All Classes and Interfaces
Class
Description
A 4 element axis angle represented by single precision floating point
x,y,z,angle components.
The
About Dialog class is the help | about window for JSpecView.TODO: adf-2007.out causes failure reading basis functions
A reader for ADF output.
A reader for various AFLOW file types.
FHI-aims (http://www.fhi-berlin.mpg.de/aims) geometry.in file format
samples of relevant lines in geometry.in file are included as comments below
modified (May 1, 2011, hansonr@stolaf.edu) to account for atom/atom_frac lines
and to bring it into compliance with other load options (such as overriding
file-based symmetry or unit cell parameters).
A method to allow a JavaScript Ajax
A method to allow a JavaScript AJAX adapter to
deliver web content to JSmol.
For handling URL file IO via AJAX in JavaScript version
TRIPOS simple Alchemy reader.
class
AnIMLExporter contains static methods to export a Graph as
as AnIML.A reader for AMPAC output.
A reader for AMS output subclassing the older AdfReader.
Representation of a XML Source.
The
Annotation class stores the spectral x and pixel y values of an
annotation text along with its textA parser for output from 3DNA web service.
An interface to Jmol.Console.
The Main Class or Entry point of the JSpecView Application.
ArrayDataReader subclasses BufferedReader and overrides its
read, readLine, mark, and reset methods so that JmolAdapter
works with String[] arrays without any further adaptation.
note: YOU MUST RELEASE THE ITERATOR
A JFrame that allows for choosing an Atomset to view.
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
This class is used to transfer text or an image into the clipboard and to get tet from the clipboard.
AwtDialog extends JDialog, interpreting DialogManager's requests in terms of Swing and AWT.
A implementation of the
FileFilter that filters out all files
except those with extensions that are added.just a class I made to separate the construction of the AnnotationDialogs
from their use
generic 2D drawing methods -- AWT version
generic 2D drawing methods -- AWT version
JSVPanel class represents a View combining one or more GraphSets, each with
one or more JDXSpectra.
all popup-related awt/swing class references are in this file.
Dialog to set print preferences for JSpecview.
A javax.swing implementation of SwingComponent
that mirrors org.jmol.awtjs.swing for compatibility with
compilation with java2script.
A simple class that throws up a white rectangle that has a single centered
label.
byte converter
A very simple Binary CIF file reader extention of MMCifReader extends
CifReader.
Bilbao Crystallographic Database file reader
see, for example, http://www.cryst.ehu.es/cryst/compstru.html Comparison of
Crystal Structures with the same Symmetry
Note that this reader scrapes HTML.
DCD binary trajectory file reader.
A "BioPolymer" is a constructed set of contiguous (probably connected) "Monomers",
which may be one of Alpha (Calpha atoms), Amino (Calpha + backbone),
Phosphorus (P atoms), Nucleic (DNA/RNA), or Carbohydrate.
a class used by ModelLoader to handle all loading
of operations specific to PDB/mmCIF files.
Mps stands for Model-Polymer-Shape
When a Cartoon is instantiated with a call to setSize(),
it creates an MpsShape for each BioPolymer in the model set.
src: http://www.javaworld.com/article/2077542/learn-java/java-tip-43--how-to-
read-8--and-24-bit-microsoft-windows-bitmaps-in-java-applications.html
see also: http://en.wikipedia.org/wiki/BMP_file_format
Modified by Bob Hanson hansonr@stolaf.edu
The BoxInfo class holds critical information about boundboxes.
A class to read Bruker ZIP files and directories.
a fast 32-bit BitSet optimized for Java2Script -- about 25 times faster than
java.util.BitSet
A Binary Space Partitioning Forest
a Binary Space Partitioning Tree
Base class for both the compress and decompress classes.
A class to represent and produce Brillouin zone polyhedra and Wigner-Seitz
cells.
Note: Color table is now in javajs/util/CU.java
CASTEP (http://www.castep.org) .cell file format relevant section of .cell
file are included as comments below
preliminary .castep, .phonon frequency reader
-- hansonr@stolaf.edu 9/2011
-- Many thanks to Keith Refson for his assistance with this implementation
-- atom's mass is encoded as bfactor
-- FILTER options include
"q=n" where n is an integer
"q={1/4 1/4 0}"
"q=ALL"
-- for non-simple fractions, you must use the exact form of the wavevector description:
-- load "xxx.phonon" FILTER "q=(-0.083333 0.083333 0.500000)
-- for simple fractions, you can also just specify SUPERCELL {a b c} where
the number of cells matches a given wavevector -- SUPERCELL {4 4 1}, for example
note: following was never implemented?
-- following this with ".1" ".2" etc.
An input stream that decompresses from the BZip2 format (without the file
header chars) to be read as any other stream.
Minimal ChemDraw CDXML writer just converts CDX to CDXML involving just the
basic necessities for XmlCDXReader.
A reader for ChemDraw binary CDX files.
A reader for TOPOS systre file Crystal Graph Data format.
Something like a PyMOL Compiled Graphical Object, but more interesting!
A Model is a collection of Chains of Groups of Atoms.
A legacy Chime-compatible messenger.
Fully implemented 2016.12.1
see http://journals.iucr.org/j/issues/2016/01/00/aj5269/index.html
Will deliver JSON versions of the data while file reading and Java List/Map structures when
called by
x = getProperty("cifInfo", filename)
Validated using the test-data suite by John Bollinger (John.Bollinger@stjude.org)
found at https://github.com/COMCIFS/cif_api
Preliminary Cif2 reader.
A CIF 1.0 tokenizer class for dealing with quoted strings in CIF files.
A true line-free CIF file reader for CIF files.
An XCrysDen XSF writer
see http://www.xcrysden.org/doc/XSF.html
A fully validated relatively efficient implementation of Cahn-Ingold-Prelog
rules for assigning R/S, M/P, and E/Z stereochemical descriptors.
A helper class to handle application-specific analysis and store
information needed by CIPChirality and CIPDataSmiles.
A subclass that allows Jmol processing of SMILES using
"...smiles...".find("SMILES","chirality")
An optional class to track digraph paths to decisions.
Implements flat circle drawing/filling routines.
The abstract class for the client protocol that defines members
common to both the server-side and client-side protocols.
Represents the connection to the GestureServer.
ClientToServerProtocol implements the Client side protocol.
A reader for CrystalMaker CMDF binary/text files.
class
CMLExporter contains static methods to export a Graph as
as CIML.An XCrysDen XSF writer
see http://www.xcrysden.org/doc/XSF.html
ColoredAnnotation is a label on the spectrum; not an integralRegion
This a representation of the Display Scheme for the spectral display.
CommandHistory keeps a command history and responds to key events
Implements a queue for a bash-like command history.
Contains conversion methods that are needed by several elements of the
Gesture Server.
The
Coordinate class stores the x and y values of a coordinate.A reader of OUT and OUTP files for CRYSTAL
http://www.crystal.unito.it/
CSF file reader based on CIF idea -- fluid property fields.
ColorUtility
Iterator used for finding all points within a box or a hemi-box
Gaussian cube file format
http://www.cup.uni-muenchen.de/oc/zipse/lv18099/orb_MOLDEN.html
this is good because it is source code
http://ftp.ccl.net/cca/software/SOURCES/C/scarecrow/gcube2plt.c
http://www.nersc.gov/nusers/resources/software/apps/chemistry/gaussian/g98/00000430.htm
distances are in Bohrs because we are reading Gaussian cube OUTPUT files
not Gaussian cube INPUT files.
change QS.MAX_TYPE_SUPPORTED if you implement this
adds spherical H orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds spherical I orbital contributions
adds 7 spherical F orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 9 spherical G orbital contributions
adds 10 cartesian F orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 15 cartesian G orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 21 cartesian H orbital contributions
change QS.MAX_TYPE_SUPPORTED if you implement this
adds 28 cartesian I orbital contributions
Just a simple abstract class to join a String reader and a String[]
reader under the same BufferedReader umbrella.
A class to insert a JavaScript debug statement for Firefox or Chrome debugger
Default implementation of the logger.
created to remove ambiguities and make a simpler DecimalFormat
A reader for Dgrid BASISFILE data.
Dialogs include Integration, PeakListing, Views, OverlayLegend, and Measurements
These dialogs have been generalized for platform independence.'
This manager is subclassed as AwtDialogManager and JsDialogManager, which apply their
own interpretation of how to create the dialog and get its event callbacks.
DialogParams handles all the platform-independent
needs of AwtAnnotationDialog and subclasses of it.
DisplaySchemesProcessor loads and saves the display schemes of
Jspecview.The original non-JSON parser for output from 3DNA web service.
A parser for output from 3DNA web service.
Eigenvalues and eigenvectors of a real matrix.
This interface must be implemented by all user-defined events.
This is an enumeration of all event types currently available.
FoldingAtHome json reader.
JFileChooser with possibility to fix size and location
A simple Dropping class to allow files to be dragged onto a target.
A simple Dropping class to allow files to be dragged onto a target.
File previsualisation before opening
open a set of models residing in different files
This reader is for current.xyz files generated by Folding@Home project
(see http://folding.stanford.edu)
I have not found a precise description of the file format.
Provides font support using a int fid
(Font ID) as an index into font table.
A generic interface for font queries.
MMFF94 implementation 5/14/2012
- fully validated for atom types and charges
- reasonably well validated for energies (see below)
- TODO: add UFF for preliminary/backup calculation
Reader for Gaussian fchk files
for vibrational modes, add Freq=(SaveNormalModes,Raman,VibRot)
also allows appended freq data
Reader for Gaussian 94/98/03/09 output files.
Reader for Gaussian Wfn files -- not implemented yet
A collection of all methods necessary for initialization of and communication with the applet.
GenericColor allows both java.awt.Color and org.jmol.awtjs.swing.Color to be
handled by methods that need not distinguish between them.
The overall parent of all popup classes in Jmol and JSmol.
Class abandoned as unnecessary in SwingJS
NBO file nn reader will pull in other files as necessary
acknowledgments: Grange Hermitage, Frank Weinhold
upgrade to NBO 6 allows reading of resonance structures, including base structure
J2SRequireImport is needed because we use ArrayUtil in a static method
Defines the interface that all user-defined gestures must implement.
The main gesture server class.
This class is a place for the enum GestureType to stand.
Reads Ghemical (
http://www.uku.fi/~thassine/ghemical)
molecular mechanics (*.mm1gp) files.
GifEncoder extensively adapted for Jmol by Bob Hanson
Color quantization roughly follows the GIMP method
"dither Floyd-Steinberg (normal)" but with some twists.
Provides high-level graphics primitives for 3D visualization for the software
renderers.
Represents a group of touch points
for the gesture server.
The essential container for every atom.
The language list is now in org.jmol.i18n.Language -- Bob Hanson, 12/16/12
implementing translations in JavaScript
Problems identified (Bob Hanson) --
-- Coordinates for the asymmetric unit are conventional.
Enum for hydrogen bonding donor/acceptor type
Implementation of hermite curves for drawing smoothed curves
that pass through specified points.
The history file contains data from previous uses of Jmol.
The window.Event in HTML5
See SwingController.
Support for .hin, HyperChem's native file format.
Generic abstract image creator:
(1) set parameters
(2) encode the image bytes, if necessary
(3) generate the image
This class adapts Richard Apodaca's 2020 molfile-to-inchi LLVM-derived Web Assembly
implementation of IUPAC InChI v.
Represents a connection to the input device.
from IntegralGraph
a data structure for integration settings
Dialog for managing the integral listing for a Spectrum within a GraphSet
Exception thrown for invalid SMILES String
methods in j2s JavaScript accessed in Jmol
Jaguar reader tested for the two samples files in CVS.
A reader for Jana M50+M40 file pairs.
A preliminary reader for JCAMP-DX files having ##$MODELS= and ##$PEAKS=
records
Designed by Robert Lancashire and Bob Hanson
specifications (by example here):
##$MODELS= acetophenone
DSViewer 3D 0
17 17 0 0 0 0 0 0 0 0999 V2000 ...
There is really no need here for awt.Dialog.
spectrum data AS READ FROM FILE
JDXDecompressor contains static methods to decompress the data part of
JCAMP-DX spectra that have been compressed using DIF, FIX, SQZ or PAC
formats.
class
JDXExporter contains methods for exporting a
JCAMP-DX Spectrum in one of the compression formats DIF, FIX, PAC, SQZ or
as x, y values.could be a spectrum or a source
Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS.
JDXFileReader reads JDX data, including complex BLOCK files that
contain NTUPLE blocks or nested BLOCK data.JDXSource is representation of all the data in the JCAMP-DX file
or source.A simple implementation of a Swing JTextPane.
Do nothing , support for JSME code splitting.
A callback meant to be used by
Java2Script rendition of Jmol using HTML5-only or WebGL-based graphics
The JmolAdapter interface defines the API used by the JmolViewer to
read external files and fetch atom properties necessary for rendering.
This is the API of methods that are available to JavaScript
via LiveConnect to the Jmol applet.
JmolData file reader, for a modified PDB format
An abstract popup class that is
instantiated for a given platform and
context as one of:
an independent class utilizing only org.jmol.api.JmolNode, not org.jmol.modelset.Atom
for use in finding molecules in models and SMILES strings
An abstract popup class that is
instantiated for a given platform and
context as one of:
Provides access to resources (for example, strings and images).
listen to atom selections in a Jmol Viewer
methods in JSmol JavaScript accessed in Jmol
allows Jmol to implement multitouch testing using the mouse
press CTRL-LEFT and drag twice for a two-stroke multitouch gesture
that will be sent to the server in an interlaced fashion.
JmolViewer is the main API for the Viewer class.
JpegEncoder - The JPEG main program which performs a jpeg compression of an
image.
just a class I made to separate the construction of the AnnotationDialogs
from their use
A DialogManager for JavaScript.
A class to output WebGL graphics.
A flag that this object is really a JavaScript function that, for example,
might be called from setTimeout().
generic 2D drawing methods for JSpecView -- JavaScript version
generic 2D drawing methods -- JavaScript version
called by JSmol JavaScript methods using
this._applet.xxxx()
a very simple JSON parser for JSON objects that are compatible with JavaScript
A gross simplification of https://github.com/douglascrockford/JSON-java
A SUBSET of JSON with similarly to window.JSON.parse():
In JavaScript returns "null" for a null value, not null
-- requires quoted strings for keys and values
-- does not allow /xxx/ objects
a client of a JsonNioService -- just needs notices of the service shutting
down or indicating that a banner needs to be changed.
A class for interacting with Jmol over local sockets.
JSVPanel class represents a View combining one or more GraphSets, each with one or more JDXSpectra.
The Main Class or Entry point of the JSpecView Application.
JavaScript 2D canvas version requires Ajax-based URL stream processing.
For menus, popup-related awt/swing class references are in this file.
JSpecView Applet class.
Entry point for the web.
A signed applet that has an Advanced...
JSVException is the base class from which all exceptions in JSpecView
is inherited.
This class encapsulates all general functionality of applet and app.
and interface for JSpecView for the Jmol application
Reads the entire contents of a ZIP file as though it were one straight file
Skips and entry that contains '\0'
Allows for a moderate amount of buffered reading via mark()
A simple implementation of a Swing JTextPane.
A borderless rectangle, like the applet, that contains the application for
use in kiosk-style displays, as for example projected on the wall as in
http://molecularPlayground.org
A simple class to read a designated number of bytes from a
file and then return them line by line, skipping lines that
start with #, and including the \n or \r characters at line ends.
VectorDataReader subclasses BufferedReader and overrides its
read, readLine, mark, and reset methods so that JmolAdapter
works with Vector arrays without any further adaptation.
Represents a 2D location with float values.
Logger mechanism.
Interface used for the logging mechanism.
created to remove ambiguities in add and remove
A single precision floating point 3 by 3 matrix.
A base class for both M3 and M4 to conserve code size.
A single precision floating point 4 by 4 matrix.
The Main Class or Entry point of the JSpecView Application.
streamlined and refined for Jmol by Bob Hanson
from http://math.nist.gov/javanumerics/jama/
Jama = Java Matrix class.
Amber Coordinate File Reader
not a stand-alone reader -- must be after COORD keyword in LOAD command
A reader for Amber Molecular Dynamics topology files --
requires subsequent COORD "xxxx.mdcrd" file
Calculates the difference between calculated and experimental values for coloring table
The
Measurement class stores an annotation that is a measurementDialog for managing the measurement list
for a Spectrum within a GraphSet
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.
an abstract class subclasssed by BioShapeRenderer, DrawRenderer, and IsosurfaceRenderer
A simple MessagePack reader.
not implemented -- would be a force toward a given position in space
mmCIF files are recognized prior to class creation.
JmolData RCSB MMTF (macromolecular transmission format) file reader
see https://github.com/rcsb/mmtf/blob/master/spec.md
Note added 2024.01.19
Jose Duarte 2:03 PM (email)
to MMTF-Users From July 2024 the PDB file archive will not be offered in the
compressed MMTF format anymore.
An abstract popup class that is instantiated for a given platform and context
as one of:
An abstract popup class that is instantiated for a given platform and context
as one of:
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
A minimal multi-file reader for TRIPOS SYBYL mol2 files.
3D only
A molecular structure and orbital reader for MolDen files.
A reader for MDLI mol and sdf files.
A class to maintain information about biomolecule groups that are (potentially)
part of biopolymers -- peptides, nucleic acid strands, or complex carbohydrates.
Mopac Archive reader -- presumes "zMatrix" is really Cartesians
use FILTER "NOCENTER" to NOT center atoms in unit cell
use CENTROID for complete molecules with centroids within unit cell
use PACKED CENTROID for complete molecules with any atoms within unit cell
Reads Mopac 2007 GRAPHF output files
Reads Mopac 93, 6, 7, 2002, or 2009 output files
General methods for reading molecular orbital data, including embedded output
from the NBO program.
JavaScript interface from JmolJSmol.js via handleOldJvm10Event (for now)
Modulated Structure Reader Interface
generalized modulated structure reader class for CIF and Jana
-- includes Fourier, Crenel, Sawtooth, Legendre; displacement, occupancy, and Uij
-- handles up to 6 modulation wave vectors
-- commensurate and incommensurate, including composites
-- not handling _cell_commen_t_section_1
Navigator is a user input mechanism that utilizes the keypad to drive through
the model.
Defines the port the server will be listening for connections on.
Implements some lost interfaces.
Class for calculating NOE intensities by full matrix relaxation approach.
Provides access to resources (for example, strings and images).
Provides quantization of normalized vectors so that shading for
lighting calculations can be handled by a simple index lookup
extends CartoonRenderer for nucleics
A reader for NWChem 4.6
NWChem is a quantum chemistry program developed at
Pacific Northwest National Laboratory.
A generic output method.
A (preliminary) reader for OPTIMADE resources.
Reads ORCA input and output files
Reads ORCA input and output files
Dialog for showing the legend or key for overlaid plots in a
JSVPanel.P2N file reader.
A 3 element point that is represented by single precision floating point
x,y,z coordinates.
A 3 element point that is represented by signed integer x,y,z coordinates.
A 4 element point that is represented by single precision floating point
x,y,z,w coordinates.
Enum for animation mode.
JSVPanel class draws a plot from the data contained a instance of a
Graph.Super-simplified for JavaScript
PDB file reader.
An XCrysDen XSF writer
see http://www.xcrysden.org/doc/XSF.html
A relatively primitive PDF generator that just makes a document with an image
in it.
A class that creates the PDF document specific to JSpecView using
javajs.export.PDFCreator.
a data structure for peak lists
Dialog for managing the peak listing
for a Spectrum within a GraphSet
WebGL interface
JavaScript 2D canvas version requires Ajax-based URL stream processing.
A class called by reflection from IsosurfaceMesh from the Jmol command
WRITE xxxx.pmesh (ascii)
or
WRITE xxxx.pmb (binary)
Modified by Bob Hanson hansonr@stolaf.edu to be a subclass of ImageEncoder
and to use javajs.util.OutputChannel instead of just returning bytes.
Just a marker for resourceClass.getClass().getResource(resourceName);
Jmol now reads the PO files directly for its translations.
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)
A dialog for controling the creation of a povray input file from a Chemframe
and a display.
see http://netpbm.sourceforge.net/doc/ppm.html
PQR file reader.
Note added 4/2015 BH:
Well, it turns out that the calculation of the intermediate pixel z value
in all methods involving rasterization of lines is incorrect and has been
incorrect since Jmol's inception.
Dialog to change the preferences for the application.
PrintLayout class stores all the information needed from the
PrintLayoutDialogThe PropertyManager handles all operations relating to delivery of properties
with the getProperty() method, or its specifically cast forms
getPropertyString() or getPropertyJSON().
Reader for Psi3 output files.
a combination of Parsing and Text-related utility classes
crude PWmat atom.config reader
http://pwmatus.com/manual
A writer for PWMAT atom.config files.
PyMOL PSE (binary Python session) file reader.
A reader for Q-Chem 2.1 and 3.2
Q-Chem is a quantum chemistry program developed
by Q-Chem, Inc.
A molecular structure and orbital reader for MolDen files.
A very experimental class for writing QCJSON files.
A general Java class for working with QCShema units and array types.
Constants and static methods for quantum shells.
Allows modification of the planes prior to isosurface creation
Used by Noncovalent Interaction Calculation for progressive readers
A general helper class for a variety of stream and reader functionality
including:
stream and byte magic-number decoding for PNG, PNGJ, ZIP, and GZIP streams
various stream/reader methods, including UTF-encoded stream reading
reflection-protected access to a CIF parser and ZIP tools
Interesting thing here is that JavaScript is 3x faster than Java in handling strings.
SwingComponent interface common to javax.swing and org.jmol.awtjs.swing
Can be augmented as needed, provided classes of org.jmol.awtjs.swing are also
updated.
Stores information
about scale and range that
JSVPanel needs to to display a
graph with a single plot.Error handling for ScriptEvaluator, ScriptProcess, and ScriptParams
Reverse Polish Notation Engine for IF, SET, and @{...}
Just a (not so simple?) RPN processor that can handle boolean, int, float,
String, Point3f, BitSet, Array, Hashtable, Matrix3f, Matrix4f
-- Bob Hanson 2/16/2007
The ScriptParam class holds methods used to parse parameters
in Jmol scripts.
ScriptToken takes care of script command processing
Represents the server to client connection.
All functions.
Shape now encompasses:
AtomShape (abstract)
|
Balls, Dots, Ellipsoids, Halos, Labels, Polyhedra, Stars, Vectors
|
GeoSurface
BioShapeCollection (abstract)
|
Backbone, Cartoon, MeshRibbon, Ribbons, Rockets, Strands, Trace
Dipoles
FontLineShape (abstract)
|
Axes, Bbcage, Frank, Uccage
Measures
MeshCollection (abstract)
| |
Draw Isosurface
|
LcaoCartoon, MolecularOrbital, Pmesh
Sticks
|
Hsticks, Sssticks
TextShape (abstract)
|
Echo, Hover
A reader for SHELX output (RES) files.
BH note: this reader was never set up to read Z-matrix structures such as benzenev4.1.fdf
SIESTA http://www.icmab.es/siesta/
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
SINGLE_POINT_GESTURE
only passes single-touch gestures.
This class represents an atom in a
SmilesMolecule.Bond in a SmilesMolecule
Double bond, allene, square planar and tetrahedral stereochemistry only
not octahedral or trigonal bipyramidal.
Originating author: Nicholas Vervelle
A class to handle a variety of SMILES/SMARTS-related functions, including: --
determining if two SMILES strings are equivalent -- determining the molecular
formula of a SMILES or SMARTS string -- searching for specific runs of atoms
in a 3D model -- searching for specific runs of atoms in a SMILES description
-- generating valid (though not canonical) SMILES and bioSMILES strings --
getting atom-atom correlation maps to be used with biomolecular alignment
methods
Parses a SMILES string or SMARTS pattern to create a
SmilesSearch.A class to build and carry out a SMILES or SMARTS match
This class relates to stereochemical issues
A general class to deal with Hermann-Mauguin or Hall names
Bob Hanson 9/2006
references: International Tables for Crystallography Vol.
A relatively simple space group finder given a unit cell.
The Client interface must be implemented in all clients wishing
to connect to the Sparsh-UI gesture server.
A class to isolate Spartan file reading methods from the rest of Jmol.
JDXSpectrum implements the Interface Spectrum for the display of
JDX Files.
Implements high performance rendering of shaded spheres.
StateCreator handles all aspects of working with the "state" as
generally defined, including
-- creating the state script
-- general output, including logging
-- handling undo/redo
-- processing SYNC directives
Called by reflection only; all state generation script here, for
modularization in JavaScript
The StatusManager class handles all details of status reporting, including:
1) saving the message in a queue that replaces the "callback" mechanism,
2) sending messages off to the console, and
3) delivering messages back to the main Jmol.java class in app or applet
to handle differences in capabilities, including true callbacks.
Class that holds the surface status information that the surface tool needs.
ScriptVariable class
class
SVGExporter contains static methods to export a Graph as
as SVG.SwingController is an interface that org.jmol.awtjs.swing classes will need.
A class to handle requests for information about space groups and symmetry
operations.
Script token class.
A generic 3 element tuple that is represented by single precision floating
point x,y and z coordinates.
A generic 3 element tuple that is represented by double precision floating
point x,y and z coordinates.
A 3-element tuple represented by signed integer x,y,z coordinates.
A generic 4 element tuple that is represented by single precision floating
point x,y,z and w coordinates.
simple Tinker format requires Tinker:: prefix:
load Tinker::mydata.xyz
1/2014 hansonr@stolaf.edu
see https://github.com/COMCIFS/TopoCif
Basic idea:
We have TLinks, TNodes, and TAtoms
TLinks each have two TNodes and may also be associated with bridging TAtom
sets.
Represents a touch point.
Defines the types of touches that can ocurr in sparsh-UI:
Birth, Move, and Death.
An adaptation of Marching Cubes that allows for indicating edges on triangles.
renders triangles
TWO_POINT_GESTURE
This gesture requires two points of contact, but its type is not initially
defined.
a class pseudoprivate to the org.jmol.symmetry and org.jmol.applet.smarter.FileSymmetry
to be accessed generally only through the SymmetryInterface API
adds vertices and offsets orientation,
and a variety of additional calculations that in
principle could be put in SimpleUnitCell
if desired, but for now are in this optional package.
A 3-element vector that is represented by single precision floating point
x,y,z coordinates.
A reader for Accelrys V3000 files.
A 3 element vector that is represented by double precision floating point
x,y,z coordinates.
http://cms.mpi.univie.ac.at/vasp/vasp/CHGCAR_file.html
very simple reader of just the header information.
http://cms.mpi.univie.ac.at/vasp/
adjusted for AFLOW options - adding element names, environment radius on atom line
http://cms.mpi.univie.ac.at/vasp/
A class to allow for more complex vibrations and associated
phenomena, such as modulated crystals.
Stores information that
GraphSet needs
to display a view with one or more spectra.Dialog for managing overlaying spectra and closing files
Visible class - for prediction of colour from visible spectrum
see
Robert J.
A molecular orbital reader for WebMO files.
A reader for Wein2k DFT files.
A class to calculate, store, and retrieve Wyckoff information as per
BCS nph-trgen at
https://www.cryst.ehu.es/cgi-bin/cryst/programs//nph-trgen?gnum=146&what=wpos&trmat=2/3a+1/3b+1/3c,-1/3a+1/3b+1/3c,-1/3a-2/3b+1/3c&unconv=R%203%20:R&from=ita
For the 611 standard setting in ITA GENPOS, we are just reading the json file and
loading its information.
A crude ArgusLab .agl file Reader - http://www.planaria-software.com/
Use this reader as a template for adding new XML readers.
A reader for CambridgeSoft CDXML files.
An chem3d c3xml reader
A CML2 Reader -
If passed a bufferedReader (from a file or inline string), we
generate a SAX parser and use callbacks to construct an
AtomSetCollection.
a SAX handler -- Java only
A Molpro 2005 reader
An abstract class accessing MOReader -- currently just for XmlMolproReader only.
An Odyssey xodydata reader
QuantumEspresso XML reader
A generic XML reader template -- by itself, does nothing.
A very simplistic XML generator
Vasp vasprun.xml reader
An XML reader for Materials Studio .xsd files http://accelrys.com/products/materials-studio/
Bob Hanson hansonr@stolaf.edu 6/3/09
An XCrysDen XSF writer.
A class used by AtomSetCollection for building the symmetry of a model and
generating new atoms based on that symmetry.
A class only used by adapter.smarter.XtalSymmetry while building the
file-based model.
Minnesota SuperComputer Center XYZ file format
simple symmetry extension via load command:
9/2006 hansonr@stolaf.edu
setAtomCoord(atom)
applySymmetryAndSetTrajectory()
extended to read XYZI files (Bob's invention -- allows isotope numbers)
extended to read XYZ files with fractional charges as, for example:
http://www.ccl.net/cca/software/SOURCES/FORTRAN/molden/test/reacpth.xyz
http://web.archive.org/web/20000120031517/www.msc.edu/msc/docs/xmol/v1.3/g94toxyz.c
Note the JSmol/HTML5 must use its own version of java.util.zip.ZipOutputStream.
Bob Hanson -- using this for Jmol; added ZStream.getBytes(s)
ZStream
deprecated? Not for public use in the future.
Class to export Wavefront OBJ files.
STereoLithography file format exporter
for 3D printing.
A basic VRML generator.