Package org.biojava.nbio.structure.contact

Class StructureInterfaceList

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Iterable<StructureInterface>
    public class StructureInterfaceList
extends java.lang.Object
implements java.io.Serializable, java.lang.Iterable<StructureInterface>
    A list of interfaces between 2 molecules (2 sets of atoms)
    Author:
    duarte_j
    See Also:
    Serialized Form

    • Method Summary

      All Methods Static Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      void add​(StructureInterface interf)  
      void calcAsas()
      Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
      void calcAsas​(int nSpherePoints, int nThreads, int cofactorSizeToUse)
      Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together.
      static StructureInterfaceList calculateInterfaces​(Structure struc)
      Calculates the interfaces for a structure using default parameters
      StructureInterface get​(int id)
      Gets the interface corresponding to given id.
      java.util.List<StructureInterfaceCluster> getClusters()
      Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
      java.util.List<StructureInterfaceCluster> getClusters​(double contactOverlapScoreClusterCutoff)
      Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
      java.util.Iterator<StructureInterface> iterator()  
      void removeInterfacesBelowArea()
      Removes from this interface list all interfaces with areas below the default cutoff area
      void removeInterfacesBelowArea​(double area)
      Removes from this interface list all interfaces with areas below the given cutoff area
      int size()  
      void sort()
      Sorts the interface list and reassigns ids based on new sorting
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

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

      • Methods inherited from interface java.lang.Iterable

        forEach, spliterator

    • Field Detail

      • DEFAULT_MINIMUM_INTERFACE_AREA

        public static final double DEFAULT_MINIMUM_INTERFACE_AREA
        Default minimum area for a contact between two chains to be considered a valid interface.
        See Also:
        Constant Field Values

      • DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF

        public static final double DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF
        Any 2 interfaces with contact overlap score larger than this value will be considered to be clustered
        See Also:
        Constant Field Values

    • Constructor Detail

      • StructureInterfaceList

        public StructureInterfaceList()

    • Method Detail

      • size

        public int size()

      • get

        public StructureInterface get​(int id)
        Gets the interface corresponding to given id. The ids go from 1 to n If sort() was called then the order is descendent by area.
        Parameters:
        id -
        Returns:

      • calcAsas

        public void calcAsas()
        Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together. Also sorts the interfaces based on calculated BSA areas (descending).

        Uses default parameters

      • calcAsas

        public void calcAsas​(int nSpherePoints,
                     int nThreads,
                     int cofactorSizeToUse)
        Calculates ASAs for all interfaces in list, both for the unbound chains and for the complex of the two chains together. Also sorts the interfaces based on calculated BSA areas (descending)
        Parameters:
        nSpherePoints -
        nThreads -
        cofactorSizeToUse - the minimum size of cofactor molecule (non-chain HET atoms) that will be used

      • sort

        public void sort()
        Sorts the interface list and reassigns ids based on new sorting

      • removeInterfacesBelowArea

        public void removeInterfacesBelowArea()
        Removes from this interface list all interfaces with areas below the default cutoff area
        See Also:
        DEFAULT_MINIMUM_INTERFACE_AREA

      • removeInterfacesBelowArea

        public void removeInterfacesBelowArea​(double area)
        Removes from this interface list all interfaces with areas below the given cutoff area
        Parameters:
        area -

      • getClusters

        public java.util.List<StructureInterfaceCluster> getClusters()
        Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces. Subsequent calls will use the cached value without recomputing the clusters. The contact overlap score cutoff to consider a pair in the same cluster is the value DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF
        Returns:

      • getClusters

        public java.util.List<StructureInterfaceCluster> getClusters​(double contactOverlapScoreClusterCutoff)
        Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces. Subsequent calls will use the cached value without recomputing the clusters.
        Parameters:
        contactOverlapScoreClusterCutoff - the contact overlap score above which a pair will be clustered
        Returns:

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object

      • calculateInterfaces

        public static StructureInterfaceList calculateInterfaces​(Structure struc)
        Calculates the interfaces for a structure using default parameters
        Parameters:
        struc -
        Returns: