Author: bugman
Date: Wed Apr 3 10:16:05 2013
New Revision: 19309
URL: http://svn.gna.org/viewcvs/relax?rev=19309&view=rev
Log:
Merged revisions 19306-19308 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r19306 | bugman | 2013-04-02 12:59:57 +0200 (Tue, 02 Apr 2013) | 3 lines
Import rearrangements.
........
r19307 | bugman | 2013-04-02 13:00:36 +0200 (Tue, 02 Apr 2013) | 3 lines
Missing imports of the lib.float.isInf() function.
........
r19308 | bugman | 2013-04-02 15:23:42 +0200 (Tue, 02 Apr 2013) | 5 lines
Modified the bug_20674_ct_analysis_failure.py system test script to use
self._execute_uf().
This allows the test to operate as a GUI test, which was failing.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/specific_analyses/consistency_tests.py
branches/relax_disp/specific_analyses/jw_mapping.py
branches/relax_disp/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Apr 3 10:16:05 2013
@@ -1,1 +1,1 @@
-/trunk:1-19304
+/trunk:1-19308
Modified: branches/relax_disp/specific_analyses/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/consistency_tests.py?rev=19309&r1=19308&r2=19309&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/consistency_tests.py (original)
+++ branches/relax_disp/specific_analyses/consistency_tests.py Wed Apr 3
10:16:05 2013
@@ -28,16 +28,17 @@
from warnings import warn
# relax module imports.
+from lib.errors import RelaxError, RelaxFuncSetupError,
RelaxNoSequenceError, RelaxNoValueError, RelaxSpinTypeError
+from lib.float import isInf
+from lib.physical_constants import N15_CSA, NH_BOND_LENGTH, h_bar, mu0,
return_gyromagnetic_ratio
+from lib.warnings import RelaxDeselectWarning
+import specific_analyses
from pipe_control.interatomic import return_interatom_list
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
from pipe_control import pipes
-from target_functions.consistency_tests import Consistency
-from lib.physical_constants import N15_CSA, NH_BOND_LENGTH, h_bar, mu0,
return_gyromagnetic_ratio
-from lib.errors import RelaxError, RelaxFuncSetupError,
RelaxNoSequenceError, RelaxNoValueError, RelaxSpinTypeError
-from lib.warnings import RelaxDeselectWarning
-import specific_analyses
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
+from target_functions.consistency_tests import Consistency
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
Modified: branches/relax_disp/specific_analyses/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/jw_mapping.py?rev=19309&r1=19308&r2=19309&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/jw_mapping.py (original)
+++ branches/relax_disp/specific_analyses/jw_mapping.py Wed Apr 3 10:16:05
2013
@@ -27,16 +27,17 @@
from warnings import warn
# relax module imports.
+from lib.errors import RelaxError, RelaxFuncSetupError,
RelaxNoSequenceError, RelaxNoValueError, RelaxSpinTypeError
+from lib.float import isInf
+from lib.physical_constants import N15_CSA, NH_BOND_LENGTH, h_bar, mu0,
return_gyromagnetic_ratio
+from lib.warnings import RelaxDeselectWarning
+import specific_analyses
+from specific_analyses.api_base import API_base
+from specific_analyses.api_common import API_common
from pipe_control.interatomic import return_interatom_list
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin,
spin_loop
from pipe_control import pipes
from target_functions.jw_mapping import Mapping
-from lib.physical_constants import N15_CSA, NH_BOND_LENGTH, h_bar, mu0,
return_gyromagnetic_ratio
-from lib.errors import RelaxError, RelaxFuncSetupError,
RelaxNoSequenceError, RelaxNoValueError, RelaxSpinTypeError
-from lib.warnings import RelaxDeselectWarning
-import specific_analyses
-from specific_analyses.api_base import API_base
-from specific_analyses.api_common import API_common
from user_functions.data import Uf_tables; uf_tables = Uf_tables()
from user_functions.objects import Desc_container
Modified:
branches/relax_disp/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py?rev=19309&r1=19308&r2=19309&view=diff
==============================================================================
---
branches/relax_disp/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py
(original)
+++
branches/relax_disp/test_suite/system_tests/scripts/bug_20674_ct_analysis_failure.py
Wed Apr 3 10:16:05 2013
@@ -9,56 +9,55 @@
# Create the run.
-name = 'consistency'
-pipe.create(name, 'ct')
+self._execute_uf(uf_name='pipe.create', pipe_name='consistency',
pipe_type='ct')
# The data directory.
path = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'consistency_testing'+sep+'bug_20674_ct_analysis_failure'
# Load the PDB file.
-structure.read_pdb(file='2QFK_MONOMERHabc5.pdb', dir=path, read_mol=None,
set_mol_name=None, read_model=None, set_model_num=None)
+self._execute_uf(uf_name='structure.read_pdb', file='2QFK_MONOMERHabc5.pdb',
dir=path, read_mol=None, set_mol_name=None, read_model=None,
set_model_num=None)
# Set up the 15N and 1H spins (both backbone and Trp indole sidechains).
-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')
+self._execute_uf(uf_name='structure.load_spins', spin_id='@N', ave_pos=True)
+self._execute_uf(uf_name='structure.load_spins', spin_id='@H', ave_pos=True)
+self._execute_uf(uf_name='spin.isotope', isotope='15N', spin_id='@N')
+self._execute_uf(uf_name='spin.isotope', isotope='1H', spin_id='@H')
# Load the relaxation data.
-bruker.read(ri_id='r1_700', file='T1 dhp 700.txt', dir=path)
-bruker.read(ri_id='r2_700', file='T2 dhp 700.txt', dir=path)
-bruker.read(ri_id='noe_700', file='NOE dhp 700.txt', dir=path)
+self._execute_uf(uf_name='bruker.read', ri_id='r1_700', file='T1 dhp
700.txt', dir=path)
+self._execute_uf(uf_name='bruker.read', ri_id='r2_700', file='T2 dhp
700.txt', dir=path)
+self._execute_uf(uf_name='bruker.read', ri_id='noe_700', file='NOE dhp
700.txt', dir=path)
# 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=1.02 * 1e-10)
+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=1.02 * 1e-10)
# Define the chemical shift relaxation interaction.
-value.set(val=-172 * 1e-6, param='csa')
+self._execute_uf(uf_name='value.set', val=-172 * 1e-6, param='csa')
# Set the angle between the 15N-1H vector and the principal axis of the 15N
chemical shift tensor
-value.set(val=15.7, param='orientation')
+self._execute_uf(uf_name='value.set', val=15.7, param='orientation')
# Set the approximate correlation time.
-value.set(val=13 * 1e-9, param='tc')
+self._execute_uf(uf_name='value.set', val=13 * 1e-9, param='tc')
# Set the frequency.
-consistency_tests.set_frq(frq=700.17 * 1e6)
+self._execute_uf(uf_name='consistency_tests.set_frq', frq=700.17 * 1e6)
# Consistency tests.
-calc()
+self._execute_uf(uf_name='calc')
# Monte Carlo simulations.
-monte_carlo.setup(number=10)
-monte_carlo.create_data()
-calc()
-monte_carlo.error_analysis()
+self._execute_uf(uf_name='monte_carlo.setup', number=10)
+self._execute_uf(uf_name='monte_carlo.create_data')
+self._execute_uf(uf_name='calc')
+self._execute_uf(uf_name='monte_carlo.error_analysis')
# Create grace files.
-grace.write(y_data_type='j0', file='devnull', force=True)
-grace.write(y_data_type='f_eta', file='devnull', force=True)
-grace.write(y_data_type='f_r2', file='devnull', force=True)
+self._execute_uf(uf_name='grace.write', y_data_type='j0', file='devnull',
force=True)
+self._execute_uf(uf_name='grace.write', y_data_type='f_eta', file='devnull',
force=True)
+self._execute_uf(uf_name='grace.write', y_data_type='f_r2', file='devnull',
force=True)
# Finish.
-results.write(file='devnull', force=True)
-state.save('devnull')
+self._execute_uf(uf_name='results.write', file='devnull', force=True)
+self._execute_uf(uf_name='state.save', state='devnull')
r19309 - in /branches/relax_disp: ./ specific_analyses/ test_suite/system_tests/scripts/