Package org.jmol.util
package org.jmol.util
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ClassDescriptionThe 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.sptNote: Color table is now in javajs/util/CU.javaImplements a queue for a bash-like command history.Default implementation of the logger.sort from smallest to largest absoluteProvides 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 methodan independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom for use in finding molecules in models and SMILES stringsLogger 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 functionsA 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 occupancyProvides quantization of normalized vectors so that shading for lighting calculations can be handled by a simple index lookupthe 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 CIPJust the bare minimum for CIP, and non-BioSMILESgeneral-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) periodicityAn 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.