Downloads:

720

Downloads of v 4.10.0.20161116:

455

Last Update:

11/16/2016

Package Maintainer(s):

Software Author(s):

  • Nicolas Guex
  • Alexandre Diemand
  • Manuel C. Peitsch
  • and Torsten Schwede

Tags:

deepview pdbviewer chemistry protein modeling

DeepView - Swiss PdbViewer

4.10.0.20161116 | Updated: 11/16/2016

Downloads:

720

Downloads of v 4.10.0.20161116:

455

Maintainer(s):

Software Author(s):

  • Nicolas Guex
  • Alexandre Diemand
  • Manuel C. Peitsch
  • and Torsten Schwede

DeepView - Swiss PdbViewer 4.10.0.20161116

All Checks are Passing

2 Passing Test


Validation Testing Passed


Verification Testing Passed

Details

To install DeepView - Swiss PdbViewer, run the following command from the command line or from PowerShell:

>

To upgrade DeepView - Swiss PdbViewer, run the following command from the command line or from PowerShell:

>

To uninstall DeepView - Swiss PdbViewer, 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 deepview -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 deepview -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 deepview installed
  win_chocolatey:
    name: deepview
    state: present
    version: 4.10.0.20161116
    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 'deepview' do
  action    :install
  version  '4.10.0.20161116'
  source   'STEP 3 URL'
end

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


Chocolatey::Ensure-Package
(
    Name: deepview,
    Version: 4.10.0.20161116,
    Source: STEP 3 URL
);

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


cChocoPackageInstaller deepview
{
   Name     = 'deepview'
   Ensure   = 'Present'
   Version  = '4.10.0.20161116'
   Source   = 'STEP 3 URL'
}

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


package { 'deepview':
  provider => 'chocolatey',
  ensure   => '4.10.0.20161116',
  source   => 'STEP 3 URL',
}

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


salt '*' chocolatey.install deepview version="4.10.0.20161116" 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 by moderator flcdrg on 11/24/2016.

Description

Swiss-PdbViewer (aka DeepView) is an application that provides a user friendly interface allowing to analyze several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface.

Swiss-PdbViewer (aka DeepView) has been developped since 1994 by Nicolas Guex. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB) at the Structural Bioinformatics Group at the Biozentrum in Basel.

Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing.

Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modeling tools are integrated and residues can be mutated.

Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. An example can be found here.


tools\chocolateyInstall.ps1
$packageName = 'deepview'

$InstallDir = Split-path (Split-path $MyInvocation.MyCommand.Definition)

$InstallArgs = @{
   PackageName = $packageName
   Url = 'http://spdbv.vital-it.ch/download/binaries/SPDBV_4.10_PC.zip' 
   UnzipLocation = $InstallDir
   checkSum = '369C0C9B6E058BB67C86DC24D711D6A655E5E023D639FCDA13EC2FE272DE1858'
   checkSumType = 'sha256'
}
Install-ChocolateyZipPackage @InstallArgs

$target   = Join-Path $InstallDir 'SPDBV_4.10_PC\spdbv.exe'
$shortcut = Join-Path ([System.Environment]::GetFolderPath('Desktop')) 'Swiss-PdbViewer.lnk'

Install-ChocolateyShortcut -ShortcutFilePath $shortcut -TargetPath $target

tools\chocolateyUninstall.ps1
$desktop = ([System.Environment]::GetFolderPath('Desktop'))
$shortcut = Join-Path $desktop 'Swiss-PdbViewer.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
DeepView - Swiss PdbViewer 4.10 265 Wednesday, April 27, 2016 Approved

This package has no dependencies.

Discussion for the DeepView - Swiss PdbViewer Package

Ground Rules:

  • This discussion is only about DeepView - Swiss PdbViewer and the DeepView - Swiss PdbViewer 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 DeepView - Swiss PdbViewer, or tell us what needs improvement.
  • Share your experiences with the package, or extra configuration or gotchas that you've found.
  • If you use a url, the comment will be flagged for moderation until you've been whitelisted. Disqus moderated comments are approved on a weekly schedule if not sooner. It could take between 1-5 days for your comment to show up.
comments powered by Disqus