Author: bugman
Date: Fri Jun 14 18:12:29 2013
New Revision: 20128
URL: http://svn.gna.org/viewcvs/relax?rev=20128&view=rev
Log:
Merged revisions 20125-20127 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r20125 | bugman | 2013-06-14 18:05:28 +0200 (Fri, 14 Jun 2013) | 3 lines
Added the j_coupling module to the pipe_control __all__ list.
........
r20126 | bugman | 2013-06-14 18:07:44 +0200 (Fri, 14 Jun 2013) | 5 lines
Fix for the pipe_control.rdc.q_factors() for T = J+D type data.
The Q factor normalisation was incorrect, as the J coupling should be
subtracted from T first.
........
r20127 | bugman | 2013-06-14 18:12:11 +0200 (Fri, 14 Jun 2013) | 5 lines
Unit test fixes for the N-state model.
This is needed due to the recent package rearrangements.
........
Modified:
branches/relax_disp/ (props changed)
branches/relax_disp/pipe_control/__init__.py
branches/relax_disp/pipe_control/rdc.py
branches/relax_disp/test_suite/unit_tests/_specific_analyses/test_n_state_model.py
Propchange: branches/relax_disp/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Fri Jun 14 18:12:29 2013
@@ -1,1 +1,1 @@
-/trunk:1-20123
+/trunk:1-20127
Modified: branches/relax_disp/pipe_control/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/__init__.py?rev=20128&r1=20127&r2=20128&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/__init__.py (original)
+++ branches/relax_disp/pipe_control/__init__.py Fri Jun 14 18:12:29 2013
@@ -35,6 +35,7 @@
'fix',
'grace',
'interatomic',
+ 'j_coupling',
'minimise',
'model_selection',
'mol_res_spin',
Modified: branches/relax_disp/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/rdc.py?rev=20128&r1=20127&r2=20128&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/rdc.py (original)
+++ branches/relax_disp/pipe_control/rdc.py Fri Jun 14 18:12:29 2013
@@ -39,7 +39,7 @@
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin
from lib.alignment.rdc import ave_rdc_tensor
from lib.physical_constants import dipolar_constant,
return_gyromagnetic_ratio
-from lib.errors import RelaxError, RelaxNoAlignError, RelaxNoRDCError,
RelaxNoSequenceError, RelaxSpinTypeError
+from lib.errors import RelaxError, RelaxNoAlignError, RelaxNoJError,
RelaxNoRDCError, RelaxNoSequenceError, RelaxSpinTypeError
from lib.io import extract_data, open_write_file, strip, write_data
from lib.warnings import RelaxWarning
@@ -468,6 +468,11 @@
rdc_data = True
if hasattr(interatom, 'rdc_bc') and align_id in interatom.rdc_bc:
rdc_bc_data = True
+ j_flag = True
+ if align_id in cdp.rdc_data_types and
cdp.rdc_data_types[align_id] == 'T':
+ j_flag = True
+ if not hasattr(interatom, 'j_coupling'):
+ raise RelaxNoJError
# Skip containers without RDC data.
if not hasattr(interatom, 'rdc') or not hasattr(interatom,
'rdc_bc') or not align_id in interatom.rdc or interatom.rdc[align_id] == None
or not align_id in interatom.rdc_bc or interatom.rdc_bc[align_id] == None:
@@ -481,7 +486,10 @@
sse = sse + (interatom.rdc[align_id] -
interatom.rdc_bc[align_id])**2
# Sum the RDCs squared (for one type of normalisation).
- D2_sum = D2_sum + interatom.rdc[align_id]**2
+ if j_flag:
+ D2_sum = D2_sum + (interatom.rdc[align_id] -
interatom.j_coupling)**2
+ else:
+ D2_sum = D2_sum + interatom.rdc[align_id]**2
# Gyromagnetic ratios.
g1 = return_gyromagnetic_ratio(spin1.isotope)
Modified:
branches/relax_disp/test_suite/unit_tests/_specific_analyses/test_n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/test_suite/unit_tests/_specific_analyses/test_n_state_model.py?rev=20128&r1=20127&r2=20128&view=diff
==============================================================================
---
branches/relax_disp/test_suite/unit_tests/_specific_analyses/test_n_state_model.py
(original)
+++
branches/relax_disp/test_suite/unit_tests/_specific_analyses/test_n_state_model.py
Fri Jun 14 18:12:29 2013
@@ -24,7 +24,7 @@
from unittest import TestCase
# relax module imports.
-from specific_analyses import n_state_model
+from specific_analyses.n_state_model import parameters
from test_suite.unit_tests.n_state_model_testing_base import
N_state_model_base_class
@@ -32,11 +32,11 @@
"""Unit tests for the functions of the 'specific_analyses.n_state_model'
module."""
# Place the specific_analyses.n_state_model module into the class
namespace.
- n_state_model_fns = n_state_model.N_state_model()
+ n_state_model_fns = parameters
- def test__assemble_param_vector(self):
- """Test the operation of the
specific_analyses.n_state_model._assemble_param_vector() method."""
+ def test_assemble_param_vector(self):
+ """Test the operation of the
specific_analyses.n_state_model.parameters.assemble_param_vector() method."""
# Set up the N, probabilities and Euler angles.
cdp.N = 3
@@ -50,7 +50,7 @@
cdp.align_tensors = None
# Get the parameter vector.
- param_vector = self.n_state_model_fns._assemble_param_vector()
+ param_vector = self.n_state_model_fns.assemble_param_vector()
# The correct result.
vector_true = [0.1, 0.3, 0.0, pi/2, 1.0, pi/2, pi, 3*pi/2, pi,
3*pi/2, 2*pi]
@@ -61,8 +61,8 @@
self.assertEqual(param_vector[i], vector_true[i])
- def test__disassemble_param_vector(self):
- """Test the operation of the
specific_analyses.n_state_model._disassemble_param_vector() method."""
+ def test_disassemble_param_vector(self):
+ """Test the operation of the
specific_analyses.n_state_model.parameters.disassemble_param_vector()
method."""
# Set up the initial N, probabilities and Euler angles.
cdp.N = 3
@@ -76,7 +76,7 @@
param_vector = [0.1, 0.3, 0.0, pi/2, 1.0, pi/2, pi, 3*pi/2, pi,
3*pi/2, 2*pi]
# Disassemble the parameter vector.
- self.n_state_model_fns._disassemble_param_vector(param_vector,
data_types=['tensor'])
+ self.n_state_model_fns.disassemble_param_vector(param_vector,
data_types=['tensor'])
# Check the probabilities.
self.assertEqual(cdp.probs, [0.1, 0.3, 0.6])
r20128 - in /branches/relax_disp: ./ pipe_control/ test_suite/unit_tests/_specific_analyses/