Downloads:

73,810

Downloads of v 14.18.1:

2,266

Last Update:

6/12/2017

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.

14.18.1 | Updated: 6/12/2017

Downloads:

73,810

Downloads of v 14.18.1:

2,266

Maintainer(s):

Software Author(s):

  • The Jmol Development Team

Tags:

jmol chemistry molecule rendering viewer java

Jmol molecule viewer 14.18.1

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: 14.18.1
    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  '14.18.1'
  source   'STEP 3 URL'
end

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


Chocolatey::Ensure-Package
(
    Name: jmol,
    Version: 14.18.1,
    Source: STEP 3 URL
);

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


cChocoPackageInstaller jmol
{
   Name     = 'jmol'
   Ensure   = 'Present'
   Version  = '14.18.1'
   Source   = 'STEP 3 URL'
}

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


package { 'jmol':
  provider => 'chocolatey',
  ensure   => '14.18.1',
  source   => 'STEP 3 URL',
}

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


salt '*' chocolatey.install jmol version="14.18.1" 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.

Private CDN cached downloads available for licensed customers. Never experience 404 breakages again! Learn more...

This package was approved as a trusted package on 6/12/2017.

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 
$packageName = 'Jmol'

$url        = 'https://sourceforge.net/projects/jmol/files/Jmol/Version%2014.18/Jmol%2014.18.1/Jmol-14.18.1-binary.zip'
$Checksum   = '93a5b12b0e694274a16fc12d7a2f23bbbdec860c1316da0cace56df6a42fb3b2'
$installDir = Split-Path (Split-Path -parent $script:MyInvocation.MyCommand.Path)

$installArgs = @{
   packageName   = $packageName
   url           = $url
   Checksum      = $Checksum
   ChecksumType  = 'sha256'
   UnzipLocation = $installDir
}

Install-ChocolateyZipPackage @installArgs

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

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 14.29.54 241 Saturday, October 12, 2019 Approved
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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