Hi Ed,
I looked at the code using svn diff with revision number...
It seems that line 225 of generic_fns/structure/geometric.py was changed
from :
R = centre_of_mass()
to
CoM = centre_of_mass()
So, should we change the following calls to 'R' to calls to 'CoM' ? Or
am I completely wrong..?
Cheers,
Séb
Edward d'Auvergne wrote:
> Hi,
>
> Yeah, I noticed that problem in your test. I'll try to hunt down a
> little later where we lost this R array (the origin set to the centre
> of mass). It should be documented in the changes in this method
> (using svn diff with revision numbers will be useful) that have
> occurred in the 1.3 line.
>
> Regards,
>
> Edward
>
>
> On Tue, Jul 8, 2008 at 3:32 PM, Sébastien Morin
> <[EMAIL PROTECTED]> wrote:
>
>> Hi Ed,
>>
>> Everything seems cool ! I get to know the code much more, but may make
>> some errors and introduce new bugs...
>>
>> Additionally, I a currently stuck with the message error for
>> diffusion_tensor system test :
>>
>> ========
>> line :
>> Traceback (most recent call last):
>> File
>> "/home/semor/pse-4/collaborations/relax/relax-1.3/test_suite/system_tests/diffusion_tensor.py",
>> line 109, in test_createDiffTensor
>> self.relax.interpreter._Structure.create_diff_tensor_pdb(file='devnull')
>> 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 263, in create_diff_tensor_pdb
>> res_num = generate_vector_residues(structure=structure,
>> vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit,
>> atom_name='Dpar', res_name_vect='AXS', sim_vectors=sim_vectors,
>> chain_id=chain_id, res_num=res_num, origin=R, scale=scale, neg=True)
>> NameError: global name 'R' is not defined
>> ========
>>
>> I tried (pessimistly) setting R to different things :
>>
>> - pipe.diff_tensor.rotation
>> - centre_of_mass()
>> - eye(3)
>> - None
>>
>> but none would work (!) and I am now without idea... Do you have any
>> clue ? Did I break something somewhere else yesterday ?
>>
>> Moreover, the system test doesn't stop at the first instance of
>> structure.create_diff_tensor_pdb(), but at the second, the first being
>> the one for the sphere. Hence, the sphere representation doesn't fail,
>> but I tried it with a script of my own and it yields an empty pdb
>> (except for the header). Would you have a tensor pdb I could look at so
>> when the code works again, I know the file is correctly formatted..?
>>
>> Regards,
>>
>>
>> Séb
>>
>>
>>
>>
>> Edward d'Auvergne wrote:
>>
>>> Hi,
>>>
>>> With the fixes you've been making and the changes I made to the
>>> structural object code, I think the diffusion tensor representation
>>> should soon be functioning again. Do you see any real technical
>>> issues preventing this? I hope my changes haven't caused you too many
>>> problems. They were necessary though, as the PDB reading and writing
>>> code was broken.
>>>
>>> Regards,
>>>
>>> Edward
>>>
>>>
>>> On Tue, Jul 8, 2008 at 6:42 AM, <[EMAIL PROTECTED]> wrote:
>>>
>>>
>>>> Author: semor
>>>> Date: Tue Jul 8 06:42:46 2008
>>>> New Revision: 6834
>>>>
>>>> URL: http://svn.gna.org/viewcvs/relax?rev=6834&view=rev
>>>> Log:
>>>> Corrected a typo introduced in r6815.
>>>>
>>>>
>>>> Modified:
>>>> 1.3/generic_fns/structure/geometric.py
>>>>
>>>> Modified: 1.3/generic_fns/structure/geometric.py
>>>> URL:
>>>> http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=6834&r1=6833&r2=6834&view=diff
>>>> ==============================================================================
>>>> --- 1.3/generic_fns/structure/geometric.py (original)
>>>> +++ 1.3/generic_fns/structure/geometric.py Tue Jul 8 06:42:46 2008
>>>> @@ -611,7 +611,7 @@
>>>> atom_id_ext = ''
>>>>
>>>> # The origin atom.
>>>> - structure.atom_add(pdb_record='HETATM',
>>>> atom_num='R_vect'+atom_id_ext, atom_name=R, res_name=res_name_vect,
>>>> chain_id=chain_id, res_num=res_num, pos=origin, segment_id=None,
>>>> element='C', struct_index=None)
>>>> + structure.atom_add(pdb_record='HETATM',
>>>> atom_num='R_vect'+atom_id_ext, atom_name='R', res_name=res_name_vect,
>>>> chain_id=chain_id, res_num=res_num, pos=origin, segment_id=None,
>>>> element='C', struct_index=None)
>>>>
>>>> # Create the PDB residue representing the vector.
>>>> structure.atom_add(pdb_record='HETATM',
>>>> atom_num=atom_name+atom_id_ext, atom_name=atom_name,
>>>> res_name=res_name_vect, chain_id=chain_id, res_num=res_num,
>>>> pos=origin+vector*scale, segment_id=None, element='C', struct_index=None)
>>>>
>>>>
>>>> _______________________________________________
>>>> relax (http://nmr-relax.com)
>>>>
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>>>>
>>> _______________________________________________
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>>
>
>
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