Author: bugman
Date: Fri Jan 23 11:23:12 2009
New Revision: 8627
URL: http://svn.gna.org/viewcvs/relax?rev=8627&view=rev
Log:
Wrote 3 system tests for the new design of the structural data handling.
These include:
test_read_pdb_mol_2_model_internal()
test_read_pdb_model_2_mol_internal()
test_read_pdb_complex_internal()
Modified:
branches/multi_structure/test_suite/system_tests/structure.py
Modified: branches/multi_structure/test_suite/system_tests/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/test_suite/system_tests/structure.py?rev=8627&r1=8626&r2=8627&view=diff
==============================================================================
--- branches/multi_structure/test_suite/system_tests/structure.py (original)
+++ branches/multi_structure/test_suite/system_tests/structure.py Fri Jan 23
11:23:12 2009
@@ -227,6 +227,125 @@
self.relax.interpreter._Structure.load_spins()
+ def test_read_pdb_mol_2_model_internal(self):
+ """Load a few 'lactose_MCMM4_S1_*.pdb' PDB files as models (using
the internal 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='internal', set_model_num=1)
+ self.relax.interpreter._Structure.read_pdb(file=files[1], dir=path,
parser='internal', set_model_num=1)
+ self.relax.interpreter._Structure.read_pdb(file=files[2], dir=path,
parser='internal', 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), 3)
+ self.assertEqual(len(cdp.structure.structural_data[0].mol), 1)
+ self.assertEqual(len(cdp.structure.structural_data[1].mol), 1)
+ self.assertEqual(len(cdp.structure.structural_data[2].mol), 1)
+
+ i = 0
+ for model in cdp.structure.structural_data:
+ self.assertEqual(model.mol[0].file_name, files[i])
+ self.assertEqual(model.mol[0].file_path, path)
+ self.assertEqual(model.mol[0].file_model, 1)
+ self.assertEqual(model.mol[0].file_mol_num, 1)
+ i = i + 1
+
+
+ def test_read_pdb_model_2_mol_internal(self):
+ """Load the 2 models of the 'gromacs_phthalic_acid.pdb' PDB file as
separate molecules of the same model (using the internal 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='internal', read_model=1, set_model_num=1)
+
self.relax.interpreter._Structure.read_pdb(file='gromacs_phthalic_acid.pdb',
dir=path, parser='internal', 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_internal(self):
+ """Test the packing of models and molecules using
'gromacs_phthalic_acid.pdb' and 'lactose_MCMM4_S1_*.pdb' (using the internal
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='internal')
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_1.pdb',
dir=path, parser='internal', set_model_num=1)
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_2.pdb',
dir=path, parser='internal', set_model_num=2)
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_3.pdb',
dir=path, parser='internal', set_model_num=1)
+
self.relax.interpreter._Structure.read_pdb(file='lactose/lactose_MCMM4_S1_4.pdb',
dir=path, parser='internal', set_model_num=2)
+
+ # 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(model.mol)):
+ 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)
+
+
def test_read_pdb_scientific1(self):
"""Load the '1F35_N_H_molmol.pdb' PDB file (using the Scientific
python structural object PDB reader)."""
r8627 - /branches/multi_structure/test_suite/system_tests/structure.py