Re: [bug #11860] Feature request for diffusion tensor representation -- July 03, 2008

Hi Ed,

I added test for the diffusion tensor PDB creation. I put stuff with the
system tests for diffusion tensors. Maybe this is not the right place
for that. If you prefer, I can move the new test to the
'test_suite/system_tests/scripts' subdirectory. Moreover, for testing
the structure.create_diff_tensor_pdb() function, I used the
'Ap4Aase_res1-12.pdb' file. Is this fine ?

Regards,


Séb




Edward d'Auvergne wrote:

Hi,

The system test is very basic to implement.  Essentially you just have
a script and data (made to be as small as possible but still trigger
the problem, less than 10 kb, and randomised to protect unpublished
data if necessary).  These things are then packaged into the
test_suite/system_tests/scripts and test_suite/shared_data/ directory,
and executed by the test suite just as you would execute it on the
command line.  If files are generated by the script, these can be
automatically lost by the file being called 'devnull' or be put into a
temporary file for later checking.  After the script is run, you can
optionally add a few checks to see if it did what you wanted.

Cheers,

Edward


On Wed, Jun 25, 2008 at 2:53 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:

Hi Ed,

First, thanks a lot for all the recent work !

I'll try to have a look at this and take some time to add tests as you
proposed. However, this may have to wait for next week.

Regards,


Séb




Edward d'Auvergne wrote:

Hi,

This bug is because the code that is being executed has not yet been
converted to the new relax design.  There are many parts of relax 1.3
which are still awaiting conversion, although this line should soon be
reasonably usable.  For feature requests, I would like to first
implement system tests (and then maybe unit tests) and then make the
code functional again.  If you would like to try to add a system test
for this feature yourself, that may speed up the process.  These tests
are essentially just an ordinary relax script with a few checks at the
end to make sure the script functioned as it should have.  Otherwise
I'll add the test and then convert the code.

Regards,

Edward



On Sun, Jun 22, 2008 at 6:41 PM, Sébastien Morin
<NO-REPLY.INVALID-ADDRESS@xxxxxxx> wrote:

URL:
 <http://gna.org/bugs/?11860>

                Summary: Feature request for diffusion tensor 
representation
                Project: relax
           Submitted by: semor
           Submitted on: Sunday 06/22/2008 at 12:41
               Category: relax's source code
               Severity: 3 - Normal
               Priority: 5 - Normal
                 Status: None
                Privacy: Public
            Assigned to: bugman
        Originator Name:
       Originator Email:
            Open/Closed: Open
        Discussion Lock: Any
                Release: Repository: 1.3 line
       Operating System: All systems

   _______________________________________________________

Details:

[ As asked by Edward d'Auvergne after a personal communication, here is 
a bug
report for a feature request... ]
------

Hi,

I would like to create a pdb representation of the optimized diffusion 
tensor
for my system.

Using the sample script 'diff_tensor_pdb.py', I get the following error :

================================================
relax> state.save(state='relax_state_20082206_123756', dir_name=None,
force=False, compress_type=1)
Opening the file 'relax_state_20082206_123701.bz2' for writing.
Traceback (most recent call last):
 File "./diff_tensor_pdb.py", line 20, in ?
   structure.create_diff_tensor_pdb(file=tensor_file, force=1)
 File
"/home/semor/pse-4/collaborations/relax/relax-1.3/prompt/structure.py", 
line
164, in create_diff_tensor_pdb
   raise RelaxBoolError, ('force flag', force)
RelaxBoolError: RelaxError: The force flag boolean argument 1 must 
either be
True or False.
================================================


Removing the 'force' argument from the 
'structure.create_diff_tensor_pdb()'
function, I get the following error :

================================================
relax> state.save(state='relax_state_20082206_123329', dir_name=None,
force=False, compress_type=1)
Opening the file 'relax_state_20082206_123329.bz2' for writing.
Traceback (most recent call last):
 File "./diff_tensor_pdb.py", line 20, in ?
   structure.create_diff_tensor_pdb(file=tensor_file)
 File
"/home/semor/pse-4/collaborations/relax/relax-1.3/prompt/structure.py", 
line
167, in create_diff_tensor_pdb
   generic_fns.structure.geometric.create_diff_tensor_pdb(scale=scale,
file=file, dir=dir, force=force)
 File
"/home/semor/pse-4/collaborations/relax/relax-1.3/generic_fns/structure/geometric.py",
line 193, in create_diff_tensor_pdb
   raise RelaxNoTensorError, 'diffusion'
RelaxNoTensorError: RelaxError: No diffusion tensor data exists.
================================================

I know relax-1.3 isn't ready for complete use, however, I would like to 
ask
for the fixing of this part of the code which isn't available in the 1.2
line...

================================================
line : 1.3
revision : 6425
================================================


Thanks a lot !


Séb




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Re: [bug #11860] Feature request for diffusion tensor representation

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