Author: bugman
Date: Thu Feb 19 14:22:50 2015
New Revision: 27667
URL: http://svn.gna.org/viewcvs/relax?rev=27667&view=rev
Log:
Created the Structure.test_bug_23293_missing_hetatm system test.
This is to catch bug #23293 (https://gna.org/bugs/?23293), the PDB HETATM
loading error whereby the
last HETATM record is sometimes not read from the PDB file.
Added:
trunk/test_suite/shared_data/structures/bug_23293_missing_hetatm.pdb
Modified:
trunk/test_suite/system_tests/structure.py
Added: trunk/test_suite/shared_data/structures/bug_23293_missing_hetatm.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/structures/bug_23293_missing_hetatm.pdb?rev=27667&view=auto
==============================================================================
--- trunk/test_suite/shared_data/structures/bug_23293_missing_hetatm.pdb
(added)
+++ trunk/test_suite/shared_data/structures/bug_23293_missing_hetatm.pdb
Thu Feb 19 14:22:50 2015
@@ -0,0 +1,27 @@
+HET CA A 501 1
+HET CA A 502 1
+HET CA B 503 1
+HET CA B 504 1
+HET CA B 505 1
+HET CA B 506 1
+HETNAM CA UNKNOWN
+FORMUL 1 CA CA1
+MODEL 1
+ATOM 1 N LEU A 1 1.000 -2.000 20.000 1.00 0.00
N
+ATOM 2 H LEU A 1 2.000 -2.000 20.000 1.00 0.00
H
+TER 3 LEU A 1
+HETATM 4 CA CA A 501 17.000 12.000 14.000 1.00 0.00
CA
+HETATM 5 CA CA A 502 6.000 9.000 14.000 1.00 0.00
CA
+ATOM 6 N LEU B 1 9.000 -9.000 27.000 1.00 0.00
N
+ATOM 7 H LEU B 1 8.000 -8.000 27.000 1.00 0.00
H
+TER 8 LEU B 1
+HETATM 9 CA CA B 503 17.000 12.000 14.000 1.00 0.00
CA
+HETATM 10 CA CA B 504 6.000 9.000 14.000 1.00 0.00
CA
+ATOM 11 N LEU C 1 12.000 -12.000 7.000 1.00 0.00
N
+ATOM 12 H LEU C 1 11.000 -12.000 7.000 1.00 0.00
H
+TER 13 LEU C 1
+HETATM 14 CA CA C 505 31.000 -10.000 -0.000 1.00 0.00
CA
+HETATM 15 CA CA C 506 31.000 -19.000 6.000 1.00 0.00
CA
+ENDMDL
+MASTER 0 0 6 0 0 0 0 0 12 3 0 0
+END
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=27667&r1=27666&r2=27667&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu Feb 19 14:22:50 2015
@@ -831,6 +831,58 @@
"ATOM 1 N Phe A 1 1.000 1.000 1.000 1.00
0.00 N \n",
"TER 2 Phe A 1
\n",
"MASTER 0 0 0 0 0 0 0 0 1 1
0 0 \n",
+ "END
\n"
+ ]
+
+ # Check the created PDB file.
+ lines = file.readlines()
+ self.strip_remarks(lines)
+ self.assertEqual(len(contents), len(lines))
+ for i in range(len(lines)):
+ self.assertEqual(contents[i], lines[i])
+
+
+ def test_bug_23293_missing_hetatm(self):
+ """Catch U{bug #23293<https://gna.org/bugs/?23293>}, the PDB HETATM
loading error whereby the last HETATM record is sometimes not read from the
PDB file."""
+
+ # 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_23293_missing_hetatm.pdb',
dir=path)
+
+ # Create a PDB file.
+ file = DummyFileObject()
+ self.interpreter.structure.write_pdb(file=file, force=True)
+
+ # The file contents, without remarks, as they should be.
+ contents = [
+ "HET CA A 501 1
\n",
+ "HET CA A 502 1
\n",
+ "HET CA B 503 1
\n",
+ "HET CA B 504 1
\n",
+ "HET CA B 505 1
\n",
+ "HET CA B 506 1
\n",
+ "HETNAM CA UNKNOWN
\n",
+ "FORMUL 1 CA CA1
\n",
+ "MODEL 1
\n",
+ "ATOM 1 N LEU A 1 1.000 -2.000 20.000 1.00
0.00 N \n",
+ "ATOM 2 H LEU A 1 2.000 -2.000 20.000 1.00
0.00 H \n",
+ "TER 3 LEU A 1
\n",
+ "HETATM 4 CA CA A 501 17.000 12.000 14.000 1.00
0.00 CA \n",
+ "HETATM 5 CA CA A 502 6.000 9.000 14.000 1.00
0.00 CA \n",
+ "ATOM 6 N LEU B 1 9.000 -9.000 27.000 1.00
0.00 N \n",
+ "ATOM 7 H LEU B 1 8.000 -8.000 27.000 1.00
0.00 H \n",
+ "TER 8 LEU B 1
\n",
+ "HETATM 9 CA CA B 503 17.000 12.000 14.000 1.00
0.00 CA \n",
+ "HETATM 10 CA CA B 504 6.000 9.000 14.000 1.00
0.00 CA \n",
+ "ATOM 11 N LEU C 1 12.000 -12.000 7.000 1.00
0.00 N \n",
+ "ATOM 12 H LEU C 1 11.000 -12.000 7.000 1.00
0.00 H \n",
+ "TER 13 LEU C 1
\n",
+ "HETATM 14 CA CA C 505 31.000 -10.000 -0.000 1.00
0.00 CA \n",
+ "HETATM 15 CA CA C 506 31.000 -19.000 6.000 1.00
0.00 CA \n",
+ "ENDMDL
\n",
+ "MASTER 0 0 6 0 0 0 0 0 12 3
0 0 \n",
"END
\n"
]
r27667 - in /trunk/test_suite: shared_data/structures/bug_23293_missing_hetatm.pdb system_tests/structure.py