Author: bugman
Date: Thu Feb 19 15:25:40 2015
New Revision: 27676
URL: http://svn.gna.org/viewcvs/relax?rev=27676&view=rev
Log:
Created the Structure.test_multi_model_and_multi_molecule system test.
This is used to check the loading and writing of a multi-model and
multi-molecule PDB file. The
test shows that this functions correctly.
Added:
trunk/test_suite/shared_data/structures/multi_model_and_mol_test.pdb
Modified:
trunk/test_suite/system_tests/structure.py
Added: trunk/test_suite/shared_data/structures/multi_model_and_mol_test.pdb
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/shared_data/structures/multi_model_and_mol_test.pdb?rev=27676&view=auto
==============================================================================
--- trunk/test_suite/shared_data/structures/multi_model_and_mol_test.pdb
(added)
+++ trunk/test_suite/shared_data/structures/multi_model_and_mol_test.pdb
Thu Feb 19 15:25:40 2015
@@ -0,0 +1,24 @@
+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
+ATOM 4 N LEU B 1 9.000 -9.000 27.000 1.00 0.00 N
+ATOM 5 H LEU B 1 8.000 -8.000 27.000 1.00 0.00 H
+TER 6 LEU B 1
+ATOM 7 N LEU C 1 12.000 -12.000 7.000 1.00 0.00 N
+ATOM 8 H LEU C 1 11.000 -12.000 7.000 1.00 0.00 H
+TER 9 LEU C 1
+ENDMDL
+MODEL 2
+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
+ATOM 4 N LEU B 1 9.000 -9.000 27.000 1.00 0.00 N
+ATOM 5 H LEU B 1 8.000 -8.000 27.000 1.00 0.00 H
+TER 6 LEU B 1
+ATOM 7 N LEU C 1 12.000 -12.000 7.000 1.00 0.00 N
+ATOM 8 H LEU C 1 11.000 -12.000 7.000 1.00 0.00 H
+TER 9 LEU C 1
+ENDMDL
+MASTER 0 0 0 0 0 0 0 0 6 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=27676&r1=27675&r2=27676&view=diff
==============================================================================
--- trunk/test_suite/system_tests/structure.py (original)
+++ trunk/test_suite/system_tests/structure.py Thu Feb 19 15:25:40 2015
@@ -3930,6 +3930,55 @@
self.assertEqual(cdp.structure.sheets[1], sheets[1])
+ def test_multi_model_and_multi_molecule(self):
+ """Test the loading and writing of a multi-model and multi-molecule
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('multi_model_and_mol_test.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 = [
+ "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",
+ "ATOM 4 N LEU B 1 9.000 -9.000 27.000 1.00
0.00 N \n",
+ "ATOM 5 H LEU B 1 8.000 -8.000 27.000 1.00
0.00 H \n",
+ "TER 6 LEU B 1
\n",
+ "ATOM 7 N LEU C 1 12.000 -12.000 7.000 1.00
0.00 N \n",
+ "ATOM 8 H LEU C 1 11.000 -12.000 7.000 1.00
0.00 H \n",
+ "TER 9 LEU C 1
\n",
+ "ENDMDL
\n",
+ "MODEL 2
\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",
+ "ATOM 4 N LEU B 1 9.000 -9.000 27.000 1.00
0.00 N \n",
+ "ATOM 5 H LEU B 1 8.000 -8.000 27.000 1.00
0.00 H \n",
+ "TER 6 LEU B 1
\n",
+ "ATOM 7 N LEU C 1 12.000 -12.000 7.000 1.00
0.00 N \n",
+ "ATOM 8 H LEU C 1 11.000 -12.000 7.000 1.00
0.00 H \n",
+ "TER 9 LEU C 1
\n",
+ "ENDMDL
\n",
+ "MASTER 0 0 0 0 0 0 0 0 6 3 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_pdb_combined_secondary_structure(self):
"""Test the handling of secondary structure metadata when combining
multiple PDB structures."""
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