Author: bugman
Date: Sat Mar 23 09:06:15 2013
New Revision: 19035
URL: http://svn.gna.org/viewcvs/relax?rev=19035&view=rev
Log:
Renamed the lib.nmr package to lib.alignment.
Added:
trunk/lib/alignment/
- copied from r19029, trunk/lib/nmr/
trunk/test_suite/unit_tests/_lib/_alignment/
- copied from r19029, trunk/test_suite/unit_tests/_lib/_nmr/
Removed:
trunk/lib/nmr/
trunk/test_suite/unit_tests/_lib/_nmr/
Modified:
trunk/generic_fns/pcs.py
trunk/generic_fns/rdc.py
trunk/lib/__init__.py
trunk/target_functions/frame_order/__init__.py
trunk/target_functions/n_state_model.py
trunk/test_suite/unit_tests/_lib/__init__.py
trunk/test_suite/unit_tests/_lib/_alignment/test___init__.py
Modified: trunk/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/pcs.py?rev=19035&r1=19034&r2=19035&view=diff
==============================================================================
--- trunk/generic_fns/pcs.py (original)
+++ trunk/generic_fns/pcs.py Sat Mar 23 09:06:15 2013
@@ -35,7 +35,7 @@
from generic_fns import grace, pipes
from generic_fns.align_tensor import get_tensor_index
from generic_fns.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_index_loop, spin_loop
-from lib.nmr.pcs import ave_pcs_tensor, pcs_tensor
+from lib.alignment.pcs import ave_pcs_tensor, pcs_tensor
from lib.geometry.vectors import random_unit_vector
from lib.physical_constants import g1H, pcs_constant
from lib.errors import RelaxError, RelaxAlignError, RelaxNoAlignError,
RelaxNoPdbError, RelaxNoPCSError, RelaxNoSequenceError, RelaxPCSError
Modified: trunk/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/rdc.py?rev=19035&r1=19034&r2=19035&view=diff
==============================================================================
--- trunk/generic_fns/rdc.py (original)
+++ trunk/generic_fns/rdc.py Sat Mar 23 09:06:15 2013
@@ -37,7 +37,7 @@
from generic_fns.align_tensor import get_tensor_index
from generic_fns.interatomic import consistent_interatomic_data,
create_interatom, interatomic_loop, return_interatom
from generic_fns.mol_res_spin import exists_mol_res_spin_data, return_spin
-from lib.nmr.rdc import ave_rdc_tensor
+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.io import extract_data, open_write_file, write_data
Modified: trunk/lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/__init__.py?rev=19035&r1=19034&r2=19035&view=diff
==============================================================================
--- trunk/lib/__init__.py (original)
+++ trunk/lib/__init__.py Sat Mar 23 09:06:15 2013
@@ -23,12 +23,12 @@
"""The relax-lib package - a collection of functions, objects, and methods
for the study of dynamics."""
__all__ = [
+ 'alignment',
'ansi',
'errors',
'float',
'geometry',
'io',
- 'nmr',
'physical_constants',
'structure',
'text',
Modified: trunk/target_functions/frame_order/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/frame_order/__init__.py?rev=19035&r1=19034&r2=19035&view=diff
==============================================================================
--- trunk/target_functions/frame_order/__init__.py (original)
+++ trunk/target_functions/frame_order/__init__.py Sat Mar 23 09:06:15 2013
@@ -32,7 +32,7 @@
from lib.float import isNaN
from generic_fns.frame_order import print_frame_order_2nd_degree
from extern.sobol.sobol_lib import i4_sobol
-from lib.nmr.alignment_tensor import to_5D, to_tensor
+from lib.alignment.alignment_tensor import to_5D, to_tensor
from target_functions.chi2 import chi2
from target_functions.coord_transform import spherical_to_cartesian
from target_functions.frame_order.matrix_ops import Data,
reduce_alignment_tensor
@@ -46,9 +46,9 @@
from target_functions.frame_order.pseudo_ellipse_torsionless import
compile_2nd_matrix_pseudo_ellipse_torsionless,
pcs_numeric_int_pseudo_ellipse_torsionless,
pcs_numeric_int_pseudo_ellipse_torsionless_qrint
from target_functions.kronecker_product import kron_prod
from target_functions import order_parameters
-from lib.nmr.pcs import pcs_tensor
+from lib.alignment.pcs import pcs_tensor
from lib.geometry.rotations import euler_to_R_zyz, two_vect_to_R
-from lib.nmr.rdc import rdc_tensor
+from lib.alignment.rdc import rdc_tensor
from lib.physical_constants import pcs_constant
from lib.errors import RelaxError
Modified: trunk/target_functions/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/n_state_model.py?rev=19035&r1=19034&r2=19035&view=diff
==============================================================================
--- trunk/target_functions/n_state_model.py (original)
+++ trunk/target_functions/n_state_model.py Sat Mar 23 09:06:15 2013
@@ -25,12 +25,12 @@
# relax module imports.
from lib.float import isNaN
-from lib.nmr.alignment_tensor import dAi_dAxx, dAi_dAyy, dAi_dAxy, dAi_dAxz,
dAi_dAyz, to_tensor
+from lib.alignment.alignment_tensor import dAi_dAxx, dAi_dAyy, dAi_dAxy,
dAi_dAxz, dAi_dAyz, to_tensor
from target_functions.chi2 import chi2, dchi2_element, d2chi2_element
from target_functions.paramag_centre import vectors_single_centre,
vectors_centre_per_state
-from lib.nmr.pcs import ave_pcs_tensor, ave_pcs_tensor_ddeltaij_dAmn,
ave_pcs_tensor_ddeltaij_dc, pcs_constant_grad, pcs_tensor
+from lib.alignment.pcs import ave_pcs_tensor, ave_pcs_tensor_ddeltaij_dAmn,
ave_pcs_tensor_ddeltaij_dc, pcs_constant_grad, pcs_tensor
from lib.geometry.rotations import euler_to_R_zyz
-from lib.nmr.rdc import ave_rdc_tensor, ave_rdc_tensor_dDij_dAmn, rdc_tensor
+from lib.alignment.rdc import ave_rdc_tensor, ave_rdc_tensor_dDij_dAmn,
rdc_tensor
from lib.physical_constants import pcs_constant
from lib.errors import RelaxError, RelaxImplementError
Modified: trunk/test_suite/unit_tests/_lib/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/__init__.py?rev=19035&r1=19034&r2=19035&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_lib/__init__.py (original)
+++ trunk/test_suite/unit_tests/_lib/__init__.py Sat Mar 23 09:06:15 2013
@@ -21,6 +21,7 @@
__all__ = [
+ '_alignment'
'_geometry'
'_text'
'test_float',
Modified: trunk/test_suite/unit_tests/_lib/_alignment/test___init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/test_suite/unit_tests/_lib/_alignment/test___init__.py?rev=19035&r1=19029&r2=19035&view=diff
==============================================================================
--- trunk/test_suite/unit_tests/_lib/_alignment/test___init__.py (original)
+++ trunk/test_suite/unit_tests/_lib/_alignment/test___init__.py Sat Mar 23
09:06:15 2013
@@ -29,11 +29,11 @@
class Test___init__(PackageTestCase):
- """Unit tests for the lib.nmr package."""
+ """Unit tests for the lib.alignment package."""
def setUp(self):
"""Set up for the package checking."""
- self.package = lib.nmr
- self.package_name = 'lib.nmr'
+ self.package = lib.alignment
+ self.package_name = 'lib.alignment'
self.package_path = sys.path[0] + sep + 'lib' + sep + 'nmr'
r19035 - in /trunk: generic_fns/ lib/ lib/alignment/ lib/nmr/ target_functions/ target_functions/frame_order/ test_suite/uni...