Author: bugman
Date: Wed Apr 23 18:44:01 2008
New Revision: 5952
URL: http://svn.gna.org/viewcvs/relax?rev=5952&view=rev
Log:
Added a system test for the loading of spins from a small molecule.
This uses the Scientific Python PDB data object.
Added:
1.3/test_suite/system_tests/load_spins.py
1.3/test_suite/system_tests/scripts/load_spins_from_small_molecule.py
Modified:
1.3/test_suite/system_tests/__init__.py
Modified: 1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=5952&r1=5951&r2=5952&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/__init__.py (original)
+++ 1.3/test_suite/system_tests/__init__.py Wed Apr 23 18:44:01 2008
@@ -36,6 +36,7 @@
from diffusion_tensor import Diffusion_tensor
from generic import Generic
from jw_mapping import Jw
+from load_spins import Load_spins
from model_free import Mf
from model_selection import Modsel
from n_state_model import N_state_model
@@ -49,6 +50,7 @@
'diffusion_tensor',
'generic',
'jw_mapping',
+ 'load_spins',
'model_free',
'model_selection',
'n_state_model',
@@ -80,6 +82,7 @@
suite_array.append(TestLoader().loadTestsFromTestCase(Diffusion_tensor))
suite_array.append(TestLoader().loadTestsFromTestCase(Generic))
suite_array.append(TestLoader().loadTestsFromTestCase(Jw))
+ suite_array.append(TestLoader().loadTestsFromTestCase(Load_spins))
suite_array.append(TestLoader().loadTestsFromTestCase(Mf))
suite_array.append(TestLoader().loadTestsFromTestCase(Modsel))
suite_array.append(TestLoader().loadTestsFromTestCase(Relax_fit))
Added: 1.3/test_suite/system_tests/load_spins.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/load_spins.py?rev=5952&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/load_spins.py (added)
+++ 1.3/test_suite/system_tests/load_spins.py Wed Apr 23 18:44:01 2008
@@ -1,0 +1,74 @@
+###############################################################################
+#
#
+# Copyright (C) 2008 Edward d'Auvergne
#
+#
#
+# This file is part of the program relax.
#
+#
#
+# relax is free software; you can redistribute it and/or modify
#
+# it under the terms of the GNU General Public License as published by
#
+# the Free Software Foundation; either version 2 of the License, or
#
+# (at your option) any later version.
#
+#
#
+# relax is distributed in the hope that it will be useful,
#
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
+# GNU General Public License for more details.
#
+#
#
+# You should have received a copy of the GNU General Public License
#
+# along with relax; if not, write to the Free Software
#
+# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
#
+#
#
+###############################################################################
+
+
+# Python module imports.
+from unittest import TestCase
+
+# relax module imports.
+from data import Data as relax_data_store
+
+
+class Load_spins(TestCase):
+ """TestCase class for the loading of spins into the
molecule/residue/spin data structure."""
+
+ def setUp(self):
+ """Set up for all the functional tests."""
+
+ # Create the data pipe.
+ self.relax.interpreter._Pipe.create('mf', 'mf')
+
+
+ def tearDown(self):
+ """Reset the relax data storage object."""
+
+ relax_data_store.__reset__()
+
+
+ def test_load_spins_from_small_molecule(self):
+ """Test the loading of spins from a small molecule using the
Scientific Python PDB data object."""
+
+ # Execute a relax script.
+
self.relax.interpreter.run(script_file='test_suite/system_tests/scripts/load_spins_from_small_molecule.py')
+
+ # Alias the current data pipe.
+ cdp = relax_data_store[relax_data_store.current_pipe]
+
+ # Test the molecule and residue data.
+ self.assertEqual(len(cdp.mol), 1)
+ self.assertEqual(cdp.mol[0].name, 'PYR')
+ self.assertEqual(len(cdp.mol[0].res), 1)
+ self.assertEqual(cdp.mol[0].res[0].num, 1)
+ self.assertEqual(cdp.mol[0].res[0].name, 'PYR')
+
+ # Spin info.
+ nums = [4, 6, 8, 10, 33, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45,
46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 15, 16, 28, 30]
+ names = ['H1', 'H2', 'H3', 'H4', 'H5', 'H6', 'H7', 'H8', 'H9',
'H10', 'H11', 'H12', 'H13', 'H14', 'H15', 'H16', 'H17', 'H18', 'H19', 'H20',
'H21', 'H22', 'H23', 'H24', 'H25', 'H26', 'H27', 'H28', 'C5', 'C6', 'C19',
'C23']
+ elements = ['H']*28 + ['C']*4
+
+ # Loop over the spin containers, testing each.
+ self.assertEqual(len(cdp.mol[0].res[0].spin), 32)
+ for i in xrange(len(cdp.mol[0].res[0].spin)):
+ self.assertEqual(cdp.mol[0].res[0].spin[i].num, nums[i])
+ self.assertEqual(cdp.mol[0].res[0].spin[i].name, names[i])
+ self.assertEqual(cdp.mol[0].res[0].spin[i].element, elements[i])
+ self.assert_(hasattr(cdp.mol[0].res[0].spin[i], 'pos'))
Added: 1.3/test_suite/system_tests/scripts/load_spins_from_small_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/load_spins_from_small_molecule.py?rev=5952&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/load_spins_from_small_molecule.py
(added)
+++ 1.3/test_suite/system_tests/scripts/load_spins_from_small_molecule.py Wed
Apr 23 18:44:01 2008
@@ -1,0 +1,16 @@
+"""Load a number of spin systems for a small molecule."""
+
+import sys
+
+
+# Read in the small molecule.
+structure.read_pdb(file='gromacs_phthalic_acid.pdb', dir=sys.path[-1] +
'/test_suite/shared_data/structures')
+
+# Load all protons.
+structure.load_spins(spin_id='@*H*')
+
+# Load a few carbons.
+structure.load_spins(spin_id='@C5')
+structure.load_spins(spin_id='@C6')
+structure.load_spins(spin_id='@C19')
+structure.load_spins(spin_id='@C23')
r5952 - in /1.3/test_suite/system_tests: __init__.py load_spins.py scripts/load_spins_from_small_molecule.py