| Interface | Description |
|---|---|
| LoggerInterface |
Interface used for the logging mechanism.
|
| Node | |
| SimpleEdge |
minimal bond interface for SMILES and CIP
|
| SimpleNode |
Just the bare minimum for CIP, and non-BioSMILES
|
| Class | Description |
|---|---|
| BoxInfo |
The BoxInfo class holds critical information about boundboxes.
|
| BSUtil | |
| BZone |
class to represent and produce Brillouin zone polyhedra and Wigner-Seitz
cells
based on https://chemapps.stolaf.edu/jmol/jsmol/spt/ext/xtal/bz.spt
|
| C |
Note: Color table is now in javajs/util/CU.java
|
| ColorEncoder | |
| CommandHistory |
Implements a queue for a bash-like command history.
|
| ContactPair | |
| DefaultLogger |
Default implementation of the logger.
|
| Edge | |
| EigenSort |
sort from smallest to largest absolute
|
| Elements | |
| Escape | |
| Font |
Provides font support using a byte fid
(Font ID) as an index into font table.
|
| GData | |
| GenericApplet |
A collection of all methods necessary for initialization of and communication with the applet,
whether it be JavaScript or Java.
|
| Geodesic |
J2SRequireImport is needed because we use ArrayUtil in a static method
|
| Int2IntHash | |
| Int2IntHashEntry | |
| JmolAudio | |
| 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
|
| JSONWriter | |
| Logger |
Logger mechanism.
|
| MeshCapper |
A class to properly cap a convoluted, closed slice of an isosurface
inspired by: Computational Geometry: Algorithms and Applications Mark de
Berg, Marc van Kreveld, Mark Overmars, and Otfried Schwarzkopf
Springer-Verlag, Berlin Heidelberg 1997 Chapter 3.
|
| MeshSlicer | |
| MeshSurface | |
| Modulation |
A class to allow for more complex vibrations and associated phenomena, such
as modulated crystals, including Fourier series, Crenel functions, and
sawtooth functions
|
| ModulationSet |
A class to group a set of modulations for an atom as a "vibration" Extends V3
so that it will be a displacement, and its value will be an occupancy
|
| MolWriter | |
| Normix |
Provides quantization of normalized vectors so that shading for
lighting calculations can be handled by a simple index lookup
|
| Parser | |
| PatternMatcher | |
| 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)
|
| Rectangle | |
| Rgb16 | |
| Shader |
All functions.
|
| 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
|
| TempArray | |
| Tensor | |
| TriangleData |
An adaptation of Marching Cubes that allows for indicating edges on triangles.
|
| Triangulator | |
| Txt | |
| Vibration |
A class to allow for more complex vibrations and associated
phenomena, such as modulated crystals.
|
| Enum | Description |
|---|---|
| Edge.EnumBondOrder |