Author: bugman
Date: Thu Feb 21 10:54:10 2008
New Revision: 5089
URL: http://svn.gna.org/viewcvs/relax?rev=5089&view=rev
Log:
Merged the N-state model branch back into the 1.3 line.
The command used was:
svn merge -r3692:HEAD
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/N_state_model/ .
Although the branch was not complete, the future changes to the N-state model
code will not affect
the rest of relax. However, the merger was done because this branch was
requiring significant
changes to the structural/PDB code (further abstractions and other API
improvements). This caused
a lot of individual changes to the generic_fns.stucture module being ported
to the branch using
svnmerge, just for debugging. The merger is best for both the branch and the
stability of the 1.3
line.
Added:
1.3/data/align_tensor.py
- copied unchanged from r5088,
branches/N_state_model/data/align_tensor.py
1.3/generic_fns/align_tensor.py
- copied unchanged from r5088,
branches/N_state_model/generic_fns/align_tensor.py
1.3/maths_fns/n_state_model.py
- copied unchanged from r5088,
branches/N_state_model/maths_fns/n_state_model.py
1.3/prompt/align_tensor.py
- copied unchanged from r5088,
branches/N_state_model/prompt/align_tensor.py
1.3/prompt/n_state_model.py
- copied unchanged from r5088,
branches/N_state_model/prompt/n_state_model.py
1.3/sample_scripts/N_state_model.py
- copied unchanged from r5088,
branches/N_state_model/sample_scripts/N_state_model.py
1.3/specific_fns/n_state_model.py
- copied unchanged from r5088,
branches/N_state_model/specific_fns/n_state_model.py
1.3/test_suite/system_tests/n_state_model.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/system_tests/n_state_model.py
1.3/test_suite/system_tests/scripts/5_state_xz.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/system_tests/scripts/5_state_xz.py
1.3/test_suite/unit_tests/_data/test_align_tensor.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/_data/test_align_tensor.py
1.3/test_suite/unit_tests/_generic_fns/test_align_tensor.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/_generic_fns/test_align_tensor.py
1.3/test_suite/unit_tests/_maths_fns/test_n_state_model.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/_maths_fns/test_n_state_model.py
1.3/test_suite/unit_tests/_prompt/test_align_tensor.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/_prompt/test_align_tensor.py
1.3/test_suite/unit_tests/_prompt/test_n_state_model.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/_prompt/test_n_state_model.py
1.3/test_suite/unit_tests/_specific_fns/test_n_state_model.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/_specific_fns/test_n_state_model.py
1.3/test_suite/unit_tests/align_tensor_testing_base.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/align_tensor_testing_base.py
1.3/test_suite/unit_tests/n_state_model_testing_base.py
- copied unchanged from r5088,
branches/N_state_model/test_suite/unit_tests/n_state_model_testing_base.py
Modified:
1.3/generic_fns/pipes.py
1.3/maths_fns/chi2.py
1.3/prompt/interpreter.py
1.3/prompt/pipe.py
1.3/prompt/value.py
1.3/relax_errors.py
1.3/specific_fns/__init__.py
1.3/specific_fns/setup.py
1.3/test_suite/system_tests/__init__.py
Modified: 1.3/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/pipes.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/generic_fns/pipes.py (original)
+++ 1.3/generic_fns/pipes.py Thu Feb 21 10:54:10 2008
@@ -73,6 +73,7 @@
@param pipe_type: The new data pipe type which can be one of the
following:
'jw': Reduced spectral density mapping,
'mf': Model-free analysis,
+ 'N-state': N-state model of domain dynamics,
'noe': Steady state NOE calculation,
'relax_fit': Relaxation curve fitting,
'srls': SRLS analysis.
@@ -80,7 +81,7 @@
"""
# List of valid data pipe types.
- valid = ['jw', 'mf', 'noe', 'relax_fit', 'srls']
+ valid = ['jw', 'mf', 'N-state', 'noe', 'relax_fit', 'srls']
# Test if pipe_type is valid.
if not pipe_type in valid:
Modified: 1.3/maths_fns/chi2.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/chi2.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/maths_fns/chi2.py (original)
+++ 1.3/maths_fns/chi2.py Thu Feb 21 10:54:10 2008
@@ -60,7 +60,7 @@
"""
# Calculate the chi-squared statistic.
- return sum((1.0 / errors * (data - back_calc_vals))**2)
+ return sum((1.0 / errors * (data - back_calc_vals))**2, axis=0)
# Chi-squared gradient.
@@ -99,7 +99,7 @@
"""
# Calculate the chi-squared gradient.
- return -2.0 * sum(1.0 / (errors**2) * (data - back_calc_vals) *
back_calc_grad)
+ return -2.0 * sum(1.0 / (errors**2) * (data - back_calc_vals) *
back_calc_grad, axis=0)
# Chi-squared Hessian.
@@ -144,8 +144,8 @@
"""
# Calculate the chi-squared Hessian.
- #return 2.0 * sum(1.0 / (errors**2) * (back_calc_grad_j *
back_calc_grad_k - (data - back_calc_vals) * back_calc_hess))
- #return 2.0 * sum((back_calc_grad_j * back_calc_grad_k - (data -
back_calc_vals) * back_calc_hess) / errors**2)
+ #return 2.0 * sum(1.0 / (errors**2) * (back_calc_grad_j *
back_calc_grad_k - (data - back_calc_vals) * back_calc_hess), axis=0)
+ #return 2.0 * sum((back_calc_grad_j * back_calc_grad_k - (data -
back_calc_vals) * back_calc_hess) / errors**2, axis=0)
# Calculate the chi-squared Hessian.
# This is faster than the above sums, and having the errors term first
appears to minimise roundoff errors.
Modified: 1.3/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/interpreter.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/prompt/interpreter.py (original)
+++ 1.3/prompt/interpreter.py Thu Feb 21 10:54:10 2008
@@ -49,6 +49,7 @@
from model_selection import Modsel
# User classes.
+from align_tensor import Align_tensor
from dasha import Dasha
from diffusion_tensor import Diffusion_tensor
from grace import Grace
@@ -57,6 +58,7 @@
from molmol import Molmol
from molecule import Molecule
from monte_carlo import Monte_carlo
+from n_state_model import N_state_model
from noe import Noe
from palmer import Palmer
from residue import Residue
@@ -125,6 +127,7 @@
self._system = system
# Place the user classes into the interpreter class namespace.
+ self._Align_tensor = Align_tensor(relax)
self._Dasha = Dasha(relax)
self._Diffusion_tensor = Diffusion_tensor(relax)
self._OpenDX = OpenDX(relax)
@@ -134,6 +137,7 @@
self._Molmol = Molmol(relax)
self._Molecule = Molecule(relax)
self._Monte_carlo = Monte_carlo(relax)
+ self._N_state_model = N_state_model(relax)
self._Noe = Noe(relax)
self._Palmer = Palmer(relax)
self._Residue = Residue(relax)
@@ -187,6 +191,7 @@
model_selection = self._Modsel.model_selection
# Place the user classes in the local namespace.
+ align_tensor = self._Align_tensor
dasha = self._Dasha
diffusion_tensor = self._Diffusion_tensor
dx = self._OpenDX
@@ -196,6 +201,7 @@
molmol = self._Molmol
molecule = self._Molecule
monte_carlo = self._Monte_carlo
+ n_state_model = self._N_state_model
noe = self._Noe
palmer = self._Palmer
structure = self._Structure
Modified: 1.3/prompt/pipe.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/pipe.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/prompt/pipe.py (original)
+++ 1.3/prompt/pipe.py Thu Feb 21 10:54:10 2008
@@ -112,6 +112,7 @@
'jw': Reduced spectral density mapping,
'mf': Model-free analysis,
+ 'N-state': N-state model of domain motions,
'noe': Steady state NOE calculation,
'relax_fit': Relaxation curve fitting,
'srls': SRLS analysis.
Modified: 1.3/prompt/value.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/value.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/prompt/value.py (original)
+++ 1.3/prompt/value.py Thu Feb 21 10:54:10 2008
@@ -32,6 +32,7 @@
from specific_fns.model_free import Model_free
from specific_fns.jw_mapping import Jw_mapping
from specific_fns.relax_fit import Relax_fit
+from specific_fns.n_state_model import N_state_model
from specific_fns.noe import Noe
@@ -509,12 +510,15 @@
copy.__doc__ = copy.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n"
copy.__doc__ = copy.__doc__ + Relax_fit.set_doc.__doc__ + "\n"
copy.__doc__ = copy.__doc__ + Relax_fit.return_data_name.__doc__ + "\n"
+ copy.__doc__ = copy.__doc__ + N_state_model.set_doc.__doc__ + "\n"
+ copy.__doc__ = copy.__doc__ + N_state_model.return_data_name.__doc__ +
"\n"
# Display function.
display.__doc__ = display.__doc__ + "\n\n" + regexp_doc() + "\n"
display.__doc__ = display.__doc__ + Model_free.return_data_name.__doc__
+ "\n\n"
display.__doc__ = display.__doc__ + Jw_mapping.return_data_name.__doc__
+ "\n"
display.__doc__ = display.__doc__ + Relax_fit.return_data_name.__doc__ +
"\n"
+ display.__doc__ = display.__doc__ +
N_state_model.return_data_name.__doc__ + "\n"
# Read function.
read.__doc__ = read.__doc__ + "\n\n" + regexp_doc() + "\n"
@@ -524,6 +528,8 @@
read.__doc__ = read.__doc__ + Jw_mapping.return_data_name.__doc__ + "\n"
read.__doc__ = read.__doc__ + Relax_fit.set_doc.__doc__ + "\n"
read.__doc__ = read.__doc__ + Relax_fit.return_data_name.__doc__ + "\n"
+ read.__doc__ = read.__doc__ + N_state_model.set_doc.__doc__ + "\n"
+ read.__doc__ = read.__doc__ + N_state_model.return_data_name.__doc__ +
"\n"
# Set function.
set.__doc__ = set.__doc__ + "\n\n" + regexp_doc() + "\n"
@@ -539,6 +545,9 @@
set.__doc__ = set.__doc__ + Relax_fit.set_doc.__doc__ + "\n"
set.__doc__ = set.__doc__ + Relax_fit.return_data_name.__doc__ + "\n"
set.__doc__ = set.__doc__ + Relax_fit.default_value.__doc__ + "\n\n"
+ set.__doc__ = set.__doc__ + N_state_model.set_doc.__doc__ + "\n"
+ set.__doc__ = set.__doc__ + N_state_model.return_data_name.__doc__ + "\n"
+ set.__doc__ = set.__doc__ + N_state_model.default_value.__doc__ + "\n\n"
# Write function.
write.__doc__ = write.__doc__ + "\n\n" + regexp_doc() + "\n"
@@ -546,3 +555,4 @@
write.__doc__ = write.__doc__ + Jw_mapping.return_data_name.__doc__ +
"\n\n"
write.__doc__ = write.__doc__ + Noe.return_data_name.__doc__ + "\n"
write.__doc__ = write.__doc__ + Relax_fit.return_data_name.__doc__ + "\n"
+ write.__doc__ = write.__doc__ + N_state_model.return_data_name.__doc__ +
"\n"
Modified: 1.3/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_errors.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/relax_errors.py (original)
+++ 1.3/relax_errors.py Thu Feb 21 10:54:10 2008
@@ -375,6 +375,13 @@
if Debug:
self.save_state()
+# None or list of strings.
+class RelaxNoneListstrError(BaseError):
+ def __init__(self, name, value):
+ self.text = "The " + name + " argument " + `value` + " must either
be an array of strings or None."
+ if Debug:
+ self.save_state()
+
# None or number.
class RelaxNoneNumError(BaseError):
def __init__(self, name, value):
@@ -621,8 +628,11 @@
# The model has not been setup.
class RelaxNoModelError(BaseError):
- def __init__(self, pipe):
- self.text = "The models corresponding to the data pipe " + `pipe` +
" have not been setup."
+ def __init__(self, name=None):
+ if name != None:
+ self.text = "The " + name + " model has not been setup."
+ else:
+ self.text = "The model has not been setup."
if Debug:
self.save_state()
Modified: 1.3/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/__init__.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/specific_fns/__init__.py (original)
+++ 1.3/specific_fns/__init__.py Thu Feb 21 10:54:10 2008
@@ -29,6 +29,7 @@
'hybrid',
'jw_mapping',
'model_free',
+ 'n_state_model',
'noe',
'relax_data',
'relax_fit']
Modified: 1.3/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/setup.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/specific_fns/setup.py (original)
+++ 1.3/specific_fns/setup.py Thu Feb 21 10:54:10 2008
@@ -24,6 +24,7 @@
from specific_fns.hybrid import Hybrid
from specific_fns.jw_mapping import Jw_mapping
from specific_fns.model_free import Model_free
+from specific_fns.n_state_model import N_state_model
from specific_fns.noe import Noe
from specific_fns.relax_fit import Relax_fit
from relax_errors import RelaxError, RelaxFuncSetupError
@@ -33,6 +34,7 @@
hybrid_obj = Hybrid()
jw_mapping_obj = Jw_mapping()
model_free_obj = Model_free()
+n_state_model_obj = N_state_model()
noe_obj = Noe()
relax_fit_obj = Relax_fit()
@@ -229,6 +231,10 @@
if function_type == 'noe':
return noe_obj
+ # The N-state model.
+ if function_type == 'N-state':
+ return n_state_model_obj
+
# Relaxation curve fitting.
if function_type == 'relax_fit':
return relax_fit_obj
@@ -256,6 +262,10 @@
if function_type == 'noe':
return "NOE calculations"
+ # The N-state model.
+ if function_type == 'N-state':
+ return "the N-state model"
+
# Relaxation curve fitting.
if function_type == 'relax_fit':
return "relaxation curve fitting"
Modified: 1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/test_suite/system_tests/__init__.py?rev=5089&r1=5088&r2=5089&view=diff
==============================================================================
--- 1.3/test_suite/system_tests/__init__.py (original)
+++ 1.3/test_suite/system_tests/__init__.py Thu Feb 21 10:54:10 2008
@@ -33,6 +33,7 @@
from jw_mapping import Jw
from model_free import Mf
from model_selection import Modsel
+from n_state_model import N_state_model
from pipe_create import Pipe_create
from relax_fit import Relax_fit
from sequence import Sequence
@@ -78,6 +79,7 @@
suite_array.append(TestLoader().loadTestsFromTestCase(Relax_fit))
suite_array.append(TestLoader().loadTestsFromTestCase(Sequence))
suite_array.append(TestLoader().loadTestsFromTestCase(Pipe_create))
+ suite_array.append(TestLoader().loadTestsFromTestCase(N_state_model))
# Add the relax namespace to each TestCase object.
for i in xrange(len(suite_array)):
r5089 - in /1.3: ./ data/ generic_fns/ maths_fns/ prompt/ sample_scripts/ specific_fns/ test_suite/system_tests/ test_suite/...