Author: michaelbieri
Date: Wed May 19 01:01:07 2010
New Revision: 11190
URL: http://svn.gna.org/viewcvs/relax?rev=11190&view=rev
Log:
Merged revisions 11185-11189 via svnmerge from
svn+ssh://michaelbieri@xxxxxxxxxxx/svn/relax/1.3
........
r11185 | bugman | 2010-05-12 00:48:07 +1000 (Wed, 12 May 2010) | 3 lines
Added some checks to properly inform the user as to what data is missing.
........
r11186 | bugman | 2010-05-14 23:53:21 +1000 (Fri, 14 May 2010) | 3 lines
Docstring fix for the vect_dist_spherical_angles() function.
........
r11187 | bugman | 2010-05-18 22:15:13 +1000 (Tue, 18 May 2010) | 5 lines
Added a check for the RDC RMS based Q-factor.
This is to check that relax matches both of Pales' Q-factors - which it
does.
........
r11188 | bugman | 2010-05-19 01:54:30 +1000 (Wed, 19 May 2010) | 3 lines
Broke some nasty circular import caused by importing the generic_fns.grace
module.
........
r11189 | bugman | 2010-05-19 02:32:14 +1000 (Wed, 19 May 2010) | 3 lines
Set names are now only written if they are not None.
........
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/generic_fns/grace.py
branches/bieri_gui/generic_fns/structure/geometric.py
branches/bieri_gui/specific_fns/n_state_model.py
branches/bieri_gui/test_suite/system_tests/n_state_model.py
Propchange: branches/bieri_gui/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed May 19 01:01:07 2010
@@ -1,1 +1,1 @@
-/1.3:1-11176
+/1.3:1-11189
Modified: branches/bieri_gui/generic_fns/grace.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/grace.py?rev=11190&r1=11189&r2=11190&view=diff
==============================================================================
--- branches/bieri_gui/generic_fns/grace.py (original)
+++ branches/bieri_gui/generic_fns/grace.py Wed May 19 01:01:07 2010
@@ -35,7 +35,7 @@
from relax_errors import RelaxError, RelaxNoSequenceError, RelaxNoSimError
from relax_io import get_file_path, open_write_file, test_binary
from relax_warnings import RelaxWarning
-from specific_fns.setup import get_specific_fn
+import specific_fns
def determine_seq_type(spin_id=None):
@@ -89,8 +89,8 @@
data_list = False
# Specific x and y value returning functions.
- x_return_value = y_return_value = get_specific_fn('return_value',
pipes.get_type())
- x_return_conversion_factor = y_return_conversion_factor =
get_specific_fn('return_conversion_factor', pipes.get_type())
+ x_return_value = y_return_value =
specific_fns.setup.get_specific_fn('return_value', pipes.get_type())
+ x_return_conversion_factor = y_return_conversion_factor =
specific_fns.setup.get_specific_fn('return_conversion_factor',
pipes.get_type())
# Test if the X-axis data type is a minimisation statistic.
if x_data_type != 'spin' and
generic_fns.minimise.return_data_name(x_data_type):
@@ -474,8 +474,8 @@
analysis_spec = True
# Specific value and error, conversion factor, and units
returning functions.
- return_units = get_specific_fn('return_units', pipes.get_type())
- return_grace_string = get_specific_fn('return_grace_string',
pipes.get_type())
+ return_units =
specific_fns.setup.get_specific_fn('return_units', pipes.get_type())
+ return_grace_string =
specific_fns.setup.get_specific_fn('return_grace_string', pipes.get_type())
# Test if the axis data type is a minimisation statistic.
if data_type[i] and data_type[i] != 'spin' and
generic_fns.minimise.return_data_name(data_type[i]):
@@ -598,5 +598,5 @@
file.write("@ s%i line color %s\n" % (i, set_colours[i]))
# Legend.
- if set_names:
+ if set_names and set_names[i]:
file.write("@ s%i legend \"%s\"\n" % (i, set_names[i]))
Modified: branches/bieri_gui/generic_fns/structure/geometric.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/generic_fns/structure/geometric.py?rev=11190&r1=11189&r2=11190&view=diff
==============================================================================
--- branches/bieri_gui/generic_fns/structure/geometric.py (original)
+++ branches/bieri_gui/generic_fns/structure/geometric.py Wed May 19 01:01:07
2010
@@ -1062,7 +1062,7 @@
@keyword distribution: The type of point distribution to use. This can
be 'uniform' or 'regular'.
@type distribution: str
@return: The distribution of vectors on a sphere.
- @rtype: list of rank-1, 3D numpy arrays, array of float,
array of float
+ @rtype: list of rank-1, 3D numpy arrays
"""
# Get the polar and azimuthal angles for the distribution.
Modified: branches/bieri_gui/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/specific_fns/n_state_model.py?rev=11190&r1=11189&r2=11190&view=diff
==============================================================================
--- branches/bieri_gui/specific_fns/n_state_model.py (original)
+++ branches/bieri_gui/specific_fns/n_state_model.py Wed May 19 01:01:07 2010
@@ -48,7 +48,7 @@
from maths_fns.potential import quad_pot
from maths_fns.rotation_matrix import two_vect_to_R, euler_to_R_zyz
from physical_constants import dipolar_constant, g1H, pcs_constant,
return_gyromagnetic_ratio
-from relax_errors import RelaxError, RelaxInfError, RelaxModelError,
RelaxNaNError, RelaxNoModelError, RelaxNoTensorError
+from relax_errors import RelaxError, RelaxInfError, RelaxModelError,
RelaxNaNError, RelaxNoModelError, RelaxNoTensorError, RelaxNoValueError,
RelaxProtonTypeError, RelaxSpinTypeError
from relax_io import open_write_file
from relax_warnings import RelaxWarning, RelaxDeselectWarning
@@ -888,6 +888,14 @@
else:
unit_vect.append(vect)
+ # Checks.
+ if not hasattr(spin, 'heteronuc_type'):
+ raise RelaxSpinTypeError
+ if not hasattr(spin, 'proton_type'):
+ raise RelaxProtonTypeError
+ if not hasattr(spin, 'r'):
+ raise RelaxNoValueError("bond length")
+
# Gyromagnetic ratios.
gx = return_gyromagnetic_ratio(spin.heteronuc_type)
gh = return_gyromagnetic_ratio(spin.proton_type)
@@ -907,6 +915,10 @@
# Check.
if unit_vect[i] != None and len(unit_vect[i]) != num:
raise RelaxError, "The number of bond vectors for all spins
do no match:\n%s" % unit_vect
+
+ # Missing unit vectors.
+ if num == None:
+ raise RelaxError, "No bond vectors could be found."
# Update None entries.
for i in range(len(unit_vect)):
Modified: branches/bieri_gui/test_suite/system_tests/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/n_state_model.py?rev=11190&r1=11189&r2=11190&view=diff
==============================================================================
--- branches/bieri_gui/test_suite/system_tests/n_state_model.py (original)
+++ branches/bieri_gui/test_suite/system_tests/n_state_model.py Wed May 19
01:01:07 2010
@@ -266,6 +266,7 @@
self.assertAlmostEqual(cdp.align_tensors[0].Ayz, -0.00015125)
self.assertAlmostEqual(cdp.chi2, 23.5877482365) #
Pales: 23.709
self.assertAlmostEqual(cdp.q_rdc, 0.078460000413257444) #
Pales (Q Saupe): 0.079
+ self.assertAlmostEqual(cdp.q_rdc_norm2, 0.14049691097282743) #
Pales (Q RDC_RMS): 0.141
def test_lactose_n_state_fixed(self):
r11190 - in /branches/bieri_gui: ./ generic_fns/ generic_fns/structure/ specific_fns/ test_suite/system_tests/