Issue launching Autodock Vina screening using OPAL web service on 0.8

[Zachary Shaw]

I cant seem to get the web services to work. I am not fluent in computer language so please bear with me. Here is a copy of the debugging log:

Exception occurred in traits notification handler for object: <enthought.logger.plugin.view.logger_view.LoggerView object="" at="" 0x20ab7e10="">, trait: log_records, old value: [], new value: [<logging.LogRecord instance="" at="" 0x32bdb328="">]
Traceback (most recent call last):
File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/Traits-3.3.0-py2.6-macosx-10.4-i386.egg/enthought/traits/trait_notifiers.py", line 512, in rebind_call_4
object, trait_name, old, new )
File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/Traits-3.3.0-py2.6-macosx-10.4-i386.egg/enthought/traits/trait_notifiers.py", line 598, in dispatch
handler( args )
File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/Traits-3.3.0-py2.6-macosx-10.4-i386.egg/enthought/traits/ui/editor.py", line 353, in update_editor
self.update_editor()
File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/TraitsBackendWX-3.3.0-py2.6.egg/enthought/traits/ui/wx/tabular_editor.py", line 460, in update_editor
control.EnsureVisible( top + pn - 2 )
File "/Library/MGLTools/PyRx/Python.framework/Versions/2.6/lib/python2.6/site-packages/wx/_controls.py", line 4707, in EnsureVisible
return _controls.ListCtrl_EnsureVisible(args, **kwargs)
PyAssertionError: C++ assertion "index >= 0 && (size_t)index < GetItemCount()" failed at /BUILD/wxPython-src-2.8.11.0/src/generic/listctrl.cpp(4636) in EnsureVisible(): invalid index in EnsureVisible

And here is the log text:

ERROR|2016-03-02 10:49:02,753|Failed to lunch at http://nbcr-222.ucsd.edu/opal2/services/autodockvina_screening_1.1.2
Error message: [Errno 8] nodename nor servname provided, or not known

Thank you for your time.

[Sarkis Dallakian]

Thank you for the message Zachary. The URL for the web services has changed. I've posted the updated URL at http://mgl.scripps.edu/forum/viewtopic.php?f=25&t=3092&p=7644 and http://mgl.scripps.edu/forum/viewtopic.php?f=25&t=2791&p=7032

I don't know if anyone was able to run this with updated URLs using PyRx 0.8. I've included the updated URL's in the latest supported version of 0.9.x. Last time I checked it was still working with PyRx version 0.9.x.

[Zachary Shaw]

I tried updating the URI but i am still having issues getting it to work VIA web service. I will play around with it some more and if i still cant get it to work, I will probably just upgrade. I used the software to run vina locally on my laptop and i like how neatly it organizes everything for docking. It makes docking a large library of molecules very efficient, except when my 6 year old Macbook Pro is doing the computing haha. So if I can't get the web service to work the upgrade would be worth that to me. One last question, is there an easier way to load ligands faster than one at a time? Say i have 1000 ligands i want to screen. Individually it will take a while. If i can find the hidden folder where it stores the ligands in the program, can I just click and drag them all to this folder and click refresh in the PyRx app and they all be there?
Thanks again for your time and prompt response. It is greatly appreciated!

[Sarkis Dallakian]

Thank you for the feedback. Glad you like how neatly it organizes everything for docking and sorry about the web services URL changes. In the latest version you can add multiple (e.g. 1000) ligands at once. You can also click and drag prepared ligand pdbqt files to the hidden folder (~/.PyRx_workspace/Ligands in the latest version) and click refresh as you wrote. These ligand files need to be in pdbqt format that AutoDock and Vina can use. Otherwise, you can use PyRx to prepare them for docking with Vina or AutoDock.

[SMITA JAIN]

I am facing these problems in PyRx
Failed to connect to http://kryptonite.nbcr.net/opal2/services
<urlopen error="" <span="">[Errno 11001] getaddrinfo failed>
Error in : <bound method="" runautogrid.tryrun="" of="" <pyrx.autogridpage.runautogrid;="" proxy="" <swig="" object="" type="" 'wxpanel="" *'="" at="" 0xa4e1398=""> >>
Python 2.6.5 (r265:79096, Mar 19 2010, 21:48:26) [MSC v.1500 32 bit (Intel)] on win32
Type "help", "copyright", "credits" or "license" for more information.</bound></urlopen>

Traceback (most recent call last):
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\wxMainFrame.py", line 304, in TryCommand
retObject = command(*args, kw)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\autogridPage.py", line 229, in TryRun
self.processPanel.Start()
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\webServices.py", line 657, in Start
resp = self.appServicePort.launchJob(self.req)
File "C:\Program Files (x86)\PyRx\lib\site-packages\PyRx\AppService\AppService_client.py", line 58, in launchJob
self.binding.Send(None, None, request, soapaction="http://nbcr.sdsc.edu/opal/launchJob", kw)
File "C:\Program Files (x86)\PyRx\lib\site-packages\ZSI\client.py", line 291, in Send
self.h.connect()
File "C:\Program Files (x86)\PyRx\lib\httplib.py", line 716, in connect
self.timeout)
File "C:\Program Files (x86)\PyRx\lib\socket.py", line 500, in create_connection
for res in getaddrinfo(host, port, 0, SOCK_STREAM):
gaierror: [Errno 11001] getaddrinfo failed

[Sarkis Dallakian]

This service has been retired. New version includes option to run jobs in a local cluster in a cloud.