Author: bugman
Date: Mon Nov 17 11:12:42 2014
New Revision: 26593
URL: http://svn.gna.org/viewcvs/relax?rev=26593&view=rev
Log:
Merged revisions 26592 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r26592 | bugman | 2014-11-17 11:12:16 +0100 (Mon, 17 Nov 2014) | 6 lines
Created the Mf.test_dauvergne_protocol_sphere system test.
This catches bug #22963 (https://gna.org/bugs/?22963): Using '@N*' to
define the interatomic
interactions for a model-free analysis fails when using non-backbone 15N
spins.
........
Modified:
branches/frame_order_cleanup/ (props changed)
branches/frame_order_cleanup/test_suite/system_tests/model_free.py
Propchange: branches/frame_order_cleanup/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Mon Nov 17 11:12:42 2014
@@ -1 +1 @@
-/trunk:1-26589
+/trunk:1-26592
Modified: branches/frame_order_cleanup/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/test_suite/system_tests/model_free.py?rev=26593&r1=26592&r2=26593&view=diff
==============================================================================
--- branches/frame_order_cleanup/test_suite/system_tests/model_free.py
(original)
+++ branches/frame_order_cleanup/test_suite/system_tests/model_free.py Mon
Nov 17 11:12:42 2014
@@ -29,6 +29,7 @@
from tempfile import mkdtemp
# relax module imports.
+from auto_analyses.dauvergne_protocol import dAuvergne_protocol
from data_store import Relax_data_store; ds = Relax_data_store()
import dep_check
from pipe_control import pipes
@@ -758,6 +759,57 @@
self.assert_(path.isfile(file_path))
+ def test_dauvergne_protocol_sphere(self):
+ """Catch a failure when loading relaxation data."""
+
+ # The data directory.
+ dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'model_free'+sep+'sphere'
+
+ # Reset relax.
+ self.interpreter.reset()
+
+ # Set up a data pipe and bundle.
+ self.interpreter.pipe.create('sphere test', 'mf', bundle='sphere
test')
+
+ # Load the sequence.
+ self.interpreter.sequence.read(file='noe.500.out', dir=dir,
spin_id_col=None, mol_name_col=1, res_num_col=2, res_name_col=3,
spin_num_col=4, spin_name_col=5, sep=None, spin_id=None)
+
+ # Load the relaxation data.
+ self.interpreter.relax_data.read(ri_id='r1.500', ri_type='R1',
frq=500000000.0, file='r1.500.out', dir=dir, spin_id_col=None,
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, sep=None, spin_id=None)
+ self.interpreter.relax_data.read(ri_id='r2.500', ri_type='R2',
frq=500000000.0, file='r2.500.out', dir=dir, spin_id_col=None,
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, sep=None, spin_id=None)
+ self.interpreter.relax_data.read(ri_id='noe.500', ri_type='NOE',
frq=500000000.0, file='noe.500.out', dir=dir, spin_id_col=None,
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, sep=None, spin_id=None)
+ self.interpreter.relax_data.read(ri_id='r1.900', ri_type='R1',
frq=900000000.0, file='r1.900.out', dir=dir, spin_id_col=None,
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, sep=None, spin_id=None)
+ self.interpreter.relax_data.read(ri_id='r2.900', ri_type='R2',
frq=900000000.0, file='r2.900.out', dir=dir, spin_id_col=None,
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, sep=None, spin_id=None)
+ self.interpreter.relax_data.read(ri_id='noe.900', ri_type='NOE',
frq=900000000.0, file='noe.900.out', dir=dir, spin_id_col=None,
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, sep=None, spin_id=None)
+ self.interpreter.relax_data.peak_intensity_type(ri_id='noe.900',
type='height')
+ self.interpreter.relax_data.peak_intensity_type(ri_id='r2.900',
type='height')
+ self.interpreter.relax_data.peak_intensity_type(ri_id='r1.900',
type='height')
+ self.interpreter.relax_data.peak_intensity_type(ri_id='noe.500',
type='height')
+ self.interpreter.relax_data.peak_intensity_type(ri_id='r2.500',
type='height')
+ self.interpreter.relax_data.peak_intensity_type(ri_id='r1.500',
type='height')
+ self.interpreter.relax_data.peak_intensity_type(ri_id='r1.500',
type='height')
+
+ # Set up the interatomic interactions.
+ self.interpreter.structure.read_pdb(file='sphere.pdb', dir=dir,
read_mol=None, set_mol_name=None, read_model=None, set_model_num=None,
alt_loc=None, verbosity=1, merge=False)
+ self.interpreter.structure.get_pos(spin_id=None, ave_pos=True)
+ self.interpreter.interatom.define(spin_id1='@N*', spin_id2='@H*',
direct_bond=True, spin_selection=True, pipe=None)
+ self.interpreter.interatom.set_dist(spin_id1='@N*', spin_id2='@H*',
ave_dist=1.02e-10, unit='meter')
+ self.interpreter.interatom.unit_vectors(ave=True)
+
+ # Set the CSA value.
+ self.interpreter.value.set(val=-0.000172, param='csa', index=0,
spin_id='@N*', error=False, force=True)
+
+ # Set up the isotope information.
+ self.interpreter.spin.isotope(isotope='15N', spin_id='@N*',
force=True)
+ self.interpreter.spin.isotope(isotope='1H', spin_id='@H*',
force=True)
+
+ # Create a temporary directory for dumping files.
+ ds.tmpdir = mkdtemp()
+
+ # The dauvergne_protocol model-free auto-analysis.
+ dAuvergne_protocol(pipe_name='sphere test', pipe_bundle='sphere
test', results_dir=ds.tmpdir, diff_model=['local_tm', 'sphere'],
mf_models=['m1', 'm2'], local_tm_models=['tm0', 'tm1'], grid_inc=3,
diff_tensor_grid_inc={'sphere': 5, 'prolate': 5, 'oblate': 5, 'ellipsoid':
3}, min_algor='newton', mc_sim_num=2, max_iter=1, conv_loop=True)
+
+
def test_generate_ri(self):
"""Back-calculate relaxation data."""
r26593 - in /branches/frame_order_cleanup: ./ test_suite/system_tests/model_free.py