Package org.jmol.util


package org.jmol.util
  • Class
    Description
    The BoxInfo class holds critical information about boundboxes.
     
    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
    Note: Color table is now in javajs/util/CU.java
     
    Implements a queue for a bash-like command history.
     
    Default implementation of the logger.
     
     
    sort from smallest to largest absolute
     
     
    Provides font support using a int fid (Font ID) as an index into font table.
     
    A collection of all methods necessary for initialization of and communication with the applet.
    J2SRequireImport is needed because we use ArrayUtil in a static method
     
     
     
    an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES strings
     
    Logger mechanism.
    Interface used for the logging mechanism.
    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.
     
     
    A class to allow for more complex vibrations and associated phenomena, such as modulated crystals, including Fourier series, Crenel functions, and sawtooth functions
    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
     
    Provides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookup
     
     
    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)
     
     
    All functions.
    minimal bond interface for SMILES and CIP
    Just the bare minimum for CIP, and non-BioSMILES
    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
     
     
    An adaptation of Marching Cubes that allows for indicating edges on triangles.
     
     
    A class to allow for more complex vibrations and associated phenomena, such as modulated crystals.