| Name | Description | Type | Package | Framework |
| Atom | Class | org.jscience.chemistry.gui.extended.molecule | JScience | |
| AtomVector | Tripos AtomVector classFields inherited from class java. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| Bond | Class | org.jscience.chemistry.gui.extended.molecule | JScience | |
| BondVector | Tripos BondVector classFields inherited from class java. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| Matrix3D | A fairly conventional 3D matrix object that can transform sets of 3D points and perform a variety of manipulations on the transform. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| Molecule | Tripos base molecule classSee Also:AtomVector, | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| MoleculeVector | Tripos MoleculeVector classFields inherited from class java. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| MolTranslateMOL2 | Translates Tripos MOL2 files to/from Tripos Java Molecule format. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| Parser | Reads and parses a Tripos Java Molecule (JMol) stream into a JMol class. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| PropAttributes | This is a base class which the Atom and Bond classes include. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| PropAttributesInter | Interface | org.jscience.chemistry.gui.extended.molecule | JScience | |
| Renderer | An implementation of a JViewer's renderer interface for drawing and manipulating a Molecule. | Class | org.jscience.chemistry.gui.extended.molecule | JScience |
| Ring | Class | org.jscience.chemistry.gui.extended.molecule | JScience | |
| RingVector | Tripos RingVector classSee Also:Serialized Form | Class | org.jscience.chemistry.gui.extended.molecule | JScience |