PyRx – Python Prescription

I’m glad to report that PyRx has been used to win Coronavirus Drug Discovery Competition. Congratulations and HUGE THANK YOU to Matt O’Connor who used deep learning techniques for molecule generation and PyRx to evaluate binding affinities (https://github.com/mattroconnor/deep_learning_coronavirus_cure). He identified Remdesivir as a potential COVID-2019 treatment, which Sage Health will be donating to the Wuhan institute of Virology for further analysis.

Happy to see that the free version is still working on Windows (since 2011), unlike Mac version, that gives me nothing but headaches. We do not plan to increase the price of PyRx anytime soon and hope that our website and the store will remain online during these troublesome times.

As you may know, you can use Vina Wizard > Analyze Results page to load multiple Vina outputs (*_out.pdbqt). For AutoDock, if you have already gone through the wizard, produced dlg (docking log) files and want to load them again, you can go through the wizard again to load them. PyRx won’t run AutoDock and will load the results instead, if all dlg files are in their places. PyRx stores dlg files in subfolders and since a file browser won’t let you select multiple files from different folders, it’s not currently possible to load dlg files using a file browser.

I’ve created a new script to enable this. Download load_dlgs.py and use PyRx > File > Run Python Script or click on Python icon on the toolbar on upper left to open this file. It opens Choose Docking Log Files dialog where you can select multiple dlg files. Please note that some of the PyRx functions, such as recently introduced Show Interactions, won’t work and will through error messages if you load dlg files this way.

We are pleased to announce the release of PyRx 0.9.8. Major changes in this release include:

• Added Show Interactions tool in Analyze Results tab for AutoDock and Vina Wizard. Click on the pink icon (highlighted in yellow in the image below) to select receptor and ligand atoms that are in close contacts to each other. It also shows hydogen bonds as green lines if there are any hydrogen bonding interactions.



• Added a new tool in the toolbar for selecting residues inside a sphere. By default, it will place the center of the sphere at a center of the current selection, or if nothing is selected, it will place the center at the center of the first molecule in the 3D scene.

  

  The center and radius of the sphere can be changed by clicking on a sphere and zooming or panning. To enter numerical values for center and radius use Navigator > TVTK, expand the tree and double-click on SphereRepresentation.

  

• You can now run Vina jobs on Amazon Web Services and pay as you go for the resources used.

  

  Read HPC and AWS article to learn how to use this.

There has been recent changes in Vina web services that makes it impossible to run Vina in Remote (Opal Web Services) mode. I’ve uploaded new updates to fix this.  Please use PyRx > Help > Check for Updates… menu to apply this update if you are using Linux or PyRx 0.9.7 or higher on Windows. Unfortunately PyRx update procedure doesn’t work on Mac OS X or on Windows with PyRx 0.9.6 and earlier versions. Please use the following steps to update PyRx instead.

Step 1, visit https://sourceforge.net/p/pyrx/code/HEAD/tree/PyRxDev/ and click on Download Snapshot.

Step 2, uncompress this downloaded file and locate PyRxDev/PyRx folder.

Step 3, make a backup copy of the following folder, by renaming it to PyRx.bak for instance, in case PyRx fails to start after this update:

• Windows PyRx 0.9.6 or earlier – C:\Program Files (x86)\PyRx\$Version\Lib\site-packages\PyRx
• Windows PyRx 0.9.7 or older – C:\Program Files\PyRx\$Version\Lib\site-packages\PyRx
• Mac OS X – /Library/PyRx/$Version/Python.framework/Versions/2.6/lib/python2.6/site-packages/PyRx

$Version here is the version number of PyRx (e.g. 0.9.6)

Step 4, replace this folder with the one you downloaded above.

If you have updated PyRx previously using Help > Check for Updates… menu, delete .PyRx_workspace\update from your home directory.

Please let me know if you have questions or need more information.

We are pleased to announce the release of PyRx 0.9.7. We have upgraded Python interpreter on Windows to 64 bit version that allows users to work with larger molecules. Other major changes in this release include:

For Inverse Virtual Screening with Vina, we now have preferences page where users can specify maximum number of Macromolecules to load.

Added Lipinski Rule of Fives in Open Babel table filter.

Open Bable table now includes logP, number of hydrogen bond donors (#HBD) and acceptors (#HBA) columns.

Implemented Max Runtime in PyRx > Edit > Preferences. Users can change this to terminate all local jobs that take more than Max Runtime (in minutes) to run.

PyRx 0.9.6 users can update to this release using PyRx > Help > Check for Updates… menu. The list of changes for 0.9.6 version is available at PyRx 0.9.6 Release Announcement.

We are pleased to announce the release of PyRx 0.9.6. Major changes in this release include:

When making pdbqt for Macromolecules that have atoms at alternate locations, users can now generate all possible combinations.

Individual residues can now be displayed as Balls and Sticks.

A new option to choose Formula_Title for the name of the ligands when making AutoDock Ligand pdqt files using Open Babel widget. Use PyRx > Edit > Preferences, click on + icon next to Open Babel and select AutoDock Ligand. You’ll see a new option there next to “Name Converted Ligand Using”. There are two options: Title or Formula_Title. If you select Formula_Title, next time when PyRx makes AutoDock ligands using Open Bable, it will name ligands accordingly.

Option to toggle on and off balloon widget shown below.

PyRx 0.9.5 users can update to this release using PyRx > Help > Check for Updates… menu. The list of changes for 0.9.5 version is available at PyRx 0.9.5 Release Announcement.

 We are pleased to announce the release of PyRx 0.9.5. Major changes in this release include:

• Fixed a bug when toggling hydrogen bonds using toolbar icon.
• PyRx can now run docking for molecules that have quotes in their names, like in 3-hydroxy-5_7_3’_4’_5′-pentamethoxyflavone.
• Added balloon widget to draw labels when the mouse stays above a molecule. This can be helpful when there are multiple molecules in 3D scene. The mouse cursors changes to busy when you move the mouse over a molecule. You can disable this by deleting a single line – https://sourceforge.net/p/pyrx/code/278/tree/PyRxDev/PyRx/mayaviEngine.py#l110 . Let me know if you don’t like this feature; I can add an option to disable this in the next release of PyRx, if needed.

• Added RMSD from reference structure column to AutoDock Analyze Results table.

• When making flexible residues, PyRx is now using options defined in receptor preparation preferences to decide what type of changes to do.

PyRx 0.9.2, 0.9.3 and 0.9.4 users can update to this release using PyRx > Help > Check for Updates… menu. The list of changes for 0.9.4 version is available at PyRx 0.9.4 Release Announcement.

2016 has been a great year for PyRx. We have passed 35k downloads, which is excellent for a scientific software. There have been many new publications mentioning PyRx; it’s nice seeing PyRx used for research ranging from Anticancer to Zika. PyRx now has a Facebook page and we also run Facebook and Googe AdWords advertising. The best news for 2016 is that we moved to our new headquarters with a beautiful view of Bonita Golf course shown in the photo below. Have a great holiday season!