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PyRx Binary Distribution PDF Print

  • Windows

    PyRx-0.9.2-Setup.exe   $159.99   buy now

    PyRx version 0.8 is available for free: PyRx-0.8-Setup.exe (93 MB)

    Troubleshooting - Installation Problems

    If you have previous version of PyRx installed and are having problems installing the new version, please remove C:\Program Files\PyRx folder using Unlocker, for instance, prior to installing this new version.

    Troubleshooting - Startup Problems

    Please install Microsoft Visual C++ 2008 Redistributable Package if PyRx fails to start. Also, make sure you can install and run Python 2.6 independent of PyRx. Visit the forum for additional instructions. Check also instructions on how to install PyRx from Source written below.

  • Linux

    64-bit PyRx 0.9.2  $159.99   buy now

    PyRx version 0.9 for 32-bit Linux is available for free: PyRx-0.9-Linux-x86-Install (122 MB)

    To start the installer grant execute permission and run it.

    chmod +x PyRx-0.9-Linux-x86-Install
    ./PyRx-0.9-Linux-x86-Install

    This installer is build on Fedora Core 13. If you are using Fedora Core 10 or RHEL5 please try PyRx-0.7-Linux-x86-RHEL5-Install (171 MB).

    Troubleshooting Installation Problems

    64-bit OS users need to have 32-bit X11 libraries installed. See, for instance, Installing 32-bit Support into 64-bit Fedora 11. You can also use Open Discovery that comes with working PyRx binaries installed.

    If you are getting the following error while running the installer, then please try downloading again or try another mirror.

    application-specific initialization failed: Can't find a usable init.tcl in the following directories: 
    /installkitvfs/lib/tcl /installkitvfs/lib/tcl8.5  /home/damon/src/installkit/glibc24/out/lib/tcl8.5  /sdc2/applications/lib/tcl8.5 /sdc2/lib/tcl8.5  /sdc2/applications/library /sdc2/library /sdc2/tcl8.5.7/library  /tcl8.5.7/library
    This probably means that Tcl wasn't installed properly.

    This happens when download was incomplete. Please make sure that the file you downloaded is 122MB in size.

    For 64-bit RHEL/CentOS 6.x you can also try PyRx-0.9-x86-64.tar.gz. After the download is complete run:

    tar -xzvf PyRx-0.9-x86-64.tar.gz
    ./usr/local/PyRx-0.9/run.sh
    

     Troubleshooting Startup Problems

    If PyRx fails to start due to a missing library, please install missing libraries or build PyRx from source. In the Ubuntu 12.04 or 13.04, for instance, you need to have ia32-libs-multiarch and libjpeg62 installed.

    sudo apt-get install libjpeg62:i386 ia32-libs-multiarch

    You might also need to install additional packages depending on your system configuration. Please see this post for more information.

    See also: 3D Acceleration on Ubuntu 10.04 (LTS 64bit) and Installing the missing dependencies on Fedora 8.

  • Mac OS X

    PyRx-0.9.2.dmg   $159.99   buy now

    To install PyRx open PyRx-0.9.2.dmg in Finder, Control-click or right click on PyRx-0.9.2 and select Open. Once PyRx is successfully installed, PyRx.app will be available under Applications folder.

  • Source

    Instructions for Installing PyRx from Source

    PyRx depends on many packages that might not be easy to install.

    Please try binary installer corresponding to your OS first (see above).

    If that fails, you'll need to install the following list of packages that PyRx depends on.

    Please note that some familiarity with development tools is needed to install all these packages.

    • Python - a programming/scripting language - python.org.

    • AutoDockTools, used to generate input files - mgltools.scripps.edu.

    • wxPython for cross-platform GUI - wxpython.org.

    • The Visualization ToolKit (VTK) for 3D computer graphics - vtk.org by Kitware, Inc.

    • Enthought Tool Suite, including Traits, for application building blocks - code.enthought.com.

    • Opal Toolkit for running AutoDock remotely using Web services - opal.nbcr.net.

      You'll need to install Python Opal Web Service Client. PyRx is set to use ws.nbcr.net servicer by default.
      If you are planning to create your own grid/cloud, you'll need to install Opal Server as well.
    • Open Babel for importing SDF files, removing salts and energy minimization - openbabel.org.

    • AutoDock, used as a docking software - http://autodock.scripps.edu (optional).

      Only remote execution mode is enabled if PyRx can't find autodock binaries.

    • ePMV, embedded Python Molecular Viewer - epmv.scripps.edu.

    Congradulations if you managed to install all the dependencies and read this far.

    You are now only a few clicks away from using PyRx. Download and uppack PyRx-0.9-Source.zip (760 KB). The latest version of PyRx source code is also available at https://sourceforge.net/projects/pyrx/develop Now, do standard python install:

    python setup.py install
    

    Starting PyRx on Different Platforms

    Windows Users - double click on runPyRx.py or run python runPyRx.py from command line.


    Linux Users - add MGLTools to your PYTHONPATH:
    csh - setenv PYTHONPATH/usr/local/MGLTools-$Version/MGLToolsPckgs:/usr/local/MGLTools-$Version/lib/python2.6/site-packages
    bash - PYTHONPATH="/usr/local/MGLTools-$Version/MGLToolsPckgs:/usr/local/MGLTools-$Version/lib/python2.6/site-packages"
    Run "python runPyRx.py" from command line.
    Mac OS X Users - add MGLTools to your PYTHONPATH:
    export PYTHONPATH="/Library/MGLTools/$Version/MGLToolsPckgs/:/Library/MGLTools/$Version/lib/python2.6/site-packages"
    Run pythonw runPyRx.py from command line.


 Please see PyRx 0.9.2 Release Announcement for the list of new features and bug fixes. Older versions of PyRx are available for free from http://sourceforge.net/projects/pyrx/files.

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Last Updated on Friday, 26 September 2014 07:03
 
Simplified BSD License PDF Print
Written by Sargis Dallakyan   

It took a great deal of effort to write PyRx and make it available under open source license. We have developed PyRx in our spare time in the hope that it will be useful, but without any warranty. This is exactly the same warranty that proprietary software companies offer: none.


Please watch Which Open Source License is Best? to learn more about open source licenses. Here is the Simplified BSD License for PyRx which is short and permissive free software licence.


Copyright (c) [2008-Forever], Sargis Dallakyan and individual contributors. All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

    * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
    * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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Last Updated on Monday, 13 February 2012 14:32
 
Known Issues and Feature Requests PDF Print
Written by Sargis Dallakyan   
  • An incomplete download is the most common reason for non working installers. Make sure your download is complete before running installers.
  • "Customize Filter" widget for table editor causes crash on Windows and Mac.
  • PyRx crashes on Linux when there are no hardware 3D accelerated (OpenGL) drivers avialable. See Using hardware accelerated 3D renderer on Linux and Installing Nvidia Driver on CentOS 6 for instuctions on how to install OpenGL drivers.
  • On Mac OS X, 3D Scene tab needs to be resized when switching between different tabs, otherwise it doesn't redraw properly.

Please visit FAQ page for information on how to submit a bug or request a new feature.

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Last Updated on Saturday, 06 September 2014 14:56