Uses of Class
edu.sdsc.mbt.Structure

Packages that use Structure

Default Package
edu.sdsc.mbt
edu.sdsc.mbt.util	This package provides classes which implement extra functionality on top of the core MBT classes (that is, capabilities that are not absolutely required by, or would otherwise overcomplicate, the core classes).
edu.sdsc.sirius.builder
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.rasmol
edu.sdsc.sirius.util
edu.sdsc.sirius.viewers

Uses of Structure in

Methods in Default Package with parameters of type Structure

void	Viewer.removeRamachandranDialog(Structure structure)
RamachandranViewer	Viewer.getRamachandranViewer(Structure structure)
void	Viewer.displayRamachandranPlot(Structure structure)

Uses of Structure in edu.sdsc.mbt

Fields in edu.sdsc.mbt declared as Structure

Structure

StructureComponent.structure The Structure to which a StructureComponent instance belongs.

Methods in edu.sdsc.mbt that return Structure

Structure	StructureMap.getStructure() Returns the Structure object used to construct this StructureMap.
Structure	StructureComponent.getStructure() Get the Structure to which a StructureComponent instance belongs.

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

void	StructureComponent.setStructure(Structure structure) Set the Structure to which a StructureComponent instance belongs.

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

StructureMap(Structure structure)
Constructs a StructureMap object for a given Structure.

StructureComponentIterator(Structure structure, StructureComponentFilter filter)
Construct a StructureComponentIterator for the given structure using the given filter to describe the desired subset.

Uses of Structure in edu.sdsc.mbt.util

Methods in edu.sdsc.mbt.util with parameters of type Structure

static java.util.Vector	BondFactory.generateBonds(Structure structure) Return a vector of Bond objects extracted from a Structure using 1.8 as the bondLimit distance.
static java.util.Vector	BondFactory.generateBonds(Structure structure, double bondLimit) Return a vector of Bond objects extracted from a Structure using the specified bondLimit distance.
static double[][]	AtomStats.getAtomCoordinateBounds(Structure structure) Return the coordinate bounds for given a Structure.
static double[]	AtomStats.getAtomCoordinateAverage(Structure structure) Return the coordinate average for a Structure's atom coordinates.

Constructors in edu.sdsc.mbt.util with parameters of type Structure

DerivedInformation(Structure structure)

DerivedInformation(Structure structure, StructureMap structureMap)

Uses of Structure in edu.sdsc.sirius.builder

Methods in edu.sdsc.sirius.builder with parameters of type Structure

static void	FragmentUtil.addCustomFragment(Structure structure, java.lang.String name, java.util.Vector attachments, double[] lookAt, double[] up)
static void	FragmentRegistry.addCustomFragment(Structure structure, java.lang.String name, java.util.Vector attachments, double[] lookAt, double[] up)

Uses of Structure in edu.sdsc.sirius.io

Methods in edu.sdsc.sirius.io that return Structure

Structure	StructureEntry.getStructure() Returns the Structure object holding the 3D information.
Structure	PdbEntryLoader.loadStructure(java.net.URL url, int number) Returns a reference to a Structure read from the given URL object.
Structure	PdbEntryLoader.loadStructure(java.io.File file, int number)
Structure	PdbEntryLoader.loadStructure(java.io.BufferedInputStream bufferedInputStream, int number) Returns a reference to a Structure read from the given (uncompressed) InputStream.
Structure	Mol2EntryLoader.loadStructure(java.io.File file) Returns a reference to a Structure read from the given File object.
Structure	Mol2EntryLoader.loadStructure(java.net.URL url) Returns a reference to a Structure read from the given URL object.
Structure	Mol2EntryLoader.loadStructure(java.io.BufferedInputStream bufferedInputStream) Returns a reference to a Structure read from the given (uncompressed) InputStream.

Methods in edu.sdsc.sirius.io with parameters of type Structure

void	StructureEntry.setStructure(Structure s) Sets a Structure object created to represent the 3D structural information

Uses of Structure in edu.sdsc.sirius.rasmol

Methods in edu.sdsc.sirius.rasmol with parameters of type Structure

void	RasmolReader.setStructure(Structure s)
void	RasmolReader.clear(Structure s)

Uses of Structure in edu.sdsc.sirius.util

Methods in edu.sdsc.sirius.util that return Structure

static Structure	IOHandler.readPDB(java.io.File file)
static Structure	IOHandler.getStructure(java.util.Hashtable components, java.lang.String n)

Methods in edu.sdsc.sirius.util with parameters of type Structure

static void	StructureMath.transformStructure(Location start, Location target, Structure structure)
static void	StructureMath.checkHydrogens(Structure structure, StructureViewer viewer, float pH) This method runs through the structure and adds hydrogens where necessary, based on tabulated element valencies.
static void	StructureMath.updateBondOrders(Structure structure) This method checks whether the structure is a protein or DNA and assigns correct bond orders in case they have not been assigned.
static double	StructureMath.getRMSD(Structure structure1, Structure structure2)
static void	StructureMath.superimpose(Structure structure1, java.util.Vector atoms1, Structure structure2, java.util.Vector atoms2) This method performs RMSD minimization structure superposition.
void	Manager.displayRamachandranPlot(Structure structure)
void	Manager.removeRamachandranDialog(Structure structure)
RamachandranViewer	Manager.getRamachandranViewer(Structure structure)
static void	IOHandler.saveStructureFile(Structure structure, Manager parent)
static java.lang.String	IOHandler.convertStructureToSDF(Structure structure, java.lang.String name, java.util.HashMap initial)
static java.lang.String	IOHandler.convertStructureToPdb(Structure structure, Manager parent)
static void	IOHandler.savePdb(Structure structure, java.lang.String fname, Manager parent, java.util.HashMap initial)
static java.lang.String	IOHandler.convertMol2ToString(Structure structure, boolean fragment, StructureViewer viewer, java.util.HashMap atomMap) Flag fragment denotes whether this string will be used to write out a custom fragment.
static java.util.Vector	DataService.parseResidueList(Structure structure, Chain chain, java.lang.String input)

Uses of Structure in edu.sdsc.sirius.viewers

Methods in edu.sdsc.sirius.viewers that return Structure

Structure	StructureViewer.getIndependentStructure()
Structure	StructureViewer.getStructure(Entry e)
Structure	RamachandranViewer.getStructure()

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

void	StructureViewer.checkDummyAtoms(Structure structure, boolean updateView)
void	StructureViewer.updateCoordinates(Structure structure, double[] coordinates, float[] charges, boolean updateSS, boolean centerView)
void	StructureViewer.removeMonitors(Structure structure, boolean update) Remove all monitors for a specific structure.
void	StructureViewer.setRenderables(Structure structure, java.util.Vector renderables) Sets list of renderables for a specific structure
void	StructureViewer.updateBoundWaters(Structure structure, boolean update)
java.lang.String	StructureViewer.getStructureName(Structure structure)
void	StructureViewer.setIndependentStructure(Structure independentStructure)
void	StructureViewer.renameStructure(Structure structure, java.lang.String name)
void	StructureViewer.alignStructures(Structure structure1, int subset1, java.lang.String set1, Structure structure2, int subset2, java.lang.String set2, StructureAlignmentDialog dialog) This method uses a local copy of compiled CE executable.
void	StructureViewer.superimposeStructures(Structure structure1, Structure structure2, boolean useAll) This method transforms coordinates of the second structure to be as close in 3D as possible to the first structure.
void	StructureViewer.saveInitialCoordinates(Structure structure)
void	StructureViewer.restoreInitialCoordinates(Structure structure)
java.util.HashMap	StructureViewer.getInitialCoordinates(Structure structure)
Entry	StructureViewer.getEntry(Structure structure)
void	RamachandranViewer.connect(Structure structure, int index)

Constructors in edu.sdsc.sirius.viewers with parameters of type Structure

RamachandranViewer(Structure structure)