# Package org.jmol.util

package org.jmol.util

Class
Description
BoxInfo
The BoxInfo class holds critical information about boundboxes.
BSUtil
BZone
A class to represent and produce Brillouin zone polyhedra and Wigner-Seitz cells.
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
Elements
Escape
Font
Provides font support using a int 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.
Geodesic
J2SRequireImport is needed because we use ArrayUtil in a static method
Int2IntHash
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.
LoggerInterface
Interface used for the logging 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
Node
Normix
Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
Parser
PatternMatcher
PatternMatcher.JSPattern
Super-simplified for JavaScript
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) associated symmetry operation (generating equivalent atoms in UnitCell.java)
Rectangle
Rgb16
Shader
All functions.
SimpleEdge
minimal bond interface for SMILES and CIP
SimpleNode
Just the bare minimum for CIP, and non-BioSMILES
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.