Author: bugman
Date: Thu Nov 14 15:00:49 2013
New Revision: 21450
URL: http://svn.gna.org/viewcvs/relax?rev=21450&view=rev
Log:
Started to add better pseudo-atom support for the PCS.
The new pipe_control.pcs.setup_pseudoatom_pcs() function has been added to
deselect the spins which
are members of a pseudo-atom. The return_pcs_data() function in the same
module now calls this
function and builds a list of pseudo-atom flags for use in the target
function (though it is still
unused).
Modified:
trunk/pipe_control/pcs.py
trunk/specific_analyses/n_state_model/__init__.py
trunk/target_functions/n_state_model.py
Modified: trunk/pipe_control/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/pcs.py?rev=21450&r1=21449&r2=21450&view=diff
==============================================================================
--- trunk/pipe_control/pcs.py (original)
+++ trunk/pipe_control/pcs.py Thu Nov 14 15:00:49 2013
@@ -25,7 +25,7 @@
# Python module imports.
from copy import deepcopy
from math import pi, sqrt
-from numpy import array, float64, ones, std, zeros
+from numpy import array, float64, int32, ones, std, zeros
from numpy.linalg import norm
from random import gauss
import sys
@@ -40,7 +40,7 @@
from lib.warnings import RelaxWarning, RelaxNoSpinWarning
from pipe_control import grace, pipes
from pipe_control.align_tensor import get_tensor_index, get_tensor_object,
opt_uses_align_data, opt_uses_tensor
-from pipe_control.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, return_spin, spin_index_loop, spin_loop
+from pipe_control.mol_res_spin import exists_mol_res_spin_data,
generate_spin_id_unique, is_pseudoatom, return_spin, spin_index_loop,
spin_loop
def back_calc(align_id=None):
@@ -756,11 +756,12 @@
@type sim_index: None or int
@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 unit vectors connecting the paramagnetic
centre (the electron spin) to the spin.
- the PCS weight.
- - the nuclear spin.
- - the pseudocontact shift constants.
- @rtype: tuple of (numpy rank-2 array, numpy rank-2 array,
numpy rank-2 array, numpy rank-1 array, numpy rank-1 array)
+ - the experimental temperatures.
+ - the spectrometer frequencies.
+ - pseudo_flags, the list of flags indicating if
the interatomic data contains a pseudo-atom (as 1's and 0's).
+ @rtype: tuple of (numpy rank-2 float64 array, numpy rank-2
float64 array, numpy rank-2 float64 array, list of float, list of float,
numpy rank-1 int32 array)
"""
# Data setup tests.
@@ -771,12 +772,16 @@
if not hasattr(cdp, 'spectrometer_frq'):
raise RelaxError("The spectrometer frequencies of the experiments
have not been set.")
+ # Sort out pseudo-atoms first. This only needs to be called once.
+ setup_pseudoatom_pcs()
+
# Initialise.
pcs = []
pcs_err = []
pcs_weight = []
temp = []
frq = []
+ pseudo_flags = []
# The PCS data.
for i in range(len(cdp.align_ids)):
@@ -843,17 +848,25 @@
# Spin index.
j = j + 1
+ # Pseudo-atom.
+ for spin in spin_loop():
+ if is_pseudoatom(spin):
+ pseudo_flags.append(1)
+ else:
+ pseudo_flags.append(0)
+
# Convert to numpy objects.
pcs = array(pcs, float64)
pcs_err = array(pcs_err, float64)
pcs_weight = array(pcs_weight, float64)
+ pseudo_flags = array(pseudo_flags, int32)
# Convert the PCS from ppm to no units.
pcs = pcs * 1e-6
pcs_err = pcs_err * 1e-6
# Return the data structures.
- return pcs, pcs_err, pcs_weight, temp, frq
+ return pcs, pcs_err, pcs_weight, temp, frq, pseudo_flags
def set_errors(align_id=None, spin_id=None, sd=None):
@@ -893,6 +906,26 @@
# Set the error.
for id in align_ids:
spin.pcs_err[id] = sd
+
+
+def setup_pseudoatom_pcs():
+ """Make sure that the spin systems are properly set up for pseudo-atoms
and PCSs.
+
+ All spin data containers which are a member of a pseudo-atom will be
deselected.
+ """
+
+ # Loop over all spin data containers.
+ for pseudospin, pseudospin_id in spin_loop(return_id=True):
+ # No pseudo-atom, so do nothing.
+ if not is_pseudoatom(pseudospin):
+ return
+
+ # Loop over the atoms of the pseudo-atom.
+ for spin, spin_id in pseudoatom_loop(pseudospin, return_id=True):
+ # Deselect if needed.
+ if spin.select:
+ warn(RelaxWarning("Deselecting the '%s' spin as it is a
member of the '%s' pseudo-atom system." % (spin_id, pseudospin_id)))
+ spin.select = False
def structural_noise(align_id=None, rmsd=0.2, sim_num=1000, file=None,
dir=None, force=False):
Modified: trunk/specific_analyses/n_state_model/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/specific_analyses/n_state_model/__init__.py?rev=21450&r1=21449&r2=21450&view=diff
==============================================================================
--- trunk/specific_analyses/n_state_model/__init__.py (original)
+++ trunk/specific_analyses/n_state_model/__init__.py Thu Nov 14 15:00:49 2013
@@ -534,7 +534,7 @@
# Get the data structures for optimisation using PCSs as base data
sets.
pcs, pcs_err, pcs_weight, temp, frq = None, None, None, None, None
if 'pcs' in data_types:
- pcs, pcs_err, pcs_weight, temp, frq =
return_pcs_data(sim_index=sim_index)
+ pcs, pcs_err, pcs_weight, temp, frq, pcs_pseudo_flags =
return_pcs_data(sim_index=sim_index)
# Get the data structures for optimisation using RDCs as base data
sets.
rdcs, rdc_err, rdc_weight, rdc_vector, rdc_dj, absolute_rdc,
T_flags, j_couplings, rdc_pseudo_flags = None, None, None, None, None, None,
None, None, None
@@ -568,7 +568,7 @@
centre_fixed = cdp.paramag_centre_fixed
# Set up the class instance containing the target function.
- model = N_state_opt(model=cdp.model, N=cdp.N,
init_params=param_vector, probs=probs, full_tensors=full_tensors,
red_data=red_tensor_elem, red_errors=red_tensor_err,
full_in_ref_frame=full_in_ref_frame, fixed_tensors=fixed_tensors, pcs=pcs,
rdcs=rdcs, pcs_errors=pcs_err, rdc_errors=rdc_err, T_flags=T_flags,
j_couplings=j_couplings, rdc_pseudo_flags=rdc_pseudo_flags,
pcs_weights=pcs_weight, rdc_weights=rdc_weight, rdc_vect=rdc_vector,
temp=temp, frq=frq, dip_const=rdc_dj, absolute_rdc=absolute_rdc,
atomic_pos=atomic_pos, paramag_centre=paramag_centre,
scaling_matrix=scaling_matrix, centre_fixed=centre_fixed)
+ model = N_state_opt(model=cdp.model, N=cdp.N,
init_params=param_vector, probs=probs, full_tensors=full_tensors,
red_data=red_tensor_elem, red_errors=red_tensor_err,
full_in_ref_frame=full_in_ref_frame, fixed_tensors=fixed_tensors, pcs=pcs,
rdcs=rdcs, pcs_errors=pcs_err, rdc_errors=rdc_err, T_flags=T_flags,
j_couplings=j_couplings, rdc_pseudo_flags=rdc_pseudo_flags,
pcs_pseudo_flags=pcs_pseudo_flags, pcs_weights=pcs_weight,
rdc_weights=rdc_weight, rdc_vect=rdc_vector, temp=temp, frq=frq,
dip_const=rdc_dj, absolute_rdc=absolute_rdc, atomic_pos=atomic_pos,
paramag_centre=paramag_centre, scaling_matrix=scaling_matrix,
centre_fixed=centre_fixed)
# Return the data.
return model, param_vector, data_types, scaling_matrix
Modified: trunk/target_functions/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/target_functions/n_state_model.py?rev=21450&r1=21449&r2=21450&view=diff
==============================================================================
--- trunk/target_functions/n_state_model.py (original)
+++ trunk/target_functions/n_state_model.py Thu Nov 14 15:00:49 2013
@@ -38,7 +38,7 @@
class N_state_opt:
"""Class containing the target function of the optimisation of the
N-state model."""
- def __init__(self, model=None, N=None, init_params=None, probs=None,
full_tensors=None, red_data=None, red_errors=None, full_in_ref_frame=None,
fixed_tensors=None, pcs=None, pcs_errors=None, pcs_weights=None, rdcs=None,
rdc_errors=None, rdc_weights=None, rdc_vect=None, T_flags=None,
j_couplings=None, rdc_pseudo_flags=None, temp=None, frq=None, dip_const=None,
absolute_rdc=None, atomic_pos=None, paramag_centre=None, scaling_matrix=None,
centre_fixed=True):
+ def __init__(self, model=None, N=None, init_params=None, probs=None,
full_tensors=None, red_data=None, red_errors=None, full_in_ref_frame=None,
fixed_tensors=None, pcs=None, pcs_errors=None, pcs_weights=None, rdcs=None,
rdc_errors=None, rdc_weights=None, rdc_vect=None, T_flags=None,
j_couplings=None, rdc_pseudo_flags=None, pcs_pseudo_flags=None, temp=None,
frq=None, dip_const=None, absolute_rdc=None, atomic_pos=None,
paramag_centre=None, scaling_matrix=None, centre_fixed=True):
"""Set up the class instance for optimisation.
The N-state models
@@ -141,6 +141,8 @@
@type j_couplings: numpy rank-1 array
@keyword rdc_pseudo_flags: The array of flags specifying if one of
the atoms of the interatomic pair for the RDC are pseudo-atoms. The indices
correspond to the interatomic pairs.
@type rdc_pseudo_flags: numpy rank-1 int32 array
+ @keyword pcs_pseudo_flags: The array of flags specifying if one of
the atoms of the interatomic pair for the PCS are pseudo-atoms. The indices
correspond to the interatomic pairs.
+ @type pcs_pseudo_flags: numpy rank-1 int32 array
@keyword temp: The temperature of each experiment, used
for the PCS.
@type temp: numpy rank-1 array
@keyword frq: The frequency of each alignment, used
for the PCS.
@@ -171,6 +173,7 @@
self.T_flags = T_flags
self.j_couplings = j_couplings
self.rdc_pseudo_flags = rdc_pseudo_flags
+ self.pcs_pseudo_flags = pcs_pseudo_flags
self.temp = temp
self.frq = frq
self.atomic_pos = atomic_pos
r21450 - in /trunk: pipe_control/pcs.py specific_analyses/n_state_model/__init__.py target_functions/n_state_model.py