Uses of Class
org.biojava.nbio.structure.contact.Pair

Packages that use Pair

Package	Description
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.contact

Uses of Pair in org.biojava.nbio.structure.align.util

Methods in org.biojava.nbio.structure.align.util that return Pair

Modifier and Type	Method and Description
Pair<Atom>	RotationAxis.getAxisEnds(Atom[] atoms) Find a segment of the axis that covers the specified set of atoms.

Uses of Pair in org.biojava.nbio.structure.contact

Methods in org.biojava.nbio.structure.contact that return Pair

Modifier and Type	Method and Description
Pair<List<Group>>	StructureInterface.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>	StructureInterface.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>
Pair<List<Group>>	StructureInterface.getInterfacingResidues(double minAsaForSurface) Returns the residues belonging to the interface, i.e. the residues at the surface with BSA>0
Pair<String>	StructureInterface.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[]>	StructureInterface.getMolecules()
Pair<Group>	GroupContact.getPair()
Pair<Atom>	AtomContact.getPair()
Pair<Chain>	StructureInterface.getParentChains() Finds the parent chains by looking up the references of first atom of each side of this interface
Pair<Compound>	StructureInterface.getParentCompounds() Finds the parent compounds by looking up the references of first atom of each side of this interface
Pair<List<Group>>	StructureInterface.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
Pair<List<Group>>	StructureInterface.getSurfaceResidues(double minAsaForSurface) Returns the residues belonging to the surface
Pair<CrystalTransform>	StructureInterface.getTransforms() Return the 2 crystal transform operations performed on each of the molecules of this interface.

Methods in org.biojava.nbio.structure.contact with parameters of type Pair

Modifier and Type	Method and Description
void	StructureInterface.setMoleculeIds(Pair<String> moleculeIds)
void	StructureInterface.setMolecules(Pair<Atom[]> molecules)
void	AtomContact.setPair(Pair<Atom> pair)
void	GroupContact.setPair(Pair<Group> pair)
void	StructureInterface.setTransforms(Pair<CrystalTransform> transforms)

Constructors in org.biojava.nbio.structure.contact with parameters of type Pair

Constructor and Description
AtomContact(Pair<Atom> pair, double distance)