ADL: MGL Tools BOINC Port

Jack Shultz jshultz at hydrogenathome.org
Wed Apr 8 12:45:18 PDT 2009


Its been a couple months since I touched these MGL Tools scripts. I
had it working and I think I broke it.

I'm troubleshooting an issue here

C:\Documents and Settings\All Users\Application Data\BOINC\slots\0>..\..\project
s\hydrogenathome.org\Python25\python.exe ..\..\projects\hydrogenathome.org\MGLTo
olsPckgs\AutoDockTools\Utilities24\prepare_receptor4.py -r receptor.pdb
Traceback (most recent call last):
  File "..\..\projects\hydrogenathome.org\MGLToolsPckgs\AutoDockTools\Utilities2
4\prepare_receptor4.py", line 138, in <module>
    mol = mols[0]
TypeError: 'NoneType' object is unsubscriptable

C:\Documents and Settings\All Users\Application Data\BOINC\slots\0>

Any ideas?


On Tue, Jul 29, 2008 at 12:48 PM, Sargis Dallakyan <sargis at scripps.edu> wrote:
> Hi Jack,
>
> The same procedure should work on Linux too. Since all the Linux machines
> have Python pre-installed and since AutoDockTools utility scripts can be run
> with all currently available versions of Python, I would just put all
> packages somewhere under BOINC tree, call them with default system Python
> and insert the path into sys.path. You can also set the environment variable
> PYTHONPATH to point to the allocation where MGLTools packages are stored
> instead of inserting the path into sys.path. The end result should be the
> same.
>
> Good luck,
> Sargis
>
> Jack Shultz wrote:
>>
>> I got it working on Windows. Any recommendations for Linux?
>>
>> On Thu, Jul 10, 2008 at 1:10 PM, Sargis Dallakyan <sargis at scripps.edu>
>> wrote:
>>>
>>> Hi Jack,
>>>
>>> Redistribution of MGL Tools is encouraged for academic purposes so there
>>> should be not problem with license violation. You can remove mslib,
>>> UTpackages, and stride from MGLToolsPckgs folder since they are not
>>> needed
>>> for command line usage of AutoDockTools utilities. In fact, you can keep
>>> only the following packages if you are planning of using only
>>> AutoDockTools
>>> utility scripts:
>>>
>>> AutoDockTools
>>> mglutil
>>> MolKit
>>> Pmv
>>> PyBabel
>>> Support
>>>
>>> These are platform independent packages and should work on any machine
>>> that
>>> have Python installed. Python, by default, searches for packages under
>>> site-packages, however, you can uncompress them under the BOINC sub
>>> directories as long as you tell python where to find them. On Windows,
>>> for
>>> instance, our installer crates sitecustomize.py file under
>>> C:\Python25\Lib
>>> that contains the following code
>>>
>>> mglroot = 'C:\Program Files\MGLTools 1.5.2'# specify mglroot here
>>> import sys, os
>>> path = os.path.join(mglroot, "MGLToolsPckgs")
>>> sys.path.insert(0,path)
>>>
>>> Python sources this file every time it starts thats why our packages can
>>> be
>>> imported from C:\Program Files\MGLTools 1.5.2\MGLToolsPckgs.
>>>
>>> For BOINC, you can uncompress MGLTools packages under the BOINC sub
>>> directories and run them either by using a script that sets sys.path as
>>> in
>>> the example above or by setting PYTHONPATH env variable:
>>> http://docs.python.org/tut/node8.html#searchPath
>>>
>>> Hope this helps,
>>> Sargis
>>>
>>> Jack Shultz wrote:
>>>>
>>>> Hi Sargis,
>>>>
>>>> I'm trying to refine my methods even more on Hydrogen at Home. I
>>>> currently have 6 python scripts ported to stand alone binaries that
>>>> are about 10 MB each. Going forward, I think it would make more sense
>>>> to have the entire MGL Tools package installed on the clients
>>>> computer. I am unsure whether this is a violation of the license
>>>> because the windows binary installer requires signing though I don't
>>>> see anything stating redistribution is wrong for academic purposes. If
>>>> it is ok, I wonder if you could tell me if there were a way where I
>>>> could uncompress the python packages anywhere on the computer and get
>>>> python to import them.
>>>>
>>>> For example, if I uncompress them under the BOINC sub directories, I
>>>> am unable to execute them. They will execute if they are installed
>>>> under the Program Files.
>>>>
>>>> Jack
>>>>
>>>
>>
>
>



-- 
Jack

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http://hydrogenathome.org


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