Ok, I've reverted to the original behaviour while still fixing the bug
(https://gna.org/bugs/?11378). So now if relax doesn't find the
relevant atoms for the XH vector, the spin is deselected and the
'xh_vect' structure is non-existent for that spin. The bug is fixed,
and the test-suite passes.
Cheers,
Edward
On Thu, Mar 27, 2008 at 4:56 PM, Sébastien Morin
<sebastien.morin.1@xxxxxxxxx> wrote:
Hi Ed,
I just updated my 1.2 version of relax so bug 11378 is solved.
I ran the test-suite and found out that solving this bug caused the
angles test to fail :
Angle calculation tests:
The user function angles()
.......................................................... [ Failed ]
In the angles test, a pDB is read. Here are the lines :
# Read a PDB file.
self.relax.interpreter._PDB.pdb(run, file='test.pdb',
dir=sys.path[-1] + '/test_suite/data', model=1, heteronuc='N', proton='H')
I don't have time right now to take a look at this...
Do you have any idea ?
Ciao !
Séb :)
edward@xxxxxxxxxxxxx wrote:
> Author: bugman
> Date: Thu Mar 27 11:23:55 2008
> New Revision: 5235
>
> URL: http://svn.gna.org/viewcvs/relax?rev=5235&view=rev
> Log:
> Fix for bug #11378 (https://gna.org/bugs/?11378).
>
> This bug was reported by Ryan Hoffman (https://gna.org/users/rydog).
>
> The fix was to set the xh_vect variable to None rather than deleting it
when the proton or
> heteronucleus is not found by the pdb() user function, and to also
deselect that spin.
>
>
> Modified:
> 1.2/generic_fns/pdb.py
>
> Modified: 1.2/generic_fns/pdb.py
> URL:
http://svn.gna.org/viewcvs/relax/1.2/generic_fns/pdb.py?rev=5235&r1=5234&r2=5235&view=diff
>
==============================================================================
> --- 1.2/generic_fns/pdb.py (original)
> +++ 1.2/generic_fns/pdb.py Thu Mar 27 11:23:55 2008
> @@ -287,9 +287,10 @@
>
> # Average the vectors and convert xh_vect from an array of
vectors to a vector.
> for i in xrange(len(self.relax.data.res[self.run])):
> - # No vectors.
> + # No vectors - deselect the residue.
> if self.relax.data.res[self.run][i].xh_vect[0] == None:
> - del self.relax.data.res[self.run][i].xh_vect
> + self.relax.data.res[self.run][i].xh_vect = None
> + self.relax.data.res[self.run][i].select = 0
> continue
>
> # Average vectors.
>
>
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Re: r5235 - /1.2/generic_fns/pdb.py