Author: bugman
Date: Thu Jun 28 14:17:56 2012
New Revision: 17090
URL: http://svn.gna.org/viewcvs/relax?rev=17090&view=rev
Log:
Created the new Interatomic system test class for testing out the interatomic
data containers.
Added:
branches/interatomic/test_suite/system_tests/interatomic.py
- copied, changed from r17079,
branches/interatomic/test_suite/system_tests/mol_res_spin.py
branches/interatomic/test_suite/system_tests/scripts/interatomic_tests.py
Modified:
branches/interatomic/test_suite/system_tests/__init__.py
Modified: branches/interatomic/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/__init__.py?rev=17090&r1=17089&r2=17090&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/__init__.py (original)
+++ branches/interatomic/test_suite/system_tests/__init__.py Thu Jun 28
14:17:56 2012
@@ -42,6 +42,7 @@
from frame_order import Frame_order
from generic import Generic
from grace import Grace
+from interatomic import Interatomic
from jw_mapping import Jw
from load_spins import Load_spins
from model_elimination import Modelim
@@ -75,6 +76,7 @@
'frame_order',
'generic',
'grace',
+ 'interatomic',
'jw_mapping',
'load_spins',
'model_elimination',
@@ -158,6 +160,7 @@
suite_array.append(TestLoader().loadTestsFromTestCase(Frame_order))
suite_array.append(TestLoader().loadTestsFromTestCase(Generic))
suite_array.append(TestLoader().loadTestsFromTestCase(Grace))
+
suite_array.append(TestLoader().loadTestsFromTestCase(Interatomic))
suite_array.append(TestLoader().loadTestsFromTestCase(Jw))
suite_array.append(TestLoader().loadTestsFromTestCase(Load_spins))
suite_array.append(TestLoader().loadTestsFromTestCase(Modelim))
Copied: branches/interatomic/test_suite/system_tests/interatomic.py (from
r17079, branches/interatomic/test_suite/system_tests/mol_res_spin.py)
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/interatomic.py?p2=branches/interatomic/test_suite/system_tests/interatomic.py&p1=branches/interatomic/test_suite/system_tests/mol_res_spin.py&r1=17079&r2=17090&rev=17090&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/mol_res_spin.py (original)
+++ branches/interatomic/test_suite/system_tests/interatomic.py Thu Jun 28
14:17:56 2012
@@ -21,7 +21,7 @@
###############################################################################
# Module docstring.
-"""System tests of the molecule, residue, and spin sequence operators."""
+"""System tests of the interatomic data container operations."""
# Python module imports.
@@ -33,32 +33,23 @@
from status import Status; status = Status()
-class Mol_res_spin(SystemTestCase):
- """Class for testing the mol_res_spin functions."""
+class Interatomic(SystemTestCase):
+ """Class for testing the interatomic functions."""
- def setUp(self):
- """Set up for all the functional tests."""
+ def test_manipulation(self):
+ """Test the manipulation of interatomic data containers."""
- # Create the data pipe.
- self.interpreter.pipe.create('mf', 'mf')
+ # Execute the script.
+ self.script_exec(status.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'interatomic_tests.py')
+ # The data.
+ select = [True]*5 + [False]*2 + [True]*5 + [False]*2
- def test_residue_delete(self):
- """Test residue deletion."""
+ # Check the data.
+ self.assertEqual(len(cdp.interatomic), 14)
+ for i in range(len(cdp.interatomic)):
+ # A print out to know where the problem is.
+ print("Checking container: %-30s %-30s" %
(cdp.interatomic[i].spin_id1, cdp.interatomic[i].spin_id2))
- # Read a PDB file.
- self.interpreter.structure.read_pdb(file='sphere.pdb',
dir=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'sphere')
-
- # Load the spins.
- self.interpreter.structure.load_spins()
-
- # Test the original sequence data.
- self.assertEqual(len(cdp.mol), 1)
- self.assertEqual(len(cdp.mol[0].res), 9)
-
- # Delete the first residue.
- self.interpreter.residue.delete(res_id='#sphere_mol1:1')
-
- # Test the remaining sequence data.
- self.assertEqual(len(cdp.mol), 1)
- self.assertEqual(len(cdp.mol[0].res), 8)
+ # The container checks.
+ self.assertEqual(cdp.interatomic[i].select, select[i])
Added:
branches/interatomic/test_suite/system_tests/scripts/interatomic_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/interatomic_tests.py?rev=17090&view=auto
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/interatomic_tests.py
(added)
+++ branches/interatomic/test_suite/system_tests/scripts/interatomic_tests.py
Thu Jun 28 14:17:56 2012
@@ -1,0 +1,39 @@
+"""Script for checking operations on interatomic data containers."""
+
+# Python module imports.
+from os import sep
+
+# relax module imports.
+from status import Status; status = Status()
+
+
+# Path of the files.
+str_path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
+
+# Create a data pipe.
+self._execute_uf(uf_name='pipe.create', pipe_name="interatom testing",
pipe_type='N-state')
+
+# Load the structures.
+NUM_STR = 4
+for i in range(NUM_STR):
+ self._execute_uf(uf_name='structure.read_pdb',
file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, parser='internal',
set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
+
+# Load the sequence information.
+self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C*',
ave_pos=False)
+self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@H*',
ave_pos=False)
+
+# Deselect the CH2 protons (the rotation of these doesn't work in the model,
but the carbon doesn't move).
+self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H6')
+self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H7')
+self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H17')
+self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H18')
+
+# Create the interatomic data containers.
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@C*',
spin_id2='@H*', direct_bond=True)
+
+# Deselect all.
+self._execute_uf(uf_name='deselect.interatom')
+
+# Select the non-CH2 bonds.
+for i in [1, 2, 3, 4, 5, 7, 8, 9, 10, 11]:
+ self._execute_uf(uf_name='select.interatom', spin_id1=':UNK@C%i'%i)
r17090 - in /branches/interatomic/test_suite/system_tests: __init__.py interatomic.py scripts/interatomic_tests.py