Uses of Package
org.proteinshader.structure

Packages that use org.proteinshader.structure

org.proteinshader.graphics	Holds the drawing classes: Ribbon, Tube, FrenetFrames, Sphere, and Cylinder.
org.proteinshader.graphics.adapter	Holds the StructureToGraphics class, which is used to manage the use of the drawing classes and OpenGL display lists.
org.proteinshader.graphics.displaylists	Holds the classes needed to manage OpenGL display lists, which are used to cache reusable geometry for spheres, cylinders, ribbon segments, and tube segments.
org.proteinshader.graphics.utils	Holds a testing utility, class SegmentRenderer, which can be used for drawing ribbon and tube segments on-the-fly, rather than using cached geometry in the form of OpenGL display lists.
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.gui.viewing	Holds important helper classes that the Renderer uses to control the view: Camera, Rotation, Lighting, etc.
org.proteinshader.structure	Holds the classes that store information from a Protein Data Bank file: Structure, Model, Chain, AminoAcid, Heterogen, Water, Atom, Bond, Helix, BetaStrand, Loop, etc.
org.proteinshader.structure.factory	Holds the factory classes needed for generating the Segment objects that hold the information needed for rendering ribbon and tube segments.
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.sort	Holds the DrawableSorter class, which is needed for sorting Drawable objects based on their distance from the camera.
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.
org.proteinshader.structure.visitor.modifiers	Holds helper classes for the ModifierVisitor class, which is used to modify Drawable objects (Atoms, Bonds, and Segments).

Classes in org.proteinshader.structure used by org.proteinshader.graphics

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.

Classes in org.proteinshader.structure used by org.proteinshader.graphics.adapter

Atom
Extends abstract class Drawable to add data that is unique to an atom (atomID, type, temperature, occupancy, radius, etc.).

Bond
Extends abstract class Drawable to add data that is unique to a bond between two atoms.

Drawable
This abstract class defines attributes and methods that are shared by all drawable objects, including the xyz-coordinates for the Drawable's center and methods that will allow each object to be sorted based on distance from the camera.

Model
A Model serves as a container for one or more Chains.

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.

Classes in org.proteinshader.structure used by org.proteinshader.graphics.displaylists

Model
A Model serves as a container for one or more Chains.

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.

Classes in org.proteinshader.structure used by org.proteinshader.graphics.utils

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.

Classes in org.proteinshader.structure used by org.proteinshader.gui

Atom
Extends abstract class Drawable to add data that is unique to an atom (atomID, type, temperature, occupancy, radius, etc.).

Chain
A Chain serves as a container for Residues (AminoAcid, Heterogen, and Water) and Regions (Loop, Helix, and BetaStrand).

Model
A Model serves as a container for one or more Chains.

Residue
This abstract class serves as a container for one or more Atoms.

Structure
Structure is the top-level container for objects that store information on a protein structure from the Protein Data Bank.

Classes in org.proteinshader.structure used by org.proteinshader.gui.components.controlpanel

Atom
Extends abstract class Drawable to add data that is unique to an atom (atomID, type, temperature, occupancy, radius, etc.).

Chain
A Chain serves as a container for Residues (AminoAcid, Heterogen, and Water) and Regions (Loop, Helix, and BetaStrand).

Model
A Model serves as a container for one or more Chains.

Residue
This abstract class serves as a container for one or more Atoms.

Structure
Structure is the top-level container for objects that store information on a protein structure from the Protein Data Bank.

Classes in org.proteinshader.structure used by org.proteinshader.gui.viewing

Drawable
This abstract class defines attributes and methods that are shared by all drawable objects, including the xyz-coordinates for the Drawable's center and methods that will allow each object to be sorted based on distance from the camera.

Classes in org.proteinshader.structure used by org.proteinshader.structure

AminoAcid
This concrete subclass of the abstract class Residue stores information on an amino acid in a PDB structure entry.

Atom
Extends abstract class Drawable to add data that is unique to an atom (atomID, type, temperature, occupancy, radius, etc.).

BetaStrand
This concrete subclass of Region holds information specific to a protein BetaStrand.

Bond
Extends abstract class Drawable to add data that is unique to a bond between two atoms.

Category
A Category object serves as a container for the Records in a PDB structure entry.

Chain
A Chain serves as a container for Residues (AminoAcid, Heterogen, and Water) and Regions (Loop, Helix, and BetaStrand).

Description
A Description object serves as a container for the Category objects that hold Records describing a PDB structure entry.

Drawable
This abstract class defines attributes and methods that are shared by all drawable objects, including the xyz-coordinates for the Drawable's center and methods that will allow each object to be sorted based on distance from the camera.

Helix
This concrete subclass of Region holds information specific to a protein Helix.

Heterogen
This concrete subclass of the abstract class Residue stores information on a heterogen in a PDB structure entry.

IDTest
This interface declares a processID() method that is intended to be used as a helper method for constructors that need to perform tests and/or any modifications on an ID.

Loop
This concrete subclass of Region holds information on the general "loop" regions found between well-defined regions of secondary structure (helices and beta-strands).

Model
A Model serves as a container for one or more Chains.

Record
A Record object serves as a container for the lines of a PDB record.

Region
Abstract class that contains references to a region of a Chain of AminoAcids.

Residue
This abstract class serves as a container for one or more Atoms.

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.

Water
This concrete subclass of the abstract class Residue stores information on a water molecule in a PDB structure entry.

Classes in org.proteinshader.structure used by org.proteinshader.structure.factory

Region
Abstract class that contains references to a region of a Chain of AminoAcids.

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.

Classes in org.proteinshader.structure used by org.proteinshader.structure.io

Structure
Structure is the top-level container for objects that store information on a protein structure from the Protein Data Bank.

Classes in org.proteinshader.structure used by org.proteinshader.structure.io.demos

Structure
Structure is the top-level container for objects that store information on a protein structure from the Protein Data Bank.

Classes in org.proteinshader.structure used by org.proteinshader.structure.sort

Drawable
This abstract class defines attributes and methods that are shared by all drawable objects, including the xyz-coordinates for the Drawable's center and methods that will allow each object to be sorted based on distance from the camera.

Classes in org.proteinshader.structure used by org.proteinshader.structure.visitor

AminoAcid
This concrete subclass of the abstract class Residue stores information on an amino acid in a PDB structure entry.

Atom
Extends abstract class Drawable to add data that is unique to an atom (atomID, type, temperature, occupancy, radius, etc.).

BetaStrand
This concrete subclass of Region holds information specific to a protein BetaStrand.

Bond
Extends abstract class Drawable to add data that is unique to a bond between two atoms.

Chain
A Chain serves as a container for Residues (AminoAcid, Heterogen, and Water) and Regions (Loop, Helix, and BetaStrand).

Description
A Description object serves as a container for the Category objects that hold Records describing a PDB structure entry.

Drawable
This abstract class defines attributes and methods that are shared by all drawable objects, including the xyz-coordinates for the Drawable's center and methods that will allow each object to be sorted based on distance from the camera.

Helix
This concrete subclass of Region holds information specific to a protein Helix.

Heterogen
This concrete subclass of the abstract class Residue stores information on a heterogen in a PDB structure entry.

Loop
This concrete subclass of Region holds information on the general "loop" regions found between well-defined regions of secondary structure (helices and beta-strands).

Model
A Model serves as a container for one or more Chains.

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.

Structure
Structure is the top-level container for objects that store information on a protein structure from the Protein Data Bank.

Water
This concrete subclass of the abstract class Residue stores information on a water molecule in a PDB structure entry.

Classes in org.proteinshader.structure used by org.proteinshader.structure.visitor.demos

Structure
Structure is the top-level container for objects that store information on a protein structure from the Protein Data Bank.

Classes in org.proteinshader.structure used by org.proteinshader.structure.visitor.modifiers

Atom
Extends abstract class Drawable to add data that is unique to an atom (atomID, type, temperature, occupancy, radius, etc.).

Drawable
This abstract class defines attributes and methods that are shared by all drawable objects, including the xyz-coordinates for the Drawable's center and methods that will allow each object to be sorted based on distance from the camera.

Segment
When a protein is drawn as a tube-like structure, a Segment is a length of the tube that corresponds to an AminoAcid.