Author: bugman
Date: Wed Feb 4 10:33:25 2009
New Revision: 8725
URL: http://svn.gna.org/viewcvs/relax?rev=8725&view=rev
Log:
Duplicated 5 systems tests of the internal PDB reader for the Scientific
python PDB reader.
Modified:
1.3/test_suite/system_tests/structure.py
Modified: 1.3/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/structure.py?rev=8725&r1=8724&r2=8725&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/structure.py (original)
+++ 1.3/test_suite/system_tests/structure.py Wed Feb 4 10:33:25 2009
@@ -458,3 +458,155 @@
# And now all the rest of the atoms.
self.relax.interpreter._Structure.load_spins()
+
+
+ def test_read_pdb_scientific6(self):
+ """Load the 'lactose_MCMM4_S1_1.pdb' and 'lactose_MCMM4_S1_2.pdb'
PDB files as 2 separate structures (using the Scientific python structural
object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures/lactose'
+
+ # Read the PDB twice.
+
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, parser='scientific')
+
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_2.pdb',
dir=path, parser='scientific')
+
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
+
+ def test_read_pdb_scientific7(self):
+ """Load the 'lactose_MCMM4_S1_1.pdb' PDB file twice as 2 separate
structures (using the Scientific python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures/lactose'
+
+ # Read the PDB twice.
+
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, parser='scientific')
+
self.relax.interpreter._Structure.read_pdb(file='lactose_MCMM4_S1_1.pdb',
dir=path, parser='scientific')
+
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
+
+ def test_read_pdb_mol_2_model_scientific(self):
+ """Load a few 'lactose_MCMM4_S1_*.pdb' PDB files as models (using
the Scientific python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures/lactose'
+
+ # Files.
+ files = ['lactose_MCMM4_S1_1.pdb',
+ 'lactose_MCMM4_S1_2.pdb',
+ 'lactose_MCMM4_S1_3.pdb']
+
+ # Read the PDBs.
+ self.relax.interpreter._Structure.read_pdb(file=files[0], dir=path,
parser='scientific', set_model_num=1)
+ self.relax.interpreter._Structure.read_pdb(file=files[1], dir=path,
parser='scientific', set_model_num=1)
+ self.relax.interpreter._Structure.read_pdb(file=files[2], dir=path,
parser='scientific', set_model_num=1)
+
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Test the structural data.
+ self.assert_(hasattr(cdp, 'structure'))
+ self.assert_(hasattr(cdp.structure, 'structural_data'))
+ self.assertEqual(len(cdp.structure.structural_data), 1)
+ self.assertEqual(len(cdp.structure.structural_data[0].mol), 3)
+
+ i = 0
+ for mol in cdp.structure.structural_data[0].mol:
+ self.assertEqual(mol.file_name, files[i])
+ self.assertEqual(mol.file_path, path)
+ self.assertEqual(mol.file_model, 1)
+ self.assertEqual(mol.file_mol_num, 1)
+ i = i + 1
+
+
+ def test_read_pdb_model_2_mol_scientific(self):
+ """Load the 2 models of the 'gromacs_phthalic_acid.pdb' PDB file as
separate molecules of the same model (using the Scientific python structural
object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB models.
+
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='scientific', read_model=1, set_model_num=1)
+
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='scientific', read_model=2, set_model_num=1)
+
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Test the structural data.
+ self.assert_(hasattr(cdp, 'structure'))
+ self.assert_(hasattr(cdp.structure, 'structural_data'))
+ self.assertEqual(len(cdp.structure.structural_data), 1)
+ self.assertEqual(len(cdp.structure.structural_data[0].mol), 2)
+
+ i = 0
+ for mol in cdp.structure.structural_data[0].mol:
+ self.assertEqual(mol.file_name, 'gromacs_phthalic_acid.pdb')
+ self.assertEqual(mol.file_path, path)
+ self.assertEqual(mol.file_model, i+1)
+ self.assertEqual(mol.file_mol_num, 1)
+ i = i + 1
+
+
+ def test_read_pdb_complex_scientific(self):
+ """Test the packing of models and molecules using
'gromacs_phthalic_acid.pdb' and 'lactose_MCMM4_S1_*.pdb' (using the
Scientific python structural object PDB reader)."""
+
+ # Path of the files.
+ path = sys.path[-1] + '/test_suite/shared_data/structures'
+
+ # Read the PDB models.
+
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='scientific')
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_1.pdb',
dir=path, parser='scientific', set_model_num=1,
set_mol_name='lactose_MCMM4_S1')
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_2.pdb',
dir=path, parser='scientific', set_model_num=2,
set_mol_name='lactose_MCMM4_S1')
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_3.pdb',
dir=path, parser='scientific', set_model_num=1,
set_mol_name='lactose_MCMM4_S1b')
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_4.pdb',
dir=path, parser='scientific', set_model_num=2,
set_mol_name='lactose_MCMM4_S1b')
+
+ # Try loading a few protons.
+ self.relax.interpreter._Structure.load_spins('@*H*')
+
+ # And now all the rest of the atoms.
+ self.relax.interpreter._Structure.load_spins()
+
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Test the structural data.
+ self.assert_(hasattr(cdp, 'structure'))
+ self.assert_(hasattr(cdp.structure, 'structural_data'))
+ self.assertEqual(len(cdp.structure.structural_data), 2)
+ self.assertEqual(len(cdp.structure.structural_data[0].mol), 3)
+ self.assertEqual(len(cdp.structure.structural_data[1].mol), 3)
+
+ files = [['gromacs_phthalic_acid.pdb', 'lactose_MCMM4_S1_1.pdb',
'lactose_MCMM4_S1_3.pdb'],
+ ['gromacs_phthalic_acid.pdb', 'lactose_MCMM4_S1_2.pdb',
'lactose_MCMM4_S1_4.pdb']]
+ paths = [[path, path+sep+'lactose', path+sep+'lactose'],
+ [path, path+sep+'lactose', path+sep+'lactose']]
+ models = [[1, 1, 1], [2, 1, 1]]
+
+ for i in range(len(cdp.structure.structural_data)):
+ for j in range(len(cdp.structure.structural_data[i].mol)):
+ mol = cdp.structure.structural_data[i].mol[j]
+ self.assertEqual(mol.file_name, files[i][j])
+ self.assertEqual(mol.file_path, paths[i][j])
+ self.assertEqual(mol.file_model, models[i][j])
+ self.assertEqual(mol.file_mol_num, 1)
r8725 - /1.3/test_suite/system_tests/structure.py