Author: bugman
Date: Wed Mar 27 13:41:12 2013
New Revision: 19185
URL: http://svn.gna.org/viewcvs/relax?rev=19185&view=rev
Log:
Ported r8338 from the old relax_disp branch into the new branch (partly
manually).
The changes not made by hand come from the command:
svn merge -r8337:8338
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/branches/relax_disp/specific_fns/@r18123
specific_analyses
All changes not in the specific_analyses package were hand edited.
.....
r8338 | semor | 2009-01-08 17:17:32 +0100 (Thu, 08 Jan 2009) | 7 lines
Changed paths:
M /branches/relax_disp/generic_fns/pipes.py
M /branches/relax_disp/prompt/__init__.py
M /branches/relax_disp/prompt/interpreter.py
M /branches/relax_disp/prompt/pipe.py
M /branches/relax_disp/specific_fns/__init__.py
M /branches/relax_disp/specific_fns/relax_disp.py
M /branches/relax_disp/specific_fns/setup.py
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/pipe_control/pipes.py
branches/relax_disp/specific_analyses/__init__.py
branches/relax_disp/specific_analyses/relax_disp.py
branches/relax_disp/specific_analyses/setup.py
branches/relax_disp/user_functions/pipe.py
Modified: branches/relax_disp/pipe_control/pipes.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/pipe_control/pipes.py?rev=19185&r1=19184&r2=19185&view=diff
==============================================================================
--- branches/relax_disp/pipe_control/pipes.py (original)
+++ branches/relax_disp/pipe_control/pipes.py Wed Mar 27 13:41:12 2013
@@ -35,7 +35,7 @@
# List of valid data pipe types and descriptions.
-VALID_TYPES = ['ct', 'frame order', 'jw', 'hybrid', 'mf', 'N-state', 'noe',
'relax_fit']
+VALID_TYPES = ['ct', 'frame order', 'jw', 'hybrid', 'mf', 'N-state', 'noe',
'relax_disp', 'relax_fit']
PIPE_DESC = {
'ct': 'Consistency testing',
'frame order': 'Frame Order theories',
@@ -44,6 +44,7 @@
'mf': 'Model-free analysis',
'N-state': 'N-state model or ensemble analysis',
'noe': 'Steady state NOE calculation',
+ 'relax_disp': 'Relaxation dispersion',
'relax_fit': 'Relaxation curve fitting'
}
PIPE_DESC_LIST = []
Modified: branches/relax_disp/specific_analyses/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/__init__.py?rev=19185&r1=19184&r2=19185&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/__init__.py (original)
+++ branches/relax_disp/specific_analyses/__init__.py Wed Mar 27 13:41:12 2013
@@ -33,6 +33,7 @@
'model_free',
'n_state_model',
'noe',
+ 'relax_disp',
'relax_fit',
'setup'
]
Modified: branches/relax_disp/specific_analyses/relax_disp.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp.py?rev=19185&r1=19184&r2=19185&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp.py Wed Mar 27 13:41:12
2013
@@ -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_analyses/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/setup.py?rev=19185&r1=19184&r2=19185&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/setup.py (original)
+++ branches/relax_disp/specific_analyses/setup.py Wed Mar 27 13:41:12 2013
@@ -31,6 +31,7 @@
from specific_analyses.model_free import Model_free
from specific_analyses.n_state_model import N_state_model
from specific_analyses.noe import Noe
+from specific_analyses.relax_disp import Relax_disp
from specific_analyses.relax_fit import Relax_fit
from lib.errors import RelaxError, RelaxFuncSetupError
@@ -43,6 +44,7 @@
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()
@@ -280,6 +282,10 @@
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
@@ -319,6 +325,10 @@
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"
Modified: branches/relax_disp/user_functions/pipe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/user_functions/pipe.py?rev=19185&r1=19184&r2=19185&view=diff
==============================================================================
--- branches/relax_disp/user_functions/pipe.py (original)
+++ branches/relax_disp/user_functions/pipe.py Wed Mar 27 13:41:12 2013
@@ -193,6 +193,7 @@
uf.desc[-1].add_item_list_element("'mf'", "Model-free analysis,")
uf.desc[-1].add_item_list_element("'N-state'", "N-state model of domain
motions,")
uf.desc[-1].add_item_list_element("'noe'", "Steady state NOE calculation,")
+uf.desc[-1].add_item_list_element("'relax_disp'", "Relaxation dispersion
curve fitting,")
uf.desc[-1].add_item_list_element("'relax_fit'", "Relaxation curve fitting,")
uf.desc[-1].add_paragraph("The pipe bundling concept is simply a way of
grouping data pipes together. This is useful for a number of purposes:")
uf.desc[-1].add_list_element("The grouping or categorisation of data pipes,
for example when multiple related analyses are performed.")
r19185 - in /branches/relax_disp: pipe_control/ specific_analyses/ user_functions/