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| Interface Summary | |
|---|---|
| JmolNode | |
| LoggerInterface | Interface used for the logging mechanism. |
| Class Summary | |
|---|---|
| ArrayUtil | |
| Base64 | |
| BinaryDocument | |
| BitSetUtil | |
| BoxInfo | |
| CifDataReader | |
| ColorEncoder | |
| CommandHistory | Implements a queue for a bash-like command history. |
| CompoundDocument | |
| ContactPair | |
| DCT | |
| DefaultLogger | Default implementation of the logger. |
| Dimension | |
| Eigen | Eigenvalues and eigenvectors of a real (n x n) symmetric matrix. |
| Elements | |
| Escape | |
| FastBitSet | |
| Huffman | |
| Int2IntHash | |
| Int2IntHash.Entry | |
| JmolEdge | |
| JmolMolecule | an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings |
| JpegEncoder | |
| JpegInfo | |
| KfDocument | |
| LimitedLineReader | |
| Logger | Logger mechanism. |
| Measure | |
| MeshSurface | |
| OutputStringBuffer | |
| Parser | |
| Point3fi | the Point3fi class allows storage of critical information involving an atom, picked bond, or measurement point, including: xyz position screen position screen radius (-1 for a simple point) index (for atoms or for an associated bond that has be picked) associated modelIndex (for measurement points) |
| Quadric | |
| Quaternion | |
| Rectangle | |
| SimpleUnitCell | general-purpose simple unit cell for calculations and as a super-class of unitcell, which is only part of Symmetry allows one-dimensional (polymer) and two-dimensional (slab) periodicity |
| SlowBitSet | |
| SurfaceFileTyper | |
| TempArray | |
| TextFormat | |
| TriangleData | |
| XmlReader | |
| XmlUtil | |
| ZipUtil | |
| Enum Summary | |
|---|---|
| JmolEdge.EnumBondOrder | |
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