ADL: Error message from ADT when attempting to analyze a vina output

Paul Rigor (uci) paul.rigor at uci.edu
Wed Mar 10 20:48:22 PST 2010


Hi all,

Sorry, here are the two files:
error output
source code

Thanks again,
Paul

On Wed, Mar 10, 2010 at 8:46 PM, Paul Rigor (uci) <paul.rigor at uci.edu>wrote:

> Hi,
>
> I'm using ADT to analyze an autodock vina output.  The pdbqt file contains
> multiple molecules where each could have multiple conformations.  As such, I
> selected 'multiple molecules' from Analyze -> Dockings -> Open AutoDock vina
> results.
>
>
> The program chokes with the following message (which I've also attached).
>  I looked at the incriminating file and the line the error message points
> to.  It looks like that autoanalyzeCommands.py::doit() method is bogus!
>
> It doesn't analyze the set of multiple molecules and only runs the
> appropriate code when select 'multiple conformations' from the GUI.  What's
> going on here?
>
> Thanks!
> Paul
>
>
> Python 2.5.1 (r251:54863, Nov 13 2007, 11:10:08)
> [GCC 4.0.1 (Apple Inc. build 5465)] on darwin
> Type "copyright", "credits" or "license()" for more information.
>
>     ****************************************************************
>     Personal firewall software may warn about the connection IDLE
>     makes to its subprocess using this computer's internal loopback
>     interface.  This connection is not visible on any external
>     interface and no data is sent to or received from the Internet.
>     ****************************************************************
>
> IDLE 1.2.1      ==== No Subprocess ====
> >>> ERROR *********************************************
> Traceback (most recent call last):
>   File "/Library/MGLTools/1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line
> 735, in tryto
>     result = apply( command, args, kw )
> TypeError: doit() got an unexpected keyword argument 'modelsAs'
> over-all best vina_energy= ERROR
> *********************************************
> Traceback (most recent call last):
>   File "/Library/MGLTools/1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line
> 735, in tryto
>     result = apply( command, args, kw )
>   File
> "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py",
> line 3083, in doit
>     print "over-all best vina_energy=", m.vina_results[0][0]
> UnboundLocalError: local variable 'm' referenced before assignment
>
>
> --
> Paul Rigor
> Pre-doctoral BIT Fellow and Graduate Student
> Institute for Genomics and Bioinformatics
> Donald Bren School of Information and Computer Sciences
> University of California, Irvine
> http://www.ics.uci.edu/~prigor
>



-- 
Paul Rigor
Pre-doctoral BIT Fellow and Graduate Student
Institute for Genomics and Bioinformatics
Donald Bren School of Information and Computer Sciences
University of California, Irvine
http://www.ics.uci.edu/~prigor
-------------- next part --------------
Python 2.5.1 (r251:54863, Nov 13 2007, 11:10:08) 
[GCC 4.0.1 (Apple Inc. build 5465)] on darwin
Type "copyright", "credits" or "license()" for more information.

    ****************************************************************
    Personal firewall software may warn about the connection IDLE
    makes to its subprocess using this computer's internal loopback
    interface.  This connection is not visible on any external
    interface and no data is sent to or received from the Internet.
    ****************************************************************
    
IDLE 1.2.1      ==== No Subprocess ====
>>> ERROR *********************************************
Traceback (most recent call last):
  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line 735, in tryto
    result = apply( command, args, kw )
TypeError: doit() got an unexpected keyword argument 'modelsAs'
over-all best vina_energy= ERROR *********************************************
Traceback (most recent call last):
  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/ViewerFramework/VF.py", line 735, in tryto
    result = apply( command, args, kw )
  File "/Library/MGLTools/1.5.4/MGLToolsPckgs/AutoDockTools/autoanalyzeCommands.py", line 3083, in doit
    print "over-all best vina_energy=", m.vina_results[0][0]
UnboundLocalError: local variable 'm' referenced before assignment
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