Author: bugman
Date: Fri Feb 20 11:49:51 2015
New Revision: 27695
URL: http://svn.gna.org/viewcvs/relax?rev=27695&view=rev
Log:
Created the Structure.test_bug_23295_ss_metadata_merge system test.
This is to catch bug #23295 (https://gna.org/bugs/?23295), the PDB secondary
structure HELIX and
SHEET records not updated when merging molecules. This uses the
'2BE6_secondary_structure.pdb'
structure file and 'test.py' relax script contents as the test, checking the
HELIX and SHEET
records.
Added:
trunk/test_suite/shared_data/structures/2BE6_secondary_structure.pdb
Modified:
trunk/test_suite/system_tests/structure.py
Added: trunk/test_suite/shared_data/structures/2BE6_secondary_structure.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/structures/2BE6_secondary_structure.pdb?rev=27695&view=auto
==============================================================================
--- trunk/test_suite/shared_data/structures/2BE6_secondary_structure.pdb
(added)
+++ trunk/test_suite/shared_data/structures/2BE6_secondary_structure.pdb
Fri Feb 20 11:49:51 2015
@@ -0,0 +1,58 @@
+HELIX 1 1 THR A 5 ASP A 20 1 16
+HELIX 2 2 THR A 28 LEU A 39 1 12
+HELIX 3 3 THR A 44 ASP A 56 1 13
+HELIX 4 4 PHE A 65 MET A 76 1 12
+HELIX 5 5 SER A 81 ASP A 93 1 13
+HELIX 6 6 SER A 101 LEU A 112 1 12
+HELIX 7 7 THR A 117 ASP A 129 1 13
+HELIX 8 8 TYR A 138 THR A 146 1 9
+HELIX 9 9 VAL D 1615 GLY D 1638 1 24
+HELIX 10 10 THR B 5 ASP B 20 1 16
+HELIX 11 11 THR B 28 LEU B 39 1 12
+HELIX 12 12 THR B 44 ASP B 56 1 13
+HELIX 13 13 PHE B 65 ASP B 78 1 14
+HELIX 14 14 GLU B 82 ASP B 93 1 12
+HELIX 15 15 SER B 101 GLY B 113 1 13
+HELIX 16 16 THR B 117 ASP B 129 1 13
+HELIX 17 17 TYR B 138 MET B 145 1 8
+HELIX 18 18 GLU E 1612 GLN E 1625 1 14
+HELIX 19 19 THR C 5 ASP C 20 1 16
+HELIX 20 20 THR C 28 LEU C 39 1 12
+HELIX 21 21 THR C 44 ASP C 56 1 13
+HELIX 22 22 PHE C 65 LYS C 75 1 11
+HELIX 23 23 GLU C 82 ASP C 93 1 12
+HELIX 24 24 SER C 101 LEU C 112 1 12
+HELIX 25 25 THR C 117 ASP C 129 1 13
+HELIX 26 26 TYR C 138 MET C 145 1 8
+HELIX 27 27 LYS F 1617 GLU F 1636 1 20
+SHEET 1 A 2 THR A 26 ILE A 27 0
+SHEET 2 A 2 ILE A 63 ASP A 64 -1 O ILE A 63 N ILE A 27
+SHEET 1 B 2 TYR A 99 ILE A 100 0
+SHEET 2 B 2 VAL A 136 ASN A 137 -1 O VAL A 136 N ILE A 100
+SHEET 1 C 2 THR B 26 ILE B 27 0
+SHEET 2 C 2 ILE B 63 ASP B 64 -1 O ILE B 63 N ILE B 27
+SHEET 1 D 2 TYR B 99 ILE B 100 0
+SHEET 2 D 2 VAL B 136 ASN B 137 -1 O VAL B 136 N ILE B 100
+SHEET 1 E 2 THR C 26 ILE C 27 0
+SHEET 2 E 2 ILE C 63 ASP C 64 -1 O ILE C 63 N ILE C 27
+SHEET 1 F 2 TYR C 99 ILE C 100 0
+SHEET 2 F 2 VAL C 136 ASN C 137 -1 O VAL C 136 N ILE C 100
+ATOM 1 N GLN A 3 -60.666 10.102 -15.189 1.00 45.02
N
+ATOM 2 CA GLN A 3 -59.700 9.668 -14.130 1.00 44.75
C
+TER 1125 THR A 146
+ATOM 1126 N GLU D1612 -37.971 8.936 -10.792 1.00 53.47
N
+ATOM 1127 CA GLU D1612 -36.823 8.395 -11.580 1.00 53.22
C
+TER 1362 VAL D1640
+ATOM 1363 N LEU B 4 -31.701 6.217 18.025 1.00 34.14
N
+ATOM 1364 CA LEU B 4 -30.741 7.335 17.723 1.00 34.28
C
+TER 2461 THR B 146
+ATOM 2462 N GLU E1612 -30.878 6.788 -3.987 1.00 23.15
N
+ATOM 2463 CA GLU E1612 -30.212 5.774 -3.112 1.00 23.48
C
+TER 2568 GLN E1625
+ATOM 2569 N LEU C 4 -15.700 1.591 -13.009 1.00 30.41
N
+ATOM 2570 CA LEU C 4 -14.296 1.964 -13.370 1.00 29.61
C
+TER 3661 THR C 146
+ATOM 3662 N VAL F1615 -13.922 9.423 -41.313 1.00 35.39
N
+ATOM 3663 CA VAL F1615 -14.225 8.920 -39.939 1.00 35.66
C
+TER 3857 GLU F1636
+END
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27695&r1=27694&r2=27695&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Fri Feb 20 11:49:51 2015
@@ -926,6 +926,120 @@
self.assertEqual(len(contents), len(lines))
for i in range(len(lines)):
self.assertEqual(contents[i], lines[i])
+
+
+ def test_bug_23295_ss_metadata_merge(self):
+ """Catch U{bug #23295<https://gna.org/bugs/?23295>}, the PDB
secondary structure HELIX and SHEET records not updated when merging
molecules."""
+
+ # 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('2BE6_secondary_structure.pdb',
dir=path, read_mol=[1, 4], set_mol_name='CaM A')
+ self.interpreter.structure.read_pdb('2BE6_secondary_structure.pdb',
dir=path, read_mol=[2, 5], set_mol_name='CaM B')
+ self.interpreter.structure.read_pdb('2BE6_secondary_structure.pdb',
dir=path, read_mol=[3, 6], set_mol_name='CaM C')
+
+ # Create a PDB file.
+ file = DummyFileObject()
+ self.interpreter.structure.write_pdb(file=file, force=True)
+
+ # The HELIX and SHEET contents, as they should be.
+ # First, the original contents:
+ # "HELIX 1 1 THR A 5 ASP A 20 1
16 "
+ # "HELIX 2 2 THR A 28 LEU A 39 1
12 "
+ # "HELIX 3 3 THR A 44 ASP A 56 1
13 "
+ # "HELIX 4 4 PHE A 65 MET A 76 1
12 "
+ # "HELIX 5 5 SER A 81 ASP A 93 1
13 "
+ # "HELIX 6 6 SER A 101 LEU A 112 1
12 "
+ # "HELIX 7 7 THR A 117 ASP A 129 1
13 "
+ # "HELIX 8 8 TYR A 138 THR A 146 1
9 "
+ # "HELIX 9 9 VAL D 1615 GLY D 1638 1
24 "
+ # "HELIX 10 10 THR B 5 ASP B 20 1
16 "
+ # "HELIX 11 11 THR B 28 LEU B 39 1
12 "
+ # "HELIX 12 12 THR B 44 ASP B 56 1
13 "
+ # "HELIX 13 13 PHE B 65 ASP B 78 1
14 "
+ # "HELIX 14 14 GLU B 82 ASP B 93 1
12 "
+ # "HELIX 15 15 SER B 101 GLY B 113 1
13 "
+ # "HELIX 16 16 THR B 117 ASP B 129 1
13 "
+ # "HELIX 17 17 TYR B 138 MET B 145 1
8 "
+ # "HELIX 18 18 GLU E 1612 GLN E 1625 1
14 "
+ # "HELIX 19 19 THR C 5 ASP C 20 1
16 "
+ # "HELIX 20 20 THR C 28 LEU C 39 1
12 "
+ # "HELIX 21 21 THR C 44 ASP C 56 1
13 "
+ # "HELIX 22 22 PHE C 65 LYS C 75 1
11 "
+ # "HELIX 23 23 GLU C 82 ASP C 93 1
12 "
+ # "HELIX 24 24 SER C 101 LEU C 112 1
12 "
+ # "HELIX 25 25 THR C 117 ASP C 129 1
13 "
+ # "HELIX 26 26 TYR C 138 MET C 145 1
8 "
+ # "HELIX 27 27 LYS F 1617 GLU F 1636 1
20 "
+ # "SHEET 1 A 2 THR A 26 ILE A 27 0
"
+ # "SHEET 2 A 2 ILE A 63 ASP A 64 -1 O ILE A 63 N
ILE A 27 "
+ # "SHEET 1 B 2 TYR A 99 ILE A 100 0
"
+ # "SHEET 2 B 2 VAL A 136 ASN A 137 -1 O VAL A 136 N
ILE A 100 "
+ # "SHEET 1 C 2 THR B 26 ILE B 27 0
"
+ # "SHEET 2 C 2 ILE B 63 ASP B 64 -1 O ILE B 63 N
ILE B 27 "
+ # "SHEET 1 D 2 TYR B 99 ILE B 100 0
"
+ # "SHEET 2 D 2 VAL B 136 ASN B 137 -1 O VAL B 136 N
ILE B 100 "
+ # "SHEET 1 E 2 THR C 26 ILE C 27 0
"
+ # "SHEET 2 E 2 ILE C 63 ASP C 64 -1 O ILE C 63 N
ILE C 27 "
+ # "SHEET 1 F 2 TYR C 99 ILE C 100 0
"
+ # "SHEET 2 F 2 VAL C 136 ASN C 137 -1 O VAL C 136 N
ILE C 100 "
+ # Then the modified contents:
+ contents = [
+ "HELIX 1 1 THR A 5 ASP A 20 1
16 \n",
+ "HELIX 2 2 THR A 28 LEU A 39 1
12 \n",
+ "HELIX 3 3 THR A 44 ASP A 56 1
13 \n",
+ "HELIX 4 4 PHE A 65 MET A 76 1
12 \n",
+ "HELIX 5 5 SER A 81 ASP A 93 1
13 \n",
+ "HELIX 6 6 SER A 101 LEU A 112 1
12 \n",
+ "HELIX 7 7 THR A 117 ASP A 129 1
13 \n",
+ "HELIX 8 8 TYR A 138 THR A 146 1
9 \n",
+ "HELIX 9 9 VAL A 1615 GLY A 1638 1
24 \n",
+ "HELIX 10 10 THR B 5 ASP B 20 1
16 \n",
+ "HELIX 11 11 THR B 28 LEU B 39 1
12 \n",
+ "HELIX 12 12 THR B 44 ASP B 56 1
13 \n",
+ "HELIX 13 13 PHE B 65 ASP B 78 1
14 \n",
+ "HELIX 14 14 GLU B 82 ASP B 93 1
12 \n",
+ "HELIX 15 15 SER B 101 GLY B 113 1
13 \n",
+ "HELIX 16 16 THR B 117 ASP B 129 1
13 \n",
+ "HELIX 17 17 TYR B 138 MET B 145 1
8 \n",
+ "HELIX 18 18 GLU B 1612 GLN B 1625 1
14 \n",
+ "HELIX 19 19 THR C 5 ASP C 20 1
16 \n",
+ "HELIX 20 20 THR C 28 LEU C 39 1
12 \n",
+ "HELIX 21 21 THR C 44 ASP C 56 1
13 \n",
+ "HELIX 22 22 PHE C 65 LYS C 75 1
11 \n",
+ "HELIX 23 23 GLU C 82 ASP C 93 1
12 \n",
+ "HELIX 24 24 SER C 101 LEU C 112 1
12 \n",
+ "HELIX 25 25 THR C 117 ASP C 129 1
13 \n",
+ "HELIX 26 26 TYR C 138 MET C 145 1
8 \n",
+ "HELIX 27 27 LYS C 1617 GLU C 1636 1
20 \n",
+ "SHEET 1 A 2 THR A 26 ILE A 27 0
\n",
+ "SHEET 2 A 2 ILE A 63 ASP A 64 -1 O ILE A 63 N ILE
A 27 \n",
+ "SHEET 1 B 2 TYR A 99 ILE A 100 0
\n",
+ "SHEET 2 B 2 VAL A 136 ASN A 137 -1 O VAL A 136 N ILE
A 100 \n",
+ "SHEET 1 C 2 THR B 26 ILE B 27 0
\n",
+ "SHEET 2 C 2 ILE B 63 ASP B 64 -1 O ILE B 63 N ILE
B 27 \n",
+ "SHEET 1 D 2 TYR B 99 ILE B 100 0
\n",
+ "SHEET 2 D 2 VAL B 136 ASN B 137 -1 O VAL B 136 N ILE
B 100 \n",
+ "SHEET 1 E 2 THR C 26 ILE C 27 0
\n",
+ "SHEET 2 E 2 ILE C 63 ASP C 64 -1 O ILE C 63 N ILE
C 27 \n",
+ "SHEET 1 F 2 TYR C 99 ILE C 100 0
\n",
+ "SHEET 2 F 2 VAL C 136 ASN C 137 -1 O VAL C 136 N ILE
C 100 \n",
+ ]
+
+ # Check the created PDB file.
+ lines = file.readlines()
+ index = 0
+ for line in lines:
+ # Skip non-secondary structure records.
+ if not search('^HELIX', line) and not search('^SHEET', line):
+ continue
+
+ # Check the line.
+ self.assertEqual(contents[index], line)
+
+ # Increment the secondary structure index.
+ index += 1
def test_bug_sr_2998_broken_conect_records(self):
r27695 - in /trunk/test_suite: shared_data/structures/2BE6_secondary_structure.pdb system_tests/structure.py