Author: semor
Date: Thu Apr 3 04:18:35 2008
New Revision: 5249
URL: http://svn.gna.org/viewcvs/relax?rev=5249&view=rev
Log:
Merged revisions 5236,5238,5240,5247 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r5236 | bugman | 2008-03-27 06:32:40 -0400 (Thu, 27 Mar 2008) | 9 lines
Fix for bug #11378 (https://gna.org/bugs/?11378).
This bug was reported by Ryan Hoffman (https://gna.org/users/rydog).
The fix for the 1.3 line is very different to that for the 1.2 line. These
functions have changed
significantly, and the pdb() user function doesn't exist any more! The
concept is similar though.
The xh_vect variable is now set to None rather than being non-existant, and
the spin is deselected.
........
r5238 | bugman | 2008-03-28 04:44:20 -0400 (Fri, 28 Mar 2008) | 5 lines
Partially reverted r5236, the 'xh_vect' structure does not exist rather
than being set to None.
See the post by Seb at
https://mail.gna.org/public/relax-devel/2008-03/msg00008.html.
........
r5240 | bugman | 2008-03-28 05:06:06 -0400 (Fri, 28 Mar 2008) | 7 lines
Fix for bug #11383 (https://gna.org/bugs/?11383).
This was reported by Ryan Hoffman (https://gna.org/users/rydog).
The relax_data.display() user function is now functional again.
........
r5247 | semor | 2008-04-02 21:59:22 -0400 (Wed, 02 Apr 2008) | 3 lines
Changes to the jw_mapping and model-free codes to reflect the model-free
changes of r5220...
........
Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/generic_fns/structure.py
branches/consistency_tests_1.3/generic_fns/value.py
branches/consistency_tests_1.3/specific_fns/relax_data.py
branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py
Propchange: branches/consistency_tests_1.3/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Apr 3 04:18:35 2008
@@ -1,1 +1,1 @@
-/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433,4440-4461,4473,4476-4493,4523-4551,4567-4577,4579,4585-4586,4618-4623,4659,4662-4693,4698-4759,4778-4792,4796-4839,4841-4850,4854-4888,4898-5047,5056-5115,5117-5233
+/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433,4440-4461,4473,4476-4493,4523-4551,4567-4577,4579,4585-4586,4618-4623,4659,4662-4693,4698-4759,4778-4792,4796-4839,4841-4850,4854-4888,4898-5047,5056-5115,5117-5233,5236-5247
Modified: branches/consistency_tests_1.3/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/structure.py?rev=5249&r1=5248&r2=5249&view=diff
==============================================================================
--- branches/consistency_tests_1.3/generic_fns/structure.py (original)
+++ branches/consistency_tests_1.3/generic_fns/structure.py Thu Apr 3
04:18:35 2008
@@ -1224,9 +1224,11 @@
# Calculate the vector.
vector = xh_vector(spin)
- # Set the vector.
+ # Set the vector and deselect the spin if the vector doesn't exist.
if vector != None:
- spin.xh_vect = vector
+ spin.xh_vect = vector
+ else:
+ spin.select = False
def uniform_vect_dist_spherical_angles(inc=20):
Modified: branches/consistency_tests_1.3/generic_fns/value.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/generic_fns/value.py?rev=5249&r1=5248&r2=5249&view=diff
==============================================================================
--- branches/consistency_tests_1.3/generic_fns/value.py (original)
+++ branches/consistency_tests_1.3/generic_fns/value.py Thu Apr 3 04:18:35
2008
@@ -583,13 +583,13 @@
file.close()
- def write_data(self, file, return_value=None):
+ def write_data(self, run=None, param=None, file=None, return_value=None):
"""Function for writing data."""
# Get the value and error returning function if required.
if not return_value:
# Function type.
- self.function_type =
relax_data_store.run_types[relax_data_store.run_names.index(self.run)]
+ self.function_type =
relax_data_store.run_types[relax_data_store.run_names.index(run)]
# Specific value and error returning function.
return_value = self.relax.specific_setup.setup('return_value',
self.function_type)
@@ -598,12 +598,12 @@
file.write("%-5s%-6s%-30s%-30s\n" % ('Num', 'Name', 'Value',
'Error'))
# Loop over the sequence.
- for i in xrange(len(relax_data_store.res[self.run])):
- # Remap the data structure 'relax_data_store.res[self.run][i]'.
- data = relax_data_store.res[self.run][i]
+ for i in xrange(len(relax_data_store.res[run])):
+ # Remap the data structure 'relax_data_store.res[run][i]'.
+ data = relax_data_store.res[run][i]
# Get the value and error.
- value, error = return_value(self.run, i, self.param)
+ value, error = return_value(run, i, param)
# Write the data.
file.write("%-5i%-6s%-30s%-30s\n" % (data.num, data.name,
`value`, `error`))
Modified: branches/consistency_tests_1.3/specific_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/specific_fns/relax_data.py?rev=5249&r1=5248&r2=5249&view=diff
==============================================================================
--- branches/consistency_tests_1.3/specific_fns/relax_data.py (original)
+++ branches/consistency_tests_1.3/specific_fns/relax_data.py Thu Apr 3
04:18:35 2008
@@ -477,7 +477,7 @@
raise RelaxNoRiError, (self.ri_label, self.frq_label)
# Print the data.
- self.relax.generic.value.write_data(self.run, (self.ri_label,
self.frq_label), sys.stdout, return_value=self.return_value)
+ self.relax.generic.value.write_data(run=self.run,
param=(self.ri_label, self.frq_label), file=sys.stdout,
return_value=self.return_value)
def find_index(self, data, ri_label, frq_label):
Modified:
branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py?rev=5249&r1=5248&r2=5249&view=diff
==============================================================================
---
branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py
(original)
+++
branches/consistency_tests_1.3/test_suite/unit_tests/value_testing_base.py
Thu Apr 3 04:18:35 2008
@@ -3116,7 +3116,7 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].csa, -160e-6)
- def test_set_jw_all_spins_nucleus(self):
+ def test_set_jw_all_spins_heteronucleus(self):
"""Set the RSDM heteronucleus type for all spins.
The functions tested are both generic_fns.value.set() and
prompt.value.set().
@@ -3272,7 +3272,7 @@
self.assertAlmostEqual(cdp.mol[0].res[1].spin[0].csa, -172e-6)
- def test_set_jw_defaults_nucleus(self):
+ def test_set_jw_defaults_heteronucleus(self):
"""Set the RSDM heteronucleus type to the default value.
The functions tested are both generic_fns.value.set() and
prompt.value.set().
@@ -3408,7 +3408,7 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].csa, -160e-6)
- def test_set_jw_single_spin_nucleus(self):
+ def test_set_jw_single_spin_heteronucleus(self):
"""Set the RSDM heteronucleus type for a single spin.
The functions tested are both generic_fns.value.set() and
prompt.value.set().
@@ -3682,7 +3682,7 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].csa, -172e-6)
- def test_set_mf_all_spins_nucleus(self):
+ def test_set_mf_all_spins_heteronucleus(self):
"""Set the model-free heteronucleus type for all spins.
The functions tested are both generic_fns.value.set() and
prompt.value.set().
@@ -3946,7 +3946,7 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].csa, -172 * 1e-6)
- def test_set_mf_defaults_nucleus(self):
+ def test_set_mf_defaults_heteronucleus(self):
"""Set the model-free heteronucleus type to the default value.
The functions tested are both generic_fns.value.set() and
prompt.value.set().
@@ -4188,7 +4188,7 @@
self.assertEqual(cdp.mol[0].res[1].spin[0].csa, -172e-6)
- def test_set_mf_single_spin_nucleus(self):
+ def test_set_mf_single_spin_heteronucleus(self):
"""Set the model-free heteronucleus type for a single spin.
The functions tested are both generic_fns.value.set() and
prompt.value.set().
r5249 - in /branches/consistency_tests_1.3: ./ generic_fns/ specific_fns/ test_suite/unit_tests/