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.basepairs
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	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.basepairs

Methods in org.biojava.nbio.structure.basepairs that return types with arguments of type Pair

Modifier and Type	Method	Description
List<Pair<Group>>	BasePairParameters.findPairs(List<Chain> chains)	This method performs a search for base pairs in the structure.
List<Pair<Group>>	MismatchedBasePairParameters.findPairs(List<Chain> chains)	This is an implementation for finding non-canonical base pairs when there may be missing or overhanging bases.
List<Pair<Group>>	TertiaryBasePairParameters.findPairs(List<Chain> chains)	This is an alternative implementation of findPair() that looks for anything that would fit the criteria for a base-pair, useful for the context of tertiary structure of RNA.

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

Modifier and Type	Method	Description
javax.vecmath.Matrix4d	BasePairParameters.basePairReferenceFrame(Pair<Group> pair)	This method calculates the central frame (4x4 transformation matrix) of a single base pair.

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

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

Modifier and Type	Method	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<Integer>	Contact.getIndexPair()
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<Atom>	AtomContact.getPair()
Pair<Group>	GroupContact.getPair()
Pair<Chain>	StructureInterface.getParentChains()	Finds the parent chains by looking up the references of first atom of each side of this interface
Pair<EntityInfo>	StructureInterface.getParentCompounds()	Finds the parent entities 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	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	Description
AtomContact(Pair<Atom> pair, double distance)