Author: bugman
Date: Wed Mar 4 11:39:09 2009
New Revision: 8899
URL: http://svn.gna.org/viewcvs/relax?rev=8899&view=rev
Log:
Merged revisions 8893-8898 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8893 | bugman | 2009-02-27 18:58:24 +0100 (Fri, 27 Feb 2009) | 3 lines
The diagonalised alignment tensor is now being created (and is being done
correctly).
........
r8894 | bugman | 2009-03-02 17:26:48 +0100 (Mon, 02 Mar 2009) | 5 lines
Fix for the calc_tensor_diag() function.
The algorithm for finding Ayy was broken.
........
r8895 | bugman | 2009-03-02 17:34:06 +0100 (Mon, 02 Mar 2009) | 5 lines
Fix for the test_name_argfail_mol_id() unit test.
The mol_id can be None, i.e. for naming unnamed molecules.
........
r8896 | bugman | 2009-03-02 17:35:33 +0100 (Mon, 02 Mar 2009) | 3 lines
Fixed the check for None in molecule.name().
........
r8897 | bugman | 2009-03-02 17:42:04 +0100 (Mon, 02 Mar 2009) | 5 lines
Allowed the spin_num arg of spin.create() to be None.
This is useful for polymers where the name is important rather than number.
........
r8898 | bugman | 2009-03-04 10:32:28 +0100 (Wed, 04 Mar 2009) | 3 lines
Fix for the test_create_argfail_spin_num() unit test.
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/data/align_tensor.py
branches/bmrb/prompt/molecule.py
branches/bmrb/prompt/spin.py
branches/bmrb/test_suite/unit_tests/_prompt/test_molecule.py
branches/bmrb/test_suite/unit_tests/_prompt/test_spin.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Mar 4 11:39:09 2009
@@ -1,1 +1,1 @@
-/1.3:1-8881
+/1.3:1-8898
Modified: branches/bmrb/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/data/align_tensor.py?rev=8899&r1=8898&r2=8899&view=diff
==============================================================================
--- branches/bmrb/data/align_tensor.py (original)
+++ branches/bmrb/data/align_tensor.py Wed Mar 4 11:39:09 2009
@@ -24,6 +24,7 @@
from re import search
from math import cos, sin
from numpy import dot, float64, identity, transpose, zeros
+from numpy.linalg import eigvals
from types import ListType
# relax module imports.
@@ -505,8 +506,8 @@
return tensor
-def calc_tensor_diag(rotation, tensor):
- """Function for calculating the diagonalised alignment tensor.
+def calc_tensor_diag(tensor):
+ """Calculate the diagonalised alignment tensor.
The diagonalised alignment tensor is defined as::
@@ -514,10 +515,8 @@
tensor = | 0 Ayy' 0 |.
| 0 0 Azz'|
- The diagonalised alignment tensor is calculated using the tensor and the
rotation matrix
- through the equation::
-
- R^T . tensor_diag . R.
+ The diagonalised alignment tensor is calculated by eigenvalue
decomposition.
+
@param rotation: The rotation matrix.
@type rotation: numpy array ((3, 3), float64)
@@ -527,8 +526,28 @@
@rtype: numpy array ((3, 3), float64)
"""
- # Rotation (R^T . tensor_diag . R).
- return dot(transpose(rotation), dot(tensor_diag, rotation))
+ # The eigenvalues.
+ vals = eigvals(tensor)
+
+ # Find the |x| < |y| < |z| indices.
+ abs_vals = abs(vals).tolist()
+ Axx_index = abs_vals.index(min(abs_vals))
+ Azz_index = abs_vals.index(max(abs_vals))
+ last_index = range(3)
+ last_index.pop(max(Axx_index, Azz_index))
+ last_index.pop(min(Axx_index, Azz_index))
+ Ayy_index = last_index[0]
+
+ # Empty tensor.
+ tensor_diag = zeros((3, 3), float64)
+
+ # Fill the elements.
+ tensor_diag[0, 0] = vals[Axx_index]
+ tensor_diag[1, 1] = vals[Ayy_index]
+ tensor_diag[2, 2] = vals[Azz_index]
+
+ # Return the tensor.
+ return tensor_diag
def dependency_generator():
@@ -561,10 +580,10 @@
yield ('Axx_unit', ['alpha', 'beta', 'gamma'],
['alpha', 'beta', 'gamma'])
yield ('Ayy_unit', ['alpha', 'beta', 'gamma'],
['alpha', 'beta', 'gamma'])
yield ('Azz_unit', ['alpha', 'beta'],
['alpha', 'beta'])
- yield ('tensor_diag', ['Axx', 'Ayy', 'Axy', 'Axz', 'Ayz'],
['tensor', 'rotation'])
yield ('rotation', ['alpha', 'beta', 'gamma'],
['Axx_unit', 'Ayy_unit', 'Azz_unit'])
yield ('tensor', ['Axx', 'Ayy', 'Axy', 'Axz', 'Ayz'],
['Axx', 'Ayy', 'Azz', 'Axy', 'Axz', 'Ayz'])
yield ('tensor_5D', ['Axx', 'Ayy', 'Axy', 'Axz', 'Ayz'],
['Axx', 'Ayy', 'Azz', 'Axy', 'Axz', 'Ayz'])
+ yield ('tensor_diag', ['Axx', 'Ayy', 'Axy', 'Axz', 'Ayz'],
['tensor'])
Modified: branches/bmrb/prompt/molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/molecule.py?rev=8899&r1=8898&r2=8899&view=diff
==============================================================================
--- branches/bmrb/prompt/molecule.py (original)
+++ branches/bmrb/prompt/molecule.py Wed Mar 4 11:39:09 2009
@@ -242,7 +242,7 @@
print text
# Residue identification string.
- if mol_id and type(mol_id) != str:
+ if mol_id != None and type(mol_id) != str:
raise RelaxNoneStrError, ('molecule identification string',
mol_id)
# New molecule name.
Modified: branches/bmrb/prompt/spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/prompt/spin.py?rev=8899&r1=8898&r2=8899&view=diff
==============================================================================
--- branches/bmrb/prompt/spin.py (original)
+++ branches/bmrb/prompt/spin.py Wed Mar 4 11:39:09 2009
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2008 Edward d'Auvergne
#
+# Copyright (C) 2007-2009 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -30,7 +30,7 @@
# relax module imports.
import help
from generic_fns.mol_res_spin import copy_spin, create_spin, delete_spin,
display_spin, id_string_doc, name_spin, number_spin
-from relax_errors import RelaxIntError, RelaxNoneIntError,
RelaxNoneStrError, RelaxStrError
+from relax_errors import RelaxNoneIntError, RelaxNoneStrError, RelaxStrError
class Spin:
@@ -157,8 +157,8 @@
print text
# Spin number.
- if type(spin_num) != int:
- raise RelaxIntError, ('spin number', spin_num)
+ if spin_num != None and type(spin_num) != int:
+ raise RelaxNoneIntError, ('spin number', spin_num)
# Spin name.
if spin_name != None and type(spin_name) != str:
Modified: branches/bmrb/test_suite/unit_tests/_prompt/test_molecule.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_prompt/test_molecule.py?rev=8899&r1=8898&r2=8899&view=diff
==============================================================================
--- branches/bmrb/test_suite/unit_tests/_prompt/test_molecule.py (original)
+++ branches/bmrb/test_suite/unit_tests/_prompt/test_molecule.py Wed Mar 4
11:39:09 2009
@@ -139,12 +139,12 @@
# Loop over the data types.
for data in DATA_TYPES:
- # Catch the str arguments, and skip them.
- if data[0] == 'str':
+ # Catch the None and str arguments, and skip them.
+ if data[0] == 'None' or data[0] == 'str':
continue
# The argument test.
- self.assertRaises(RelaxStrError, self.molecule_fns.name,
mol_id=data[1])
+ self.assertRaises(RelaxNoneStrError, self.molecule_fns.name,
mol_id=data[1])
def test_name_argfail_name(self):
Modified: branches/bmrb/test_suite/unit_tests/_prompt/test_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_prompt/test_spin.py?rev=8899&r1=8898&r2=8899&view=diff
==============================================================================
--- branches/bmrb/test_suite/unit_tests/_prompt/test_spin.py (original)
+++ branches/bmrb/test_suite/unit_tests/_prompt/test_spin.py Wed Mar 4
11:39:09 2009
@@ -98,11 +98,11 @@
# Loop over the data types.
for data in DATA_TYPES:
# Catch the int and bin arguments, and skip them.
- if data[0] == 'int' or data[0] == 'bin':
- continue
-
- # The argument test.
- self.assertRaises(RelaxIntError, self.spin_fns.create,
spin_num=data[1], spin_name='NH')
+ if data[0] == 'None' or data[0] == 'int' or data[0] == 'bin':
+ continue
+
+ # The argument test.
+ self.assertRaises(RelaxNoneIntError, self.spin_fns.create,
spin_num=data[1], spin_name='NH')
def test_create_argfail_spin_name(self):
r8899 - in /branches/bmrb: ./ data/ prompt/ test_suite/unit_tests/_prompt/