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24 """The model-free specific code."""
25
26
27
28 __all__ = [ 'bmrb',
29 'macro_base',
30 'main',
31 'mf_minimise',
32 'molmol',
33 'multi_processor_commands',
34 'pymol',
35 'results'
36 ]
37
38
39 from bmrb import Bmrb
40 from generic_fns import diffusion_tensor, relax_data
41 from main import Model_free_main
42 from mf_minimise import Mf_minimise
43 from molmol import Molmol
44 from physical_constants import N15_CSA, NH_BOND_LENGTH
45 from pymol import Pymol
46 from results import Results
47 from specific_fns.api_base import API_base
48 from specific_fns.api_common import API_common
49
50
51 -class Model_free(Model_free_main, Mf_minimise, Results, Bmrb, API_base, API_common):
52 """Parent class containing all the model-free specific functions."""
53
55 """Initialise the class by placing API_common methods into the API."""
56
57
58 super(Model_free, self).__init__()
59
60
61 self.base_data_loop = self._base_data_loop_spin
62 self.return_error = self._return_error_relax_data
63 self.return_value = self._return_value_general
64 self.sim_pack_data = self._sim_pack_relax_data
65 self.test_grid_ops = self._test_grid_ops_general
66
67
68 self._molmol_macros = Molmol()
69 self._pymol_macros = Pymol()
70
71
72 self.pymol_macro = self._pymol_macros.create_macro
73 self.molmol_macro = self._molmol_macros.create_macro
74
75
76 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)
77 self.PARAMS.add('Diso', scope='global', default=diffusion_tensor.default_value('Diso'), py_type=float, set='params', err=True, sim=True)
78 self.PARAMS.add('Dx', scope='global', default=diffusion_tensor.default_value('Dx'), py_type=float, set='params', err=True, sim=True)
79 self.PARAMS.add('Dy', scope='global', default=diffusion_tensor.default_value('Dy'), py_type=float, set='params', err=True, sim=True)
80 self.PARAMS.add('Dz', scope='global', default=diffusion_tensor.default_value('Dz'), py_type=float, set='params', err=True, sim=True)
81 self.PARAMS.add('Dpar', scope='global', default=diffusion_tensor.default_value('Dpar'), py_type=float, set='params', err=True, sim=True)
82 self.PARAMS.add('Dper', scope='global', default=diffusion_tensor.default_value('Dper'), py_type=float, set='params', err=True, sim=True)
83 self.PARAMS.add('Da', scope='global', default=diffusion_tensor.default_value('Da'), py_type=float, set='params', err=True, sim=True)
84 self.PARAMS.add('Dratio', scope='global', default=diffusion_tensor.default_value('Dratio'), py_type=float, set='params', err=True, sim=True)
85 self.PARAMS.add('Dr', scope='global', default=diffusion_tensor.default_value('Dr'), py_type=float, set='params', err=True, sim=True)
86 self.PARAMS.add('alpha', scope='global', default=diffusion_tensor.default_value('alpha'), py_type=float, set='params', err=True, sim=True)
87 self.PARAMS.add('beta', scope='global', default=diffusion_tensor.default_value('beta'), py_type=float, set='params', err=True, sim=True)
88 self.PARAMS.add('gamma', scope='global', default=diffusion_tensor.default_value('gamma'), py_type=float, set='params', err=True, sim=True)
89 self.PARAMS.add('theta', scope='global', default=diffusion_tensor.default_value('theta'), py_type=float, set='params', err=True, sim=True)
90 self.PARAMS.add('phi', scope='global', default=diffusion_tensor.default_value('phi'), py_type=float, set='params', err=True, sim=True)
91
92
93 self.PARAMS.add('proton_type', scope='spin', default='1H', desc='The proton spin type', py_type=str)
94 self.PARAMS.add('heteronuc_type', scope='spin', default='15N', desc='The heteronucleus spin type', py_type=str)
95 self.PARAMS.add('attached_proton', scope='spin', default='H', desc='The name of the attached proton', py_type=str)
96 self.PARAMS.add('model', scope='spin', desc='The model', py_type=str)
97 self.PARAMS.add('equation', scope='spin', desc='The model equation', py_type=str)
98 self.PARAMS.add('params', scope='spin', desc='The model parameters', py_type=list)
99 self.PARAMS.add('xh_vect', scope='spin', desc='XH bond vector', py_type=list)
100 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)
101 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)
102 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)
103 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)
104 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)
105 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)
106 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)
107 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)
108 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)
109 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)
110
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112 self.PARAMS.add_min_data(min_stats_global=True, min_stats_spin=True)
113
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115 self.PARAMS.add('ri_data', scope='spin', desc=relax_data.return_data_desc('ri_data'), py_type=dict, err=False, sim=True)
116 self.PARAMS.add('ri_data_err', scope='spin', desc=relax_data.return_data_desc('ri_data_err'), py_type=dict, err=False, sim=False)
117