Author: semor
Date: Thu Jan 8 17:17:32 2009
New Revision: 8338
URL: http://svn.gna.org/viewcvs/relax?rev=8338&view=rev
Log:
Fixed many formatting errors and made the 'relax_disp' code accessible
(pipes, interpreter, etc).
These changes also include a coming back to using the C code
'math_fns/relax_fit.py' since there is
still no such code associated to relaxation dispersion. This will allow
workingin the code without
relax crashing and complaining about the lack of a C module name
'relax_disp.py'.
Modified:
branches/relax_disp/generic_fns/pipes.py
branches/relax_disp/prompt/__init__.py
branches/relax_disp/prompt/interpreter.py
branches/relax_disp/prompt/pipe.py
branches/relax_disp/specific_fns/__init__.py
branches/relax_disp/specific_fns/relax_disp.py
branches/relax_disp/specific_fns/setup.py
Modified: branches/relax_disp/generic_fns/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/generic_fns/pipes.py?rev=8338&r1=8337&r2=8338&view=diff
==============================================================================
--- branches/relax_disp/generic_fns/pipes.py (original)
+++ branches/relax_disp/generic_fns/pipes.py Thu Jan 8 17:17:32 2009
@@ -74,8 +74,8 @@
'mf': Model-free analysis,
'N-state': N-state model of domain dynamics,
'noe': Steady state NOE calculation,
+ 'relax_disp': Relaxation dispersion,
'relax_fit': Relaxation curve fitting,
- 'relax_disp': Relaxation dispersion,
'srls': SRLS analysis.
@type pipe_type: str
@keyword switch: If True, this new pipe will be switched to,
otherwise the current data pipe
Modified: branches/relax_disp/prompt/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/__init__.py?rev=8338&r1=8337&r2=8338&view=diff
==============================================================================
--- branches/relax_disp/prompt/__init__.py (original)
+++ branches/relax_disp/prompt/__init__.py Thu Jan 8 17:17:32 2009
@@ -46,6 +46,7 @@
'palmer',
'pymol',
'relax_data',
+ 'relax_disp',
'relax_fit',
'reset',
'pipe',
Modified: branches/relax_disp/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/interpreter.py?rev=8338&r1=8337&r2=8338&view=diff
==============================================================================
--- branches/relax_disp/prompt/interpreter.py (original)
+++ branches/relax_disp/prompt/interpreter.py Thu Jan 8 17:17:32 2009
@@ -77,6 +77,7 @@
from pymol import Pymol
from rdc import RDC
from relax_data import Relax_data
+from relax_disp import Relax_disp
from relax_fit import Relax_fit
from results import Results
from pipe import Pipe
@@ -162,6 +163,7 @@
self._Pymol = Pymol(relax)
self._RDC = RDC(relax)
self._Relax_data = Relax_data(relax)
+ self._Relax_disp = Relax_disp(relax)
self._Relax_fit = Relax_fit(relax)
self._Results = Results(relax)
self._Pipe = Pipe(relax)
@@ -231,6 +233,7 @@
pymol = self._Pymol
rdc = self._RDC
relax_data = self._Relax_data
+ relax_disp = self._Relax_disp
relax_fit = self._Relax_fit
residue = self._Residue
results = self._Results
Modified: branches/relax_disp/prompt/pipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/prompt/pipe.py?rev=8338&r1=8337&r2=8338&view=diff
==============================================================================
--- branches/relax_disp/prompt/pipe.py (original)
+++ branches/relax_disp/prompt/pipe.py Thu Jan 8 17:17:32 2009
@@ -118,6 +118,7 @@
'mf': Model-free analysis,
'N-state': N-state model of domain motions,
'noe': Steady state NOE calculation,
+ 'relax_disp': Relaxation dispersion curve fitting,
'relax_fit': Relaxation curve fitting,
'srls': SRLS analysis.
Modified: branches/relax_disp/specific_fns/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/__init__.py?rev=8338&r1=8337&r2=8338&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/__init__.py (original)
+++ branches/relax_disp/specific_fns/__init__.py Thu Jan 8 17:17:32 2009
@@ -32,4 +32,5 @@
'model_free',
'n_state_model',
'noe',
+ 'relax_disp',
'relax_fit']
Modified: branches/relax_disp/specific_fns/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/relax_disp.py?rev=8338&r1=8337&r2=8338&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/relax_disp.py (original)
+++ branches/relax_disp/specific_fns/relax_disp.py Thu Jan 8 17:17:32 2009
@@ -39,7 +39,7 @@
# C modules.
if C_module_exp_fn:
- from maths_fns.relax_disp import setup, func, dfunc, d2func, back_calc_I
+ from maths_fns.relax_fit import setup, func, dfunc, d2func, back_calc_I
class Relax_disp(Common_functions):
@@ -196,12 +196,12 @@
if not hasattr(cdp, 'cpmg_frqs'):
cdp.cpmg_frqs = [None] * len(cdp.spectrum_ids)
- # Index not present in the global CPMG frequency data structure.
- while 1:
- if index > len(cdp.cpmg_frqs) - 1:
- cdp.cpmg_frqs.append(None)
- else:
- break
+ # Index not present in the global CPMG frequency data structure.
+ while 1:
+ if index > len(cdp.cpmg_frqs) - 1:
+ cdp.cpmg_frqs.append(None)
+ else:
+ break
# Add the frequency at the correct position.
cdp.cpmg_frqs[index] = frq
@@ -445,17 +445,17 @@
if not exists_mol_res_spin_data():
raise RelaxNoSequenceError
- # CPMG relaxation dispersion experiments.
- if exp = 'cpmg':
- print "CPMG relaxation dispersion experiments."
-
- # R1rho relaxation dispersion experiments.
- elif exp = 'r1rho':
- print "R1rho relaxation dispersion experiments."
-
- # Invalid relaxation dispersion experiment.
- else:
- raise RelaxError, "The relaxation dispersion experiment '" + exp
+ "' is invalid."
+ # CPMG relaxation dispersion experiments.
+ if exp == 'cpmg':
+ print "CPMG relaxation dispersion experiments."
+
+ # R1rho relaxation dispersion experiments.
+ elif exp == 'r1rho':
+ print "R1rho relaxation dispersion experiments."
+
+ # Invalid relaxation dispersion experiment.
+ else:
+ raise RelaxError, "The relaxation dispersion experiment '" + exp
+ "' is invalid."
def grid_search(self, lower=None, upper=None, inc=None,
constraints=True, verbosity=1, sim_index=None):
Modified: branches/relax_disp/specific_fns/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_fns/setup.py?rev=8338&r1=8337&r2=8338&view=diff
==============================================================================
--- branches/relax_disp/specific_fns/setup.py (original)
+++ branches/relax_disp/specific_fns/setup.py Thu Jan 8 17:17:32 2009
@@ -27,6 +27,7 @@
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_disp import Relax_disp
from specific_fns.relax_fit import Relax_fit
from relax_errors import RelaxError, RelaxFuncSetupError
@@ -38,6 +39,7 @@
model_free_obj = Model_free()
n_state_model_obj = N_state_model()
noe_obj = Noe()
+relax_disp_obj = Relax_disp()
relax_fit_obj = Relax_fit()
@@ -265,6 +267,10 @@
if function_type == 'N-state':
return n_state_model_obj
+ # Relaxation dispersion curve fitting.
+ if function_type == 'relax_disp':
+ return relax_disp_obj
+
# Relaxation curve fitting.
if function_type == 'relax_fit':
return relax_fit_obj
@@ -300,6 +306,10 @@
if function_type == 'N-state':
return "the N-state model"
+ # Relaxation dispersion curve fitting.
+ if function_type == 'relax_disp':
+ return "relaxation dispersion curve fitting"
+
# Relaxation curve fitting.
if function_type == 'relax_fit':
return "relaxation curve fitting"
r8338 - in /branches/relax_disp: generic_fns/ prompt/ specific_fns/