Author: bugman
Date: Thu May 15 13:07:47 2014
New Revision: 23187
URL: http://svn.gna.org/viewcvs/relax?rev=23187&view=rev
Log:
Created the Structure.test_bug_22041_atom_numbering system test to catch bug
#22041.
This was reported at https://gna.org/bugs/?22041.
The problem is that the structure.write_pdb user function does not create the
correct atom serial
numbers.
Modified:
trunk/test_suite/system_tests/structure.py
Modified: trunk/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/system_tests/structure.py?rev=23187&r1=23186&r2=23187&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu May 15 13:07:47 2014
@@ -142,6 +142,58 @@
# Load the file.
self.interpreter.structure.read_pdb('SpUreE_dimer_H_new', dir=path)
+
+
+ def test_bug_22041_atom_numbering(self):
+ """Catch U{bug #22041<https://gna.org/bugs/?22041>}, the atom serial
number not being sequential from 1 onwards."""
+
+ # Path of the structure file.
+ path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'
+
+ # Read a PDB file twice as two different molecules.
+ self.interpreter.structure.read_pdb('1RTE_trunc.pdb', dir=path,
set_mol_name='N-dom')
+ self.interpreter.structure.read_pdb('1RTE_trunc.pdb', dir=path,
set_mol_name='C-dom')
+
+ # Create a PDB file.
+ file = DummyFileObject()
+ self.interpreter.structure.write_pdb(file=file, force=True)
+
+ # The file contents, as they should be.
+ contents = [
+ "REMARK 4 THIS FILE COMPLIES WITH FORMAT V. 3.30, JUL-2011.
\n",
+ "REMARK 40 CREATED BY RELAX (HTTP://WWW.NMR-RELAX.COM).
\n",
+ "HET CYN A 445 1
\n",
+ "HET CYN B 445 1
\n",
+ "HETNAM CYN UNKNOWN
\n",
+ "FORMUL 1 CYN C1
\n",
+ "ATOM 1 N LEU A 3 49.617 4.693 46.426 1.00
0.00 N \n",
+ "ATOM 2 CA LEU A 3 49.432 5.476 45.190 1.00
0.00 C \n",
+ "ATOM 3 C LEU A 3 50.346 4.980 44.055 1.00
0.00 C \n",
+ "ATOM 4 O LEU A 3 49.924 4.868 42.889 1.00
0.00 O \n",
+ "ATOM 5 CB LEU A 3 49.673 6.968 45.457 1.00
0.00 C \n",
+ "ATOM 6 CG LEU A 3 49.804 7.863 44.222 1.00
0.00 C \n",
+ "ATOM 7 CD1 LEU A 3 48.564 7.837 43.327 1.00
0.00 C \n",
+ "ATOM 8 CD2 LEU A 3 50.075 9.282 44.625 1.00
0.00 C \n",
+ "TER 9 LEU A 3
\n",
+ "HETATM 10 C CYN A 445 29.160 13.127 62.533 1.00
0.00 C \n",
+ "ATOM 11 N LEU B 3 49.617 4.693 46.426 1.00
0.00 N \n",
+ "ATOM 12 CA LEU B 3 49.432 5.476 45.190 1.00
0.00 C \n",
+ "ATOM 13 C LEU B 3 50.346 4.980 44.055 1.00
0.00 C \n",
+ "ATOM 14 O LEU B 3 49.924 4.868 42.889 1.00
0.00 O \n",
+ "ATOM 15 CB LEU B 3 49.673 6.968 45.457 1.00
0.00 C \n",
+ "ATOM 16 CG LEU B 3 49.804 7.863 44.222 1.00
0.00 C \n",
+ "ATOM 17 CD1 LEU B 3 48.564 7.837 43.327 1.00
0.00 C \n",
+ "ATOM 18 CD2 LEU B 3 50.075 9.282 44.625 1.00
0.00 C \n",
+ "TER 19 LEU B 3
\n",
+ "HETATM 20 C CYN B 445 29.160 13.127 62.533 1.00
0.00 C \n",
+ "MASTER 0 0 2 0 0 0 0 0 18 2
0 0 \n",
+ "END
\n"
+ ]
+
+ # Check the created PDB file.
+ lines = file.readlines()
+ for i in range(len(lines)):
+ self.assertEqual(contents[i], lines[i])
def test_delete_empty(self):
r23187 - /trunk/test_suite/system_tests/structure.py