Re: r6834 - /1.3/generic_fns/structure/geometric.py -- July 08, 2008 - 15:56

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
<sebastien.morin.1@xxxxxxxxx> 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,  <sebastien.morin.1@xxxxxxxxx> 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)
> > >
> > >
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