Author: bugman
Date: Mon Mar 11 14:19:58 2013
New Revision: 18770
URL: http://svn.gna.org/viewcvs/relax?rev=18770&view=rev
Log:
Updated the rigid_test.py frame order system test script so that it can run
as a GUI test.
The self._execute_uf() method needs to be used to call user function. This
was causing 8 GUI test
failures.
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/rigid_test.py
Modified:
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/rigid_test.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/rigid_test.py?rev=18770&r1=18769&r2=18770&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/rigid_test.py
(original)
+++
branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/rigid_test.py
Mon Mar 11 14:19:58 2013
@@ -40,20 +40,20 @@
# Create the data pipe.
-pipe.create(pipe_name='rigid test', pipe_type='frame order')
+self._execute_uf(uf_name='pipe.create', pipe_name='rigid test',
pipe_type='frame order')
# Read the structures.
-structure.read_pdb('displaced.pdb', dir=PATH, set_mol_name='fancy_mol')
+self._execute_uf(uf_name='structure.read_pdb', file='displaced.pdb',
dir=PATH, set_mol_name='fancy_mol')
# Set up the 15N and 1H spins.
-structure.load_spins()
-spin.isotope(isotope='15N', spin_id='@N')
-spin.isotope(isotope='1H', spin_id='@H')
+self._execute_uf(uf_name='structure.load_spins')
+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.
-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')
# The lanthanides and data files.
ln = ['dy', 'tb', 'tm', 'er', 'yb', 'ho']
@@ -77,65 +77,65 @@
# Loop over the alignments.
for i in range(len(ln)):
# Load the RDCs.
- rdc.read(align_id=ln[i], file=rdc_files[i], dir=PATH, spin_id1_col=1,
spin_id2_col=2, data_col=3, error_col=4)
+ self._execute_uf(uf_name='rdc.read', align_id=ln[i], file=rdc_files[i],
dir=PATH, spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
# The PCS (only a subset of ~5 spins for fast initial optimisations).
- pcs.read(align_id=ln[i], file=pcs_files[i], dir=PATH, mol_name_col=1,
res_num_col=2, spin_name_col=5, data_col=6, error_col=7)
+ self._execute_uf(uf_name='pcs.read', align_id=ln[i], file=pcs_files[i],
dir=PATH, mol_name_col=1, res_num_col=2, spin_name_col=5, data_col=6,
error_col=7)
# The temperature and field strength.
- temperature(id=ln[i], temp=303.0)
- frq.set(id=ln[i], frq=800.0, units="MHz")
+ self._execute_uf(uf_name='temperature', id=ln[i], temp=303.0)
+ self._execute_uf(uf_name='frq.set', id=ln[i], frq=800.0, units="MHz")
# Load the tensors (the full tensors).
-align_tensor.init(tensor='Dy fixed', align_id='dy',
params=(-0.000283041921495, 0.00017331020651, 0.000348144461756,
0.00109678563394, -0.000261126459214), param_types=2)
-align_tensor.init(tensor='Dy fixed', align_id='dy',
params=(1.32405973595e-05, 1.69451339335e-05, 1.11420056339e-05,
1.2902359091e-05, 1.06231229491e-05), param_types=2, errors=True)
-align_tensor.init(tensor='Tb fixed', align_id='tb',
params=(0.000167738428636, -0.000311103377008, 0.000231043994111,
0.000927908442481, -0.00042448381621), param_types=2)
-align_tensor.init(tensor='Tb fixed', align_id='tb',
params=(9.23106516114e-06, 1.23864406564e-05, 9.25138110416e-06,
1.0025121852e-05, 8.6027985631e-06), param_types=2, errors=True)
-align_tensor.init(tensor='Tm fixed', align_id='tm',
params=(-0.000214531334757, 0.000250016686133, -0.000318452894707,
-0.000566585709341, 0.000458689017372), param_types=2)
-align_tensor.init(tensor='Tm fixed', align_id='tm',
params=(8.18656207912e-06, 1.09649975373e-05, 8.43998269558e-06,
8.63599444168e-06, 7.95937745247e-06), param_types=2, errors=True)
-align_tensor.init(tensor='Er fixed', align_id='er',
params=(-9.34632913359e-05, 7.71986454118e-05, -0.000234020357448,
-0.000363596427557, 0.000177874820425), param_types=2)
-align_tensor.init(tensor='Er fixed', align_id='er',
params=(6.32851257036e-06, 9.3721066722e-06, 7.36682050165e-06,
7.52806731357e-06, 9.79003188793e-06), param_types=2, errors=True)
-align_tensor.init(tensor='Yb fixed', align_id='yb',
params=(2.20524016343e-05, -6.04903356962e-05, -0.000114723702615,
-0.000214855846027, 0.000143730520814), param_types=2)
-align_tensor.init(tensor='Yb fixed', align_id='yb',
params=(4.2812326053e-06, 5.43186247053e-06, 4.83605375312e-06,
5.10468453851e-06, 4.31847329676e-06), param_types=2, errors=True)
-align_tensor.init(tensor='Ho fixed', align_id='ho',
params=(-6.99147985047e-05, -8.00899711508e-06, 0.000102219102441,
0.000424559081645, -0.000255281322523), param_types=2)
-align_tensor.init(tensor='Ho fixed', align_id='ho',
params=(7.74711876341e-06, 9.55677606858e-06, 9.13852550558e-06,
7.82230105216e-06, 7.33515152376e-06), param_types=2, errors=True)
+self._execute_uf(uf_name='align_tensor.init', tensor='Dy fixed',
align_id='dy', params=(-0.000283041921495, 0.00017331020651,
0.000348144461756, 0.00109678563394, -0.000261126459214), param_types=2)
+self._execute_uf(uf_name='align_tensor.init', tensor='Dy fixed',
align_id='dy', params=(1.32405973595e-05, 1.69451339335e-05,
1.11420056339e-05, 1.2902359091e-05, 1.06231229491e-05), param_types=2,
errors=True)
+self._execute_uf(uf_name='align_tensor.init', tensor='Tb fixed',
align_id='tb', params=(0.000167738428636, -0.000311103377008,
0.000231043994111, 0.000927908442481, -0.00042448381621), param_types=2)
+self._execute_uf(uf_name='align_tensor.init', tensor='Tb fixed',
align_id='tb', params=(9.23106516114e-06, 1.23864406564e-05,
9.25138110416e-06, 1.0025121852e-05, 8.6027985631e-06), param_types=2,
errors=True)
+self._execute_uf(uf_name='align_tensor.init', tensor='Tm fixed',
align_id='tm', params=(-0.000214531334757, 0.000250016686133,
-0.000318452894707, -0.000566585709341, 0.000458689017372), param_types=2)
+self._execute_uf(uf_name='align_tensor.init', tensor='Tm fixed',
align_id='tm', params=(8.18656207912e-06, 1.09649975373e-05,
8.43998269558e-06, 8.63599444168e-06, 7.95937745247e-06), param_types=2,
errors=True)
+self._execute_uf(uf_name='align_tensor.init', tensor='Er fixed',
align_id='er', params=(-9.34632913359e-05, 7.71986454118e-05,
-0.000234020357448, -0.000363596427557, 0.000177874820425), param_types=2)
+self._execute_uf(uf_name='align_tensor.init', tensor='Er fixed',
align_id='er', params=(6.32851257036e-06, 9.3721066722e-06,
7.36682050165e-06, 7.52806731357e-06, 9.79003188793e-06), param_types=2,
errors=True)
+self._execute_uf(uf_name='align_tensor.init', tensor='Yb fixed',
align_id='yb', params=(2.20524016343e-05, -6.04903356962e-05,
-0.000114723702615, -0.000214855846027, 0.000143730520814), param_types=2)
+self._execute_uf(uf_name='align_tensor.init', tensor='Yb fixed',
align_id='yb', params=(4.2812326053e-06, 5.43186247053e-06,
4.83605375312e-06, 5.10468453851e-06, 4.31847329676e-06), param_types=2,
errors=True)
+self._execute_uf(uf_name='align_tensor.init', tensor='Ho fixed',
align_id='ho', params=(-6.99147985047e-05, -8.00899711508e-06,
0.000102219102441, 0.000424559081645, -0.000255281322523), param_types=2)
+self._execute_uf(uf_name='align_tensor.init', tensor='Ho fixed',
align_id='ho', params=(7.74711876341e-06, 9.55677606858e-06,
9.13852550558e-06, 7.82230105216e-06, 7.33515152376e-06), param_types=2,
errors=True)
# Define the domains.
-domain(id='moving', spin_id=":0-100")
-domain(id='fixed', spin_id=":101-200")
+self._execute_uf(uf_name='domain', id='moving', spin_id=":0-100")
+self._execute_uf(uf_name='domain', id='fixed', spin_id=":101-200")
# The tensor domains and reductions.
full = ['Dy fixed', 'Tb fixed', 'Tm fixed', 'Er fixed', 'Yb fixed', 'Ho
fixed']
red = ['Dy moving', 'Tb moving', 'Tm moving', 'Er moving', 'Yb moving', 'Ho
moving']
for i in range(len(full)):
# Initialise the reduced tensors (fitted during optimisation).
- align_tensor.init(tensor=red[i], align_id=ln[i], params=(0, 0, 0, 0, 0))
+ self._execute_uf(uf_name='align_tensor.init', tensor=red[i],
align_id=ln[i], params=(0, 0, 0, 0, 0))
# Set the domain info.
- align_tensor.set_domain(tensor=full[i], domain='fixed')
- align_tensor.set_domain(tensor=red[i], domain='moving')
+ self._execute_uf(uf_name='align_tensor.set_domain', tensor=full[i],
domain='fixed')
+ self._execute_uf(uf_name='align_tensor.set_domain', tensor=red[i],
domain='moving')
# Specify which tensor is reduced.
- align_tensor.reduction(full_tensor=full[i], red_tensor=red[i])
+ self._execute_uf(uf_name='align_tensor.reduction', full_tensor=full[i],
red_tensor=red[i])
# Set the reference domain.
-frame_order.ref_domain('fixed')
+self._execute_uf(uf_name='frame_order.ref_domain', ref='fixed')
# Link the domains to the PDB files.
-frame_order.domain_to_pdb(domain='fixed', pdb='displaced.pdb')
+self._execute_uf(uf_name='frame_order.domain_to_pdb', domain='fixed',
pdb='displaced.pdb')
# Set up the mechanics of the displacement to the average domain position.
-frame_order.average_position(pivot='com', translation=True)
+self._execute_uf(uf_name='frame_order.average_position', pivot='com',
translation=True)
# Set the initial pivot point (should make no difference for the rigid
model).
pivot = array([0, 0, 0], float64)
-frame_order.pivot(pivot, fix=True)
+self._execute_uf(uf_name='frame_order.pivot', pivot=pivot, fix=True)
# Set the paramagnetic centre position.
-paramag.centre(pos=[-5, -7, -9])
+self._execute_uf(uf_name='paramag.centre', pos=[-5, -7, -9])
# Set the number of integration points.
-frame_order.num_int_pts(10000)
+self._execute_uf(uf_name='frame_order.num_int_pts', num=10000)
# Set the real parameter values (the inverted displacement values).
cdp.ave_pos_x = -1
@@ -157,7 +157,7 @@
ds.model = 'rigid'
# Select the Frame Order model.
-frame_order.select_model(model=ds.model)
+self._execute_uf(uf_name='frame_order.select_model', model=ds.model)
# Calculate the chi2 value.
-calc()
+self._execute_uf(uf_name='calc')
r18770 - /branches/frame_order_testing/test_suite/system_tests/scripts/frame_order/rigid_test.py