Uses of Class
org.proteinshader.structure.Structure

Packages that use Structure

org.proteinshader.gui	Holds all of the Swing GUI components and their associated listeners, including class Renderer, which is registered as a listener for the GLCanvas object that is used a drawing surface.
org.proteinshader.gui.components.controlpanel	Holds the JPanels used in the right-side retractable control panel of the GUI.
org.proteinshader.structure.io	Holds the classes needed for reading Protein Data Bank structure files.
org.proteinshader.structure.io.demos	Holds demo classes that were used for early testing of the io classes.
org.proteinshader.structure.visitor	Holds Visitor classes that know how to traverse the hierarchy of objects held by class Structure.
org.proteinshader.structure.visitor.demos	Holds demo classes that were used for early testing of the Visitor classes.

Uses of Structure in org.proteinshader.gui

Methods in org.proteinshader.gui that return Structure

Structure	MediatorImpl.getStructure() Returns the current Structure to display.
Structure	Mediator.getStructure() Returns the current Structure to display.

Uses of Structure in org.proteinshader.gui.components.controlpanel

Methods in org.proteinshader.gui.components.controlpanel with parameters of type Structure

void	ControlPanel.addNewStructure(Structure structure) The Structure is used to set the Model menu of the SelectorPanel, which will automatically set the other menus and lists of the SelectorPanel.
void	SelectorPanel.setModelMenu(Structure structure) Adds the Structure's Models to the Model menu.

Uses of Structure in org.proteinshader.structure.io

Methods in org.proteinshader.structure.io that return Structure

Structure	StructureReader.readStructure(File file) Reads a protein structure from a file and returns a Structure object.
Structure	PDBStructureReader.readStructure(File file) Reads a protein structure from a ".pdb" file and returns a Structure object.
Structure	StructureReader.readStructure(String filename) Reads a protein structure from a file and returns a Structure object.
Structure	PDBStructureReader.readStructure(String filename) Reads a protein structure from a ".pdb" file and returns a Structure object.

Constructors in org.proteinshader.structure.io with parameters of type Structure

PDBLineParser(Structure structure)
Constructs a PDBLineParser for the Structure given as an argument.

Uses of Structure in org.proteinshader.structure.io.demos

Methods in org.proteinshader.structure.io.demos with parameters of type Structure

void	PDBStructureReaderDemo.writeStructure(Structure structure, String filename) Writes a Structure to a file by using a SFWriterVisitor.
void	SegmentDemo.writeStructure(Structure structure, String filename) Writes a Structure to a file by using a SFWriterVisitor.

Uses of Structure in org.proteinshader.structure.visitor

Methods in org.proteinshader.structure.visitor with parameters of type Structure

void	Visitor.visit(Structure structure) Traverses all Models owned by the Structure.
void	SFWriterVisitor.visit(Structure structure) Writes a Structure's data to a simple text file.
void	BondGeneratorVisitor.visit(Structure structure) Generates all standard Bonds (AminoAcids and Waters) for the Structure.

Uses of Structure in org.proteinshader.structure.visitor.demos

Methods in org.proteinshader.structure.visitor.demos with parameters of type Structure

void	ModifierVisitorDemo.modify(Structure structure) The Helices of the Structure are modified by changing their shape to CYLINDER and setting all of their Atoms and Bonds to INVISIBLE.
void	VisitorDemo.testVisitor(Structure structure) Creates a Visitor and tests it by activating debug mode so that it will print the ID of each object in the Structure.
void	ModifierVisitorDemo.writeStructure(Structure structure, String filename) Writes a Structure to a file by using a SFWriterVisitor.