Author: bugman
Date: Fri Mar 28 12:17:42 2014
New Revision: 22584
URL: http://svn.gna.org/viewcvs/relax?rev=22584&view=rev
Log:
Shifted the model-free analysis specific API object to the
specific_analyses.model_free.api module.
Added:
trunk/specific_analyses/model_free/api.py
- copied, changed from r22576,
trunk/specific_analyses/model_free/__init__.py
Modified:
trunk/specific_analyses/model_free/__init__.py
Modified: trunk/specific_analyses/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/model_free/__init__.py?rev=22584&r1=22583&r2=22584&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/__init__.py (original)
+++ trunk/specific_analyses/model_free/__init__.py Fri Mar 28 12:17:42
2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2013 Edward d'Auvergne
#
+# Copyright (C) 2007-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -20,91 +20,18 @@
###############################################################################
# Module docstring.
-"""Analysis specific code for the Lipari-Szabo model-free analysis."""
+"""The Lipari-Szabo model-free analysis."""
# The available modules.
-__all__ = [ 'bmrb',
- 'macro_base',
- 'main',
- 'mf_minimise',
- 'molmol',
- 'multi_processor_commands',
- 'pymol',
- 'results'
+__all__ = [
+ 'api',
+ 'bmrb',
+ 'macro_base',
+ 'main',
+ 'mf_minimise',
+ 'molmol',
+ 'multi_processor_commands',
+ 'pymol',
+ 'results'
]
-
-# relax module imports.
-from lib.physical_constants import N15_CSA, NH_BOND_LENGTH
-from pipe_control import diffusion_tensor, relax_data
-from specific_analyses.api_base import API_base
-from specific_analyses.api_common import API_common
-from specific_analyses.model_free.bmrb import Bmrb
-from specific_analyses.model_free.main import Model_free_main
-from specific_analyses.model_free.mf_minimise import Mf_minimise
-from specific_analyses.model_free.molmol import Molmol
-from specific_analyses.model_free.pymol import Pymol
-from specific_analyses.model_free.results import Results
-
-
-class Model_free(Model_free_main, Mf_minimise, Results, Bmrb, API_base,
API_common):
- """Parent class containing all the model-free specific functions."""
-
- def __init__(self):
- """Initialise the class by placing API_common methods into the
API."""
-
- # Execute the base class __init__ method.
- super(Model_free, self).__init__()
-
- # Place methods into the API.
- self.base_data_loop = self._base_data_loop_spin
- self.return_error = self._return_error_relax_data
- self.return_value = self._return_value_general
- self.sim_pack_data = self._sim_pack_relax_data
- self.test_grid_ops = self._test_grid_ops_general
-
- # Initialise the macro classes.
- self._molmol_macros = Molmol()
- self._pymol_macros = Pymol()
-
- # Alias the macro creation methods.
- self.pymol_macro = self._pymol_macros.create_macro
- self.molmol_macro = self._molmol_macros.create_macro
-
- # Set up the global parameters.
- self.PARAMS.add('tm', scope='global',
default=diffusion_tensor.default_value('tm'), conv_factor=1e-9,
grace_string='\\xt\\f{}\\sm', units='ns', py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Diso', scope='global',
default=diffusion_tensor.default_value('Diso'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Dx', scope='global',
default=diffusion_tensor.default_value('Dx'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Dy', scope='global',
default=diffusion_tensor.default_value('Dy'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Dz', scope='global',
default=diffusion_tensor.default_value('Dz'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Dpar', scope='global',
default=diffusion_tensor.default_value('Dpar'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Dper', scope='global',
default=diffusion_tensor.default_value('Dper'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Da', scope='global',
default=diffusion_tensor.default_value('Da'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('Dratio', scope='global',
default=diffusion_tensor.default_value('Dratio'), py_type=float,
set='params', err=True, sim=True)
- self.PARAMS.add('Dr', scope='global',
default=diffusion_tensor.default_value('Dr'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('alpha', scope='global',
default=diffusion_tensor.default_value('alpha'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('beta', scope='global',
default=diffusion_tensor.default_value('beta'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('gamma', scope='global',
default=diffusion_tensor.default_value('gamma'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('theta', scope='global',
default=diffusion_tensor.default_value('theta'), py_type=float, set='params',
err=True, sim=True)
- self.PARAMS.add('phi', scope='global',
default=diffusion_tensor.default_value('phi'), py_type=float, set='params',
err=True, sim=True)
-
- # Set up the spin parameters.
- self.PARAMS.add('model', scope='spin', desc='The model', py_type=str)
- self.PARAMS.add('equation', scope='spin', desc='The model equation',
py_type=str)
- self.PARAMS.add('params', scope='spin', desc='The model parameters',
py_type=list)
- self.PARAMS.add('s2', scope='spin', default=0.8, desc='S2, the
model-free generalised order parameter (S2 = S2f.S2s)', py_type=float,
set='params', grace_string='\\qS\\v{0.4}\\z{0.71}2\\Q', err=True, sim=True)
- self.PARAMS.add('s2f', scope='spin', default=0.8, desc='S2f, the
faster motion model-free generalised order parameter', py_type=float,
set='params', grace_string='\\qS\\sf\\N\\h{-0.2}\\v{0.4}\\z{0.71}2\\Q',
err=True, sim=True)
- self.PARAMS.add('s2s', scope='spin', default=0.8, desc='S2s, the
slower motion model-free generalised order parameter', py_type=float,
set='params', grace_string='\\qS\\ss\\N\\h{-0.2}\\v{0.4}\\z{0.71}2\\Q',
err=True, sim=True)
- self.PARAMS.add('local_tm', scope='spin', default=10.0 * 1e-9,
desc='The spin specific global correlation time (seconds)', py_type=float,
set='params', grace_string='\\xt\\f{}\\sm', units='ns', err=True, sim=True)
- self.PARAMS.add('te', scope='spin', default=100.0 * 1e-12,
desc='Single motion effective internal correlation time (seconds)',
py_type=float, set='params', conv_factor=1e-12, grace_string='\\xt\\f{}\\se',
units='ps', err=True, sim=True)
- self.PARAMS.add('tf', scope='spin', default=10.0 * 1e-12,
desc='Faster motion effective internal correlation time (seconds)',
py_type=float, set='params', conv_factor=1e-12, grace_string='\\xt\\f{}\\sf',
units='ps', err=True, sim=True)
- self.PARAMS.add('ts', scope='spin', default=1000.0 * 1e-12,
desc='Slower motion effective internal correlation time (seconds)',
py_type=float, set='params', conv_factor=1e-12, grace_string='\\xt\\f{}\\ss',
units='ps', err=True, sim=True)
- self.PARAMS.add('rex', scope='spin', default=0.0, desc='Chemical
exchange relaxation (sigma_ex = Rex / omega**2)', py_type=float,
set='params', conv_factor=self._conv_factor_rex, units=self._units_rex,
grace_string='\\qR\\sex\\Q', err=True, sim=True)
- self.PARAMS.add('csa', scope='spin', default=N15_CSA, units='ppm',
desc='Chemical shift anisotropy (unitless)', py_type=float, set='params',
conv_factor=1e-6, grace_string='\\qCSA\\Q', err=True, sim=True)
-
- # Add the minimisation data.
- self.PARAMS.add_min_data(min_stats_global=True, min_stats_spin=True)
-
- # Add the relaxation data parameters.
- self.PARAMS.add('ri_data', scope='spin',
desc=relax_data.return_data_desc('ri_data'), py_type=dict, err=False,
sim=True)
- self.PARAMS.add('ri_data_err', scope='spin',
desc=relax_data.return_data_desc('ri_data_err'), py_type=dict, err=False,
sim=False)
Copied: trunk/specific_analyses/model_free/api.py (from r22576,
trunk/specific_analyses/model_free/__init__.py)
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/model_free/api.py?p2=trunk/specific_analyses/model_free/api.py&p1=trunk/specific_analyses/model_free/__init__.py&r1=22576&r2=22584&rev=22584&view=diff
==============================================================================
--- trunk/specific_analyses/model_free/__init__.py (original)
+++ trunk/specific_analyses/model_free/api.py Fri Mar 28 12:17:42 2014
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2007-2013 Edward d'Auvergne
#
+# Copyright (C) 2007-2014 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -20,22 +20,11 @@
###############################################################################
# Module docstring.
-"""Analysis specific code for the Lipari-Szabo model-free analysis."""
+"""The Lipari-Szabo model-free analysis API object."""
-# The available modules.
-__all__ = [ 'bmrb',
- 'macro_base',
- 'main',
- 'mf_minimise',
- 'molmol',
- 'multi_processor_commands',
- 'pymol',
- 'results'
-]
-
# relax module imports.
-from lib.physical_constants import N15_CSA, NH_BOND_LENGTH
+from lib.physical_constants import N15_CSA
from pipe_control import diffusion_tensor, relax_data
from specific_analyses.api_base import API_base
from specific_analyses.api_common import API_common
r22584 - in /trunk/specific_analyses/model_free: __init__.py api.py