Uses of Class
edu.sdsc.mbt.Residue

Packages that use Residue

edu.sdsc.mbt
edu.sdsc.mbt.viewables	This package provides classes which enable molecular biology data to be represented as visible/renderable viewable objects, plus, this package defines a top-level StructureDocument object to encapsulate the complete state of these objects and properties.
edu.sdsc.sirius.dialogs
edu.sdsc.sirius.io	This package provides classes which enable molecular biology data sets (such as protein structures, sequence data, etc) to be loaded into an MBT application as a Structure object.
edu.sdsc.sirius.viewers
edu.sdsc.sirius.viewers.SequenceViewerImpl
edu.sdsc.sirius.viewers.TreeViewer

Uses of Residue in edu.sdsc.mbt

Fields in edu.sdsc.mbt declared as Residue

Residue	ResidueLabelComponent.residue
Residue	Atom.residue

Methods in edu.sdsc.mbt that return Residue

Residue	StructureMap.getResidue(Atom atom) Get the Residue object to which this Atom belongs.
Residue	StructureMap.getLigandResidue(int ligandIndex) Return the Residue for a given ligand index.
Residue	StructureMap.getResidue(int residueIndex) Return the start Atom index for a given residue index.
Residue	StructureMap.getResidue(java.lang.String chainAndResidue) Get the Residue object by its chain and residue id.
Residue	Fragment.getResidue(int index)
Residue	Chain.getResidue(int index) Return the specified Residue record contained in this Chain.

Methods in edu.sdsc.mbt with parameters of type Residue

void	StructureMap.setResidueId(Residue residue, int n)
void	StructureMap.addAtom(Atom added, Residue target, boolean assignName)
void	StructureMap.addAtom(Atom atom, Residue residue, java.lang.String chainId) Simply add an atom to the records don't assign bonds (they may be added later), and assign number based on the current numbering in the structure residue is a new Residue object that will be added to the structure (subsequent atoms may be added to the same residue from the calling method)
void	StructureMap.addAtom(Atom atom, Residue residue, int position, java.lang.String chainId) Adds a new atom with the specified position of the residue (if new)
int	StructureMap.getResidueIndex(Residue residue) Get the index of the specified Residue.
void	StructureMap.computePhiPsi(Residue r, java.util.HashMap transformed)
double[]	StructureMap.getPsiPhi(Residue r)
int	Fragment.getResidueIndex(Residue residue)
int	Fragment.getResidueIndexInChain(Residue residue)
int	Chain.getResidueIndex(Residue residue) Return the specified Residue index in this Chain.
void	Chain.addResidue(Residue residue) Add a Residue record to this Chain.
void	Chain.addResidue(Residue residue, int position) Add a Residue record to this Chain at the specified position.
void	Chain.removeResidue(Residue residue)

Constructors in edu.sdsc.mbt with parameters of type Residue

ResidueLabelComponent(Residue residue, int dataType, int font, java.lang.String label)

ResidueLabelComponent(Residue residue, int dataType, int font, java.lang.String label, boolean selected, float[] color)

Uses of Residue in edu.sdsc.mbt.viewables

Methods in edu.sdsc.mbt.viewables with parameters of type Residue

void	StructureStyles.getRibbonColor(Residue residue, float[] color)
void	StructureStyles.fireGeometryChangeEvent(Residue r)
void	RibbonColorUniform.getRibbonColor(Residue residue, float[] c) Produce a color based upon the residue element type.
void	RibbonColorUniform.setRibbonColor(Residue residue, float[] c)
void	RibbonColorDefault.getRibbonColor(Residue residue, float[] c) Produce a color based upon the residue element type.
void	RibbonColorDefault.setRibbonColor(Residue residue, float[] c)
void	RibbonColor.getRibbonColor(Residue residue, float[] color) Assign appropriate color to the specified Residue
void	RibbonColor.setRibbonColor(Residue residue, float[] color) Sets color assigned to the residues in the future.
void	ResidueColorUniform.getResidueColor(Residue residue, float[] c) Produce a color based upon the residue element type.
void	ResidueColorUniform.setResidueColor(Residue residue, float[] c)
void	ResidueColorUniform.getBackgroundColor(Residue residue, float[] c)
void	ResidueColorUniform.setBackgroundColor(Residue residue, float[] c)
void	ResidueColorScaled.getResidueColor(Residue residue, float[] c) Produce a color based upon the color map values.
void	ResidueColorScaled.getBackgroundColor(Residue residue, float[] c)
void	ResidueColorScaled.setResidueColor(Residue residue, float[] c)
void	ResidueColorScaled.setBackgroundColor(Residue residue, float[] c)
void	ResidueColorDefault.getResidueColor(Residue residue, float[] c) Produce a color based upon the residue element type.
void	ResidueColorDefault.setResidueColor(Residue residue, float[] c)
void	ResidueColorDefault.getBackgroundColor(Residue residue, float[] c)
void	ResidueColorDefault.setBackgroundColor(Residue residue, float[] c)
void	ResidueColorByType.getResidueColor(Residue residue, float[] color) Produce a color based upon the residue.
void	ResidueColorByType.getBackgroundColor(Residue residue, float[] color)
void	ResidueColorByType.setResidueColor(Residue residue, float[] color)
void	ResidueColorByType.setBackgroundColor(Residue residue, float[] color)
void	ResidueColorByHydrophobicity.getResidueColor(Residue residue, float[] color) Produce a color based upon the residue element type.
void	ResidueColorByHydrophobicity.getBackgroundColor(Residue residue, float[] color)
void	ResidueColorByHydrophobicity.setResidueColor(Residue residue, float[] color)
void	ResidueColorByHydrophobicity.setBackgroundColor(Residue residue, float[] color)
void	ResidueColorByElement.getResidueColor(Residue residue, float[] c) Produce a color based upon the residue element type.
void	ResidueColorByElement.setResidueColor(Residue residue, float[] c)
void	ResidueColorByCharge.getResidueColor(Residue residue, float[] color) Produce a color based upon the residue element type.
void	ResidueColorByCharge.getBackgroundColor(Residue residue, float[] color)
void	ResidueColorByCharge.setResidueColor(Residue residue, float[] color)
void	ResidueColorByCharge.setBackgroundColor(Residue residue, float[] color)
void	ResidueColor.getResidueColor(Residue residue, float[] color) Assign appropriate color to the specified Residue
void	ResidueColor.setResidueColor(Residue residue, float[] color) Sets color assigned to the residues in the future.

Uses of Residue in edu.sdsc.sirius.dialogs

Methods in edu.sdsc.sirius.dialogs with parameters of type Residue

static java.lang.String

ResidueRenameDialog.showDialog(javax.swing.JFrame f, Residue r)

Uses of Residue in edu.sdsc.sirius.io

Fields in edu.sdsc.sirius.io declared as Residue

Residue

SideChain.residue

Uses of Residue in edu.sdsc.sirius.viewers

Methods in edu.sdsc.sirius.viewers with parameters of type Residue

void	StructureViewer.checkDummyAtoms(Residue residue) This method is a Residue-level utility optimized to run a limited check within the residue affected by a visibility event
void	StructureViewer.createLabel(Residue residue, int type, int size, java.lang.String text, boolean selected, float[] color, boolean updateView)
void	StructureViewer.registerResidueSelection(Entry e, Residue r, boolean b) Blank method for compliance with the Viewer interface.
void	StructureViewer.replaceResidue(Residue residue, java.lang.String label)
void	StructureViewer.setSelectionArea(Residue residue, double distance, boolean fullResidues)

Uses of Residue in edu.sdsc.sirius.viewers.SequenceViewerImpl

Fields in edu.sdsc.sirius.viewers.SequenceViewerImpl declared as Residue

Residue

Cell.residue

Constructors in edu.sdsc.sirius.viewers.SequenceViewerImpl with parameters of type Residue

Cell(Sequence sequence, int index, java.lang.String symbol, Residue r, int residueId)

Cell(Sequence sequence, int index, java.lang.String symbol, Residue r)

Cell(int index, java.lang.String symbol, Residue r)

Uses of Residue in edu.sdsc.sirius.viewers.TreeViewer

Methods in edu.sdsc.sirius.viewers.TreeViewer with parameters of type Residue

void	StructureBrowser.updateVisibility(Residue residue)