Re: [bug #11860] Feature request for diffusion tensor representation -- June 22, 2008 - 21:34

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
>
>
>
>
>    _______________________________________________________
>
> Reply to this item at:
>
>  <http://gna.org/bugs/?11860>
>
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