Hi Edward,
I added the residue check as you suggested. A new problem was coming out.
Firstly, a single atom 2 can be loaded properly. But if all atoms are
loaded, then it complains that the second atom exists and a new spin with
the same name can not be generated again. I guess the code can not check
properly that the atom 2 has been loaded, but I could not find the problem
in the code. Could you help me with that?
Best,
Han
On Jun 23, 2011, at 3:19 PM, hasu@xxxxxxxxxxxxxxxxx wrote:
Author: han87
Date: Thu Jun 23 15:19:45 2011
New Revision: 13180
URL: http://svn.gna.org/viewcvs/relax?rev=13180&view=rev
Log:
Debugging the user function load_spins() and changing the system test
test_read_xyz_internal2().
In the user function load_spins() in generic_fns/structure/main.py a check
whether the residue name exists or not has been included. The code is
similiar to the molecule check. Also see email:
https://mail.gna.org/public/relax-devel/2011-06/msg00226.html. And in the
system test 'test_read_xyz_internal2()' all models were loaded instead of 2
and the line for loading proton was removed.
Modified:
branches/xyz/generic_fns/structure/main.py
branches/xyz/test_suite/system_tests/structure.py
Modified: branches/xyz/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/generic_fns/structure/main.py?rev=13180&r1=13179&r2=13180&view=diff
==============================================================================
--- branches/xyz/generic_fns/structure/main.py (original)
+++ branches/xyz/generic_fns/structure/main.py Thu Jun 23 15:19:45 2011
@@ -236,11 +236,26 @@
# Add the residue if it doesn't exist.
if res_cont == None:
- # Add the residue.
- mol_cont.res.add_item(res_name=res_name, res_num=res_num)
-
- # Get the container.
- res_cont = mol_cont.res[-1]
+ # Get the unnamed residue, assuming there is only one:
+ res_cont = return_residue()
+
+ # Got something!
+ if res_cont != None:
+ # Rename the residue name if the res name is given and
the sole container is unnamed.
+ if res_cont.name == None and res_name:
+ # Print out.
+ print(("Renaming the unnamed sole residue container
to '%s'." % res_name))
+
+ # Get the name.
+ res_cont.name = res_name
+
+ # Nothing exists yet.
+ else:
+ # Add the residue.
+ mol_cont.res.add_item(res_name=res_name, res_num=res_num)
+
+ # Get the container.
+ res_cont = mol_cont.res[-1]
# Add the atom number to the ID string (atom name is ignored
because only the number is unique).
id = id + '@' + repr(atom_num)
Modified: branches/xyz/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/xyz/test_suite/system_tests/structure.py?rev=13180&r1=13179&r2=13180&view=diff
==============================================================================
--- branches/xyz/test_suite/system_tests/structure.py (original)
+++ branches/xyz/test_suite/system_tests/structure.py Thu Jun 23 15:19:45
2011
@@ -656,7 +656,7 @@
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
# Read the xyz.
-
self.interpreter.structure.read_xyz(file='SSS-cluster4-new-test.xyz',
dir=path, read_model=[1,3])
+
self.interpreter.structure.read_xyz(file='SSS-cluster4-new-test.xyz',
dir=path)
# Test the molecule name.
self.assertEqual(cdp.structure.structural_data[0].mol[0].mol_name,
'SSS-cluster4-new-test_mol1')
@@ -666,8 +666,8 @@
self.assertEqual(count_spins(), 1)
# Try loading a few protons.
- self.interpreter.structure.load_spins('@*H*')
-
- # And now all the rest of the atoms.
- self.interpreter.structure.load_spins()
-
+ #self.interpreter.structure.load_spins('@H')
+
+ # And now all the rest of the atoms.
+ self.interpreter.structure.load_spins()
+
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Re: r13180 - in /branches/xyz: generic_fns/structure/main.py test_suite/system_tests/structure.py