Author: bugman
Date: Fri Feb 1 17:05:09 2013
New Revision: 18361
URL: http://svn.gna.org/viewcvs/relax?rev=18361&view=rev
Log:
Merged revisions 18358-18360 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18358 | bugman | 2013-02-01 16:53:34 +0100 (Fri, 01 Feb 2013) | 3 lines
Created the Bmrb.test_bug_20471_structure_present to catch bug #20471
(https://gna.org/bugs/?20471).
........
r18359 | bugman | 2013-02-01 17:03:20 +0100 (Fri, 01 Feb 2013) | 7 lines
Fix for bug #20471 (https://gna.org/bugs/?20471).
The problem was that the data pipe is_empty() method was not handling
structural data correctly.
The is_empty() method now belongs to the MolContainer objects rather than
cdp.structure, and the
object cdp.structure is not always present.
........
r18360 | bugman | 2013-02-01 17:04:27 +0100 (Fri, 01 Feb 2013) | 7 lines
Fix for bug #20471 (https://gna.org/bugs/?20471).
The problem was that the data pipe is_empty() method was not handling
structural data correctly.
The is_empty() method now belongs to the MolContainer objects rather than
cdp.structure, and the
object cdp.structure is not always present.
........
Added:
branches/frame_order_testing/test_suite/shared_data/bmrb/
- copied from r18360, trunk/test_suite/shared_data/bmrb/
branches/frame_order_testing/test_suite/shared_data/structures/1RTE_H_trunc.pdb
- copied unchanged from r18360,
trunk/test_suite/shared_data/structures/1RTE_H_trunc.pdb
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/data/pipe_container.py
branches/frame_order_testing/test_suite/system_tests/bmrb.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Feb 1 17:05:09 2013
@@ -1,1 +1,1 @@
-/trunk:1-18356
+/trunk:1-18360
Modified: branches/frame_order_testing/data/pipe_container.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/data/pipe_container.py?rev=18361&r1=18360&r2=18361&view=diff
==============================================================================
--- branches/frame_order_testing/data/pipe_container.py (original)
+++ branches/frame_order_testing/data/pipe_container.py Fri Feb 1 17:05:09
2013
@@ -260,7 +260,7 @@
"""
# Is the molecule structure data object empty?
- if hasattr(self, 'structure') and not self.structure.is_empty():
+ if hasattr(self, 'structure'):
return False
# Is the molecule/residue/spin data object empty?
Modified: branches/frame_order_testing/test_suite/system_tests/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/bmrb.py?rev=18361&r1=18360&r2=18361&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/bmrb.py (original)
+++ branches/frame_order_testing/test_suite/system_tests/bmrb.py Fri Feb 1
17:05:09 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008-2012 Edward d'Auvergne
#
+# Copyright (C) 2008-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -231,6 +231,27 @@
self.assertEqual(cont_old.ri_data_err[ri_id],
cont_new.ri_data_err[ri_id])
+ def test_bug_20471_structure_present(self):
+ """Catch bug #20471 (https://gna.org/bugs/?20471), with structural
data present prior to a bmrb.read call."""
+
+ # Create the data pipe.
+ self.interpreter.pipe.create('test', 'mf')
+
+ # Load the PDB file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+ self.interpreter.structure.read_pdb(file='1RTE_H_trunc.pdb',
dir=path, read_mol=None, set_mol_name=None, read_model=None,
set_model_num=None, parser='internal', alt_loc='A')
+
+ # Set up the 15N and 1H spins.
+ self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True)
+ self.interpreter.structure.load_spins(spin_id='@H', ave_pos=True)
+ self.interpreter.spin.isotope(isotope='15N', spin_id='@N',
force=False)
+ self.interpreter.spin.isotope(isotope='1H', spin_id='@H',
force=False)
+
+ # Load the relaxation data.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'bmrb'
+ self.interpreter.bmrb.read(file='17226.txt', dir=path, version=None,
sample_conditions=None)
+
+
def test_rw_bmrb_3_0_model_free(self):
"""Write and then read a BRMB STAR formatted file containing
model-free results."""
r18361 - in /branches/frame_order_testing: ./ data/ test_suite/shared_data/bmrb/ test_suite/shared_data/structures/ test_sui...