Author: bugman
Date: Sun Aug 17 19:08:49 2008
New Revision: 7205
URL: http://svn.gna.org/viewcvs/relax?rev=7205&view=rev
Log:
Reverted the last revision, r7204, as this included too much.
The command used was:
svn merge -r7204:7203 .
Modified:
branches/rdc_analysis/generic_fns/pcs.py
branches/rdc_analysis/maths_fns/n_state_model.py
branches/rdc_analysis/specific_fns/n_state_model.py
Modified: branches/rdc_analysis/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/pcs.py?rev=7205&r1=7204&r2=7205&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/pcs.py (original)
+++ branches/rdc_analysis/generic_fns/pcs.py Sun Aug 17 19:08:49 2008
@@ -596,7 +596,7 @@
@type spin_name_col: int or None
@param spin_num_col: The column containing the spin number
information.
@type spin_num_col: int or None
- @param sep: The column separator which, if None, defaults to
whitespace.
+ @param sep: The column seperator which, if None, defaults to
whitespace.
@type sep: str or None
"""
@@ -611,12 +611,8 @@
cdp = ds[ds.current_pipe]
# Test if PCS data corresponding to 'id' already exists.
- if data_col != None and hasattr(cdp, 'pcs_ids') and id in cdp.pcs_ids:
+ if hasattr(cdp, 'pcs_ids') and id in cdp.pcs_ids:
raise RelaxPCSError, id
-
- # Either the data or error column must be supplied.
- if data_col == None and error_col == None:
- raise RelaxError, "One of either the data or error column must be
supplied."
# Minimum number of columns.
min_col_num = max(mol_name_col, res_num_col, res_name_col, spin_num_col,
spin_name_col, data_col, error_col)
@@ -630,10 +626,7 @@
header_lines = 0
for i in xrange(len(file_data)):
try:
- if data_col != None:
- float(file_data[i][data_col])
- else:
- float(file_data[i][error_col])
+ float(file_data[i][data_col])
except:
header_lines = header_lines + 1
else:
@@ -650,9 +643,9 @@
# Skip missing data.
if len(file_data[i]) <= min_col_num:
continue
- elif data_col != None and file_data[i][data_col] == 'None':
+ elif file_data[i][data_col] == 'None':
continue
- elif error_col != None and file_data[i][error_col] == 'None':
+ elif error_col and file_data[i][error_col] == 'None':
continue
# Test that the data are numbers.
@@ -661,9 +654,8 @@
int(file_data[i][res_num_col])
if spin_num_col != None:
int(file_data[i][spin_num_col])
- if data_col != None:
- float(file_data[i][data_col])
- if error_col != None:
+ float(file_data[i][data_col])
+ if error_col:
float(file_data[i][error_col])
except ValueError:
raise RelaxError, "The PCS data in the line " +
`file_data[i]` + " is invalid."
@@ -693,16 +685,9 @@
id = generate_spin_id_data_array(data=file_data[i],
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col)
# Convert the data.
- value = None
- if data_col != None:
- value = eval(file_data[i][data_col])
- error = None
- if error_col != None:
+ value = eval(file_data[i][data_col])
+ if error_col:
error = eval(file_data[i][error_col])
-
- # Test the error value (cannot be 0.0).
- if error == 0.0:
- raise RelaxError, "An invalid error value of zero has been
encountered."
# Get the corresponding spin container.
spin = return_spin(id)
@@ -710,21 +695,12 @@
raise RelaxNoSpinError, id
# Add the data.
- if data_col != None:
- # Initialise.
- if not hasattr(spin, 'pcs'):
- spin.pcs = []
-
- # Append the value.
- spin.pcs.append(value)
-
- # Add the error.
- if error_col != None:
- # Initialise.
+ if not hasattr(spin, 'pcs'):
+ spin.pcs = []
+ spin.pcs.append(value)
+ if error_col:
if not hasattr(spin, 'pcs_err'):
spin.pcs_err = []
-
- # Append the error.
spin.pcs_err.append(error)
Modified: branches/rdc_analysis/maths_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/maths_fns/n_state_model.py?rev=7205&r1=7204&r2=7205&view=diff
==============================================================================
--- branches/rdc_analysis/maths_fns/n_state_model.py (original)
+++ branches/rdc_analysis/maths_fns/n_state_model.py Sun Aug 17 19:08:49 2008
@@ -231,30 +231,18 @@
self.num_align_params = self.num_align * 5
# PCS errors.
- if self.pcs_flag:
- err = False
- for i in xrange(len(pcs_errors)):
- for j in xrange(len(pcs_errors[i])):
- if not isNaN(pcs_errors[i, j]):
- err = True
- if err:
- self.pcs_sigma_ij = pcs_errors
- else:
- # Missing errors (the values need to be small, close to
ppm units, so the chi-squared value is comparable to the RDC).
- self.pcs_sigma_ij = 0.03 * 1e-6 * ones((self.num_align,
self.num_spins), float64)
+ if pcs_errors == None:
+ # Missing errors (the values need to be small, close to ppm
units, so the chi-squared value is comparable to the RDC).
+ self.pcs_sigma_ij = 0.03 * 1e-6 * ones((self.num_align,
self.num_spins), float64)
+ else:
+ self.pcs_sigma_ij = pcs_errors
# RDC errors.
- if self.rdc_flag:
- err = False
- for i in xrange(len(rdc_errors)):
- for j in xrange(len(rdc_errors[i])):
- if not isNaN(rdc_errors[i, j]):
- err = True
- if err:
- self.rdc_sigma_ij = rdc_errors
- else:
- # Missing errors.
- self.rdc_sigma_ij = ones((self.num_align,
self.num_spins), float64)
+ if rdc_errors == None:
+ # Missing errors.
+ self.rdc_sigma_ij = ones((self.num_align, self.num_spins),
float64)
+ else:
+ self.rdc_sigma_ij = rdc_errors
# Alignment tensor function and gradient matrices.
self.A = zeros((self.num_align, 3, 3), float64)
@@ -279,9 +267,6 @@
# Change the NaN to zero.
self.Dij[i, j] = 0.0
- # Change the error to one (to avoid zero
division).
- self.rdc_sigma_ij[i, j] = 1.0
-
# Missing data matrices (PCS).
if self.pcs_flag:
self.missing_deltaij = zeros((self.num_align,
self.num_spins), float64)
@@ -293,9 +278,6 @@
# Change the NaN to zero.
self.deltaij[i, j] = 0.0
-
- # Change the error to one (to avoid zero
division).
- self.pcs_sigma_ij[i, j] = 1.0
# PCS function, gradient, and Hessian matrices.
self.deltaij_theta = zeros((self.num_align, self.num_spins),
float64)
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=7205&r1=7204&r2=7205&view=diff
==============================================================================
--- branches/rdc_analysis/specific_fns/n_state_model.py (original)
+++ branches/rdc_analysis/specific_fns/n_state_model.py Sun Aug 17 19:08:49
2008
@@ -402,7 +402,6 @@
# Initialise.
pcs = []
- pcs_err = []
unit_vect = []
r = []
pcs_const = []
@@ -419,12 +418,6 @@
# Append the PCSs to the list.
pcs.append(spin.pcs)
-
- # Append the PCS errors (or a list of None).
- if hasattr(spin, 'pcs_err'):
- pcs_err.append(spin.pcs_err)
- else:
- pcs_err.append([None]*len(spin.pcs))
# Add empty lists to the r and unit_vector lists.
unit_vect.append([])
@@ -480,16 +473,14 @@
# Initialise the numpy objects (the pcs matrix is transposed!).
pcs_numpy = zeros((len(pcs[0]), len(pcs)), float64)
- pcs_err_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 and error.
+ # Transpose and store the PCS value.
pcs_numpy[align_index, spin_index] =
pcs[spin_index][align_index]
- pcs_err_numpy[align_index, spin_index] =
pcs_err[spin_index][align_index]
# Loop over the N states.
for state_index in xrange(len(unit_vect[spin_index])):
@@ -498,10 +489,9 @@
# Convert the PCS from ppm to no units.
pcs_numpy = pcs_numpy * 1e-6
- pcs_err_numpy = pcs_err_numpy * 1e-6
# Return the data structures.
- return pcs_numpy, pcs_err_numpy, unit_vect_numpy, array(pcs_const)
+ return pcs_numpy, unit_vect_numpy, array(pcs_const)
def __minimise_setup_rdcs(self, param_vector=None, scaling_matrix=None):
@@ -520,7 +510,6 @@
# Initialise.
rdcs = []
- rdc_err = []
xh_vectors = []
dj = []
@@ -535,7 +524,6 @@
# Add rows of None if other data exists.
if hasattr(spin, 'pcs'):
rdcs.append([None]*len(cdp.align_tensors))
- rdc_err.append([None]*len(cdp.align_tensors))
xh_vectors.append([None]*3)
dj.append(None)
@@ -550,7 +538,6 @@
# Add rows of None if other data exists.
if hasattr(spin, 'pcs'):
rdcs.append([None]*len(cdp.align_tensors))
- rdc_err.append([None]*len(cdp.align_tensors))
xh_vectors.append([None]*3)
dj.append(None)
@@ -561,12 +548,6 @@
rdcs.append(spin.rdc)
xh_vectors.append(spin.xh_vect)
- # Append the PCS errors (or a list of None).
- if hasattr(spin, 'rdc_err'):
- rdc_err.append(spin.rdc_err)
- else:
- rdc_err.append([None]*len(cdp.align_tensors))
-
# Gyromagnetic ratios.
gx = return_gyromagnetic_ratio(spin.heteronuc_type)
gh = return_gyromagnetic_ratio(spin.proton_type)
@@ -576,16 +557,14 @@
# Initialise the numpy objects (the rdc matrix is transposed!).
rdcs_numpy = zeros((len(rdcs[0]), len(rdcs)), float64)
- rdc_err_numpy = zeros((len(rdcs[0]), len(rdcs)), float64)
xh_vect_numpy = zeros((len(xh_vectors), len(xh_vectors[0]), 3),
float64)
# Loop over the spins.
for spin_index in xrange(len(rdcs)):
# Loop over the alignments.
for align_index in xrange(len(rdcs[spin_index])):
- # Transpose and store the RDC value and error.
+ # Transpose and store the RDC value.
rdcs_numpy[align_index, spin_index] =
rdcs[spin_index][align_index]
- rdc_err_numpy[align_index, spin_index] =
rdc_err[spin_index][align_index]
# Loop over the N states.
for state_index in xrange(len(xh_vectors[spin_index])):
@@ -593,7 +572,7 @@
xh_vect_numpy[spin_index, state_index] =
xh_vectors[spin_index][state_index]
# Return the data structures.
- return rdcs_numpy, rdc_err_numpy, xh_vect_numpy, array(dj, float64)
+ return rdcs_numpy, xh_vect_numpy, array(dj, float64)
def __minimise_setup_tensors(self):
@@ -1102,17 +1081,17 @@
full_tensors, red_tensor_elem, red_tensor_err, full_in_ref_frame
= self.__minimise_setup_tensors()
# Get the data structures for optimisation using PCSs as base data
sets.
- pcs, pcs_err, pcs_vect, pcs_dj = None, None, None, None
+ pcs, pcs_vect, pcs_dj = None, None, None
if 'pcs' in data_types:
- pcs, pcs_err, pcs_vect, pcs_dj = self.__minimise_setup_pcs()
+ pcs, pcs_vect, pcs_dj = self.__minimise_setup_pcs()
# Get the data structures for optimisation using RDCs as base data
sets.
- rdcs, rdc_err, xh_vect, rdc_dj = None, None, None, None
+ rdcs, xh_vect, rdc_dj = None, None, None
if 'rdc' in data_types:
- rdcs, rdc_err, xh_vect, rdc_dj = self.__minimise_setup_rdcs()
+ rdcs, xh_vect, rdc_dj = self.__minimise_setup_rdcs()
# Set up the class instance containing the target function.
- model = N_state_opt(model=cdp.model, N=cdp.N,
init_params=param_vector, full_tensors=full_tensors,
red_data=red_tensor_elem, red_errors=red_tensor_err,
full_in_ref_frame=full_in_ref_frame, pcs=pcs, rdcs=rdcs, pcs_errors=pcs_err,
rdc_errors=rdc_err, pcs_vect=pcs_vect, xh_vect=xh_vect, pcs_const=pcs_dj,
dip_const=rdc_dj, scaling_matrix=scaling_matrix)
+ model = N_state_opt(model=cdp.model, N=cdp.N,
init_params=param_vector, full_tensors=full_tensors,
red_data=red_tensor_elem, red_errors=red_tensor_err,
full_in_ref_frame=full_in_ref_frame, pcs=pcs, rdcs=rdcs, pcs_vect=pcs_vect,
xh_vect=xh_vect, pcs_const=pcs_dj, dip_const=rdc_dj,
scaling_matrix=scaling_matrix)
# Minimisation.
if constraints:
r7205 - in /branches/rdc_analysis: generic_fns/pcs.py maths_fns/n_state_model.py specific_fns/n_state_model.py