Uses of Interface
org.simtk.molecularstructure.Residue

Packages that use Residue

org.simtk.molecularstructure
org.simtk.molecularstructure.atom
org.simtk.molecularstructure.nucleicacid
org.simtk.rnaml

Uses of Residue in org.simtk.molecularstructure

Classes in org.simtk.molecularstructure that implement Residue

class

ResidueClass

Fields in org.simtk.molecularstructure declared as Residue

protected Residue	ResidueClass.nextResidue
protected Residue	ResidueClass.previousResidue

Fields in org.simtk.molecularstructure with type parameters of type Residue

protected java.util.Collection<Residue>

SecondaryStructureClass.residues

Methods in org.simtk.molecularstructure that return Residue

Residue	ResidueClass.getNextResidue()
Residue	Residue.getNextResidue()
Residue	ResidueClass.getPreviousResidue()
Residue	Residue.getPreviousResidue()
Residue	BiopolymerClass.getResidue(int i)
Residue	Biopolymer.getResidue(int i)
Residue	BiopolymerClass.getResidueByNumber(int i)
Residue	Biopolymer.getResidueByNumber(int i)
Residue	BiopolymerClass.getResidueByNumber(int i, char insertionCode)
Residue	BiopolymerClass.getResidueByNumber(java.lang.String n)

Methods in org.simtk.molecularstructure that return types with arguments of type Residue

java.util.Iterator<Residue>	SecondaryStructureClass.getResidueIterator()
java.util.Iterator<Residue>	SecondaryStructure.getResidueIterator()
java.util.Collection<Residue>	SecondaryStructureClass.residues()
java.util.Collection<Residue>	SecondaryStructure.residues()
java.util.List<Residue>	BiopolymerClass.residues()
java.util.List<Residue>	Biopolymer.residues()

Methods in org.simtk.molecularstructure with parameters of type Residue

void	SecondaryStructureClass.addResidue(Residue residue)
void	SecondaryStructure.addResidue(Residue residue)
void	ResidueClass.setNextResidue(Residue r)
void	Residue.setNextResidue(Residue r)
void	ResidueClass.setPreviousResidue(Residue r)
void	Residue.setPreviousResidue(Residue r)

Constructor parameters in org.simtk.molecularstructure with type arguments of type Residue

SecondaryStructureClass(java.util.Collection<Residue> residues)

SecondaryStructureClass(java.util.Collection<Residue> residues, int resLimit)

SecondaryStructureClass(java.util.Collection<Residue> residues, int resLimit, java.lang.String source)

Uses of Residue in org.simtk.molecularstructure.atom

Methods in org.simtk.molecularstructure.atom that return Residue

Residue	AtomClass.getResidue()
Residue	Atom.getResidue()

Methods in org.simtk.molecularstructure.atom with parameters of type Residue

void	AtomClass.setResidue(Residue r)

Uses of Residue in org.simtk.molecularstructure.nucleicacid

Fields in org.simtk.molecularstructure.nucleicacid with type parameters of type Residue

protected java.util.HashMap<Residue,BasePair.EdgeType>

BasePair.edges

Methods in org.simtk.molecularstructure.nucleicacid that return Residue

Residue	BasePair.getResidue1()
Residue	BasePair.getResidue2()

Methods in org.simtk.molecularstructure.nucleicacid that return types with arguments of type Residue

java.util.Iterator<Residue>

BasePair.iterator()

Methods in org.simtk.molecularstructure.nucleicacid with parameters of type Residue

void	BasePair.addResidue(Residue r)
static BasePair	BasePair.getBasePair(Residue r1, Residue r2, java.lang.String source)
BasePair.EdgeType	BasePair.getEdge(Residue res)
java.lang.Boolean	BasePair.isBetween(Residue r1, Residue r2)
static BasePair	BasePair.makeBasePair(Residue r1, Residue r2, java.lang.String source)
void	BasePair.setEdge(Residue res, BasePair.EdgeType edgeT)
void	BasePair.setEdge(Residue res, java.lang.String edge)

Constructors in org.simtk.molecularstructure.nucleicacid with parameters of type Residue

BasePair(Residue r1, Residue r2)

Constructor parameters in org.simtk.molecularstructure.nucleicacid with type arguments of type Residue

BaseStack(java.util.Collection<Residue> residues)

BaseStack(java.util.Collection<Residue> residues, java.lang.String source)

Uses of Residue in org.simtk.rnaml

Methods in org.simtk.rnaml with parameters of type Residue

boolean

RnamlDocument.isDeemedNucleotide(Residue res, java.lang.String source)