Author: bugman
Date: Thu Oct 10 13:58:50 2013
New Revision: 21049
URL: http://svn.gna.org/viewcvs/relax?rev=21049&view=rev
Log:
Created the Structure.test_bug_21187_corrupted_pdb system test to catch bug
#21187.
The bug at https://gna.org/bugs/?21187 was reported by Martin Ballaschk
(https://gna.org/users/mab).
Added:
trunk/test_suite/shared_data/structures/bug_21187_molecule.pdb
Modified:
trunk/test_suite/system_tests/structure.py
Added: trunk/test_suite/shared_data/structures/bug_21187_molecule.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/structures/bug_21187_molecule.pdb?rev=21049&view=auto
==============================================================================
--- trunk/test_suite/shared_data/structures/bug_21187_molecule.pdb (added)
+++ trunk/test_suite/shared_data/structures/bug_21187_molecule.pdb Thu Oct 10
13:58:50 2013
@@ -1,0 +1,69 @@
+ATOM 2775 N ASP B 59 20.590 15.179 38.962 1.00 26.64
N
+ATOM 2776 CA ASP B 59 21.867 14.942 39.643 1.00 25.88
C
+ATOM 2777 C ASP B 59 22.583 13.669 39.172 1.00 24.80
C
+ATOM 2778 O ASP B 59 23.565 13.235 39.784 1.00 25.02
O
+ATOM 2779 CB ASP B 59 21.687 14.934 41.166 1.00 25.70
C
+ATOM 2780 CG ASP B 59 20.852 13.764 41.670 1.00 26.73
C
+ATOM 2781 OD1 ASP B 59 20.375 12.916 40.871 1.00 26.48
O
+ATOM 2782 OD2 ASP B 59 20.616 13.635 42.887 1.00 26.65
O
+ATOM 0 H ASP B 59 19.793 14.814 39.443 1.00 26.64
H new
+ATOM 0 HA ASP B 59 22.519 15.783 39.366 1.00 25.88
H new
+ATOM 0 HB2 ASP B 59 22.677 14.901 41.645 1.00 25.70
H new
+ATOM 0 HB3 ASP B 59 21.210 15.876 41.476 1.00 25.70
H new
+ATOM 2783 N TRP B 60 22.070 13.080 38.099 1.00 23.50
N
+ATOM 2784 CA TRP B 60 22.670 11.937 37.398 1.00 22.62
C
+ATOM 2785 C TRP B 60 22.385 10.571 38.023 1.00 22.58
C
+ATOM 2786 O TRP B 60 22.705 9.551 37.420 1.00 22.20
O
+ATOM 2787 CB TRP B 60 24.182 12.088 37.221 1.00 22.53
C
+ATOM 2788 CG TRP B 60 24.639 13.359 36.542 1.00 21.54
C
+ATOM 2789 CD1 TRP B 60 25.229 14.419 37.133 1.00 20.30
C
+ATOM 2790 CD2 TRP B 60 24.551 13.675 35.143 1.00 19.70
C
+ATOM 2791 NE1 TRP B 60 25.529 15.376 36.191 1.00 21.03
N
+ATOM 2792 CE2 TRP B 60 25.118 14.946 34.963 1.00 20.00
C
+ATOM 2793 CE3 TRP B 60 24.060 12.999 34.021 1.00 21.09
C
+ATOM 2794 CZ2 TRP B 60 25.212 15.563 33.711 1.00 19.58
C
+ATOM 2795 CZ3 TRP B 60 24.145 13.608 32.776 1.00 21.12
C
+ATOM 2796 CH2 TRP B 60 24.715 14.880 32.633 1.00 20.93
C
+ATOM 0 H TRP B 60 21.213 13.384 37.682 1.00 23.50
H new
+ATOM 0 HA TRP B 60 22.170 11.958 36.419 1.00 22.62
H new
+ATOM 0 HB2 TRP B 60 24.656 12.033 38.212 1.00 22.53
H new
+ATOM 0 HB3 TRP B 60 24.552 11.230 36.640 1.00 22.53
H new
+ATOM 0 HD1 TRP B 60 25.439 14.505 38.209 1.00 20.30
H new
+ATOM 0 HE1 TRP B 60 25.978 16.250 36.377 1.00 21.03
H new
+ATOM 0 HE3 TRP B 60 23.613 11.999 34.124 1.00 21.09
H new
+ATOM 0 HZ2 TRP B 60 25.667 16.558 33.597 1.00 19.58
H new
+ATOM 0 HZ3 TRP B 60 23.759 13.084 31.889 1.00 21.12
H new
+ATOM 0 HH2 TRP B 60 24.764 15.339 31.635 1.00 20.93
H new
+ATOM 2797 N SER B 61 21.783 10.536 39.209 1.00 22.42
N
+ATOM 2798 CA SER B 61 21.456 9.273 39.849 1.00 22.36
C
+ATOM 2799 C SER B 61 20.303 8.581 39.104 1.00 22.17
C
+ATOM 2800 O SER B 61 19.410 9.245 38.578 1.00 22.01
O
+ATOM 2801 CB SER B 61 21.097 9.482 41.319 1.00 22.72
C
+ATOM 2802 OG SER B 61 19.846 10.114 41.467 1.00 21.64
O
+ATOM 0 H SER B 61 21.520 11.348 39.730 1.00 22.42
H new
+ATOM 0 HA SER B 61 22.343 8.624 39.805 1.00 22.36
H new
+ATOM 0 HB2 SER B 61 21.080 8.510 41.834 1.00 22.72
H new
+ATOM 0 HB3 SER B 61 21.875 10.090 41.804 1.00 22.72
H new
+ATOM 0 HG SER B 61 19.942 11.092 41.279 1.00 21.64
H new
+ATOM 3209 N LEU C 9 34.356 13.147 22.748 1.00 26.70
N
+ATOM 3210 CA LEU C 9 35.075 13.681 23.899 1.00 26.05
C
+ATOM 3211 C LEU C 9 36.574 13.738 23.604 1.00 25.71
C
+ATOM 3212 O LEU C 9 37.076 13.030 22.725 1.00 24.25
O
+ATOM 3213 CB LEU C 9 34.818 12.851 25.159 1.00 26.19
C
+ATOM 3214 CG LEU C 9 33.375 12.758 25.689 1.00 26.33
C
+ATOM 3215 CD1 LEU C 9 33.317 11.975 26.987 1.00 25.47
C
+ATOM 3216 CD2 LEU C 9 32.744 14.126 25.889 1.00 26.24
C
+ATOM 3217 OXT LEU C 9 37.313 14.501 24.240 1.00 25.40
O
+ATOM 0 H LEU C 9 33.807 12.334 22.942 1.00 26.70
H new
+ATOM 0 HA LEU C 9 34.702 14.699 24.085 1.00 26.05
H new
+ATOM 0 HB2 LEU C 9 35.171 11.827 24.965 1.00 26.19
H new
+ATOM 0 HB3 LEU C 9 35.446 13.260 25.964 1.00 26.19
H new
+ATOM 0 HG LEU C 9 32.796 12.226 24.919 1.00 26.33
H new
+ATOM 0 HD11 LEU C 9 32.276 11.926 27.340 1.00 25.47
H new
+ATOM 0 HD12 LEU C 9 33.695 10.956 26.818 1.00 25.47
H new
+ATOM 0 HD13 LEU C 9 33.938 12.475 27.745 1.00 25.47
H new
+ATOM 0 HD21 LEU C 9 31.718 14.005 26.267 1.00 26.24
H new
+ATOM 0 HD22 LEU C 9 33.337 14.701 26.616 1.00 26.24
H new
+ATOM 0 HD23 LEU C 9 32.720 14.663 24.929 1.00 26.24
H new
+TER 3218 LEU C 9
+END
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=21049&r1=21048&r2=21049&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu Oct 10 13:58:50 2013
@@ -75,6 +75,24 @@
self.interpreter.structure.read_pdb('1OGT_trunc.pdb', dir=path,
alt_loc='A')
self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True)
self.interpreter.sequence.attach_protons()
+
+
+ def test_bug_21187_corrupted_pdb(self):
+ """Catch U{bug #21187<https://gna.org/bugs/?21187>}, the corrupted
PDB with all proton atoms numbers set to zero."""
+
+ # Path of the structure file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+ # Load the file.
+ self.interpreter.structure.read_pdb('bug_21187_molecule.pdb',
dir=path)
+
+ # Load the @N, @H, and @NE1 spins (needed to create the :60@0 spin
to trigger the bug later).
+ self.interpreter.structure.load_spins(spin_id='@N', ave_pos=True)
+ self.interpreter.structure.load_spins(spin_id='@NE1', ave_pos=True)
+ self.interpreter.structure.load_spins(spin_id='@H', ave_pos=True)
+
+ # Load the :60@HE1 spin - this clashes with the :60@H spin as both
have the spin ID of ':60@0'.
+ self.interpreter.structure.load_spins(spin_id='@HE1', ave_pos=True)
def test_delete_empty(self):
r21049 - in /trunk/test_suite: shared_data/structures/bug_21187_molecule.pdb system_tests/structure.py