Author: bugman
Date: Tue Jun 19 11:01:47 2012
New Revision: 16946
URL: http://svn.gna.org/viewcvs/relax?rev=16946&view=rev
Log:
Eliminated a number of the specific API parameters relating to dipole-dipole
interactions.
These are now provided by the spin.isotope user function and the dipole_pair
user functions. The
eliminated parameters are:
'r' - replaced by dipole_pair.set_dist or dipole_pair.read_dist,
'xh_vect' - replaced by dipole_pair.unit_vectors,
'heteronuc_type' - replaced by spin.isotope,
'proton_type' - replaced by spin.isotope,
'attached_proton' - replaced by dipole_pair.define.
Modified:
branches/interatomic/specific_fns/consistency_tests.py
branches/interatomic/specific_fns/frame_order.py
branches/interatomic/specific_fns/jw_mapping.py
branches/interatomic/specific_fns/model_free/__init__.py
branches/interatomic/specific_fns/n_state_model.py
Modified: branches/interatomic/specific_fns/consistency_tests.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/consistency_tests.py?rev=16946&r1=16945&r2=16946&view=diff
==============================================================================
--- branches/interatomic/specific_fns/consistency_tests.py (original)
+++ branches/interatomic/specific_fns/consistency_tests.py Tue Jun 19
11:01:47 2012
@@ -61,10 +61,7 @@
self.PARAMS.add('j0', scope='spin', desc='Spectral density value at
0 MHz (from Farrow et al. (1995) JBNMR, 6: 153-162)', py_type=float,
grace_string='\\qJ(0)\\Q', err=True, sim=True)
self.PARAMS.add('f_eta', scope='spin', desc='Eta-test (from Fushman
et al. (1998) JACS, 120: 10947-10952)', py_type=float,
grace_string='\\qF\\s\\xh\\Q', err=True, sim=True)
self.PARAMS.add('f_r2', scope='spin', desc='R2-test (from Fushman et
al. (1998) JACS, 120: 10947-10952)', py_type=float,
grace_string='\\qF\\sR2\\Q', err=True, sim=True)
- self.PARAMS.add('r', scope='spin', default=NH_BOND_LENGTH,
units='Angstrom', desc='Bond length', py_type=float, grace_string='Bond
length')
self.PARAMS.add('csa', scope='spin', default=N15_CSA, units='ppm',
desc='CSA value', py_type=float, grace_string='\\qCSA\\Q')
- self.PARAMS.add('heteronuc_type', scope='spin', default='15N',
desc='The heteronucleus type', py_type=str)
- self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The
proton type', py_type=str)
self.PARAMS.add('orientation', scope='spin', default=15.7,
units='degrees', desc="Angle between the 15N-1H vector and the principal axis
of the 15N chemical shift tensor", py_type=float, grace_string='\\q\\xq\\Q')
self.PARAMS.add('tc', scope='spin', default=13 * 1e-9, units='ns',
desc="Correlation time", py_type=float, grace_string='\\q\\xt\\f{}c\\Q')
Modified: branches/interatomic/specific_fns/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/frame_order.py?rev=16946&r1=16945&r2=16946&view=diff
==============================================================================
--- branches/interatomic/specific_fns/frame_order.py (original)
+++ branches/interatomic/specific_fns/frame_order.py Tue Jun 19 11:01:47 2012
@@ -80,10 +80,6 @@
self.PARAMS.add('cone_s1', scope='global', units='', desc='The
isotropic cone order parameter', py_type=float, set='params', err=True,
sim=True)
self.PARAMS.add('cone_sigma_max', scope='global', units='rad',
desc='The torsion angle', py_type=float, set='params', err=True, sim=True)
self.PARAMS.add('params', scope='global', desc='The model
parameters', py_type=list)
-
- # Set up the spin parameters.
- self.PARAMS.add('heteronuc_type', scope='spin', default='15N',
desc='The heteronucleus type', py_type=str)
- self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The
proton type', py_type=str)
# Add minimisation structures.
self.PARAMS.add_min_data(min_stats_global=True)
Modified: branches/interatomic/specific_fns/jw_mapping.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/jw_mapping.py?rev=16946&r1=16945&r2=16946&view=diff
==============================================================================
--- branches/interatomic/specific_fns/jw_mapping.py (original)
+++ branches/interatomic/specific_fns/jw_mapping.py Tue Jun 19 11:01:47 2012
@@ -62,10 +62,7 @@
self.PARAMS.add('j0', scope='spin', string='J(0)', desc='Spectral
density value at 0 MHz', py_type=float, set='params',
grace_string='\\qJ(0)\\Q', err=True, sim=True)
self.PARAMS.add('jwx', scope='spin', string='J(wX)', desc='Spectral
density value at the frequency of the heteronucleus', py_type=float,
set='params', grace_string='\\qJ(\\xw\\f{}\\sX\\N)\\Q', err=True, sim=True)
self.PARAMS.add('jwh', scope='spin', string='J(wH)', desc='Spectral
density value at the frequency of the proton', py_type=float, set='params',
grace_string='\\qJ(\\xw\\f{}\\sH\\N)\\Q', err=True, sim=True)
- self.PARAMS.add('r', scope='spin', default=NH_BOND_LENGTH,
units='Angstrom', desc='Bond length', py_type=float, grace_string='Bond
length')
self.PARAMS.add('csa', scope='spin', default=N15_CSA, units='ppm',
desc='CSA value', py_type=float, grace_string='\\qCSA\\Q')
- self.PARAMS.add('heteronuc_type', scope='spin', default='15N',
desc='The heteronucleus type', py_type=str)
- self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The
proton type', py_type=str)
def _set_frq(self, frq=None):
Modified: branches/interatomic/specific_fns/model_free/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/model_free/__init__.py?rev=16946&r1=16945&r2=16946&view=diff
==============================================================================
--- branches/interatomic/specific_fns/model_free/__init__.py (original)
+++ branches/interatomic/specific_fns/model_free/__init__.py Tue Jun 19
11:01:47 2012
@@ -90,13 +90,9 @@
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('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('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)
Modified: branches/interatomic/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/specific_fns/n_state_model.py?rev=16946&r1=16945&r2=16946&view=diff
==============================================================================
--- branches/interatomic/specific_fns/n_state_model.py (original)
+++ branches/interatomic/specific_fns/n_state_model.py Tue Jun 19 11:01:47
2012
@@ -75,10 +75,7 @@
self.test_grid_ops = self._test_grid_ops_general
# Set up the spin parameters.
- self.PARAMS.add('r', scope='spin', units='Angstrom', desc='Bond
length', py_type=float, grace_string='Bond length')
self.PARAMS.add('csa', scope='spin', units='ppm', desc='CSA value',
py_type=float, grace_string='\\qCSA\\Q')
- self.PARAMS.add('heteronuc_type', scope='spin', default='15N',
desc='The heteronucleus type', py_type=str)
- self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The
proton type', py_type=str)
# Add the minimisation data.
self.PARAMS.add_min_data(min_stats_global=False, min_stats_spin=True)
r16946 - in /branches/interatomic/specific_fns: ./ model_free/