Author: bugman
Date: Fri Jul 4 00:10:41 2008
New Revision: 6642
URL: http://svn.gna.org/viewcvs/relax?rev=6642&view=rev
Log:
Renamed 'self.param_set' to 'model_type'.
Modified:
1.3/generic_fns/dasha.py
1.3/specific_fns/model_free/main.py
1.3/specific_fns/model_free/results.py
Modified: 1.3/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/dasha.py?rev=6642&r1=6641&r2=6642&view=diff
==============================================================================
--- 1.3/generic_fns/dasha.py (original)
+++ 1.3/generic_fns/dasha.py Fri Jul 4 00:10:41 2008
@@ -59,14 +59,14 @@
raise RelaxNoSequenceError, self.run
# Determine the parameter set.
- self.param_set =
self.relax.specific.model_free.determine_model_type(self.run)
+ model_type =
self.relax.specific.model_free.determine_model_type(self.run)
# Test if diffusion tensor data for the run exists.
- if self.param_set != 'local_tm' and not ds.diff.has_key(self.run):
+ if model_type != 'local_tm' and not ds.diff.has_key(self.run):
raise RelaxNoTensorError, 'diffusion'
# Test if the PDB file has been loaded (for the spheroid and
ellipsoid).
- if self.param_set != 'local_tm' and ds.diff[self.run].type !=
'sphere' and not ds.pdb.has_key(self.run):
+ if model_type != 'local_tm' and ds.diff[self.run].type != 'sphere'
and not ds.pdb.has_key(self.run):
raise RelaxNoPdbError, self.run
# Test if the nucleus type has been set.
@@ -139,7 +139,7 @@
# Set the diffusion tensor.
file.write('\n# Set the diffusion tensor.\n')
- if self.param_set != 'local_tm':
+ if model_type != 'local_tm':
# Sphere.
if ds.diff[self.run].type == 'sphere':
file.write('set tr ' + `ds.diff[self.run].tm / 1e-9` + '\n')
@@ -225,7 +225,7 @@
file.write('exit\n')
# Individual residue optimisation.
- if self.param_set == 'mf':
+ if model_type == 'mf':
# Loop over the residues.
for i in xrange(len(ds.res[self.run])):
# Reassign the data.
@@ -333,7 +333,7 @@
file.write('write chi2.out F\n')
else:
- raise RelaxError, 'Optimisation of the parameter set ' +
`self.param_set` + ' currently not supported.'
+ raise RelaxError, 'Optimisation of the parameter set ' +
`model_type` + ' currently not supported.'
def execute(self, run, dir, force, binary):
Modified: 1.3/specific_fns/model_free/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/main.py?rev=6642&r1=6641&r2=6642&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/main.py (original)
+++ 1.3/specific_fns/model_free/main.py Fri Jul 4 00:10:41 2008
@@ -1066,7 +1066,7 @@
c1, c2 = args
# Get the tm value.
- if self.param_set == 'local_tm':
+ if model_type == 'local_tm':
tm = ds.res[run][i].local_tm
else:
tm = ds.diff[run].tm
@@ -1131,10 +1131,10 @@
raise RelaxNoModelError, self.run
# Determine the parameter set type.
- self.param_set = self.determine_model_type()
+ model_type = self.determine_model_type()
# Residue index.
- if self.param_set == 'mf' or self.param_set == 'local_tm':
+ if model_type == 'mf' or model_type == 'local_tm':
index = i
else:
index = None
@@ -2453,7 +2453,7 @@
# Diffusion tensor parameter errors.
####################################
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
# Spherical diffusion.
if ds.diff[self.run].type == 'sphere':
# Return the parameter array.
@@ -2501,7 +2501,7 @@
# Model-free parameter errors for the parameter set 'all'.
##########################################################
- if self.param_set == 'all':
+ if model_type == 'all':
# Loop over the sequence.
for i in xrange(len(ds.res[self.run])):
# Skip deselected residues.
@@ -2521,7 +2521,7 @@
# Model-free parameters for the parameter sets 'mf' and 'local_tm'.
###################################################################
- if self.param_set == 'mf' or self.param_set == 'local_tm':
+ if model_type == 'mf' or model_type == 'local_tm':
# Skip deselected residues.
if not ds.res[self.run][instance].select:
return
@@ -2604,7 +2604,7 @@
self.run = run
# Determine the parameter set type.
- self.param_set = self.determine_model_type()
+ model_type = self.determine_model_type()
# Get the parameter object names.
param_names = self.data_names(set='params')
@@ -2613,7 +2613,7 @@
min_names = self.data_names(set='min')
# List of diffusion tensor parameters.
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
# Spherical diffusion.
if ds.diff[self.run].type == 'sphere':
diff_params = ['tm']
@@ -2631,7 +2631,7 @@
#############################################################
# Diffusion tensor parameters and non residue specific minimisation
statistics.
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
# Loop over the parameters.
for object_name in diff_params:
# Name for the simulation object.
@@ -2651,7 +2651,7 @@
raise RelaxError, "Monte Carlo parameter values have
already been set."
# Residue specific parameters.
- if self.param_set != 'diff':
+ if model_type != 'diff':
for i in xrange(len(ds.res[self.run])):
# Skip deselected residues.
if not ds.res[self.run][i].select:
@@ -2697,7 +2697,7 @@
sim_object[self.run].append(deepcopy(object[self.run]))
# Diffusion tensor parameters and non residue specific minimisation
statistics.
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
# Loop over the parameters.
for object_name in diff_params:
# Name for the simulation object.
@@ -2715,7 +2715,7 @@
sim_object.append(deepcopy(getattr(ds.diff[self.run],
object_name)))
# Residue specific parameters.
- if self.param_set != 'diff':
+ if model_type != 'diff':
for i in xrange(len(ds.res[self.run])):
# Skip deselected residues.
if not ds.res[self.run][i].select:
@@ -2772,10 +2772,10 @@
self.run = run
# Determine the parameter set type.
- self.param_set = self.determine_model_type()
+ model_type = self.determine_model_type()
# Single instance.
- if self.param_set == 'all' or self.param_set == 'diff':
+ if model_type == 'all' or model_type == 'diff':
return ds.chi2_sim[self.run]
# Multiple instances.
@@ -2799,7 +2799,7 @@
# Diffusion tensor parameters.
##############################
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
# Spherical diffusion.
if ds.diff[self.run].type == 'sphere':
# Return the parameter array.
@@ -2847,7 +2847,7 @@
# Model-free parameters for the parameter set 'all'.
####################################################
- if self.param_set == 'all':
+ if model_type == 'all':
# Loop over the sequence.
for i in xrange(len(ds.res[self.run])):
# Skip deselected residues.
@@ -2867,7 +2867,7 @@
# Model-free parameters for the parameter sets 'mf' and 'local_tm'.
###################################################################
- if self.param_set == 'mf' or self.param_set == 'local_tm':
+ if model_type == 'mf' or model_type == 'local_tm':
# Skip deselected residues.
if not ds.res[self.run][instance].select:
return
@@ -2889,10 +2889,10 @@
self.run = run
# Determine the parameter set type.
- self.param_set = self.determine_model_type()
+ model_type = self.determine_model_type()
# Single instance.
- if self.param_set == 'all' or self.param_set == 'diff':
+ if model_type == 'all' or model_type == 'diff':
return ds.select_sim[self.run]
# Multiple instances.
@@ -2934,12 +2934,12 @@
self.run = run
# Determine the parameter set type.
- self.param_set = self.determine_model_type()
+ model_type = self.determine_model_type()
# Simulation deselect.
if sim_index != None:
# Single instance.
- if self.param_set == 'mf' or self.param_set == 'local_tm':
+ if model_type == 'mf' or model_type == 'local_tm':
ds.res[self.run][i].select_sim[sim_index] = 0
# Multiple instances.
@@ -2949,5 +2949,5 @@
# Residue deselect.
else:
# Single residue.
- if self.param_set == 'mf' or self.param_set == 'local_tm':
+ if model_type == 'mf' or model_type == 'local_tm':
ds.res[self.run][i].select = 0
Modified: 1.3/specific_fns/model_free/results.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/results.py?rev=6642&r1=6641&r2=6642&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/results.py (original)
+++ 1.3/specific_fns/model_free/results.py Fri Jul 4 00:10:41 2008
@@ -1166,7 +1166,7 @@
self.run = run
# Determine the parameter set type.
- self.param_set = self.determine_model_type()
+ model_type = self.determine_model_type()
# Header.
@@ -1174,7 +1174,7 @@
# Diffusion parameters.
diff_params = None
- if self.param_set != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
+ if model_type != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
# Sphere.
if ds.diff[self.run].type == 'sphere':
diff_params = ['tm_(s)']
@@ -1208,7 +1208,7 @@
# Diffusion parameters.
diff_type = None
diff_params = None
- if self.param_set != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
+ if model_type != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
# Sphere.
if ds.diff[self.run].type == 'sphere':
diff_type = 'sphere'
@@ -1326,7 +1326,7 @@
# Minimisation details.
try:
# Global minimisation results.
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
chi2 = `ds.chi2[self.run]`
iter = ds.iter[self.run]
f = ds.f_count[self.run]
@@ -1392,7 +1392,7 @@
ri_error.append(None)
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='value', nucleus=nucleus,
model=model, equation=equation, params=params, param_set=self.param_set,
s2=s2, s2f=s2f, s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex,
r=r, csa=csa, chi2=chi2, i=iter, f=f, g=g, h=h, warn=warn,
diff_type=diff_type, diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=heteronuc, pdb_proton=proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='value', nucleus=nucleus,
model=model, equation=equation, params=params, param_set=model_type, s2=s2,
s2f=s2f, s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r,
csa=csa, chi2=chi2, i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=heteronuc, pdb_proton=proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
# Errors.
@@ -1402,7 +1402,7 @@
if self.has_errors():
# Diffusion parameters.
diff_params = None
- if self.param_set != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
+ if model_type != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
# Sphere.
if ds.diff[self.run].type == 'sphere':
diff_params = [None]
@@ -1416,7 +1416,7 @@
diff_params = [None, None, None, None, None, None]
# Diffusion parameter errors.
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
# Sphere.
if ds.diff[self.run].type == 'sphere' and
hasattr(ds.diff[self.run], 'tm_err'):
diff_params = [`ds.diff[self.run].tm_err`]
@@ -1520,7 +1520,7 @@
xh_vect = replace(`data.xh_vect.tolist()`, ' ', '')
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='error', nucleus=nucleus,
model=model, equation=equation, params=params, param_set=self.param_set,
s2=s2, s2f=s2f, s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex,
r=r, csa=csa, diff_type=diff_type, diff_params=diff_params, pdb=pdb,
pdb_model=pdb_model, pdb_heteronuc=heteronuc, pdb_proton=proton,
xh_vect=xh_vect, ri_labels=ri_labels, remap_table=remap_table,
frq_labels=frq_labels, frq=frq, ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, data_set='error', nucleus=nucleus,
model=model, equation=equation, params=params, param_set=model_type, s2=s2,
s2f=s2f, s2s=s2s, local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r,
csa=csa, diff_type=diff_type, diff_params=diff_params, pdb=pdb,
pdb_model=pdb_model, pdb_heteronuc=heteronuc, pdb_proton=proton,
xh_vect=xh_vect, ri_labels=ri_labels, remap_table=remap_table,
frq_labels=frq_labels, frq=frq, ri=ri, ri_error=ri_error)
# Simulation values.
@@ -1532,9 +1532,9 @@
for i in xrange(ds.sim_number[self.run]):
# Diffusion parameters.
diff_params = None
- if self.param_set != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
+ if model_type != 'local_tm' and hasattr(ds, 'diff') and
ds.diff.has_key(self.run):
# Diffusion parameter simulation values.
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
# Sphere.
if ds.diff[self.run].type == 'sphere':
diff_params = [`ds.diff[self.run].tm_sim[i]`]
@@ -1580,7 +1580,7 @@
params = replace(`data.params`, ' ', '')
# Selected simulation.
- if self.param_set == 'diff' or self.param_set == 'all':
+ if model_type == 'diff' or model_type == 'all':
select_sim = ds.select_sim[self.run][i]
else:
select_sim = data.select_sim[i]
@@ -1648,7 +1648,7 @@
# Minimisation details.
try:
# Global minimisation results.
- if self.param_set == 'diff' or self.param_set ==
'all':
+ if model_type == 'diff' or model_type == 'all':
chi2 = `ds.chi2_sim[self.run][i]`
iter = ds.iter_sim[self.run][i]
f = ds.f_count_sim[self.run][i]
@@ -1707,4 +1707,4 @@
xh_vect = replace(`data.xh_vect.tolist()`, ' ', '')
# Write the line.
- self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, select_sim=select_sim,
data_set='sim_'+`i`, nucleus=nucleus, model=model, equation=equation,
params=params, param_set=self.param_set, s2=s2, s2f=s2f, s2s=s2s,
local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa, chi2=chi2,
i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=heteronuc, pdb_proton=proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
+ self.write_columnar_line(file=file, num=data.num,
name=data.name, select=data.select, select_sim=select_sim,
data_set='sim_'+`i`, nucleus=nucleus, model=model, equation=equation,
params=params, param_set=model_type, s2=s2, s2f=s2f, s2s=s2s,
local_tm=local_tm, te=te, tf=tf, ts=ts, rex=rex, r=r, csa=csa, chi2=chi2,
i=iter, f=f, g=g, h=h, warn=warn, diff_type=diff_type,
diff_params=diff_params, pdb=pdb, pdb_model=pdb_model,
pdb_heteronuc=heteronuc, pdb_proton=proton, xh_vect=xh_vect,
ri_labels=ri_labels, remap_table=remap_table, frq_labels=frq_labels, frq=frq,
ri=ri, ri_error=ri_error)
r6642 - in /1.3: generic_fns/dasha.py specific_fns/model_free/main.py specific_fns/model_free/results.py