Author: bugman
Date: Fri Dec 14 17:55:14 2012
New Revision: 18143
URL: http://svn.gna.org/viewcvs/relax?rev=18143&view=rev
Log:
Merged revisions 18138,18140-18142 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r18138 | bugman | 2012-12-14 16:45:06 +0100 (Fri, 14 Dec 2012) | 5 lines
The RelaxErrors when calling user functions in the prompt/script interface
are now more informative.
The user function is now stated. This is to better help the user work out
where the problem is.
........
r18140 | bugman | 2012-12-14 17:11:08 +0100 (Fri, 14 Dec 2012) | 3 lines
Created the Rdc.test_rdc_copy system test to demonstrate the failure of the
rdc.copy user function.
........
r18141 | bugman | 2012-12-14 17:35:35 +0100 (Fri, 14 Dec 2012) | 6 lines
Bug fix for the rdc.copy user function - it is now functional.
The code was old and untested, and still assumed that the RDC values were
held in spin containers
rather than the interatomic data containers.
........
r18142 | bugman | 2012-12-14 17:51:48 +0100 (Fri, 14 Dec 2012) | 5 lines
Created the Pcs.test_pcs_load and Pcs.test_pcs_copy system tests to check
some of the PCS user functions.
The Pcs system test class is new, and these tests check untested areas of
relax.
........
Added:
branches/frame_order_testing/test_suite/system_tests/pcs.py
- copied unchanged from r18142, trunk/test_suite/system_tests/pcs.py
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/generic_fns/rdc.py
branches/frame_order_testing/prompt/uf_objects.py
branches/frame_order_testing/test_suite/system_tests/__init__.py
branches/frame_order_testing/test_suite/system_tests/rdc.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Dec 14 17:55:14 2012
@@ -1,1 +1,1 @@
-/trunk:1-18136
+/trunk:1-18142
Modified: branches/frame_order_testing/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/generic_fns/rdc.py?rev=18143&r1=18142&r2=18143&view=diff
==============================================================================
--- branches/frame_order_testing/generic_fns/rdc.py (original)
+++ branches/frame_order_testing/generic_fns/rdc.py Fri Dec 14 17:55:14 2012
@@ -221,27 +221,27 @@
if align_id in dp_from.rdc_ids and align_id not in dp_to.rdc_ids:
dp_to.rdc_ids.append(align_id)
- # Spin loop.
- for mol_index, res_index, spin_index in spin_index_loop():
- # Alias the spin containers.
- spin_from =
dp_from.mol[mol_index].res[res_index].spin[spin_index]
- spin_to = dp_to.mol[mol_index].res[res_index].spin[spin_index]
+ # Loop over the interatomic data.
+ for i in range(len(dp_from.interatomic)):
+ # Alias the containers.
+ interatom_from = dp_from.interatomic[i]
+ interatom_to = dp_to.interatomic[i]
# No data or errors.
- if (not hasattr(spin_from, 'rdc') or not align_id in
spin_from.rdc) and (not hasattr(spin_from, 'rdc_err') or not align_id in
spin_from.rdc_err):
+ if (not hasattr(interatom_from, 'rdc') or not align_id in
interatom_from.rdc) and (not hasattr(interatom_from, 'rdc_err') or not
align_id in interatom_from.rdc_err):
continue
- # Initialise the spin data if necessary.
- if hasattr(spin_from, 'rdc') and not hasattr(spin_to, 'rdc'):
- spin_to.rdc = {}
- if hasattr(spin_from, 'rdc_err') and not hasattr(spin_to,
'rdc_err'):
- spin_to.rdc_err = {}
+ # Initialise the data structures if necessary.
+ if hasattr(interatom_from, 'rdc') and not hasattr(interatom_to,
'rdc'):
+ interatom_to.rdc = {}
+ if hasattr(interatom_from, 'rdc_err') and not
hasattr(interatom_to, 'rdc_err'):
+ interatom_to.rdc_err = {}
# Copy the value and error from pipe_from.
- if hasattr(spin_from, 'rdc'):
- spin_to.rdc[align_id] = spin_from.rdc[align_id]
- if hasattr(spin_from, 'rdc_err'):
- spin_to.rdc_err[align_id] = spin_from.rdc_err[align_id]
+ if hasattr(interatom_from, 'rdc'):
+ interatom_to.rdc[align_id] = interatom_from.rdc[align_id]
+ if hasattr(interatom_from, 'rdc_err'):
+ interatom_to.rdc_err[align_id] =
interatom_from.rdc_err[align_id]
def corr_plot(format=None, file=None, dir=None, force=False):
Modified: branches/frame_order_testing/prompt/uf_objects.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/prompt/uf_objects.py?rev=18143&r1=18142&r2=18143&view=diff
==============================================================================
--- branches/frame_order_testing/prompt/uf_objects.py (original)
+++ branches/frame_order_testing/prompt/uf_objects.py Fri Dec 14 17:55:14 2012
@@ -118,7 +118,7 @@
for name in keys:
# Unknown keyword.
if name not in self._karg_names:
- raise RelaxError("The keyword argument '%s' is unknown." %
name)
+ raise RelaxError("User function %s - the keyword argument
'%s' is unknown." % (self._name, name))
# Convert the args to keyword args if needed.
num_args = len(uf_args)
@@ -127,7 +127,7 @@
for i in range(num_args):
# Check if the keyword is already assigned.
if self._kargs[i]['name'] in keys:
- raise RelaxError("The argument '%s' and the keyword
argument '%s' cannot both be supplied." % (uf_args[i],
self._kargs[i]['name']))
+ raise RelaxError("User function %s - the argument '%s'
and the keyword argument '%s' cannot both be supplied." % (self._name,
uf_args[i], self._kargs[i]['name']))
# Add the arg as a keyword arg.
uf_kargs[self._kargs[i]['name']] = uf_args[i]
@@ -213,7 +213,7 @@
elif py_type == 'val_or_list':
arg_check.is_val_or_list(value, desc_short, size=dim,
can_be_none=can_be_none, can_be_empty=can_be_empty)
else:
- raise RelaxError("The Python object type '%s' is unknown." %
py_type)
+ raise RelaxError("User function %s - the Python object type
'%s' is unknown." % (self._name, py_type))
# Execute the functional code.
self._backend(*new_args, **uf_kargs)
Modified: branches/frame_order_testing/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/__init__.py?rev=18143&r1=18142&r2=18143&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/__init__.py
(original)
+++ branches/frame_order_testing/test_suite/system_tests/__init__.py Fri Dec
14 17:55:14 2012
@@ -52,6 +52,7 @@
from test_suite.system_tests.noe import Noe
from test_suite.system_tests.noe_restraints import Noe_restraints
from test_suite.system_tests.palmer import Palmer
+from test_suite.system_tests.pcs import Pcs
from test_suite.system_tests.peak_lists import Peak_lists
from test_suite.system_tests.pipes import Pipes
from test_suite.system_tests.rdc import Rdc
@@ -84,6 +85,7 @@
'noe',
'noe_restraints',
'palmer',
+ 'pcs'
'peak_lists'
'pipes',
'rdc',
@@ -170,6 +172,7 @@
suite_array.append(TestLoader().loadTestsFromTestCase(Noe))
suite_array.append(TestLoader().loadTestsFromTestCase(Noe_restraints))
suite_array.append(TestLoader().loadTestsFromTestCase(Palmer))
+ suite_array.append(TestLoader().loadTestsFromTestCase(Pcs))
suite_array.append(TestLoader().loadTestsFromTestCase(Peak_lists))
suite_array.append(TestLoader().loadTestsFromTestCase(Pipes))
suite_array.append(TestLoader().loadTestsFromTestCase(Rdc))
Modified: branches/frame_order_testing/test_suite/system_tests/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/rdc.py?rev=18143&r1=18142&r2=18143&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/rdc.py (original)
+++ branches/frame_order_testing/test_suite/system_tests/rdc.py Fri Dec 14
17:55:14 2012
@@ -36,6 +36,46 @@
class Rdc(SystemTestCase):
"""Class for testing RDC operations."""
+ def test_rdc_copy(self):
+ """Test the operation of the rdc.copy user function."""
+
+ # Create a data pipe.
+ self.interpreter.pipe.create('orig', 'N-state')
+
+ # Data directory.
+ dir = status.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'align_data'+sep
+
+ # Load the spins.
+ self.interpreter.sequence.read(file='tb.txt', dir=dir, spin_id_col=1)
+ self.interpreter.sequence.attach_protons()
+ self.interpreter.sequence.display()
+
+ # Load the RDCs.
+ self.interpreter.rdc.read(align_id='tb', file='tb.txt', dir=dir,
spin_id1_col=1, spin_id2_col=2, data_col=3, error_col=4)
+ self.interpreter.sequence.display()
+
+ # The RDCs.
+ rdcs = [ -26.2501958629, 9.93081766942, 7.26317614156,
-1.24840526981, 5.31803314334, 14.0362909456, 1.33652530397, -1.6021670281]
+
+ # Create a new data pipe by copying the old, then switch to it.
+ self.interpreter.pipe.copy(pipe_from='orig', pipe_to='new')
+ self.interpreter.pipe.switch(pipe_name='new')
+
+ # Delete the RDC data.
+ self.interpreter.rdc.delete()
+
+ # Copy the RDCs.
+ self.interpreter.rdc.copy(pipe_from='orig', align_id='tb')
+
+ # Checks.
+ self.assertEqual(count_spins(), 16)
+ self.assertEqual(len(cdp.interatomic), 8)
+ i = 0
+ for interatom in interatomic_loop():
+ self.assertAlmostEqual(rdcs[i], interatom.rdc['tb'])
+ i += 1
+
+
def test_rdc_load(self):
"""Test for the loading of some RDC data with the spin ID format."""
@@ -64,4 +104,3 @@
for interatom in interatomic_loop():
self.assertAlmostEqual(rdcs[i], interatom.rdc['tb'])
i += 1
-
r18143 - in /branches/frame_order_testing: ./ generic_fns/ prompt/ test_suite/system_tests/