Uses of Class
org.biojava.nbio.structure.contact.Pair
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Packages that use Pair Package Description org.biojava.nbio.structure.align.util org.biojava.nbio.structure.basepairs org.biojava.nbio.structure.contact -
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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 bsaToAsaCutoffPair<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>0Pair<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 interfacePair<EntityInfo>
StructureInterface. getParentCompounds()
Finds the parent compounds by looking up the references of first atom of each side of this interfacePair<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 bsaToAsaCutoffPair<List<Group>>
StructureInterface. getSurfaceResidues(double minAsaForSurface)
Returns the residues belonging to the surfacePair<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)
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