Package org.biojava.nbio.structure.contact

Class StructureInterface

java.lang.Object

org.biojava.nbio.structure.contact.StructureInterface

All Implemented Interfaces:

Serializable, Comparable<StructureInterface>

public class StructureInterface
extends Object
implements Serializable, Comparable<StructureInterface>

An interface between 2 molecules (2 sets of atoms).

Author:

duarte_j

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor	Description
StructureInterface()	Constructs an empty StructureInterface
StructureInterface(Atom[] firstMolecule, Atom[] secondMolecule, String firstMoleculeId, String secondMoleculeId, AtomContactSet contacts, CrystalTransform firstTransf, CrystalTransform secondTransf)	Constructs a StructureInterface

Method Summary

Modifier and Type	Method	Description
int	compareTo(StructureInterface o)
protected Atom[]	getAtomsForAsa(int cofactorSizeToUse)
StructureInterfaceCluster	getCluster()
double	getContactOverlapScore(StructureInterface other, boolean invert)	Calculates the Jaccard contact set score (intersection over union) between this StructureInterface and the given one.
AtomContactSet	getContacts()
Pair<List<Group>>	getCoreResidues(double bsaToAsaCutoff, double minAsaForSurface)	Returns the residues belonging to the interface core, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff
Pair<String>	getCrystalIds()	Returns a pair of identifiers for each of the 2 member molecules that identify them uniquely in the crystal: <molecule id (asym unit id)>+<operator id>+<crystal translation>
protected Atom[]	getFirstAtomsForAsa(int cofactorSizeToUse)
GroupAsa	getFirstGroupAsa(ResidueNumber resNum)	Gets the GroupAsa for the corresponding residue number of first chain
Map<ResidueNumber,GroupAsa>	getFirstGroupAsas()	Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.
GroupContactSet	getGroupContacts()
int	getId()
Pair<List<Group>>	getInterfacingResidues(double minAsaForSurface)	Returns the residues belonging to the interface, i.e. the residues at the surface with BSA>0
Pair<String>	getMoleculeIds()	Return the pair of identifiers identifying each of the 2 molecules of this interface in the asymmetry unit (usually the chain identifier if this interface is between 2 chains)
Pair<Atom[]>	getMolecules()
Pair<Chain>	getParentChains()	Finds the parent chains by looking up the references of first atom of each side of this interface
Pair<EntityInfo>	getParentCompounds()	Finds the parent entities by looking up the references of first atom of each side of this interface
Pair<List<Group>>	getRimResidues(double bsaToAsaCutoff, double minAsaForSurface)	Returns the residues belonging to the interface rim, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff
protected Atom[]	getSecondAtomsForAsa(int cofactorSizeToUse)
GroupAsa	getSecondGroupAsa(ResidueNumber resNum)	Gets the GroupAsa for the corresponding residue number of second chain
Map<ResidueNumber,GroupAsa>	getSecondGroupAsas()	Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.
Pair<List<Group>>	getSurfaceResidues(double minAsaForSurface)	Returns the residues belonging to the surface
double	getTotalArea()	Returns the total area buried upon formation of this interface, defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:
Pair<CrystalTransform>	getTransforms()	Return the 2 crystal transform operations performed on each of the molecules of this interface.
boolean	isHomomeric()	Returns true if the 2 molecules of this interface are the same entity (i.e. homomeric interface), false otherwise (i.e. heteromeric interface)
boolean	isInfinite()	Returns true if the transformation applied to the second molecule of this interface has an infinite character (pure translation or screw rotation) and both molecules of the interface have the same asymmetric unit identifier (chain id): in such cases the interface would lead to infinite fiber-like (linear or helical) assemblies
boolean	isIsologous()	Tell whether the interface is isologous, i.e. it is formed by the same patches of same entity on both sides.
boolean	isSymRelated()	Tells whether the interface corresponds to one mediated by crystallographic symmetry, i.e. it is between symmetry-related molecules (with same chain identifier)
void	setCluster(StructureInterfaceCluster cluster)
void	setContacts(AtomContactSet contacts)
void	setFirstGroupAsa(GroupAsa groupAsa)
void	setFirstGroupAsas(Map<ResidueNumber,GroupAsa> firstGroupAsas)
void	setId(int id)
void	setMoleculeIds(Pair<String> moleculeIds)
void	setMolecules(Pair<Atom[]> molecules)
void	setSecondGroupAsa(GroupAsa groupAsa)
void	setSecondGroupAsas(Map<ResidueNumber,GroupAsa> secondGroupAsas)
void	setTotalArea(double totalArea)
void	setTransforms(Pair<CrystalTransform> transforms)
String	toMMCIF()	Return a String representing the 2 molecules of this interface in mmCIF format.
String	toPDB()	Return a String representing the 2 molecules of this interface in PDB format.
String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

StructureInterface

public StructureInterface(Atom[] firstMolecule,
                          Atom[] secondMolecule,
                          String firstMoleculeId,
                          String secondMoleculeId,
                          AtomContactSet contacts,
                          CrystalTransform firstTransf,
                          CrystalTransform secondTransf)

Constructs a StructureInterface

Parameters:

firstMolecule - the atoms of the first molecule

secondMolecule - the atoms of the second molecule

firstMoleculeId - an identifier that identifies the first molecule within the Asymmetric Unit

secondMoleculeId - an identifier that identifies the second molecule within the Asymmetric Unit

contacts - the contacts between the 2 molecules

firstTransf - the transformation (crystal operator) applied to first molecule

secondTransf - the transformation (crystal operator) applied to second molecule

StructureInterface

public StructureInterface()

Constructs an empty StructureInterface

Method Detail

getId

public int getId()

setId

public void setId(int id)

getCrystalIds

public Pair<String> getCrystalIds()

Returns a pair of identifiers for each of the 2 member molecules that identify them uniquely in the crystal: <molecule id (asym unit id)>+<operator id>+<crystal translation>

Returns:

getTotalArea

public double getTotalArea()

Returns the total area buried upon formation of this interface, defined as: 1/2[ (ASA1u-ASA1c) + (ASA2u-ASA2u) ] , with:

ASAxu = ASA of first/second unbound chain

ASAxc = ASA of first/second complexed chain

In the area calculation HETATOM groups not part of the main protein/nucleotide chain are not included.

Returns:

setTotalArea

public void setTotalArea(double totalArea)

getContacts

public AtomContactSet getContacts()

setContacts

public void setContacts(AtomContactSet contacts)

getMolecules

public Pair<Atom[]> getMolecules()

setMolecules

public void setMolecules(Pair<Atom[]> molecules)

getMoleculeIds

public Pair<String> getMoleculeIds()

Return the pair of identifiers identifying each of the 2 molecules of this interface in the asymmetry unit (usually the chain identifier if this interface is between 2 chains)

Returns:

setMoleculeIds

public void setMoleculeIds(Pair<String> moleculeIds)

getTransforms

public Pair<CrystalTransform> getTransforms()

Return the 2 crystal transform operations performed on each of the molecules of this interface.

Returns:

setTransforms

public void setTransforms(Pair<CrystalTransform> transforms)

getFirstAtomsForAsa

protected Atom[] getFirstAtomsForAsa(int cofactorSizeToUse)

getSecondAtomsForAsa

protected Atom[] getSecondAtomsForAsa(int cofactorSizeToUse)

getAtomsForAsa

protected Atom[] getAtomsForAsa(int cofactorSizeToUse)

isSymRelated

public boolean isSymRelated()

Tells whether the interface corresponds to one mediated by crystallographic symmetry, i.e. it is between symmetry-related molecules (with same chain identifier)

Returns:

isInfinite

public boolean isInfinite()

Returns true if the transformation applied to the second molecule of this interface has an infinite character (pure translation or screw rotation) and both molecules of the interface have the same asymmetric unit identifier (chain id): in such cases the interface would lead to infinite fiber-like (linear or helical) assemblies

Returns:

isHomomeric

public boolean isHomomeric()

Returns true if the 2 molecules of this interface are the same entity (i.e. homomeric interface), false otherwise (i.e. heteromeric interface)

Returns:

true if homomeric or if either of the entities is unknonw (null Compounds), false otherwise

getFirstGroupAsas

public Map<ResidueNumber,GroupAsa> getFirstGroupAsas()

Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.

Returns:

getFirstGroupAsa

public GroupAsa getFirstGroupAsa(ResidueNumber resNum)

Gets the GroupAsa for the corresponding residue number of first chain

Parameters:

resNum -

Returns:

setFirstGroupAsa

public void setFirstGroupAsa(GroupAsa groupAsa)

setFirstGroupAsas

public void setFirstGroupAsas(Map<ResidueNumber,GroupAsa> firstGroupAsas)

setSecondGroupAsas

public void setSecondGroupAsas(Map<ResidueNumber,GroupAsa> secondGroupAsas)

getSecondGroupAsas

public Map<ResidueNumber,GroupAsa> getSecondGroupAsas()

Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.

Returns:

setSecondGroupAsa

public void setSecondGroupAsa(GroupAsa groupAsa)

getSecondGroupAsa

public GroupAsa getSecondGroupAsa(ResidueNumber resNum)

Gets the GroupAsa for the corresponding residue number of second chain

Parameters:

resNum -

Returns:

getCoreResidues

public Pair<List<Group>> getCoreResidues(double bsaToAsaCutoff,
                                         double minAsaForSurface)

Returns the residues belonging to the interface core, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is above the given bsaToAsaCutoff

Parameters:

bsaToAsaCutoff -

minAsaForSurface - the minimum ASA to consider a residue on the surface

Returns:

getRimResidues

public Pair<List<Group>> getRimResidues(double bsaToAsaCutoff,
                                        double minAsaForSurface)

Returns the residues belonging to the interface rim, defined as those residues at the interface (BSA>0) and for which the BSA/ASA ratio is below the given bsaToAsaCutoff

Parameters:

bsaToAsaCutoff -

minAsaForSurface - the minimum ASA to consider a residue on the surface

Returns:

getInterfacingResidues

public Pair<List<Group>> getInterfacingResidues(double minAsaForSurface)

Returns the residues belonging to the interface, i.e. the residues at the surface with BSA>0

Parameters:

minAsaForSurface - the minimum ASA to consider a residue on the surface

Returns:

getSurfaceResidues

public Pair<List<Group>> getSurfaceResidues(double minAsaForSurface)

Returns the residues belonging to the surface

Parameters:

minAsaForSurface - the minimum ASA to consider a residue on the surface

Returns:

getCluster

public StructureInterfaceCluster getCluster()

setCluster

public void setCluster(StructureInterfaceCluster cluster)

getContactOverlapScore

public double getContactOverlapScore(StructureInterface other,
                                     boolean invert)

Calculates the Jaccard contact set score (intersection over union) between this StructureInterface and the given one. The calculation assumes that both interfaces come from the same structure. The output will not necessarily make sense if the two interfaces come from different structures. The two sides of the given StructureInterface need to match this StructureInterface in the sense that they must come from the same Entity, i.e. their residue numbers need to align with 100% identity, except for unobserved density residues. The SEQRES indices obtained through EntityInfo.getAlignedResIndex(Group, Chain) are used to match residues, thus if no SEQRES is present or if FileParsingParameters.setAlignSeqRes(boolean) is not used, this calculation is not guaranteed to work properly.

Parameters:

other - the interface to be compared to this one

invert - if false the comparison will be done first-to-first and second-to-second, if true the match will be first-to-second and second-to-first

Returns:

the contact overlap score, range [0.0,1.0]

getGroupContacts

public GroupContactSet getGroupContacts()

isIsologous

public boolean isIsologous()

Tell whether the interface is isologous, i.e. it is formed by the same patches of same entity on both sides.

Returns:

true if isologous, false if heterologous

getParentChains

public Pair<Chain> getParentChains()

Finds the parent chains by looking up the references of first atom of each side of this interface

Returns:

getParentCompounds

public Pair<EntityInfo> getParentCompounds()

Finds the parent entities by looking up the references of first atom of each side of this interface

Returns:

toPDB

public String toPDB()

Return a String representing the 2 molecules of this interface in PDB format. If the molecule ids (i.e. chain ids) are the same for both molecules, then the second one will be replaced by the next letter in alphabet (or A for Z)

Returns:

the PDB-formatted string

toMMCIF

public String toMMCIF()

Return a String representing the 2 molecules of this interface in mmCIF format. If the molecule ids (i.e. chain ids) are the same for both molecules, then the second one will be written as chainId_operatorId (with operatorId taken from getTransforms()

Returns:

the mmCIF-formatted string

compareTo

public int compareTo(StructureInterface o)

Specified by:

compareTo in interface Comparable<StructureInterface>

toString

public String toString()

Overrides:

toString in class Object