Author: bugman
Date: Tue May 29 15:59:49 2012
New Revision: 16511
URL: http://svn.gna.org/viewcvs/relax?rev=16511&view=rev
Log:
Lots of improvements for the specification of the model-free global and spin
parameters.
Modified:
branches/uf_redesign/specific_fns/model_free/__init__.py
Modified: branches/uf_redesign/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/specific_fns/model_free/__init__.py?rev=16511&r1=16510&r2=16511&view=diff
==============================================================================
--- branches/uf_redesign/specific_fns/model_free/__init__.py (original)
+++ branches/uf_redesign/specific_fns/model_free/__init__.py Tue May 29
15:59:49 2012
@@ -37,7 +37,7 @@
# relax module imports.
from bmrb import Bmrb
-from generic_fns import diffusion_tensor
+from generic_fns import diffusion_tensor, relax_data
from main import Model_free_main
from mf_minimise import Mf_minimise
from molmol import Molmol
@@ -73,35 +73,43 @@
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, err=True, sim=True)
- self.PARAMS.add('Diso', scope='global',
default=diffusion_tensor.default_value('Diso'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('Dx', scope='global',
default=diffusion_tensor.default_value('Dx'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('Dy', scope='global',
default=diffusion_tensor.default_value('Dy'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('Dz', scope='global',
default=diffusion_tensor.default_value('Dz'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('Dpar', scope='global',
default=diffusion_tensor.default_value('Dpar'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('Dper', scope='global',
default=diffusion_tensor.default_value('Dper'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('Da', scope='global',
default=diffusion_tensor.default_value('Da'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('Dratio', scope='global',
default=diffusion_tensor.default_value('Dratio'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('alpha', scope='global',
default=diffusion_tensor.default_value('alpha'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('beta', scope='global',
default=diffusion_tensor.default_value('beta'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('gamma', scope='global',
default=diffusion_tensor.default_value('gamma'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('theta', scope='global',
default=diffusion_tensor.default_value('theta'), py_type=float, err=True,
sim=True)
- self.PARAMS.add('phi', scope='global',
default=diffusion_tensor.default_value('phi'), py_type=float, err=True,
sim=True)
+ 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('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('local_tm', scope='spin', default=10.0 * 1e-9,
desc='The spin specific global correlation time (seconds)', py_type=float,
grace_string='\\xt\\f{}\\sm', units='ns', err=True, sim=True)
- self.PARAMS.add('s2', scope='spin', default=0.8, desc='S2, the
model-free generalised order parameter (S2 = S2f.S2s)', py_type=float,
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,
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,
grace_string='\\qS\\ss\\N\\h{-0.2}\\v{0.4}\\z{0.71}2\\Q', 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, 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, 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, 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,
conv_factor=self._conv_factor_rex, units=self._units_rex,
grace_string='\\qR\\sex\\Q', err=True, sim=True)
- self.PARAMS.add('r', scope='spin', default=NH_BOND_LENGTH,
units='Angstrom', desc='Bond length (meters)', py_type=float,
conv_factor=1e-10, grace_string='Bond length', err=True, sim=True)
- self.PARAMS.add('csa', scope='spin', default=N15_CSA, units='ppm',
desc='Chemical shift anisotropy (unitless)', py_type=float, conv_factor=1e-6,
grace_string='\\qCSA\\Q', err=True, sim=True)
+ self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The
proton spin type', py_type=str)
self.PARAMS.add('heteronuc_type', scope='spin', default='15N',
desc='The heteronucleus spin type', py_type=str)
- self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The
proton spin type', py_type=str)
+ self.PARAMS.add('attached_proton', scope='spin', default='H',
desc='The name of the attached proton', py_type=str)
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('xh_vect', scope='spin', desc='XH bond vector',
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('r', scope='spin', default=NH_BOND_LENGTH,
units='Angstrom', desc='Bond length (meters)', py_type=float, set='params',
conv_factor=1e-10, grace_string='Bond length', 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)
r16511 - /branches/uf_redesign/specific_fns/model_free/__init__.py