StructureInterface (biojava 5.3.0 API)

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 and 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

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`compareTo(StructureInterface o)`
`protected Atom[]`	`getAtomsForAsa(int cofactorSizeToUse)`
`StructureInterfaceCluster`	`getCluster()`
`double`	`getContactOverlapScore(StructureInterface other, boolean invert)` Calculates the contact overlap score 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 compounds 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: 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.
`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 Compound 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`	`setId(int id)`
`void`	`setMoleculeIds(Pair<String> moleculeIds)`
`void`	`setMolecules(Pair<Atom[]> molecules)`
`void`	`setSecondGroupAsa(GroupAsa groupAsa)`
`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)
```
  - 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 contact overlap score between this StructureInterface and the given one. The two sides of the given StructureInterface need to match this StructureInterface in the sense that they must come from the same Compound (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 -
    
    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 Compound 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 compounds 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:
  - 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:
  - compareTo
```
public int compareTo(StructureInterface o)
```
    Specified by:
    
    compareTo in interface Comparable<StructureInterface>
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object

Class StructureInterface

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

StructureInterface

StructureInterface

Method Detail

getId

setId

getCrystalIds

getTotalArea

setTotalArea

getContacts

setContacts

getMolecules

setMolecules

getMoleculeIds

setMoleculeIds

getTransforms

setTransforms

getFirstAtomsForAsa

getSecondAtomsForAsa

getAtomsForAsa

isSymRelated

isInfinite

isHomomeric

getFirstGroupAsas

getFirstGroupAsa

setFirstGroupAsa

getSecondGroupAsas

setSecondGroupAsa

getSecondGroupAsa

getCoreResidues

getRimResidues

getInterfacingResidues

getSurfaceResidues

getCluster

setCluster

getContactOverlapScore

getGroupContacts

isIsologous

getParentChains

getParentCompounds

toPDB

toMMCIF

compareTo

toString