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• org.openscience.miniJmol: Javadoc index of package org.openscience.miniJmol.


Package Samples:

• org.openscience.miniJmol

Classes:

• Gaussian98Reader: A reader for Gaussian98 output. Gaussian 98 is a quantum chemistry program by Gaussian, Inc. (http://www.gaussian.com/). Molecular coordinates, energies, and normal coordinates of vibrations are read. Each set of coordinates is added to the ChemFile in the order they are found. Energies and vibrations are associated with the previously read set of coordinates. This reader was developed from a small set of example output files, and therefore, is not guaranteed to properly read all Gaussian98 output. If you have problems, please contact the author of this code, not the developers of Gaussian98.
• BaseAtomType: The basic properties of an atom are represented by the atom type. Each atom type is identified with a unique string label. To ensure that only one atom type exists for each label, atom types can not be created, but only retrieved from a static pool of BaseAtomTypes. If the pool does contain an BaseAtomType for a given label, one will be created upon the first retreival.
• XYZReader: XYZ files may contain multiple ChemFrame objects, and may have charges and vector information contained along with atom types and coordinates. XYZ files must have a number of atoms at the beginning of each line then another line (which may be blank) to identify each frame.
• PDBReader: PDB files contain a single ChemFrame object. Only the END, ATOM and HETATM command strings are processed for now, and the ATOM and HETATM entries are only used for coordinate information.
• JmolJudeEditor: A little wrapper that permit to use JmolSimpleBean. !! Add POPUP support and call useful actions like ATOM view type and others...
• Matrix3D: A fairly conventional 3D matrix object that can transform sets of 3D points and perform a variety of manipulations on the transform
• AtomTypeSet: Collection of AtomTypes. No duplicates are allowed. This class is implemented with Hashtable to allow compatability with Java 1.1.
• AtomRenderer: Drawing methods for atoms. Modified from Massimo Zaniboni in order to transform in a SwingComponent
• ReaderFactory: A factory for creating ChemFileReaders. The type of reader created is determined from the input.
• JmolSimpleBean: Subset version of JMol which appears as a componant and can be controlled with strings.
• Atom: This class stores and manipulations information and properties of atoms.
• displayPanel: Modified from Massimo Zaniboni in order to obtain a Swing component
• ChemFileReader: An interface for reading output from chemistry programs.
• DisplaySettings: Stores the display style of graphical elements.
• CMLReader: CML files contain a single ChemFrame object.
• BondRenderer: Drawing methods for bonds.
• ArrowLine
• CMLHandler
• ChemFile
• ChemFrame
• DTDResolver
• JMolCDO
• JmolApplet
• JmolBeanTest

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