Author: bugman
Date: Mon Jun 25 12:26:12 2012
New Revision: 17047
URL: http://svn.gna.org/viewcvs/relax?rev=17047&view=rev
Log:
Fixes for some of the N-state model system tests for the interatomic data
design.
Modified:
branches/interatomic/test_suite/system_tests/n_state_model.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/align_fit.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/vector_loading.py
Modified: branches/interatomic/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/n_state_model.py?rev=17047&r1=17046&r2=17047&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/n_state_model.py (original)
+++ branches/interatomic/test_suite/system_tests/n_state_model.py Mon Jun 25
12:26:12 2012
@@ -74,13 +74,14 @@
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])
+ print("The loaded vector: %s" % cdp.interatomic[0].vector[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)
+ self.assertAlmostEqual(norm(C_pos[ds.order_new[i]] -
cdp.mol[0].res[0].spin[0].pos[i]), 0.0)
+ self.assertAlmostEqual(norm(H_pos[ds.order_new[i]] -
cdp.mol[0].res[0].spin[1].pos[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)
+ self.assertAlmostEqual(norm(vect[ds.order_new[i]] -
cdp.interatomic[0].vector[i]), 0.0)
def test_5_state_xz(self):
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/align_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/align_fit.py?rev=17047&r1=17046&r2=17047&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/align_fit.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/align_fit.py
Mon Jun 25 12:26:12 2012
@@ -35,13 +35,14 @@
# Load the spins.
self._execute_uf(uf_name='structure.load_spins')
-# Load the NH vectors.
-self._execute_uf(uf_name='structure.vectors', spin_id='@N', attached='H',
ave=False)
+# Define the magnetic dipole-dipole relaxation interaction.
+dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.041 * 1e-10)
+dipole_pair.unit_vectors()
-# Set the values needed to calculate the dipolar constant.
-self._execute_uf(1.041 * 1e-10, 'r', spin_id="@N", uf_name='value.set')
-self._execute_uf('15N', 'heteronuc_type', spin_id="@N", uf_name='value.set')
-self._execute_uf('1H', 'proton_type', spin_id="@N", uf_name='value.set')
+# Set the nuclear isotope.
+self._execute_uf(uf_name='spin.isotope', isotope='15N', spin_id='@N')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H')
# RDCs.
if ds.mode in ['rdc', 'all']:
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py?rev=17047&r1=17046&r2=17047&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
Mon Jun 25 12:26:12 2012
@@ -23,13 +23,14 @@
self._execute_uf(uf_name='structure.load_spins', spin_id='@N', ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id='@H', ave_pos=False)
-# Load the NH vectors.
-self._execute_uf('H', '@N', ave=False, uf_name='structure.vectors')
+# Define the magnetic dipole-dipole relaxation interaction.
+dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
+dipole_pair.set_dist(spin_id1='@N', spin_id2='@H',
ave_dist=NH_BOND_LENGTH_RDC)
+dipole_pair.unit_vectors()
-# Set the values needed to calculate the dipolar constant.
-self._execute_uf(NH_BOND_LENGTH_RDC, 'r', uf_name='value.set')
-self._execute_uf('15N', 'heteronuc_type', uf_name='value.set')
-self._execute_uf('1H', 'proton_type', uf_name='value.set')
+# Set the nuclear isotope type.
+spin.isotope('15N', spin_id='@N')
+spin.isotope('1H', spin_id='@H')
# RDCs.
self._execute_uf(uf_name='rdc.read', align_id=tag, file='rdc_dy',
dir=DATA_PATH, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4,
neg_g_corr=True)
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/vector_loading.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/vector_loading.py?rev=17047&r1=17046&r2=17047&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/vector_loading.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/vector_loading.py
Mon Jun 25 12:26:12 2012
@@ -21,6 +21,8 @@
# Load the sequence information.
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C1',
ave_pos=False)
+self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@H1',
ave_pos=False)
# Load the CH vectors for the C atoms.
-self._execute_uf(uf_name='structure.vectors', spin_id='@C*', attached='H*',
ave=False)
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@C1',
spin_id2='@H1', direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
r17047 - in /branches/interatomic/test_suite/system_tests: ./ scripts/n_state_model/