Author: bugman
Date: Wed Jul 4 09:21:45 2012
New Revision: 17173
URL: http://svn.gna.org/viewcvs/relax?rev=17173&view=rev
Log:
A number of clean ups and rearrangements of the system test scripts.
Modified:
branches/interatomic/test_suite/system_tests/scripts/dasha.py
branches/interatomic/test_suite/system_tests/scripts/jw_mapping.py
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
branches/interatomic/test_suite/system_tests/scripts/model_free/generate_ri.py
branches/interatomic/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
branches/interatomic/test_suite/system_tests/scripts/n_state_model/lactose_n_state.py
branches/interatomic/test_suite/system_tests/scripts/palmer.py
branches/interatomic/test_suite/system_tests/scripts/xh_vector_dist.py
Modified: branches/interatomic/test_suite/system_tests/scripts/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/dasha.py?rev=17173&r1=17172&r2=17173&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/dasha.py (original)
+++ branches/interatomic/test_suite/system_tests/scripts/dasha.py Wed Jul 4
09:21:45 2012
@@ -21,36 +21,29 @@
# Create the data pipe.
pipe.create(name, 'mf')
- # Load the sequence.
+ # Set up the 15N spins.
sequence.read(status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2)
-
- # Load a PDB file.
- #structure.read_pdb('example.pdb')
+ spin.name('N')
+ spin.element(element='N', spin_id='@N')
+ spin.isotope('15N', spin_id='@N')
# Load the relaxation data.
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R1.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R2.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
- # Name the spins, then attach some protons.
- spin.name('N')
+ # Set up the diffusion tensor.
+ diffusion_tensor.init(1e-8, fixed=True)
+
+ # Generate the 1H spins for the magnetic dipole-dipole relaxation
interaction.
sequence.attach_protons()
- # Setup other values.
- diffusion_tensor.init(1e-8, fixed=True)
-
# Define the magnetic dipole-dipole relaxation interaction.
- spin.element(element='N', spin_id='@N')
- spin.element(element='H', spin_id='@H')
dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
# Define the chemical shift relaxation interaction.
value.set(-172 * 1e-6, 'csa', spin_id='@N')
-
- # Set the nuclear isotope type.
- spin.isotope('15N', spin_id='@N')
- spin.isotope('1H', spin_id='@H')
# Select the model-free model.
model_free.select_model(model=name)
Modified: branches/interatomic/test_suite/system_tests/scripts/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/jw_mapping.py?rev=17173&r1=17172&r2=17173&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/jw_mapping.py
(original)
+++ branches/interatomic/test_suite/system_tests/scripts/jw_mapping.py Wed
Jul 4 09:21:45 2012
@@ -8,24 +8,23 @@
from status import Status; status = Status()
-# Create the run.
+# Create the data pipe.
name = 'jw_mapping'
self._execute_uf(uf_name='pipe.create', pipe_name=name, pipe_type='jw')
-# Load the sequence.
+# Set up the 15N spins.
self._execute_uf(uf_name='sequence.read', file=status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2)
+self._execute_uf(uf_name='spin.name', name='N')
+self._execute_uf(uf_name='spin.element', element='N')
+self._execute_uf(uf_name='spin.isotope', isotope='15N', spin_id='@N')
# Load the relaxation data.
self._execute_uf(uf_name='relax_data.read', ri_id='R1_600', ri_type='R1',
frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R1.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
self._execute_uf(uf_name='relax_data.read', ri_id='R2_600', ri_type='R2',
frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R2.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
self._execute_uf(uf_name='relax_data.read', ri_id='NOE_600', ri_type='NOE',
frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
-# Set the spin information.
-self._execute_uf(uf_name='spin.name', name='N')
-self._execute_uf(uf_name='spin.element', element='N')
+# Generate 1H spins for the magnetic dipole-dipole relaxation interaction.
self._execute_uf(uf_name='sequence.attach_protons')
-self._execute_uf(uf_name='spin.isotope', isotope='15N', spin_id='@N')
-self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H')
# Define the magnetic dipole-dipole relaxation interaction.
self._execute_uf(uf_name='dipole_pair.define', spin_id1='@N', spin_id2='@H',
direct_bond=True)
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py?rev=17173&r1=17172&r2=17173&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/dauvergne_protocol.py
Wed Jul 4 09:21:45 2012
@@ -189,9 +189,11 @@
# Load the PDB file.
structure.read_pdb('sphere.pdb', dir=data_path)
-# Load all the N and H spins.
+# Set up the 15N and 1H spins.
structure.load_spins('@N', ave_pos=True)
structure.load_spins('@H', ave_pos=True)
+spin.isotope('15N', spin_id='@N')
+spin.isotope('1H', spin_id='@H')
# Load the relaxation data.
relax_data.read(ri_id='R1_900', ri_type='R1', frq=900*1e6,
file='r1.900.out', 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)
@@ -209,11 +211,6 @@
# Define the chemical shift relaxation interaction.
value.set(-172 * 1e-6, 'csa', spin_id='@N')
-# Set the nuclear isotope type.
-spin.isotope('15N', spin_id='@N')
-spin.isotope('1H', spin_id='@H')
-
-
# Execution.
############
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/generate_ri.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/generate_ri.py?rev=17173&r1=17172&r2=17173&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/generate_ri.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/generate_ri.py
Wed Jul 4 09:21:45 2012
@@ -46,17 +46,19 @@
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
dipole_pair.unit_vectors()
+# Define the CSA relaxation interaction.
+value.set(val=-172e-6, param='csa')
+
# Set the diffusion tensor in the PDB frame (Dxx, Dyy, Dzz, Dxy, Dxz, Dyz).
diffusion_tensor.init((1.340e7, 1.516e7, 1.691e7, 0.000e7, 0.000e7,
0.000e7), param_types=3)
-
-# Set the required values.
-value.set(val=-172e-6, param='csa')
-value.set(val=0.8, param='s2')
-value.set(val=20e-12, param='te')
# Set the spin information.
spin.isotope('15N', spin_id='@N')
spin.isotope('1H', spin_id='@H')
+
+# Set the required values.
+value.set(val=0.8, param='s2')
+value.set(val=20e-12, param='te')
# Select model-free model m2.
model_free.select_model(model='m2')
Modified:
branches/interatomic/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py?rev=17173&r1=17172&r2=17173&view=diff
==============================================================================
---
branches/interatomic/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
(original)
+++
branches/interatomic/test_suite/system_tests/scripts/model_free/opendx_s2_te_rex.py
Wed Jul 4 09:21:45 2012
@@ -12,8 +12,11 @@
# Path of the files.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'S2_0.970_te_2048_Rex_0.149'
-# Read the sequence.
+# Set up the 15N spins.
sequence.read(file='noe.500.out', dir=path, res_num_col=1, res_name_col=2)
+spin.name('N')
+spin.element('N')
+spin.isotope('15N', spin_id='@N')
# Read the relaxation data.
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.0*1e6,
file='r1.600.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
@@ -23,9 +26,8 @@
relax_data.read(ri_id='R2_500', ri_type='R2', frq=500.0*1e6,
file='r2.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
relax_data.read(ri_id='NOE_500', ri_type='NOE', frq=500.0*1e6,
file='noe.500.out', dir=path, res_num_col=1, res_name_col=2, data_col=3,
error_col=4)
-# Name the spins and set the element type.
-spin.name('N')
-spin.element('N')
+# Initialise the diffusion tensor.
+diffusion_tensor.init(1e-8, fixed=True)
# Create all attached protons.
sequence.attach_protons()
@@ -34,15 +36,8 @@
dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 * 1e-10)
-# Initialise the diffusion tensor.
-diffusion_tensor.init(1e-8, fixed=True)
-
-# Set up the CSA value.
+# Define the CSA relaxation interaction.
value.set(N15_CSA, 'csa')
-
-# Set the spin information.
-spin.isotope('15N', spin_id='@N')
-spin.isotope('1H', spin_id='@H')
# Select the model.
model_free.select_model(model='m4')
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=17173&r1=17172&r2=17173&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 Jul 4 09:21:45 2012
@@ -26,9 +26,11 @@
for i in range(NUM_STR):
self._execute_uf(uf_name='structure.read_pdb',
file='lactose_MCMM4_S1_'+repr(i+1), dir=str_path, parser='internal',
set_model_num=i+1, set_mol_name='lactose_MCMM4_S1')
-# Load the sequence information.
+# Set up the 13C and 1H spins information.
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@C*',
ave_pos=False)
self._execute_uf(uf_name='structure.load_spins', spin_id=':UNK@H*',
ave_pos=False)
+self._execute_uf(uf_name='spin.isotope', isotope='13C', spin_id='@C*')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H*')
# Deselect the CH2 protons (the rotation of these doesn't work in the model,
but the carbon doesn't move).
self._execute_uf(uf_name='deselect.spin', spin_id=':UNK@H6')
@@ -46,10 +48,6 @@
self._execute_uf(uf_name='deselect.interatom', spin_id1=':UNK@C6',
spin_id2=':UNK@H7')
self._execute_uf(uf_name='deselect.interatom', spin_id1=':UNK@C12',
spin_id2=':UNK@H17')
self._execute_uf(uf_name='deselect.interatom', spin_id1=':UNK@C12',
spin_id2=':UNK@H18')
-
-# 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']
Modified: branches/interatomic/test_suite/system_tests/scripts/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/palmer.py?rev=17173&r1=17172&r2=17173&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/palmer.py (original)
+++ branches/interatomic/test_suite/system_tests/scripts/palmer.py Wed Jul 4
09:21:45 2012
@@ -26,24 +26,24 @@
print(("\n\n# " + name + " #"))
pipe.create(name, 'mf')
- # Load the sequence.
+ # Set up the 15N spins.
sequence.read(status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2)
+ spin.name('N')
+ spin.element(element='N', spin_id='@N')
+ spin.isotope('15N', spin_id='@N')
# Load the relaxation data.
relax_data.read(ri_id='R1_600', ri_type='R1', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R1.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='R2_600', ri_type='R2', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'R2.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
relax_data.read(ri_id='NOE_600', ri_type='NOE', frq=600.0*1e6,
file=status.install_path+sep+'test_suite'+sep+'shared_data'+sep+'jw_mapping'+sep+'noe.dat',
res_num_col=1, res_name_col=2, data_col=3, error_col=4)
- # Name the spins, then attach some protons.
- spin.name('N')
+ # Set up the diffusion tensor.
+ diffusion_tensor.init(1e-8)
+
+ # Generate 1H spins for the magnetic dipole-dipole relaxation
interaction.
sequence.attach_protons()
- # Setup other values.
- diffusion_tensor.init(1e-8)
-
# Define the magnetic dipole-dipole relaxation interaction.
- spin.element(element='N', spin_id='@N')
- spin.element(element='H', spin_id='@H')
dipole_pair.define(spin_id1='@N', spin_id2='@H', direct_bond=True)
dipole_pair.set_dist(spin_id1='@N', spin_id2='@H', ave_dist=1.02 *
1e-10)
@@ -51,7 +51,6 @@
value.set(-172 * 1e-6, 'csa', spin_id='@N')
# Set the nuclear isotope type.
- spin.isotope('15N', spin_id='@N')
spin.isotope('1H', spin_id='@H')
# Select the model-free model.
Modified:
branches/interatomic/test_suite/system_tests/scripts/xh_vector_dist.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/test_suite/system_tests/scripts/xh_vector_dist.py?rev=17173&r1=17172&r2=17173&view=diff
==============================================================================
--- branches/interatomic/test_suite/system_tests/scripts/xh_vector_dist.py
(original)
+++ branches/interatomic/test_suite/system_tests/scripts/xh_vector_dist.py
Wed Jul 4 09:21:45 2012
@@ -21,8 +21,8 @@
structure.load_spins(spin_id='@N')
structure.load_spins(spin_id='@H')
-# Set the XH vectors.
-dipole_pair.define('@N', '@H')
+# Set up the XH vectors.
+dipole_pair.define(spin_id1='@N', spin_id2='@H')
dipole_pair.unit_vectors()
# Create the PDB file.
r17173 - in /branches/interatomic/test_suite/system_tests/scripts: ./ model_free/ n_state_model/