Class containing the specific methods of the Frame Order theories.
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numpy rank-1 array, numpy rank-1 array
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numpy rank-1 array
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numpy rank-2 array
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list of str
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_check_rdcs(self,
interatom,
spin1,
spin2)
Check if the RDCs for the given interatomic data container should be
used. |
source code
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str
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list of float
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_grid_row(self,
incs,
lower,
upper,
dist_type=None,
end_point=True)
Set up a row of the grid search for a given parameter. |
source code
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numpy rank-3 array, numpy rank-1 array.
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tuple of (numpy rank-2 array, numpy rank-2 array, numpy rank-2 array,
numpy rank-1 array, numpy rank-1 array)
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tuple of (numpy rank-2 array, numpy rank-2 array, numpy rank-2 array,
numpy rank-3 array, numpy rank-2 array, numpy rank-2 array)
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tuple of 3 numpy nx5D, rank-1 arrays
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_num_int_pts(self,
num=200000)
Set the number of integration points to use in the quasi-random
Sobol' sequence. |
source code
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bool
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bool
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_opt_uses_pcs(self,
align_id)
Determine if the PCS data for the given alignment ID is needed for
optimisation. |
source code
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bool
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_opt_uses_rdc(self,
align_id)
Determine if the RDC data for the given alignment ID is needed for
optimisation. |
source code
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int
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_pdb_ave_pos(self,
file=None,
dir=None,
force=False)
Create a PDB file of the molecule with the moving domains shifted to
the average position. |
source code
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_pdb_distribution(self,
file=None,
dir=None,
force=False)
Create a PDB file of a distribution of positions coving the full
dynamics of the moving domain. |
source code
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_pdb_geometric_rep(self,
file=None,
dir=None,
size=30.0,
inc=36,
force=False,
neg_cone=True)
Create a PDB file containing a geometric object representing the
frame order dynamics. |
source code
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_pdb_model(self,
ave_pos_file=' ave_pos.pdb ' ,
rep_file=' frame_order.pdb ' ,
dist_file=' domain_distribution.pdb ' ,
dir=None,
size=30.0,
inc=36,
force=False,
neg_cone=True)
Create 3 different PDB files for representing the frame order
dynamics of the system. |
source code
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_pivot(self,
pivot=None,
fix=None)
Set the pivot point for the 2 body motion. |
source code
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bool
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_quad_int(self,
flag=False)
Turn the high precision Scipy quadratic numerical integration on or
off. |
source code
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_target_fn_setup(self,
sim_index=None,
scaling=True)
Initialise the target function for optimisation or direct
calculation. |
source code
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(int, AlignTensorData instance)
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bool
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_update_model(self)
Update the model parameters as necessary. |
source code
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_unpack_opt_results(self,
results,
scaling=False,
scaling_matrix=None,
sim_index=None)
Unpack and store the Frame Order optimisation results. |
source code
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list of str
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calculate(self,
spin_id=None,
verbosity=1,
sim_index=None)
Calculate the chi-squared value for the current parameter values. |
source code
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list of floats
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duplicate_data(self,
pipe_from=None,
pipe_to=None,
model_info=None,
global_stats=False,
verbose=True)
Duplicate the data specific to a single frame order data pipe. |
source code
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bool
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list of str
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list of str
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grid_search(self,
lower=None,
upper=None,
inc=None,
constraints=False,
verbosity=0,
sim_index=None)
Perform a grid search. |
source code
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bool
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list of float
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minimise(self,
min_algor=None,
min_options=None,
func_tol=None,
grad_tol=None,
max_iterations=None,
constraints=False,
scaling=True,
verbosity=0,
sim_index=None,
lower=None,
upper=None,
inc=None)
Minimisation function. |
source code
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str
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SpinContainer instance
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tuple of (int, int, float)
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str
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list of float
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str
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list of float
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list of int
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Inherited from api_base.API_base :
back_calc_ri ,
bmrb_read ,
bmrb_write ,
constraint_algorithm ,
data_init ,
data_names ,
data_type ,
default_value ,
has_errors ,
molmol_macro ,
num_instances ,
overfit_deselect ,
pymol_macro ,
read_columnar_results ,
return_conversion_factor ,
return_data ,
return_data_desc ,
return_data_name ,
return_grace_string ,
return_value ,
set_param_values ,
set_update ,
sim_return_chi2 ,
skip_function ,
test_grid_ops
Inherited from object :
__delattr__ ,
__format__ ,
__getattribute__ ,
__hash__ ,
__new__ ,
__reduce__ ,
__reduce_ex__ ,
__repr__ ,
__setattr__ ,
__sizeof__ ,
__str__ ,
__subclasshook__
Inherited from api_common.API_common (private):
_base_data_loop_spin ,
_create_mc_relax_data ,
_data_init_dummy ,
_data_init_spin ,
_eliminate_false ,
_has_errors_spin ,
_is_spin_param_true ,
_model_loop_single_global ,
_model_loop_spin ,
_model_type_global ,
_model_type_local ,
_num_instances_spin ,
_overfit_deselect_dummy ,
_return_data_relax_data ,
_return_error_relax_data ,
_return_no_conversion_factor ,
_return_value_general ,
_set_error_spin ,
_set_param_values_global ,
_set_param_values_spin ,
_set_selected_sim_global ,
_set_selected_sim_spin ,
_set_update ,
_sim_init_values_spin ,
_sim_pack_relax_data ,
_sim_return_chi2_spin ,
_sim_return_param_spin ,
_sim_return_selected_global ,
_sim_return_selected_spin ,
_test_grid_ops_general
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