Hi Edward,
Ok, thanks! I think I need some time to fully understand this logic.
Best,
Han
On Jul 27, 2011, at 1:49 PM, Edward d'Auvergne wrote:
Hi,
The svnmerge update will clear some things up. I've now tracked this
to the load_spins() function of generic_fns/structure/main.py. The
logic is not very flexible in here, and I think we will need to
redesign this function. It is safe to do the redesign in the xyz
branch as the 1.3 line is working perfectly at the moment. The
redesign is only needed for the XYZ files. This is just because the
code was not designed with this type of flexibility in mind.
I would suggest that the logic should follow these options (the
container would be either a molecule container, a residue container,
or a spin container, and the same logic would be applied to all
three):
(1) The container name (and number) was not supplied, so check that
there is only a single container in the relax data store and that it
is unnamed and unnumbered (throw a RelaxError otherwise).
(2) The container already exists in the relax data store, so do
nothing.
(3) There is only a single container in the relax data store and
it is empty.
(4) The container does not exist, so add it.
The order of these would need to be determined. I would suggest we
also use a number of pre-written functions from relax:
- To get the ID strings, we can use
generic_fns.mol_res_spin.generate_spin_id(). This replaces all of the
'id' string manipulation in the current code.
- The container objects have is_empty() methods for determining if
they are empty. This should be used to identify if the container
should be renamed and renumbered in (3).
Because of the difficulty of this design, I might try to solve it
myself and commit the code to the xyz branch.
Regards,
Edward
On 27 July 2011 12:15, Han Sun <[email protected]> wrote:
Hi Edward,
ok, I will have a look. I think the problem is that the
return_residue
function does not work properly. I hope the 1.3 line has already
solved this
problem.
Best,
Han
On Jul 27, 2011, at 12:04 PM, Edward d'Auvergne wrote:
Hi Han,
I think you'll need to merge the 1.3 line changes into your
branch to
root out this problem. That will simplify the amount of changed
code
to search for the problem. If you don't know how to do this, see
section 9.5 of the relax manual for details
(http://www.nmr-relax.com/manual/1.3/9_5_Branches.html). Note that
svnmerge for the xyz branch has already been initialised.
Regards,
Edward
On 27 July 2011 11:52, Edward d'Auvergne <[email protected]>
wrote:
Hi,
This seems quite strange. When running the test suite, the system
tests have 11 failures and 44 errors. There appears to be a
problem
whereby all spins are being put into the first residue. I.e.
multiple
residues are no longer supported. This will require a bit of
digging.
Regards,
Edward
On 26 July 2011 18:57, Han Sun <[email protected]> wrote:
Hi Edward,
Now the test passes for reading the xyz file and loading the
spins. But
there is a problem for loading the spins in the pdb file. The
reason is
in
the generic_fns/structure/main.py function load_spins. We added
a check
to
see whether the residue name exists or not. When not, it will
add one.
And I
found this rises the problem now for loading the spins of a pdb
file
properly. Do you have a idea how to solve it?
Best,
Han
Begin forwarded message:
From: [email protected]
Date: July 26, 2011 6:47:49 PM GMT+02:00
To: [email protected]
Subject: r13900 - /branches/xyz/generic_fns/structure/main.py
Reply-To: [email protected]
Author: han87
Date: Tue Jul 26 18:47:49 2011
New Revision: 13900
URL: http://svn.gna.org/viewcvs/relax?rev=13900&view=rev
Log:
Changing the code in the generic_fns/structure/main.py
For printing out of modified spins, a test to check whether the
spin_name
exists or not is added.
Modified:
branches/xyz/generic_fns/structure/main.py
Modified: branches/xyz/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/
structure/main.py?rev=13900&r1=13899&r2=13900&view=diff
==================================================================
============
--- branches/xyz/generic_fns/structure/main.py (original)
+++ branches/xyz/generic_fns/structure/main.py Tue Jul 26
18:47:49 2011
@@ -602,7 +602,10 @@
# Print out of modified spins.
if verbosity:
- print(("Extracted " + str(spin.num) + "-" +
str(attached_name)
+ " vectors for " + repr(id) + '.'))
+ if spin.name:
+ print(("Extracted " + spin.name + "-" +
str(attached_name)
+ " vectors for " + repr(id) + '.'))
+ else:
+ print(("Extracted " + str(spin.num) + "-" +
str(attached_name) + " vectors for " + repr(id) + '.'))
# Right, catch the problem of missing vectors to prevent
massive
user
confusion!
if no_vectors:
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