Author: bugman
Date: Tue Oct 20 09:07:39 2015
New Revision: 28065
URL: http://svn.gna.org/viewcvs/relax?rev=28065&view=rev
Log:
Created the Mf.test_bug_23933_relax_data_read_ids system test.
This is designed to catch bug #23933 (https://gna.org/bugs/?23933), the
"NameError: global name
'ids' is not defined" problem when loading relaxation data.
A truncated version of the PDB file and relaxation data, the full versions of
which are attached to
the bug report, consisting solely of residues 329, 330, and 331 have been
added to the test suite
shared data directories, and the system test written to catch the NameError.
Added:
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/LARA_N_term_no_helixFH_reg.pdb
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt
(with props)
Modified:
trunk/test_suite/system_tests/model_free.py
Added:
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/LARA_N_term_no_helixFH_reg.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/LARA_N_term_no_helixFH_reg.pdb?rev=28065&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/LARA_N_term_no_helixFH_reg.pdb
(added)
+++
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/LARA_N_term_no_helixFH_reg.pdb
Tue Oct 20 09:07:39 2015
@@ -0,0 +1,46 @@
+ATOM 1 N GLN X 329 19.164 76.707 7.444 1.00 93.32
N
+ATOM 2 CA GLN X 329 18.396 77.948 7.313 1.00 94.77
C
+ATOM 3 C GLN X 329 19.316 79.169 7.331 1.00 95.15
C
+ATOM 4 O GLN X 329 18.945 80.243 6.859 1.00 98.80
O
+ATOM 5 CB GLN X 329 17.356 78.060 8.427 1.00 95.61
C
+ATOM 6 CG GLN X 329 16.064 77.308 8.156 1.00 93.83
C
+ATOM 7 CD GLN X 329 15.121 77.294 9.350 1.00 97.67
C
+ATOM 8 OE1 GLN X 329 14.384 76.328 9.556 1.00 96.17
O
+ATOM 9 NE2 GLN X 329 15.141 78.362 10.145 1.00 90.91
N
+ATOM 0 HA GLN X 329 17.938 77.922 6.459 1.00 94.77
H new
+ATOM 0 HB2 GLN X 329 17.744 77.728 9.252 1.00 95.61
H new
+ATOM 0 HB3 GLN X 329 17.149 78.997 8.568 1.00 95.61
H new
+ATOM 0 HG2 GLN X 329 15.613 77.713 7.399 1.00 93.83
H new
+ATOM 0 HG3 GLN X 329 16.274 76.395 7.906 1.00 93.83
H new
+ATOM 0 HE21 GLN X 329 15.669 79.018 9.970 1.00 90.91
H new
+ATOM 0 HE22 GLN X 329 14.626 78.396 10.833 1.00 90.91
H new
+ATOM 10 N GLN X 330 20.511 78.989 7.887 1.00 97.21
N
+ATOM 11 CA GLN X 330 21.528 80.033 7.940 1.00101.62
C
+ATOM 12 C GLN X 330 22.688 79.690 6.998 1.00103.96
C
+ATOM 13 O GLN X 330 23.834 80.084 7.233 1.00 99.45
O
+ATOM 14 CB GLN X 330 22.030 80.222 9.371 1.00106.05
C
+ATOM 15 CG GLN X 330 22.769 81.532 9.620 1.00111.68
C
+ATOM 16 CD GLN X 330 21.844 82.736 9.642 1.00110.66
C
+ATOM 17 OE1 GLN X 330 21.103 82.985 8.691 1.00114.33
O flip
+ATOM 18 NE2 GLN X 330 21.885 83.492 10.734 1.00106.35
N flip
+ATOM 0 H GLN X 330 20.756 78.248 8.248 1.00 97.21
H new
+ATOM 0 HA GLN X 330 21.137 80.872 7.650 1.00101.62
H new
+ATOM 0 HB2 GLN X 330 21.268 80.195 9.972 1.00106.05
H new
+ATOM 0 HB3 GLN X 330 22.638 79.497 9.584 1.00106.05
H new
+ATOM 0 HG2 GLN X 330 23.214 81.483 10.480 1.00111.68
H new
+ATOM 0 HG3 GLN X 330 23.421 81.672 8.918 1.00111.68
H new
+ATOM 0 HE21 GLN X 330 22.416 83.287 11.379 1.00106.35
H new
+ATOM 0 HE22 GLN X 330 21.380 84.185 10.796 1.00106.35
H new
+ATOM 19 N SER X 331 22.379 78.956 5.930 1.00106.47
N
+ATOM 20 CA SER X 331 23.396 78.493 4.982 1.00102.41
C
+ATOM 21 C SER X 331 23.614 79.457 3.809 1.00104.95
C
+ATOM 22 O SER X 331 24.323 79.129 2.857 1.00 99.41
O
+ATOM 23 CB SER X 331 23.067 77.085 4.472 1.00 93.37
C
+ATOM 24 OG SER X 331 21.928 77.092 3.631 1.00 99.94
O
+ATOM 0 H SER X 331 21.578 78.713 5.734 1.00106.47
H new
+ATOM 0 HA SER X 331 24.232 78.465 5.473 1.00102.41
H new
+ATOM 0 HB2 SER X 331 23.828 76.729 3.986 1.00 93.37
H new
+ATOM 0 HB3 SER X 331 22.911 76.495 5.226 1.00 93.37
H new
+ATOM 0 HG SER X 331 21.771 76.311 3.365 1.00 99.94
H new
+TER 845 SER X 437
+END
Added:
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt?rev=28065&view=auto
==============================================================================
---
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt
(added)
+++
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt
Tue Oct 20 09:07:39 2015
@@ -0,0 +1,2 @@
+329 0.71267 0.00665
+331 0.68828 0.01202
Propchange:
trunk/test_suite/shared_data/model_free/bug_23933_relax_data_read_ids/r1_600.txt
------------------------------------------------------------------------------
svn:eol-style = native
Modified: trunk/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/model_free.py?rev=28065&r1=28064&r2=28065&view=diff
==============================================================================
--- trunk/test_suite/system_tests/model_free.py (original)
+++ trunk/test_suite/system_tests/model_free.py Tue Oct 20 09:07:39 2015
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2006-2014 Edward d'Auvergne
#
+# Copyright (C) 2006-2015 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -478,6 +478,26 @@
# Execute the script.
self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'bug_21079_local_tm_global_selection.py')
+
+
+ def test_bug_23933_relax_data_read_ids(self):
+ """U{Bug #23933<https://gna.org/bugs/?23933>} catch, the global name
'ids' is not defined error when loading relaxation data."""
+
+ # Path of the files.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'bug_23933_relax_data_read_ids'
+
+ # Load the truncated PDB file.
+
self.interpreter.structure.read_pdb(file='LARA_N_term_no_helixFH_reg.pdb',
dir=path)
+
+ # Load the spin systems.
+ self.interpreter.structure.load_spins(spin_id='@N')
+ self.interpreter.structure.load_spins(spin_id='@H')
+ self.interpreter.structure.load_spins(spin_id='@NE1')
+ self.interpreter.structure.load_spins(spin_id='@HE1')
+
+ # Load the relaxation data.
+ self.interpreter.relax_data.read(ri_id='R1_600', ri_type='R1',
frq=600402816.0, file='r1_600.txt', dir=path, res_num_col=1, data_col=2,
error_col=3)
+
def test_create_m4(self):
r28065 - in /trunk/test_suite: shared_data/model_free/bug_23933_relax_data_read_ids/ system_tests/