Author: bugman
Date: Wed Jun 27 17:43:37 2012
New Revision: 17077
URL: http://svn.gna.org/viewcvs/relax?rev=17077&view=rev
Log:
Converted all of the N-state model system and GUI test scripts to the new
interatomic data design.
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/align_fit.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/rdc_tensor.py
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=17077&r1=17076&r2=17077&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
Wed Jun 27 17:43:37 2012
@@ -36,9 +36,9 @@
self._execute_uf(uf_name='structure.load_spins')
# 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()
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@N', spin_id2='@H',
direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@N',
spin_id2='@H', ave_dist=1.041 * 1e-10)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
# Set the nuclear isotope.
self._execute_uf(uf_name='spin.isotope', isotope='15N', spin_id='@N')
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py?rev=17077&r1=17076&r2=17077&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
Wed Jun 27 17:43:37 2012
@@ -36,13 +36,14 @@
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H17')
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H18')
-# Load the CH vectors for the C atoms.
-self._execute_uf(uf_name='structure.vectors', spin_id='@C*', attached='H*',
ave=False)
+# Define the magnetic dipole-dipole relaxation interaction.
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@C*',
spin_id2='@H*', direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@C*',
spin_id2='@H*', ave_dist=1.10 * 1e-10)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
-# Set the values needed to calculate the dipolar constant.
-self._execute_uf(1.10 * 1e-10, 'r', spin_id="@C*", uf_name='value.set')
-self._execute_uf('13C', 'heteronuc_type', spin_id="@C*", uf_name='value.set')
-self._execute_uf('1H', 'proton_type', spin_id="@C*", uf_name='value.set')
+# Set the nuclear isotope type.
+self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
# File list.
align_list = ['Dy', 'Tb', 'Tm', 'Er']
@@ -50,8 +51,8 @@
# Load the RDCs and PCSs.
for i in xrange(len(align_list)):
# The RDC.
- self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='rdc.txt', dir=data_path, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=1, data_col=i+3,
error_col=None)
- self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='rdc_err.txt', dir=data_path, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=1, data_col=None,
error_col=i+3)
+ self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='rdc.txt', dir=data_path, spin_id1_col=1, spin_id2_col=2, data_col=i+3,
error_col=None)
+ self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='rdc_err.txt', dir=data_path, spin_id1_col=1, spin_id2_col=2,
data_col=None, error_col=i+3)
self._execute_uf(uf_name='rdc.display', align_id=align_list[i])
# The PCS.
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py?rev=17077&r1=17076&r2=17077&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/metal_pos_opt.py
Wed Jun 27 17:43:37 2012
@@ -36,13 +36,14 @@
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H17')
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H18')
-# Load the CH vectors.
-self._execute_uf(uf_name='structure.vectors', spin_id='@C*', attached='H*',
ave=False)
+# Define the magnetic dipole-dipole relaxation interaction.
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@C*',
spin_id2='@H*', direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@C*',
spin_id2='@H*', ave_dist=1.10 * 1e-10)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
-# Set the values needed to calculate the dipolar constant.
-self._execute_uf(1.10 * 1e-10, 'r', spin_id="@C*", uf_name='value.set')
-self._execute_uf('13C', 'heteronuc_type', spin_id="@C*", uf_name='value.set')
-self._execute_uf('1H', 'proton_type', spin_id="@C*", uf_name='value.set')
+# Set the nuclear isotope type.
+self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
# Set the paramagnetic centre.
self._execute_uf(uf_name='paramag.centre', pos=[ -14.845, 0.969,
0.265])
@@ -59,7 +60,7 @@
# Load the RDCs and PCSs.
for i in xrange(len(align_list)):
# The RDC.
- self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='missing_rdc_%i' % i, dir=DATA_PATH, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=5, data_col=6,
error_col=None)
+ self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='missing_rdc_%i' % i, dir=DATA_PATH, spin_id1_col=1, spin_id2_col=2,
data_col=3, error_col=None)
# The PCS.
self._execute_uf(uf_name='pcs.read', align_id=align_list[i],
file='missing_pcs_%i' % i, dir=DATA_PATH, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=5, data_col=6,
error_col=None)
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/missing_data_test.py?rev=17077&r1=17076&r2=17077&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/missing_data_test.py
Wed Jun 27 17:43:37 2012
@@ -21,13 +21,14 @@
self._execute_uf(uf_name='structure.load_spins', spin_id='@C*',
ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id='@H*',
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)
+# Define the magnetic dipole-dipole relaxation interaction.
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@C*',
spin_id2='@H*', direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@C*',
spin_id2='@H*', ave_dist=1.10 * 1e-10)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
-# Set the values needed to calculate the dipolar constant.
-self._execute_uf(uf_name='value.set', val=1.10 * 1e-10, param='r',
spin_id="@C*")
-self._execute_uf(uf_name='value.set', val='13C', param='heteronuc_type',
spin_id="@C*")
-self._execute_uf(uf_name='value.set', val='1H', param='proton_type',
spin_id="@C*")
+# Set the nuclear isotope type.
+self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
# File list.
align_list = ['Dy', 'Tb', 'Tm', 'Er']
@@ -36,7 +37,7 @@
for i in xrange(len(align_list)):
# The RDC.
if i != 1:
- self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='missing_rdc_%i' % i, dir=data_path, mol_name_col=1, res_num_col=2,
res_name_col=3, spin_num_col=None, spin_name_col=5, data_col=6,
error_col=None)
+ self._execute_uf(uf_name='rdc.read', align_id=align_list[i],
file='missing_rdc_%i' % i, dir=data_path, spin_id1_col=1, spin_id2_col=2,
data_col=3, error_col=None)
self._execute_uf(uf_name='rdc.display', align_id=align_list[i])
# The PCS.
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py?rev=17077&r1=17076&r2=17077&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/monte_carlo_testing.py
Wed Jun 27 17:43:37 2012
@@ -23,16 +23,17 @@
# 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.
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@N', spin_id2='@H',
direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@N',
spin_id2='@H', ave_dist=1.041 * 1e-10)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
-# Set the values needed to calculate the dipolar constant.
-self._execute_uf(uf_name='value.set', val=1.041 * 1e-10, param='r',
spin_id="@N")
-self._execute_uf(uf_name='value.set', val='15N', param='heteronuc_type',
spin_id="@N")
-self._execute_uf(uf_name='value.set', val='1H', param='proton_type',
spin_id="@N")
+# 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.
-self._execute_uf(uf_name='rdc.read', align_id='synth', file='synth_rdc',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
+self._execute_uf(uf_name='rdc.read', align_id='synth', file='synth_rdc',
dir=DATA_PATH, spin_id1_col=1, spin_id1_col=2, data_col=3, error_col=4)
# PCSs.
self._execute_uf(uf_name='pcs.read', align_id='synth', file='synth_pcs',
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6, error_col=7)
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py?rev=17077&r1=17076&r2=17077&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/paramag_centre_fit.py
Wed Jun 27 17:43:37 2012
@@ -31,7 +31,16 @@
# Load the spins.
self._execute_uf(uf_name='structure.load_spins')
-# Deselect most spins (to speed things up).
+# Define the magnetic dipole-dipole relaxation interaction.
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@N', spin_id2='@H',
direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@N',
spin_id2='@H', ave_dist=1.041 * 1e-10)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
+
+# Set the nuclear isotope type.
+self._execute_uf(uf_name='spin.isotope', isotope='15N', spin_id='@N')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H')
+
+# Deselect most spins and interatomic data containers (to speed things up).
self._execute_uf(uf_name='deselect.spin')
self._execute_uf(uf_name='select.spin', spin_id=":83")
self._execute_uf(uf_name='select.spin', spin_id=":84")
@@ -41,18 +50,19 @@
self._execute_uf(uf_name='select.spin', spin_id=":131")
self._execute_uf(uf_name='select.spin', spin_id=":132")
self._execute_uf(uf_name='select.spin', spin_id=":148")
-
-# Load the NH vectors.
-self._execute_uf(uf_name='structure.vectors', spin_id='@N', attached='H',
ave=False)
-
-# Set the values needed to calculate the dipolar constant.
-self._execute_uf(uf_name='value.set', val=1.041 * 1e-10, param='r',
spin_id="@N")
-self._execute_uf(uf_name='value.set', val='15N', param='heteronuc_type',
spin_id="@N")
-self._execute_uf(uf_name='value.set', val='1H', param='proton_type',
spin_id="@N")
+self._execute_uf(uf_name='deselect.interatom')
+self._execute_uf(uf_name='select.interatom', spin_id1=":83")
+self._execute_uf(uf_name='select.interatom', spin_id1=":84")
+self._execute_uf(uf_name='select.interatom', spin_id1=":85")
+self._execute_uf(uf_name='select.interatom', spin_id1=":111")
+self._execute_uf(uf_name='select.interatom', spin_id1=":130")
+self._execute_uf(uf_name='select.interatom', spin_id1=":131")
+self._execute_uf(uf_name='select.interatom', spin_id1=":132")
+self._execute_uf(uf_name='select.interatom', spin_id1=":148")
# RDCs.
if ds.mode == 'all':
- self._execute_uf(uf_name='rdc.read', align_id='synth', file=rdc_file,
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6)
+ self._execute_uf(uf_name='rdc.read', align_id='synth', file=rdc_file,
dir=DATA_PATH, spin_id1_col=1, spin_id2_col=2, data_col=3)
# PCSs.
self._execute_uf(uf_name='pcs.read', align_id='synth', file=pcs_file,
dir=DATA_PATH, mol_name_col=1, res_num_col=2, res_name_col=3, spin_num_col=4,
spin_name_col=5, data_col=6)
Modified:
branches/interatomic/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py?rev=17077&r1=17076&r2=17077&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/n_state_model/pcs_to_rdc.py
Wed Jun 27 17:43:37 2012
@@ -19,13 +19,14 @@
# Load the spins.
self._execute_uf(uf_name='structure.load_spins', spin_id='@N')
-# Set the heteronucleus type.
-self._execute_uf(uf_name='value.set', val='15N', param='heteronuc_type')
-self._execute_uf(uf_name='value.set', val='1H', param='proton_type')
-self._execute_uf(uf_name='value.set', val=NH_BOND_LENGTH_RDC, param='r')
+# Define the magnetic dipole-dipole relaxation interaction.
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@N', spin_id2='@H',
direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@N',
spin_id2='@H', ave_dist=NH_BOND_LENGTH_RDC)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
-# Load the bond vectors.
-self._execute_uf(uf_name='structure.vectors', attached='H', spin_id='@N')
+# 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')
# The dipolar constant.
const = 3.0 / (2.0*pi) * dipolar_constant(g15N, g1H, NH_BOND_LENGTH_RDC)
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=17077&r1=17076&r2=17077&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
Wed Jun 27 17:43:37 2012
@@ -24,13 +24,13 @@
self._execute_uf(uf_name='structure.load_spins', spin_id='@H', ave_pos=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=NH_BOND_LENGTH_RDC)
-dipole_pair.unit_vectors()
+self._execute_uf(uf_name='dipole_pair.define', spin_id1='@N', spin_id2='@H',
direct_bond=True)
+self._execute_uf(uf_name='dipole_pair.set_dist', spin_id1='@N',
spin_id2='@H', ave_dist=NH_BOND_LENGTH_RDC)
+self._execute_uf(uf_name='dipole_pair.unit_vectors', ave=False)
# Set the nuclear isotope type.
-spin.isotope('15N', spin_id='@N')
-spin.isotope('1H', spin_id='@H')
+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.
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)
r17077 - /branches/interatomic/test_suite/system_tests/scripts/n_state_model/