StructureInterfaceList (biojava 5.3.0 API)

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:

Jose Duarte

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`DEFAULT_ASA_SPHERE_POINTS` Default number of points to use when calculating ASAs
`static double`	`DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF` Any 2 interfaces with contact overlap score larger than this value will be considered to be clustered
`static int`	`DEFAULT_MIN_COFACTOR_SIZE` Default minimum size of cofactor molecule (non-chain HET atoms) that will be used
`static double`	`DEFAULT_MINIMUM_INTERFACE_AREA` Default minimum area for a contact between two chains to be considered a valid interface.

Constructor Summary

Constructors
Constructor and Description

StructureInterfaceList()

Constructors
Constructor and Description
`StructureInterfaceList()`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add(StructureInterface interf)`
`void`	`addNcsEquivalent(StructureInterface interfaceNew, StructureInterface interfaceRef)` Add an interface to the list, possibly defining it as NCS-equivalent to an interface already in the list.
`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.
`List<StructureInterfaceCluster>`	`getClusters()` Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
`List<StructureInterfaceCluster>`	`getClusters(double contactOverlapScoreClusterCutoff)` Calculate the interface clusters for this StructureInterfaceList using a contact overlap score to measure the similarity of interfaces.
`List<StructureInterfaceCluster>`	`getClustersNcs()` Get the interface clusters for this StructureInterfaceList grouped by NCS-equivalence.
`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.
`void`	`setChainOrigNamesMap(Map<String,String> chainOrigNamesMap)` Sets a map with mapping from NCS chain names to original chain names.
`int`	`size()`
`void`	`sort()` Sorts the interface list and reassigns ids based on new sorting
`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:
    
    removeInterfacesBelowArea(double);, Constant Field Values
  - DEFAULT_ASA_SPHERE_POINTS
```
public static final int DEFAULT_ASA_SPHERE_POINTS
```
    Default number of points to use when calculating ASAs
    
    See Also:
    
    calcAsas(int, int, int), Constant Field Values
  - 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:
    
    calcAsas(int, int, int), 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
  - 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
  - getClustersNcs
```
public List<StructureInterfaceCluster> getClustersNcs()
```
    Get the interface clusters for this StructureInterfaceList grouped by NCS-equivalence. This means that for any two interfaces in the same cluster: 1. The chains forming the first interface are NCS-copies of the chains forming the second interface, in any order. 2. Relative orientation of the chains is preserved, i.e. the contacts are identical.
    
    Returns:
    
    list of StructureInterfaceCluster objects.
    
    Since:
    
    5.0.0
  - addNcsEquivalent
```
public void addNcsEquivalent(StructureInterface interfaceNew,
                             StructureInterface interfaceRef)
```
    Add an interface to the list, possibly defining it as NCS-equivalent to an interface already in the list. Used to build up the NCS clustering.
    
    Parameters:
    
    interfaceNew - an interface to be added to the list.
    
    interfaceRef - interfaceNew will be added to the cluster which contains interfaceRef. If interfaceRef is null, new cluster will be created for interfaceNew.
    
    Since:
    
    5.0.0
  - setChainOrigNamesMap
```
public void setChainOrigNamesMap(Map<String,String> chainOrigNamesMap)
```
    Sets a map with mapping from NCS chain names to original chain names. Necessary when addNcsEquivalent(StructureInterface, StructureInterface) is used and NCS equivalent interfaces exist in this list and their names need mapping when setting ASAs.
    
    Parameters:
    
    chainOrigNamesMap - a map of NCS chain name to original chain name
  - removeInterfacesBelowArea
```
public void removeInterfacesBelowArea()
```
    Removes from this interface list all interfaces with areas below the default cutoff area. Note that this must be called after calcAsas(int, int, int), otherwise all areas would be 0 and thus all removed.
    
    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. Note that this must be called after calcAsas(int, int, int), otherwise all areas would be 0 and thus all removed.
    
    Parameters:
    
    area - the minimum interface buried surface area to keep. Interfaces below this value will be removed.
  - 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. The clusters will be assigned ids by sorting descending by StructureInterfaceCluster.getTotalArea()
    
    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:

Class StructureInterfaceList

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Field Detail

DEFAULT_MINIMUM_INTERFACE_AREA

DEFAULT_ASA_SPHERE_POINTS

DEFAULT_MIN_COFACTOR_SIZE

DEFAULT_CONTACT_OVERLAP_SCORE_CLUSTER_CUTOFF

Constructor Detail

StructureInterfaceList

Method Detail

add

size

get

calcAsas

calcAsas

sort

getClustersNcs

addNcsEquivalent

setChainOrigNamesMap

removeInterfacesBelowArea

removeInterfacesBelowArea

getClusters

getClusters

iterator

toString

calculateInterfaces