Author: bugman Date: Fri Feb 20 09:27:20 2015 New Revision: 27681 URL: http://svn.gna.org/viewcvs/relax?rev=27681&view=rev Log: Merged revisions 27680 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk
........ r27680 | bugman | 2015-02-20 09:26:57 +0100 (Fri, 20 Feb 2015) | 9 lines Created the Structure.test_bug_23294_multi_mol_automerge system test. This is used to catch bug #2329 (https://gna.org/bugs/?23294), the automatic merging of PDB molecules resulting in an IndexError. It reads in the 'in.pdb' PDB file attached to the bug report, now named 'bug_23294_multi_mol_automerge.pdb', to show the IndexError. The test also checks the structure.write_pdb user function to make sure that the output PDB file contains a single merged molecule. ........ Modified: branches/nmrglue/ (props changed) branches/nmrglue/test_suite/system_tests/structure.py Propchange: branches/nmrglue/ ------------------------------------------------------------------------------ --- svnmerge-integrated (original) +++ svnmerge-integrated Fri Feb 20 09:27:20 2015 @@ -1 +1 @@ -/trunk:1-27677 +/trunk:1-27680 Modified: branches/nmrglue/test_suite/system_tests/structure.py URL: http://svn.gna.org/viewcvs/relax/branches/nmrglue/test_suite/system_tests/structure.py?rev=27681&r1=27680&r2=27681&view=diff ============================================================================== --- branches/nmrglue/test_suite/system_tests/structure.py (original) +++ branches/nmrglue/test_suite/system_tests/structure.py Fri Feb 20 09:27:20 2015 @@ -883,6 +883,39 @@ "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" + ] + + # 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_23294_multi_mol_automerge(self): + """Catch U{bug #23294<https://gna.org/bugs/?23294>}, the automatic merging of PDB molecules results in an IndexError.""" + + # 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_23294_multi_mol_automerge.pdb', dir=path, read_model=1, set_mol_name='merged mol') + + # 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 0.000 0.000 1.00 0.00 N \n", + "ATOM 2 H LEU A 1 2.000 0.000 0.000 1.00 0.00 H \n", + "ATOM 3 N GLU A 2 3.000 0.000 0.000 1.00 0.00 N \n", + "ATOM 4 H GLU A 2 4.000 0.000 0.000 1.00 0.00 H \n", + "TER 5 GLU A 2 \n", + "ENDMDL \n", "END \n" ] _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
