Author: bugman
Date: Mon May 3 00:54:06 2010
New Revision: 11173
URL: http://svn.gna.org/viewcvs/relax?rev=11173&view=rev
Log:
Added 3 system tests for the correct loading of XH bond vectors into the spin
containers.
This catches the previously fixed model looping bug.
Added:
1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py
Modified:
1.3/test_suite/system_tests/n_state_model.py
Modified: 1.3/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/n_state_model.py?rev=11173&r1=11172&r2=11173&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/n_state_model.py (original)
+++ 1.3/test_suite/system_tests/n_state_model.py Mon May 3 00:54:06 2010
@@ -23,6 +23,8 @@
# Python module imports.
import __main__
from math import pi, sqrt
+from numpy import array
+from numpy.linalg import norm
from os import listdir, sep
from shutil import rmtree
from tempfile import mkdtemp
@@ -31,6 +33,7 @@
from base_classes import SystemTestCase
from data import Relax_data_store; ds = Relax_data_store()
from generic_fns.align_tensor import calc_chi_tensor
+from generic_fns.mol_res_spin import spin_loop
class N_state_model(SystemTestCase):
@@ -45,6 +48,51 @@
# Reset the relax data storage object.
ds.__reset__()
+
+
+ def check_vectors(self):
+ """Auxiliary method for checking the correct loading of bond
vectors."""
+
+ # The new order.
+ ds.order_new =
array([ds.order_struct[ds.order_model[ds.order_model[0]]],
+
ds.order_struct[ds.order_model[ds.order_model[1]]],
+
ds.order_struct[ds.order_model[ds.order_model[2]]]])
+
+ # The atom positions.
+ C_pos = []
+ C_pos.append(array([6.250, 0.948, 1.968]))
+ C_pos.append(array([6.438, -0.139, 1.226]))
+ C_pos.append(array([6.108, -0.169, 0.378]))
+
+ H_pos = []
+ H_pos.append(array([7.243, 0.580, 1.676]))
+ H_pos.append(array([7.271, -0.291, 0.525]))
+ H_pos.append(array([5.735, 0.003, -0.639]))
+
+ # The real vectors.
+ vect = []
+ for i in range(3):
+ vect.append(H_pos[i] - C_pos[i])
+
+ # Normalise.
+ for i in range(3):
+ vect[i] = vect[i] / norm(vect[i])
+
+ # Print out.
+ print("Structure order: %s" % ds.order_struct)
+ print("Model order: %s" % ds.order_model)
+ print("New order: %s" % ds.order_new)
+ for i in range(3):
+ print("\ni = %i" % i)
+ print("The real vector: %s" % vect[i])
+ print("The reordered vector: %s" % vect[ds.order_new[i]])
+ print("The loaded vector: %s" %
cdp.mol[0].res[0].spin[0].xh_vect[i])
+
+ # Check.
+ for i in range(3):
+ self.assertAlmostEqual(norm(vect[ds.order_new[i]] -
cdp.mol[0].res[0].spin[0].xh_vect[i]), 0.0)
+ for i in range(3):
+ self.assertAlmostEqual(norm(C_pos[ds.order_new[i]] -
cdp.mol[0].res[0].spin[0].pos[i]), 0.0)
def test_5_state_xz(self):
@@ -362,10 +410,52 @@
# Check the populations.
self.assertEqual(len(cdp.probs), 3)
self.assertAlmostEqual(cdp.probs[0], 0.3)
- self.assertAlmostEqual(cdp.probs[1], 0.1)
- self.assertAlmostEqual(cdp.probs[2], 0.6)
+ self.assertAlmostEqual(cdp.probs[1], 0.6)
+ self.assertAlmostEqual(cdp.probs[2], 0.1)
# Test the optimised values.
self.assertAlmostEqual(cdp.chi2, 0.0)
self.assertAlmostEqual(cdp.q_rdc, 0.0)
self.assertAlmostEqual(cdp.q_pcs, 0.0)
+
+
+ def test_vector_loading1(self):
+ """Test the loading of inter-atomic vectors in the 'population'
N-state model."""
+
+ # Order.
+ ds.order_struct = [1, 2, 0]
+ ds.order_model = [0, 1, 2]
+
+ # Execute the script.
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'vector_loading.py')
+
+ # Check the vectors.
+ self.check_vectors()
+
+
+ def test_vector_loading2(self):
+ """Test the loading of inter-atomic vectors in the 'population'
N-state model."""
+
+ # Order.
+ ds.order_struct = [0, 1, 2]
+ ds.order_model = [2, 0, 1]
+
+ # Execute the script.
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'vector_loading.py')
+
+ # Check the vectors.
+ self.check_vectors()
+
+
+ def test_vector_loading3(self):
+ """Test the loading of inter-atomic vectors in the 'population'
N-state model."""
+
+ # Order.
+ ds.order_struct = [1, 0, 2]
+ ds.order_model = [2, 0, 1]
+
+ # Execute the script.
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'n_state_model'+sep+'vector_loading.py')
+
+ # Check the vectors.
+ self.check_vectors()
Added: 1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py?rev=11173&view=auto
==============================================================================
--- 1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py
(added)
+++ 1.3/test_suite/system_tests/scripts/n_state_model/vector_loading.py Mon
May 3 00:54:06 2010
@@ -1,0 +1,26 @@
+# Script for checking the loading of bond vectors in the correct order.
+
+# Python module imports.
+import __main__
+from os import sep
+
+# relax module imports.
+from data import Relax_data_store; ds = Relax_data_store()
+
+
+# Path of the files.
+str_path = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'structures'+sep+'lactose'
+
+
+# Create the data pipe.
+pipe.create('populations', 'N-state')
+
+# Load the structures.
+for i in range(3):
+ structure.read_pdb(file='lactose_MCMM4_S1_%i.pdb' %
(ds.order_struct[i]+1), dir=str_path, set_model_num=ds.order_model[i]+1,
set_mol_name='LE')
+
+# Load the sequence information.
+structure.load_spins(spin_id=':UNK@C1', combine_models=False, ave_pos=False)
+
+# Load the CH vectors for the C atoms.
+structure.vectors(spin_id='@C*', attached='H*', ave=False)
r11173 - in /1.3/test_suite/system_tests: n_state_model.py scripts/n_state_model/vector_loading.py