Downloads:

73,810

Downloads of v 14.21.1:

280

Last Update:

10/24/2017

Package Maintainer(s):

Software Author(s):

  • The Jmol Development Team

Tags:

jmol chemistry molecule rendering viewer java

Jmol molecule viewer

This is not the latest version of Jmol molecule viewer available.

14.21.1 | Updated: 10/24/2017

Downloads:

73,810

Downloads of v 14.21.1:

280

Maintainer(s):

Software Author(s):

  • The Jmol Development Team

Jmol molecule viewer 14.21.1

This is not the latest version of Jmol molecule viewer available.

All Checks are Passing

2 Passing Test


Validation Testing Passed


Verification Testing Passed

Details

To install Jmol molecule viewer, run the following command from the command line or from PowerShell:

>

To upgrade Jmol molecule viewer, run the following command from the command line or from PowerShell:

>

To uninstall Jmol molecule viewer, run the following command from the command line or from PowerShell:

>

NOTE: This applies to both open source and commercial editions of Chocolatey.

1. Ensure you are set for organizational deployment

Please see the organizational deployment guide

  • Open Source or Commercial:
    • Proxy Repository - Create a proxy nuget repository on Nexus, Artifactory Pro, or a proxy Chocolatey repository on ProGet. Point your upstream to https://chocolatey.org/api/v2. Packages cache on first access automatically. Make sure your choco clients are using your proxy repository as a source and NOT the default community repository. See source command for more information.
    • You can also just download the package and push it to a repository Download

3. Enter your internal repository url

(this should look similar to https://chocolatey.org/api/v2)

4. Choose your deployment method:


choco upgrade jmol -y --source="'STEP 3 URL'" [other options]

See options you can pass to upgrade.

See best practices for scripting.

Add this to a PowerShell script or use a Batch script with tools and in places where you are calling directly to Chocolatey. If you are integrating, keep in mind enhanced exit codes.

If you do use a PowerShell script, use the following to ensure bad exit codes are shown as failures:


choco upgrade jmol -y --source="'STEP 3 URL'" 
$exitCode = $LASTEXITCODE

Write-Verbose "Exit code was $exitCode"
$validExitCodes = @(0, 1605, 1614, 1641, 3010)
if ($validExitCodes -contains $exitCode) {
  Exit 0
}

Exit $exitCode

- name: Ensure jmol installed
  win_chocolatey:
    name: jmol
    state: present
    version: 14.21.1
    source: STEP 3 URL

See docs at https://docs.ansible.com/ansible/latest/modules/win_chocolatey_module.html.

Coming early 2020! Central Managment Reporting available now! More information...


chocolatey_package 'jmol' do
  action    :install
  version  '14.21.1'
  source   'STEP 3 URL'
end

See docs at https://docs.chef.io/resource_chocolatey_package.html.


Chocolatey::Ensure-Package
(
    Name: jmol,
    Version: 14.21.1,
    Source: STEP 3 URL
);

Requires Otter Chocolatey Extension. See docs at https://inedo.com/den/otter/chocolatey.


cChocoPackageInstaller jmol
{
   Name     = 'jmol'
   Ensure   = 'Present'
   Version  = '14.21.1'
   Source   = 'STEP 3 URL'
}

Requires cChoco DSC Resource. See docs at https://github.com/chocolatey/cChoco.


package { 'jmol':
  provider => 'chocolatey',
  ensure   => '14.21.1',
  source   => 'STEP 3 URL',
}

Requires Puppet Chocolatey Provider module. See docs at https://forge.puppet.com/puppetlabs/chocolatey.


salt '*' chocolatey.install jmol version="14.21.1" source="STEP 3 URL"

See docs at https://docs.saltstack.com/en/latest/ref/modules/all/salt.modules.chocolatey.html.

5. If applicable - Chocolatey configuration/installation

See infrastructure management matrix for Chocolatey configuration elements and examples.

This package was approved as a trusted package on 10/24/2017.

Description

Jmol is a free, open source molecule viewer for students, educators, and researchers in chemistry and biochemistry.

Features

  • Free, open-source software licensed under the GNU Lesser General Public License
  • Applet, Application, and Systems Integration Component*
  • Multi-language
  • Cross-platform
  • Supports all major web browsers: Internet Explorer, Mozilla and Firefox, Safari, Google Chrome, Opera, Konqueror, IceWeasel, ...
  • High-performance 3D rendering with no hardware requirements
  • File formats (see also the file formats section within Jmol Wiki):
    • MOL MDL / Elsevier / Symyx structure (classic version V2000)
    • V3000 MDL / Elsevier / Symyx structure (new version V3000)
    • SDF MDL / Elsevier / Symyx structure (multiple models)
    • CTFile MDL / Elsevier / Symyx chemical table (generic)
    • CIF Crystallographic Information File - standard from the International Union of Crystallography
    • mmCIF Macromolecular Crystallographic Information File - standard from the International Union of Crystallography
    • CML Chemical Markup Language
    • PDB Protein Data Bank - Research Collaboratory for Structural Bioinformatics
    • XYZ XYZ format, XMol file - Minnesota Supercomputer Institute
    • XYZ+vib XYZ format with added vibrational vector information
    • XYZ-FAH XYZ format for [email protected]
    • MOL2 Sybyl, Tripos
    • Alchemy Tripos
    • CSF Fujitsu CAChe chemical structure, now Fujitsu Sygress
    • GAMESS General Atomic and Molecular Electronic Structure System output (both US and UK variants) - Gordon Research Group, Iowa State University
    • Gaussian Gaussian 94/98/03 output - Gaussian, Inc.
    • Cube Gaussian, Inc.
    • Ghemical The Ghemical computational chemistry package
    • MM1GP Ghemical molecular mechanics file
    • HIN HIN / HIV files from HyperChem - Hypercube, Inc.
    • Jaguar Schrodinger, LLC
    • MOLPRO Molpro output
    • MOPAC MOPAC 93/97/2002 output (public domain)
    • MGF MOPAC 2007 (v.7.101) graphf output (public domain)
    • NWCHEM NWChem output - Pacific Northwest National Laboratory
    • odydata Odyssey data - WaveFunction, Inc.
    • xodydata Odyssey XML data - WaveFunction, Inc.
    • QOUT Q-Chem, Inc.
    • SHELX Structural Chemistry Department, University of Göttingen (Germany)
    • SMOL Spartan data - Wavefunction, Inc.
    • spinput Spartan data - Wavefunction, Inc.
    • GRO Gromos87 format from GROMACS
    • PQR Modified pdb format including charge and radius
    • Amber The Amber package of molecular simulation programs
    • JME Java Molecular Editor - Peter Ertl
    • CASTEP The CASTEP software package, uses density functional theory
    • FHI-aims Full-potential / all-electron electronic structure theory with local orbitals - Fritz-Haber-Institut der Max-Planck-Gesellschaft
    • VASP VASP / VAMP / Vienna ab-initio simulation package
    • DGrid Miroslav Kohout, Max-Planck Institute
    • ADF ADF output - Amsterdam Density Functional
    • XSD Accelrys Materials Studio
    • AGL ArgusLab
    • DFT Wien2k
    • AMPAC AMPAC output - Semichem, Inc.
    • WebMO WebMO interface to computational chemistry packages
    • Molden Electron density / molecular orbitals
    • PSI3 Output files from the PSI3 suite of quantum chemical programs
    • CRYSTAL Output files from CRYSTAL, a computational tool for solid state chemistry and physics. Theoretical Chemistry Group, Univ. Torino, Italy.
  • Files which are compressed with gzip will automatically be decompressed
  • Animations
  • Vibrations
  • Surfaces
  • Orbitals
  • Support for unit cell and symmetry operations
  • Schematic shapes for secondary structures in biomolecules
  • Measurements of distance, angle, torsion angle
  • Support for RasMol/Chime scripting language
  • JavaScript support library (Jmol.js)
  • Exports to jpg, png, gif, ppm, pdf, POV-Ray, Gaussian, Maya, vrml, x3d, idtf, web page.

tools\chocolateyInstall.ps1
$ErrorActionPreference = 'Stop'; # stop on all errors

$ToolsDir   = Split-Path -parent $MyInvocation.MyCommand.Path
$PackageDir = Split-Path -Parent $ToolsDir

# Remove previous versions
$Previous = Get-ChildItem $PackageDir -filter "jmol*" | ?{ $_.PSIsContainer }
if ($Previous) {
   $Previous | % { Remove-Item $_.FullName -Recurse -Force }
}

$installArgs = @{
   packageName  = $env:ChocolateyPackageName
   FileFullPath = (Get-ChildItem $ToolsDir -Filter "*.zip").FullName
   Destination  = $PackageDir
}

Get-ChocolateyUnzip @installArgs

$JavaExe = "$env:ProgramData\Oracle\Java\javapath\javaw.exe"
$target = (Get-ChildItem $PackageDir -filter jmol.jar -Recurse).fullname
$icon = Join-Path $PackageDir 'tools\Jmol_icon13.ico'
$launcher = Join-Path $PackageDir 'Jmol Launcher.exe'
$SGpath = Join-Path $env:ChocolateyInstall 'tools\shimgen.exe'

& $SGpath -o $launcher -p $JavaExe -c "-jar '$target'" -i $icon --gui

$shortcut = Join-Path ([Environment]::GetFolderPath("Desktop")) 'Jmol.lnk'

Install-ChocolateyShortcut -ShortcutFilePath $shortcut -TargetPath $launcher -IconLocation $icon
tools\chocolateyUninstall.ps1
$desktop = [Environment]::GetFolderPath("Desktop")
$shortcut = Join-Path $desktop 'Jmol.lnk'
 
if ([System.IO.File]::Exists($shortcut)) {
    Write-Debug "Found the desktop shortcut. Deleting it..."
    [System.IO.File]::Delete($shortcut)
}
tools\Jmol-14.21.1-binary.zip
md5: AA632678399595A5C42FA9A25E8086FC | sha1: 1C208702E0297CF3BEA03FD825EA6307045C2199 | sha256: 1FAF5C7E01E72A1C179D6C4D71F5E3163926CA3078BB2902A880A20F2F1800E5 | sha512: A82C228E8DC1978398DF5DD7B43BFD2CCEC481F24A42AD3A9D2AB11FC7AFFA79388A8F8CC64CBF4FB260AD613E3A089D75DFC10C11EB2DF7BECD4EF304D0F870
tools\LICENSE.txt
                   GNU LESSER GENERAL PUBLIC LICENSE
                       Version 3, 29 June 2007

 Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
 Everyone is permitted to copy and distribute verbatim copies
 of this license document, but changing it is not allowed.


  This version of the GNU Lesser General Public License incorporates
the terms and conditions of version 3 of the GNU General Public
License, supplemented by the additional permissions listed below.

  0. Additional Definitions.

  As used herein, "this License" refers to version 3 of the GNU Lesser
General Public License, and the "GNU GPL" refers to version 3 of the GNU
General Public License.

  "The Library" refers to a covered work governed by this License,
other than an Application or a Combined Work as defined below.

  An "Application" is any work that makes use of an interface provided
by the Library, but which is not otherwise based on the Library.
Defining a subclass of a class defined by the Library is deemed a mode
of using an interface provided by the Library.

  A "Combined Work" is a work produced by combining or linking an
Application with the Library.  The particular version of the Library
with which the Combined Work was made is also called the "Linked
Version".

  The "Minimal Corresponding Source" for a Combined Work means the
Corresponding Source for the Combined Work, excluding any source code
for portions of the Combined Work that, considered in isolation, are
based on the Application, and not on the Linked Version.

  The "Corresponding Application Code" for a Combined Work means the
object code and/or source code for the Application, including any data
and utility programs needed for reproducing the Combined Work from the
Application, but excluding the System Libraries of the Combined Work.

  1. Exception to Section 3 of the GNU GPL.

  You may convey a covered work under sections 3 and 4 of this License
without being bound by section 3 of the GNU GPL.

  2. Conveying Modified Versions.

  If you modify a copy of the Library, and, in your modifications, a
facility refers to a function or data to be supplied by an Application
that uses the facility (other than as an argument passed when the
facility is invoked), then you may convey a copy of the modified
version:

   a) under this License, provided that you make a good faith effort to
   ensure that, in the event an Application does not supply the
   function or data, the facility still operates, and performs
   whatever part of its purpose remains meaningful, or

   b) under the GNU GPL, with none of the additional permissions of
   this License applicable to that copy.

  3. Object Code Incorporating Material from Library Header Files.

  The object code form of an Application may incorporate material from
a header file that is part of the Library.  You may convey such object
code under terms of your choice, provided that, if the incorporated
material is not limited to numerical parameters, data structure
layouts and accessors, or small macros, inline functions and templates
(ten or fewer lines in length), you do both of the following:

   a) Give prominent notice with each copy of the object code that the
   Library is used in it and that the Library and its use are
   covered by this License.

   b) Accompany the object code with a copy of the GNU GPL and this license
   document.

  4. Combined Works.

  You may convey a Combined Work under terms of your choice that,
taken together, effectively do not restrict modification of the
portions of the Library contained in the Combined Work and reverse
engineering for debugging such modifications, if you also do each of
the following:

   a) Give prominent notice with each copy of the Combined Work that
   the Library is used in it and that the Library and its use are
   covered by this License.

   b) Accompany the Combined Work with a copy of the GNU GPL and this license
   document.

   c) For a Combined Work that displays copyright notices during
   execution, include the copyright notice for the Library among
   these notices, as well as a reference directing the user to the
   copies of the GNU GPL and this license document.

   d) Do one of the following:

       0) Convey the Minimal Corresponding Source under the terms of this
       License, and the Corresponding Application Code in a form
       suitable for, and under terms that permit, the user to
       recombine or relink the Application with a modified version of
       the Linked Version to produce a modified Combined Work, in the
       manner specified by section 6 of the GNU GPL for conveying
       Corresponding Source.

       1) Use a suitable shared library mechanism for linking with the
       Library.  A suitable mechanism is one that (a) uses at run time
       a copy of the Library already present on the user's computer
       system, and (b) will operate properly with a modified version
       of the Library that is interface-compatible with the Linked
       Version.

   e) Provide Installation Information, but only if you would otherwise
   be required to provide such information under section 6 of the
   GNU GPL, and only to the extent that such information is
   necessary to install and execute a modified version of the
   Combined Work produced by recombining or relinking the
   Application with a modified version of the Linked Version. (If
   you use option 4d0, the Installation Information must accompany
   the Minimal Corresponding Source and Corresponding Application
   Code. If you use option 4d1, you must provide the Installation
   Information in the manner specified by section 6 of the GNU GPL
   for conveying Corresponding Source.)

  5. Combined Libraries.

  You may place library facilities that are a work based on the
Library side by side in a single library together with other library
facilities that are not Applications and are not covered by this
License, and convey such a combined library under terms of your
choice, if you do both of the following:

   a) Accompany the combined library with a copy of the same work based
   on the Library, uncombined with any other library facilities,
   conveyed under the terms of this License.

   b) Give prominent notice with the combined library that part of it
   is a work based on the Library, and explaining where to find the
   accompanying uncombined form of the same work.

  6. Revised Versions of the GNU Lesser General Public License.

  The Free Software Foundation may publish revised and/or new versions
of the GNU Lesser General Public License from time to time. Such new
versions will be similar in spirit to the present version, but may
differ in detail to address new problems or concerns.

  Each version is given a distinguishing version number. If the
Library as you received it specifies that a certain numbered version
of the GNU Lesser General Public License "or any later version"
applies to it, you have the option of following the terms and
conditions either of that published version or of any later version
published by the Free Software Foundation. If the Library as you
received it does not specify a version number of the GNU Lesser
General Public License, you may choose any version of the GNU Lesser
General Public License ever published by the Free Software Foundation.

  If the Library as you received it specifies that a proxy can decide
whether future versions of the GNU Lesser General Public License shall
apply, that proxy's public statement of acceptance of any version is
permanent authorization for you to choose that version for the
Library.
tools\VERIFICATION.txt
VERIFICATION
Verification is intended to assist the Chocolatey moderators and community
in verifying that this package's contents are trustworthy.
 
The installer is available from SourceForge:
https://sourceforge.net/projects/jmol/files/Jmol-<Latest Version>-binary.zip

Direct Download:

Version  : 14.21.1
URL      : https://sourceforge.net/projects/jmol/files/Jmol-14.21.1-binary.zip
CheckSum : 1FAF5C7E01E72A1C179D6C4D71F5E3163926CA3078BB2902A880A20F2F1800E5


In cases where actual malware is found, the packages are subject to removal. Software sometimes has false positives. Moderators do not necessarily validate the safety of the underlying software, only that a package retrieves software from the official distribution point and/or validate embedded software against official distribution point (where distribution rights allow redistribution).

Chocolatey Pro provides runtime protection from possible malware.

Version Downloads Last Updated Status
Jmol molecule viewer 14.29.53 166 Saturday, September 28, 2019 Approved
Jmol molecule viewer 14.29.52 1410 Thursday, August 29, 2019 Approved
Jmol molecule viewer 14.29.47 1724 Wednesday, July 31, 2019 Approved
Jmol molecule viewer 14.29.46 660 Tuesday, June 18, 2019 Approved
Jmol molecule viewer 14.29.42 6774 Thursday, May 16, 2019 Approved
Jmol molecule viewer 14.29.40 3378 Tuesday, April 30, 2019 Approved
Jmol molecule viewer 14.29.36 3629 Sunday, April 14, 2019 Approved
Jmol molecule viewer 14.29.34 703 Thursday, April 11, 2019 Approved
Jmol molecule viewer 14.29.31 8577 Tuesday, March 5, 2019 Approved

Discussion for the Jmol molecule viewer Package

Ground Rules:

  • This discussion is only about Jmol molecule viewer and the Jmol molecule viewer package. If you have feedback for Chocolatey, please contact the Google Group.
  • This discussion will carry over multiple versions. If you have a comment about a particular version, please note that in your comments.
  • The maintainers of this Chocolatey Package will be notified about new comments that are posted to this Disqus thread, however, it is NOT a guarantee that you will get a response. If you do not hear back from the maintainers after posting a message below, please follow up by using the link on the left side of this page or follow this link to contact maintainers. If you still hear nothing back, please follow the package triage process.
  • Tell us what you love about the package or Jmol molecule viewer, or tell us what needs improvement.
  • Share your experiences with the package, or extra configuration or gotchas that you've found.
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