Uses of Class org.biojava.nbio.structure.ResidueNumber (biojava 5.2.0 API)

Packages that use ResidueNumber
Package	Description
org.biojava.nbio.protmod.structure
org.biojava.nbio.structure
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	Description
`ResidueNumber`	StructureGroup.`getPDBResidueNumber()`

Methods in org.biojava.nbio.protmod.structure with parameters of type ResidueNumber
Modifier and Type	Method	Description
`void`	StructureGroup.`setPDBResidueNumber(ResidueNumber resNum)`

Constructors in org.biojava.nbio.protmod.structure with parameters of type ResidueNumber
Constructor	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	Description
`protected ResidueNumber`	HetatomImpl.`residueNumber`

Methods in org.biojava.nbio.structure that return ResidueNumber
Modifier and Type	Method	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	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	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[]`	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)`	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	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	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	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.

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