| BoxInfo |
The BoxInfo class holds critical information about boundboxes.
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| BSUtil |
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| C |
Note: Color table is now in javajs/util/CU.java
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| ColorEncoder |
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| CommandHistory |
Implements a queue for a bash-like command history.
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| ContactPair |
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| DefaultLogger |
Default implementation of the logger.
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| Edge |
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| EigenSort |
sort from smallest to largest absolute
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| Elements |
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| Escape |
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| GData |
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| GenericApplet |
A collection of all methods necessary for initialization of and communication with the applet,
whether it be JavaScript or Java.
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| Geodesic |
J2SRequireImport is needed because we use ArrayUtil in a static method
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| Int2IntHash |
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| Int2IntHashEntry |
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| 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
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| Logger |
Logger mechanism.
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| 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.
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| MeshSlicer |
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| MeshSurface |
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| Modulation |
A class to allow for more complex vibrations and associated phenomena, such
as modulated crystals, including Fourier series, Crenel functions, and
sawtooth functions
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| 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
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| Normix |
Provides quantization of normalized vectors so that shading for
lighting calculations can be handled by a simple index lookup
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| Parser |
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| PatternMatcher |
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| 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)
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| Rectangle |
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| Rgb16 |
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| Shader |
All functions.
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| 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
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| TempArray |
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| Tensor |
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| TriangleData |
An adaptation of Marching Cubes that allows for indicating edges on triangles.
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| Triangulator |
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| Txt |
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| Vibration |
A class to allow for more complex vibrations and associated
phenomena, such as modulated crystals.
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