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See:
Description
| Packages | |
|---|---|
| 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.enums | Holds the enums needed by org.proteinshader.graphics and its subpackages. |
| org.proteinshader.graphics.exceptions | Holds the exception classes needed by org.proteinshader.graphics and its subpackages. |
| org.proteinshader.graphics.shader | Holds the classes needed for compiling and managing the vertex and fragment shaders used for texture mapping and custom lighting calculations. |
| org.proteinshader.graphics.textures | Holds the classes needed for creating and managing OpenGL texture objects. |
| org.proteinshader.graphics.typography | Holds the classes needed for applying text labels to the curved surfaces of tubes and ribbons. |
| 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 | Holds the gui components (JPanels and JMenus) needed by class ProteinShaderGUI. |
| org.proteinshader.gui.components.controlpanel | Holds the JPanels used in the right-side retractable control panel of the GUI. |
| org.proteinshader.gui.components.menubar | Holds the JMenus used in menu bar above the canvas. |
| org.proteinshader.gui.enums | Holds the enums needed by org.proteinshader.gui and its subpackages. |
| org.proteinshader.gui.exceptions | Holds the exception classes needed by org.proteinshader.gui and its subpackages. |
| org.proteinshader.gui.listeners | Holds the listener classes for the gui. |
| org.proteinshader.gui.listeners.controlpanel | Holds the listeners for components used in the JPanels of the right-side retractable control panel of the GUI. |
| org.proteinshader.gui.listeners.menubar | Holds the listeners for the items used in the JMenus of the menu bar above the canvas. |
| org.proteinshader.gui.utils | Holds minor utility classes needed by the Renderer. |
| org.proteinshader.gui.viewing | Holds important helper classes that the Renderer uses to control the view: Camera, Rotation, Lighting, etc. |
| org.proteinshader.math | The key classes in this package are Hermite and Quaternion, which are needed for generating the ribbons and tubes that are used to represent the backbone of a protein in a cartoon-type display. |
| 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.enums | Holds the enums needed by org.proteinshader.structure and its subpackages. |
| org.proteinshader.structure.exceptions | Holds the exception classes needed by org.proteinshader.structure and its subpackages. |
| 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.io.enums | Holds the enums needed for parsing Protein Data Bank structure files. |
| org.proteinshader.structure.io.exceptions | Holds the exception classes that may be needed when parsing Protein Data Bank structure files. |
| org.proteinshader.structure.io.filters | Holds filters for checking file extensions. |
| 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.enums | Holds enums needed by the Visitor classes. |
| org.proteinshader.structure.visitor.exceptions | Holds exception classes needed by 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). |
The ProteinShader program is a free open-source platform-independent molecular
visualization tool designed to produce illustrative renderings of proteins
that approximate what an artist might create using pen and ink.
ProteinShader is written primarily in Java, and uses JOGL (Java Bindings for
OpenGL) to call on the C language functions of OpenGL, a low-level graphics
library that is supported by most modern graphics cards. The texture
mapping and lighting calculations needed by ProteinShader are accomplished
using custom vertex and fragement shaders written in the OpenGL Shading
Language. The source code for the vertex and fragment shaders can be found
in the shaders directory of the ProteinShader distribution, while
the Java source code documented in this API can be found in the
src directory.
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