Author: bugman
Date: Fri Aug 8 16:19:24 2008
New Revision: 7121
URL: http://svn.gna.org/viewcvs/relax?rev=7121&view=rev
Log:
Wrote the __minimise_setup_pcs() method.
Modified:
branches/rdc_analysis/specific_fns/n_state_model.py
Modified: branches/rdc_analysis/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/specific_fns/n_state_model.py?rev=7121&r1=7120&r2=7121&view=diff
==============================================================================
--- branches/rdc_analysis/specific_fns/n_state_model.py (original)
+++ branches/rdc_analysis/specific_fns/n_state_model.py Fri Aug 8 16:19:24
2008
@@ -345,6 +345,100 @@
# Return the contraint objects.
return A, b
+
+
+ def __minimise_setup_pcs(self):
+ """Set up the data structures for optimisation using PCSs as base
data sets.
+
+ @return: The assembled data structures for using PCSs as the base
data for optimisation.
+ These include:
+ - the PCS values.
+ - the unit vectors connecting the paramagnetic
centre (the electron spin) to
+ the nuclear spin.
+ - the pseudocontact shift constants.
+ - the temperatures.
+ - the spectrometer frequencies.
+ @rtype: tuple of (numpy rank-2 array, numpy rank-2 array, numpy
rank-2 array, numpy
+ rank-1 array, numpy rank-1 array)
+ """
+
+ # Alias the current data pipe.
+ cdp = ds[ds.current_pipe]
+
+ # Initialise.
+ pcs = []
+ unit_vect = []
+ pcs_dj = []
+ temp = []
+ frq = []
+
+ # Spin loop.
+ for spin, spin_id in spin_loop(return_id=True):
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # Skip spins without PCS data.
+ if not hasattr(spin, 'pcs'):
+ continue
+
+ # Append the PCSs to the list.
+ pcs.append(spin.pcs)
+
+ # Gyromagnetic ratios.
+ gx = return_gyromagnetic_ratio(spin.heteronuc_type)
+ gh = return_gyromagnetic_ratio(spin.proton_type)
+
+ # Loop over the states, and calculate the PCS constant for each
(the distance changes each time).
+ pcs_dj.append([])
+ for c in range(cdp.N):
+ # Get the paramagnetic coordinates.
+ i = 0
+ for R in cdp.structure.atom_loop(atom_id=cdp.para_id,
pos_flag=True):
+ i = i + 1
+
+ # Can only be one paramagnetic centre (for now).
+ if i > 1:
+ raise RelaxError, "More than one paramagnetic centre
found."
+
+ # Calculate the electron spin to nuclear spin vector.
+ vect = spin.pos[c] - R
+
+ # The length.
+ r = norm(vect)
+
+ # Append the unit vector.
+ unit_vect.append(vect/r)
+
+ # Calculate the PCS dipolar constant (in Hertz, and the 3
comes from the alignment tensor), and append it to the list.
+ pcs_dj[-1].append(pcs_constant(gx, gh, r))
+
+ # Loop over alignments.
+ for align in cdp.align_tensors:
+ # Append the temperature.
+ temp.append(cdp.temp[align.name])
+
+ # Append the frequency.
+ frq.append(cdp.frq[align.name])
+
+ # Initialise the numpy objects (the pcs matrix is transposed!).
+ pcs_numpy = zeros((len(pcs[0]), len(pcs)), float64)
+ unit_vect_numpy = zeros((len(unit_vect), len(unit_vect[0]), 3),
float64)
+
+ # Loop over the spins.
+ for spin_index in xrange(len(pcs)):
+ # Loop over the alignments.
+ for align_index in xrange(len(pcs[spin_index])):
+ # Transpose and store the PCS value.
+ pcs_numpy[align_index, spin_index] =
pcs[spin_index][align_index]
+
+ # Loop over the N states.
+ for state_index in xrange(len(unit_vect[spin_index])):
+ # Store the unit vector.
+ unit_vect_numpy[spin_index, state_index] =
unit_vect[spin_index][state_index]
+
+ # Return the data structures.
+ return pcs_numpy, unit_vect_numpy, pcs_dj, temp, frq
def __minimise_setup_rdcs(self, param_vector=None, scaling_matrix=None):
r7121 - /branches/rdc_analysis/specific_fns/n_state_model.py