org.jmol.util
Date: 2019-10-22

# Package org.jmol.util

- Interface Summary
  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 Summary
  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 Summary
  Enum | Description
  --- | ---
  Edge.EnumBondOrder |