Uses of Class
org.biojava.nbio.structure.ResidueNumber

Packages that use ResidueNumber

Package	Description
org.biojava.nbio.protmod.structure
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.align.util
org.biojava.nbio.structure.contact
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.secstruc

Uses of ResidueNumber in org.biojava.nbio.protmod.structure

Methods in org.biojava.nbio.protmod.structure that return ResidueNumber

Modifier and Type	Method and Description
ResidueNumber	StructureGroup.getPDBResidueNumber()

Methods in org.biojava.nbio.protmod.structure with parameters of type ResidueNumber

Modifier and Type	Method and Description
void	StructureGroup.setPDBResidueNumber(ResidueNumber resNum)

Constructors in org.biojava.nbio.protmod.structure with parameters of type ResidueNumber

Constructor and Description
StructureGroup(ResidueNumber resNum, String pdbName, boolean isAminoAcid)

Uses of ResidueNumber in org.biojava.nbio.structure

Fields in org.biojava.nbio.structure declared as ResidueNumber

Modifier and Type	Field and Description
protected ResidueNumber	HetatomImpl.residueNumber

Methods in org.biojava.nbio.structure that return ResidueNumber

Modifier and Type	Method and Description
static ResidueNumber	ResidueNumber.fromString(String pdb_code) Convert a string representation of a residue number to a residue number object.
ResidueNumber	ResidueRange.getEnd()
ResidueNumber	AtomPositionMap.getFirst()
ResidueNumber	AtomPositionMap.getFirst(String chainId)
ResidueNumber	AtomPositionMap.getLast()
ResidueNumber	AtomPositionMap.getLast(String chainId)
ResidueNumber	AugmentedResidueRange.getResidue(int positionInRange) Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
ResidueNumber	ResidueRange.getResidue(int positionInRange, AtomPositionMap map) Returns the ResidueNumber that is at position positionInRange in this ResidueRange.
ResidueNumber	Group.getResidueNumber() returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
ResidueNumber	HetatomImpl.getResidueNumber() returns a dynamically created ResidueNumber for the group - this contains the chainId, resNum and insCode of the group.
ResidueNumber	ResidueRange.getStart()

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

Modifier and Type	Method and Description
NavigableMap<ResidueNumber,Integer>	AtomPositionMap.getNavMap()
Iterator<ResidueNumber>	AugmentedResidueRange.iterator() Returns a new Iterator over every ResidueNumber in this ResidueRange.
Iterator<ResidueNumber>	ResidueRange.iterator(AtomPositionMap map) Returns a new Iterator over every ResidueNumber in this ResidueRange.
Iterator<ResidueNumber>	ResidueRangeAndLength.iterator(AtomPositionMap map) Returns a new Iterator over every ResidueNumber in this ResidueRange.
static Iterator<ResidueNumber>	ResidueRange.multiIterator(AtomPositionMap map, List<? extends ResidueRange> rrs) Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.
static Iterator<ResidueNumber>	ResidueRange.multiIterator(AtomPositionMap map, ResidueRange... rrs) Returns a new Iterator over every ResidueNumber in the list of ResidueRanges.

Methods in org.biojava.nbio.structure with parameters of type ResidueNumber

Modifier and Type	Method and Description
int	ResidueNumber.compareTo(ResidueNumber other) Compare residue numbers by chain, sequence number, and insertion code
int	ResidueNumber.compareToPositional(ResidueNumber other) Compare residue numbers by sequence number and insertion code, ignoring the chain
boolean	AugmentedResidueRange.contains(ResidueNumber residueNumber)
boolean	ResidueRange.contains(ResidueNumber residueNumber, AtomPositionMap map)
Group	Chain.getGroupByPDB(ResidueNumber resNum) Get a group by its PDB residue numbering.
Group	ChainImpl.getGroupByPDB(ResidueNumber resNum) Get a group by its PDB residue numbering.
static Group	StructureTools.getGroupByPDBResidueNumber(Structure struc, ResidueNumber pdbResNum) Get a group represented by a ResidueNumber.
Group[]	Chain.getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd) Get all groups that are located between two PDB residue numbers.
Group[]	ChainImpl.getGroupsByPDB(ResidueNumber start, ResidueNumber end) Get all groups that are located between two PDB residue numbers.
Group[]	Chain.getGroupsByPDB(ResidueNumber pdbresnumStart, ResidueNumber pdbresnumEnd, boolean ignoreMissing) Get all groups that are located between two PDB residue numbers.
Group[]	ChainImpl.getGroupsByPDB(ResidueNumber start, ResidueNumber end, boolean ignoreMissing)
int	AtomPositionMap.getLength(ResidueNumber start, ResidueNumber end) Calculates the number of atoms between two ResidueNumbers, inclusive.
int	AtomPositionMap.getLengthDirectional(ResidueNumber start, ResidueNumber end) Calculates the number of atoms between two ResidueNumbers, inclusive.
Integer	AtomPositionMap.getPosition(ResidueNumber residueNumber) Gets the 0-based index of residueNumber to the matched atoms
void	Group.setResidueNumber(ResidueNumber residueNumber) sets the ResidueNumber for this Group
void	HetatomImpl.setResidueNumber(ResidueNumber residueNumber)

Method parameters in org.biojava.nbio.structure with type arguments of type ResidueNumber

Modifier and Type	Method and Description
static Map<Group,Double>	StructureTools.getGroupDistancesWithinShell(Structure structure, Atom centroid, Set<ResidueNumber> excludeResidues, double radius, boolean includeWater, boolean useAverageDistance) Finds Groups in structure that contain at least one Atom that is within radius Angstroms of centroid.
static Set<Group>	StructureTools.getGroupsWithinShell(Structure structure, Atom atom, Set<ResidueNumber> excludeResidues, double distance, boolean includeWater)

Constructors in org.biojava.nbio.structure with parameters of type ResidueNumber

Constructor and Description
AugmentedResidueRange(String chain, ResidueNumber start, ResidueNumber end, int length, AtomPositionMap map)
ResidueNumber(ResidueNumber o)
ResidueRange(String chainName, ResidueNumber start, ResidueNumber end)
ResidueRangeAndLength(String chain, ResidueNumber start, ResidueNumber end, int length)

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

Methods in org.biojava.nbio.structure.align.util with parameters of type ResidueNumber

Modifier and Type	Method and Description
static AFPChain	AlignmentTools.createAFPChain(Atom[] ca1, Atom[] ca2, ResidueNumber[] aligned1, ResidueNumber[] aligned2) Fundamentally, an alignment is just a list of aligned residues in each protein.
static AFPChain	AlignmentTools.createAFPChain(Atom[] ca1, Atom[] ca2, ResidueNumber[] aligned1, ResidueNumber[] aligned2) Fundamentally, an alignment is just a list of aligned residues in each protein.

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

Methods in org.biojava.nbio.structure.contact that return types with arguments of type ResidueNumber

Modifier and Type	Method and Description
Map<ResidueNumber,GroupAsa>	StructureInterface.getFirstGroupAsas() Gets a map of ResidueNumbers to GroupAsas for all groups of first chain.
Map<ResidueNumber,GroupAsa>	StructureInterface.getSecondGroupAsas() Gets a map of ResidueNumbers to GroupAsas for all groups of second chain.

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

Modifier and Type	Method and Description
GroupAsa	StructureInterface.getFirstGroupAsa(ResidueNumber resNum) Gets the GroupAsa for the corresponding residue number of first chain
GroupAsa	StructureInterface.getSecondGroupAsa(ResidueNumber resNum) Gets the GroupAsa for the corresponding residue number of second chain
boolean	GroupContactSet.hasContact(ResidueNumber resNumber1, ResidueNumber resNumber2) Tell whether the given pair is a contact in this GroupContactSet, the comparison is done by matching residue numbers and chain identifiers

Uses of ResidueNumber in org.biojava.nbio.structure.io

Methods in org.biojava.nbio.structure.io that return ResidueNumber

Modifier and Type	Method and Description
ResidueNumber[][]	FastaStructureParser.getResidues() For each residue in the fasta file, return the ResidueNumber in the corresponding structure.
static ResidueNumber[]	StructureSequenceMatcher.matchSequenceToStructure(ProteinSequence seq, Structure struct) Given a sequence and the corresponding Structure, get the ResidueNumber for each residue in the sequence.

Uses of ResidueNumber in org.biojava.nbio.structure.secstruc

Constructors in org.biojava.nbio.structure.secstruc with parameters of type ResidueNumber

Constructor and Description
SecStrucElement(SecStrucType type, ResidueNumber start, ResidueNumber end, int length, int index, String chainID) Create a new SSE object.