Author: bugman
Date: Tue Jan 27 10:01:41 2009
New Revision: 8659
URL: http://svn.gna.org/viewcvs/relax?rev=8659&view=rev
Log:
Created a system test for the reading of a generically formatted NOE
restraint file.
Added:
branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py
Modified:
branches/ave_noe/test_suite/system_tests/noe_restraints.py
Modified: branches/ave_noe/test_suite/system_tests/noe_restraints.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/test_suite/system_tests/noe_restraints.py?rev=8659&r1=8658&r2=8659&view=diff
==============================================================================
--- branches/ave_noe/test_suite/system_tests/noe_restraints.py (original)
+++ branches/ave_noe/test_suite/system_tests/noe_restraints.py Tue Jan 27
10:01:41 2009
@@ -89,6 +89,80 @@
# Display the sequence for debugging.
self.relax.interpreter._Sequence.display()
+
+
+ def test_read_generic_phthalic_acid(self):
+ """Test the reading of phthalic acid NOE restraints in generic
format."""
+
+ # Execute the script.
+ self.relax.interpreter.run(script_file=sys.path[-1] +
'/test_suite/system_tests/scripts/phthalic_acid_noes.py')
+
+ # The restraint data.
+ restraints = [
+ ['@H1', '@H6', 3.0, 5.0],
+ ['@H3', '@H9', 3.0, 5.0],
+ ['@H3', '@H10', 3.0, 5.0],
+ ['@H3', '@H11', 3.0, 5.0],
+ ['@H3', '@H19', 3.0, 5.0],
+ ['@H3', '@Q9', 3.0, 6.0],
+ ['@H4', '@H8', 3.0, 5.0],
+ ['@H4', '@H9', 3.0, 5.0],
+ ['@H4', '@H10', 3.0, 5.0],
+ ['@H4', '@H11', 3.0, 5.0],
+ ['@H4', '@H15', 3.0, 5.0],
+ ['@H4', '@H19', 3.0, 5.0],
+ ['@H4', '@Q9', 3.0, 6.0],
+ ['@H5', '@H9', 3.0, 5.0],
+ ['@H5', '@Q7', 3.0, 6.0],
+ ['@H5', '@Q9', 3.0, 6.0],
+ ['@H6', '@H8', 3.0, 5.0],
+ ['@H6', '@H9', 3.0, 5.0],
+ ['@H6', '@H10', 3.0, 5.0],
+ ['@H6', '@H11', 3.0, 5.0],
+ ['@H6', '@H15', 3.0, 5.0],
+ ['@H6', '@Q7', 3.0, 6.0],
+ ['@H6', '@H19', 3.0, 5.0],
+ ['@H6', '@Q9', 3.0, 6.0],
+ ['@H26', '@H1', 3.0, 5.0],
+ ['@H26', '@H8', 3.0, 5.0],
+ ['@H26', '@H9', 3.0, 5.0],
+ ['@H26', '@H10', 3.0, 5.0],
+ ['@H26', '@H11', 3.0, 5.0],
+ ['@H26', '@H15', 3.0, 5.0],
+ ['@H26', '@Q7', 3.0, 6.0],
+ ['@H26', '@H19', 3.0, 5.0],
+ ['@H26', '@Q9', 3.0, 6.0],
+ ['@H27', '@H1', 3.0, 5.0],
+ ['@H27', '@H8', 3.0, 5.0],
+ ['@H27', '@H9', 3.0, 5.0],
+ ['@H27', '@H11', 3.0, 5.0],
+ ['@H27', '@H13', 3.0, 5.0],
+ ['@H27', '@H15', 3.0, 5.0],
+ ['@H27', '@Q7', 3.0, 6.0],
+ ['@H27', '@H19', 3.0, 5.0],
+ ['@H27', '@Q9', 3.0, 6.0],
+ ['@H28', '@H1', 3.0, 5.0],
+ ['@H28', '@H8', 3.0, 5.0],
+ ['@H28', '@H9', 3.0, 5.0],
+ ['@H28', '@H11', 3.0, 5.0],
+ ['@H28', '@H15', 3.0, 5.0],
+ ['@H28', '@Q7', 3.0, 6.0],
+ ['@H28', '@H19', 3.0, 5.0],
+ ['@H28', '@Q9', 3.0, 6.0]
+ ]
+
+ # Alias the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Test that the restraints are properly set.
+ for i in range(len(restraints)):
+ # Atom ids.
+ self.assertEqual(cdp.noe_restraints[i][0], restraints[i][0])
+ self.assertEqual(cdp.noe_restraints[i][1], restraints[i][1])
+
+ # Lower and upper bound.
+ self.assertEqual(cdp.noe_restraints[i][2], restraints[i][2])
+ self.assertEqual(cdp.noe_restraints[i][3], restraints[i][3])
def test_read_xplor_rna(self):
Added: branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py?rev=8659&view=auto
==============================================================================
--- branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py
(added)
+++ branches/ave_noe/test_suite/system_tests/scripts/phthalic_acid_noes.py
Tue Jan 27 10:01:41 2009
@@ -1,0 +1,21 @@
+"""Script for testing the loading of phthalic acid NOEs from a generically
formatted file."""
+
+# Python module imports.
+import sys
+
+# Path of the relaxation data.
+DATA_PATH = sys.path[-1] + '/test_suite/shared_data/'
+
+# Create the data pipe.
+pipe.create('test', 'N-state')
+
+# Read the structure.
+structure.read_pdb('gromacs_phthalic_acid.pdb', dir=DATA_PATH+'/structures')
+
+# Load all protons as the sequence.
+structure.load_spins('@*H*', ave_pos=False)
+
+# Read the NOE restraints.
+noe.read_restraints(file='phthalic_acid', dir=DATA_PATH+'noe_restraints')
+
+
r8659 - in /branches/ave_noe/test_suite/system_tests: noe_restraints.py scripts/phthalic_acid_noes.py