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:

Jose Duarte

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field	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	Description
StructureInterfaceList()

Method Summary

Modifier and Type	Method	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
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:

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

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 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: