__init__(self,
model=None,
init_params=None,
full_tensors=None,
full_in_ref_frame=None,
rdcs=None,
rdc_errors=None,
rdc_weights=None,
rdc_vect=None,
dip_const=None,
pcs=None,
pcs_errors=None,
pcs_weights=None,
atomic_pos=None,
temp=None,
frq=None,
paramag_centre=array([ 0., 0., 0.]),
scaling_matrix=None,
num_int_pts=500,
com=None,
ave_pos_pivot=array([ 0., 0., 0.]),
ave_pos_piv_sync=True,
translation_opt=False,
pivot=None,
pivot2=None,
pivot_opt=False,
quad_int=True)
(Constructor)
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Set up the target functions for the Frame Order theories.
- Parameters:
model (str) - The name of the Frame Order model.init_params (numpy float64 array) - The initial parameter values.full_tensors (numpy nx5D, rank-1 float64 array) - An array of the {Axx, Ayy, Axy, Axz, Ayz} values for all full
alignment tensors. The format is [Axx1, Ayy1, Axy1, Axz1, Ayz1,
Axx2, Ayy2, Axy2, Axz2, Ayz2, ..., Axxn, Ayyn, Axyn, Axzn, Ayzn].full_in_ref_frame (numpy rank-1 array) - An array of flags specifying if the tensor in the reference frame
is the full or reduced tensor.rdcs (numpy rank-2 array) - The RDC lists. The first index must correspond to the different
alignment media i and the second index to the spin systems j.rdc_errors (numpy rank-2 array) - The RDC error lists. The dimensions of this argument are the
same as for 'rdcs'.rdc_weights (numpy rank-2 array) - The RDC weight lists. The dimensions of this argument are the
same as for 'rdcs'.rdc_vect (numpy rank-2 array) - The unit XH vector lists corresponding to the RDC values. The
first index must correspond to the spin systems and the second
index to the x, y, z elements.dip_const (numpy rank-1 array) - The dipolar constants for each RDC. The indices correspond to
the spin systems j.pcs (numpy rank-2 array) - The PCS lists. The first index must correspond to the different
alignment media i and the second index to the spin systems j.pcs_errors (numpy rank-2 array) - The PCS error lists. The dimensions of this argument are the
same as for 'pcs'.pcs_weights (numpy rank-2 array) - The PCS weight lists. The dimensions of this argument are the
same as for 'pcs'.atomic_pos (numpy rank-3 array) - The atomic positions of all spins for the PCS and PRE data. The
first index is the spin systems j and the second is the structure
or state c.temp (numpy rank-1 array) - The temperature of each PCS data set.frq (numpy rank-1 array) - The frequency of each PCS data set.paramag_centre (numpy rank-1, 3D array or rank-2, Nx3 array) - The paramagnetic centre position (or positions).scaling_matrix (numpy rank-2 array) - The square and diagonal scaling matrix.num_int_pts (int) - The number of points to use for the numerical integration
technique.com (numpy 3D rank-1 array) - The centre of mass of the system. This is used for defining the
rotor model systems.ave_pos_pivot (numpy 3D rank-1 array) - The pivot point to rotate all atoms about to the average domain
position. For example this can be the centre of mass of the
moving domain.ave_pos_piv_sync (bool) - A flag which if True will cause pivot point to rotate to the
average domain position to be synchronised with the motional
pivot. This will cause ave_pos_pivot argument to be ignored.translation_opt (bool) - A flag which if True will allow the pivot point of the motion to
be optimised.pivot (numpy rank-1, 3D array or None) - The pivot point for the ball-and-socket joint motion. This is
needed if PCS or PRE values are used.pivot2 (numpy rank-1, 3D array or None) - The second pivot point for the motion. This is needed if PCS or
PRE values are used and if a double-motional model is to be
optimised.pivot_opt (bool) - A flag which if True will allow the pivot point of the motion to
be optimised.quad_int (bool) - A flag which if True will perform high precision numerical
integration via the scipy.integrate quad(), dblquad() and
tplquad() integration methods rather than the rough quasi-random
numerical integration.
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