet

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Iterable<GroupContact>

    public class GroupContactSet
    extends java.lang.Object
    implements java.io.Serializable, java.lang.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 Description
      GroupContactSet()  
      GroupContactSet​(AtomContactSet atomContacts)
      Constructs a GroupContactSet by collapsing the given AtomContactSet into residue-residue (group-group) contacts.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      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
      java.util.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 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

      • 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 java.util.Iterator<GroupContact> iterator()
        Specified by:
        iterator in interface java.lang.Iterable<GroupContact>