Package org.biojava.nbio.structure.contact

Class StructureInterfaceList

java.lang.Object
org.biojava.nbio.structure.contact.StructureInterfaceList
All Implemented Interfaces:
Serializable, Iterable<StructureInterface>
public class StructureInterfaceList extends Object implements Serializable, Iterable<StructureInterface>
A list of interfaces between 2 molecules (2 sets of atoms)
Author:
duarte_j
See Also:

  • Field Details

    • 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:

    • DEFAULT_ASA_SPHERE_POINTS

      public static final int DEFAULT_ASA_SPHERE_POINTS
      Default number of points to use when calculating ASAs
      See Also:

    • DEFAULT_MIN_COFACTOR_SIZE

      public static final int DEFAULT_MIN_COFACTOR_SIZE
      Default minimum size of cofactor molecule (non-chain HET atoms) that will be used
      See Also:

    • 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:

  • Constructor Details

    • StructureInterfaceList

      public StructureInterfaceList()

  • Method Details

    • add

      public void add(StructureInterface interf)

    • 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:

    • removeInterfacesBelowArea

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

    • getClusters

      public 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 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:

    • iterator

      public Iterator<StructureInterface> iterator()
      Specified by:
      iterator in interface Iterable<StructureInterface>

    • toString

      public String toString()
      Overrides:
      toString in class Object

    • calculateInterfaces

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