Author: bugman
Date: Thu Sep 5 14:43:49 2013
New Revision: 20846
URL: http://svn.gna.org/viewcvs/relax?rev=20846&view=rev
Log:
More fixes due to the cdp.exp_type change.
This follows from http://thread.gmane.org/gmane.science.nmr.relax.devel/4530,
the thread about
supporting multiple data types such as SQ+MQ data simultaneously.
Modified:
branches/relax_disp/specific_analyses/relax_disp/api.py
branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
branches/relax_disp/specific_analyses/relax_disp/nessy.py
branches/relax_disp/specific_analyses/relax_disp/parameters.py
branches/relax_disp/specific_analyses/relax_disp/sherekhan.py
Modified: branches/relax_disp/specific_analyses/relax_disp/api.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/api.py?rev=20846&r1=20845&r2=20846&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/api.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/api.py Thu Sep 5
14:43:49 2013
@@ -163,17 +163,19 @@
return results
- def _back_calc_peak_intensities(self, spin=None, frq=None, point=None):
+ def _back_calc_peak_intensities(self, spin=None, exp_type=None,
frq=None, point=None):
"""Back-calculation of peak intensity for the given relaxation time.
- @keyword spin: The specific spin data container.
- @type spin: SpinContainer instance
- @keyword frq: The spectrometer frequency.
- @type frq: float
- @keyword point: The dispersion point data (either the spin-lock
field strength in Hz or the nu_CPMG frequency in Hz).
- @type point: float
- @return: The back-calculated peak intensities for the given
exponential curve.
- @rtype: numpy rank-1 float array
+ @keyword spin: The specific spin data container.
+ @type spin: SpinContainer instance
+ @keyword exp_type: The experiment type.
+ @type exp_type: str
+ @keyword frq: The spectrometer frequency.
+ @type frq: float
+ @keyword point: The dispersion point data (either the spin-lock
field strength in Hz or the nu_CPMG frequency in Hz).
+ @type point: float
+ @return: The back-calculated peak intensities for the
given exponential curve.
+ @rtype: numpy rank-1 float array
"""
# Check.
@@ -195,8 +197,8 @@
times = []
for time in cdp.relax_time_list:
# The data.
- values.append(average_intensity(spin=spin, frq=frq, point=point,
time=time))
- errors.append(average_intensity(spin=spin, frq=frq, point=point,
time=time, error=True))
+ values.append(average_intensity(spin=spin, exp_type=exp_type,
frq=frq, point=point, time=time))
+ errors.append(average_intensity(spin=spin, exp_type=exp_type,
frq=frq, point=point, time=time, error=True))
times.append(time)
# The scaling matrix in a diagonalised list form.
@@ -487,8 +489,8 @@
errors = []
times = []
for time in cdp.relax_time_list:
- values.append(average_intensity(spin=spin, frq=frq,
point=point, time=time, sim_index=sim_index))
- errors.append(average_intensity(spin=spin, frq=frq,
point=point, time=time, error=True))
+ values.append(average_intensity(spin=spin,
exp_type=exp_type, frq=frq, point=point, time=time, sim_index=sim_index))
+ errors.append(average_intensity(spin=spin,
exp_type=exp_type, frq=frq, point=point, time=time, error=True))
times.append(time)
# The scaling matrix in a diagonalised list form.
@@ -621,14 +623,14 @@
elif model == MODEL_NOREX:
print("The model for no chemical exchange relaxation.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
# LM63 model.
elif model == MODEL_LM63:
print("The Luz and Meiboom (1963) 2-site fast exchange model.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['phi_ex', 'kex']
@@ -636,7 +638,7 @@
elif model == MODEL_LM63_3SITE:
print("The Luz and Meiboom (1963) 3-site fast exchange model.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['phi_ex_B', 'phi_ex_C', 'kB', 'kC']
@@ -644,9 +646,9 @@
elif model == MODEL_CR72_FULL:
print("The full Carver and Richards (1972) 2-site model for all
time scales.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2a')
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2b')
params += ['pA', 'dw', 'kex']
@@ -654,7 +656,7 @@
elif model == MODEL_CR72:
print("The reduced Carver and Richards (1972) 2-site model for
all time scales, whereby the simplification R20A = R20B is assumed.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -662,7 +664,7 @@
elif model == MODEL_IT99:
print("The Ishima and Torchia (1999) CPMG 2-site model for all
time scales with pA >> pB.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['phi_ex', 'padw2', 'tex']
@@ -670,7 +672,7 @@
elif model == MODEL_TSMFK01:
print("The Tollinger, Kay et al. (2001) 2-site very-slow
exchange model, range of microsecond to second time scale.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2a')
params += ['dw', 'kA']
@@ -678,9 +680,9 @@
elif model == MODEL_NS_CPMG_2SITE_3D_FULL:
print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2a')
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2b')
params += ['pA', 'dw', 'kex']
@@ -688,7 +690,7 @@
elif model == MODEL_NS_CPMG_2SITE_3D:
print("The reduced numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using 3D magnetisation vectors,
whereby the simplification R20A = R20B is assumed.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -696,7 +698,7 @@
elif model == MODEL_NS_CPMG_2SITE_EXPANDED:
print("The numerical solution for the 2-site Bloch-McConnell
equations for CPMG data expanded using Maple by Nikolai Skrynnikov.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -704,9 +706,9 @@
elif model == MODEL_NS_CPMG_2SITE_STAR_FULL:
print("The full numerical solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2a')
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2b')
params += ['pA', 'dw', 'kex']
@@ -714,7 +716,7 @@
elif model == MODEL_NS_CPMG_2SITE_STAR:
print("The numerical reduced solution for the 2-site
Bloch-McConnell equations for CPMG data using complex conjugate matrices,
whereby the simplification R20A = R20B is assumed.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -722,7 +724,7 @@
elif model == MODEL_M61:
print("The Meiboom (1961) 2-site fast exchange model for
R1rho-type experiments.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['phi_ex', 'kex']
@@ -730,7 +732,7 @@
elif model == MODEL_M61B:
print("The Meiboom (1961) on-resonance 2-site model with skewed
populations (pA >> pB) for R1rho-type experiments.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -738,7 +740,7 @@
elif model == MODEL_DPL94:
print("The Davis, Perlman and London (1994) 2-site fast exchange
model for R1rho-type experiments.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['phi_ex', 'kex']
@@ -746,7 +748,7 @@
elif model == MODEL_TP02:
print("The Trott and Palmer (2002) off-resonance 2-site model
for R1rho-type experiments.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
@@ -754,7 +756,7 @@
elif model == MODEL_NS_R1RHO_2SITE:
print("The reduced numerical solution for the 2-site
Bloch-McConnell equations for R1rho data using 3D magnetisation vectors,
whereby the simplification R20A = R20B is assumed.")
params = []
- for exp_type, frq in loop_exp_frq():
+ for frq in loop_frq():
params.append('r2')
params += ['pA', 'dw', 'kex']
Modified: branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py?rev=20846&r1=20845&r2=20846&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/cpmgfit.py Thu Sep 5
14:43:49 2013
@@ -41,7 +41,7 @@
from pipe_control import pipes
from pipe_control.spectrometer import get_frequencies
from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
-from specific_analyses.relax_disp.disp_data import loop_frq_point,
return_param_key_from_data
+from specific_analyses.relax_disp.disp_data import loop_exp_frq_point,
return_param_key_from_data
def cpmgfit_execute(dir=None, binary='cpmgfit', force=False):
@@ -259,7 +259,7 @@
# The data.
file.write("data\n")
- for frq, point in loop_frq_point():
+ for exp_type, frq, point in loop_exp_frq_point():
# The parameter key.
param_key = return_param_key_from_data(frq=frq, point=point)
Modified: branches/relax_disp/specific_analyses/relax_disp/nessy.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/nessy.py?rev=20846&r1=20845&r2=20846&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/nessy.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/nessy.py Thu Sep 5
14:43:49 2013
@@ -32,7 +32,7 @@
from pipe_control import pipes
from pipe_control.spectrometer import get_frequencies
from pipe_control.mol_res_spin import exists_mol_res_spin_data, spin_loop
-from specific_analyses.relax_disp.disp_data import find_intensity_keys,
loop_frq, loop_frq_point_time, loop_point, return_index_from_disp_point,
return_index_from_frq
+from specific_analyses.relax_disp.disp_data import find_intensity_keys,
loop_exp_frq, loop_exp_frq_point_time, loop_point,
return_index_from_disp_point, return_index_from_frq
def nessy_input(file='save.NESSY', dir=None, spin_id=None, force=False):
@@ -281,14 +281,14 @@
raise RelaxError("A residue number of greater than 700 is
not supported in NESSY.")
# Loop over all spectrometer frequencies.
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
# Loop over all dispersion points.
field_index = 0
- for point in loop_point(skip_ref=False):
+ for point in loop_point(exp_type=exp_type, skip_ref=False):
# Indices and keys.
exp_index = return_index_from_frq(frq)
point_index = return_index_from_disp_point(point)
- keys = find_intensity_keys(frq=frq, point=point,
time=cdp.relax_time_list[0])
+ keys = find_intensity_keys(exp_type=exp_type, frq=frq,
point=point, time=cdp.relax_time_list[0])
# Convert the reference point for NESSY input.
if point == None:
@@ -320,7 +320,7 @@
frq_T = get_frequencies(units='T')
# Loop over all data points.
- for frq, point, time in loop_frq_point_time():
+ for exp_type, frq, point, time in loop_exp_frq_point_time():
# The frequency index.
frq_index = cdp.spectrometer_frq_list.index(frq)
Modified: branches/relax_disp/specific_analyses/relax_disp/parameters.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/parameters.py?rev=20846&r1=20845&r2=20846&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/parameters.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/parameters.py Thu Sep 5
14:43:49 2013
@@ -35,7 +35,7 @@
from lib.text.sectioning import subsection
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data, return_spin
-from specific_analyses.relax_disp.disp_data import count_frq, loop_cluster,
loop_frq, loop_frq_point
+from specific_analyses.relax_disp.disp_data import count_frq, loop_cluster,
loop_frq
from specific_analyses.relax_disp.variables import EXP_TYPE_LIST_VAR_TIME,
MODEL_R2EFF, MODEL_M61B
@@ -279,6 +279,7 @@
# Switch back to the original data pipe.
pipes.switch(pipe_orig)
+
def disassemble_param_vector(param_vector=None, key=None, spins=None,
sim_index=None):
"""Disassemble the parameter vector.
Modified: branches/relax_disp/specific_analyses/relax_disp/sherekhan.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_disp/specific_analyses/relax_disp/sherekhan.py?rev=20846&r1=20845&r2=20846&view=diff
==============================================================================
--- branches/relax_disp/specific_analyses/relax_disp/sherekhan.py (original)
+++ branches/relax_disp/specific_analyses/relax_disp/sherekhan.py Thu Sep 5
14:43:49 2013
@@ -40,7 +40,7 @@
from pipe_control import pipes
from pipe_control.mol_res_spin import exists_mol_res_spin_data,
return_residue, spin_loop
from pipe_control.spectrometer import get_frequencies
-from specific_analyses.relax_disp.disp_data import loop_cluster, loop_frq,
loop_point, return_param_key_from_data, spin_ids_to_containers
+from specific_analyses.relax_disp.disp_data import loop_cluster,
loop_exp_frq, loop_point, return_param_key_from_data, spin_ids_to_containers
def sherekhan_input(spin_id=None, force=False):
@@ -79,7 +79,7 @@
# Loop over the magnetic fields.
frq_index = 0
- for frq in loop_frq():
+ for exp_type, frq in loop_exp_frq():
# The ShereKhan input file for the spin cluster.
file_name = 'sherekhan_frq%s.in' % (frq_index+1)
dir_name = 'cluster%s' % (cluster_index+1)
@@ -111,7 +111,7 @@
lines.append("# %s%s\n" % (res_name, res.num))
# Loop over the dispersion points.
- for point in loop_point(skip_ref=True):
+ for point in loop_point(exp_type=exp_type, skip_ref=True):
# The parameter key.
param_key = return_param_key_from_data(frq=frq,
point=point)
r20846 - in /branches/relax_disp/specific_analyses/relax_disp: api.py cpmgfit.py nessy.py parameters.py sherekhan.py