Author: semor
Date: Wed Jan 9 19:28:21 2008
New Revision: 4576
URL: http://svn.gna.org/viewcvs/relax?rev=4576&view=rev
Log:
Completed the changes from the previous commit (4575) as the model_free
directory had been skipped.
Changed almost all instances of the 'print_flag' arg to 'verbosity' in the
specific_fns/model_free
directory. Exceptions were made for instances in generic_minimise() functions
where
'print_flag=print_flag' becomes 'print_flag=verbosity'.
This was pointed out in a post by Edward d'Auvergne at :
https://mail.gna.org/public/relax-devel/2008-01/msg00021.html (Message-id:
<7f080ed10801090840s341431f2nb75b15b137b46176@xxxxxxxxxxxxxx>)
Modified:
1.3/specific_fns/model_free/model_free.py
Modified: 1.3/specific_fns/model_free/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/model_free.py?rev=4576&r1=4575&r2=4576&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/model_free.py (original)
+++ 1.3/specific_fns/model_free/model_free.py Wed Jan 9 19:28:21 2008
@@ -406,12 +406,12 @@
return value
- def calculate(self, run=None, res_num=None, print_flag=1,
sim_index=None):
+ def calculate(self, run=None, res_num=None, verbosity=1, sim_index=None):
"""Calculation of the model-free chi-squared value."""
# Arguments.
self.run = run
- self.print_flag = print_flag
+ self.verbosity = verbosity
# Test if the sequence data for self.run is loaded.
if not relax_data_store.res.has_key(self.run):
@@ -1520,7 +1520,7 @@
return self.param_vector
- def grid_search(self, run, lower, upper, inc, constraints, print_flag,
sim_index=None):
+ def grid_search(self, run, lower, upper, inc, constraints, verbosity,
sim_index=None):
"""The grid search function."""
# Arguments.
@@ -1529,7 +1529,7 @@
self.inc = inc
# Minimisation.
- self.minimise(run=run, min_algor='grid', constraints=constraints,
print_flag=print_flag, sim_index=sim_index)
+ self.minimise(run=run, min_algor='grid', constraints=constraints,
verbosity=verbosity, sim_index=sim_index)
def grid_search_setup(self, index=None):
@@ -2016,7 +2016,7 @@
return [-100 * 1e-6, -300 * 1e-6]
- def minimise(self, run=None, min_algor=None, min_options=None,
func_tol=None, grad_tol=None, max_iterations=None, constraints=0, scaling=1,
print_flag=0, sim_index=None):
+ def minimise(self, run=None, min_algor=None, min_options=None,
func_tol=None, grad_tol=None, max_iterations=None, constraints=0, scaling=1,
verbosity, sim_index=None):
"""Model-free minimisation.
Three types of parameter sets exist for which minimisation is
different. These are:
@@ -2027,7 +2027,7 @@
# Arguments.
self.run = run
- self.print_flag = print_flag
+ self.verbosity = verbosity
# Test if the sequence data for self.run is loaded.
if not relax_data_store.res.has_key(self.run):
@@ -2083,7 +2083,7 @@
raise RelaxNoValueError, unset_param
# Print out.
- if self.print_flag >= 1:
+ if self.verbosity >= 1:
if self.param_set == 'mf':
print "Only the model-free parameters for single residues
will be used."
elif self.param_set == 'local_mf':
@@ -2181,10 +2181,10 @@
A, b = self.linear_constraints(index=index)
# Print out.
- if self.print_flag >= 1:
+ if self.verbosity >= 1:
# Individual residue stuff.
if self.param_set == 'mf' or self.param_set == 'local_tm':
- if self.print_flag >= 2:
+ if self.verbosity >= 2:
print "\n\n"
string = "Fitting to residue: " +
`relax_data_store.res[self.run][index].num` + " " +
relax_data_store.res[self.run][index].name
print "\n\n" + string
@@ -2385,9 +2385,9 @@
###############
if constraints:
- results = generic_minimise(func=self.mf.func,
dfunc=self.mf.dfunc, d2func=self.mf.d2func, args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options, func_tol=func_tol,
grad_tol=grad_tol, maxiter=max_iterations, A=A, b=b, full_output=1,
print_flag=print_flag)
+ results = generic_minimise(func=self.mf.func,
dfunc=self.mf.dfunc, d2func=self.mf.d2func, args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options, func_tol=func_tol,
grad_tol=grad_tol, maxiter=max_iterations, A=A, b=b, full_output=1,
print_flag=verbosity)
else:
- results = generic_minimise(func=self.mf.func,
dfunc=self.mf.dfunc, d2func=self.mf.d2func, args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options, func_tol=func_tol,
grad_tol=grad_tol, maxiter=max_iterations, full_output=1,
print_flag=print_flag)
+ results = generic_minimise(func=self.mf.func,
dfunc=self.mf.dfunc, d2func=self.mf.d2func, args=(), x0=self.param_vector,
min_algor=min_algor, min_options=min_options, func_tol=func_tol,
grad_tol=grad_tol, maxiter=max_iterations, full_output=1,
print_flag=verbosity)
if results == None:
return
self.param_vector, self.func, iter, fc, gc, hc, self.warning =
results
@@ -3276,7 +3276,7 @@
relax_data_store.res[self.run][i].fixed = res_fixed
- def read_columnar_pdb(self, print_flag=1):
+ def read_columnar_pdb(self, verbosity=1):
"""Function for reading the PDB file."""
# File name.
@@ -3287,7 +3287,7 @@
# Read the PDB file (if it exists).
if not pdb == 'None':
- self.relax.generic.structure.read_pdb(run=self.run, file=pdb,
model=pdb_model, fail=0, print_flag=print_flag)
+ self.relax.generic.structure.read_pdb(run=self.run, file=pdb,
model=pdb_model, fail=0, verbosity=verbosity)
return 1
else:
return 0
@@ -3333,7 +3333,7 @@
self.relax.specific.relax_data.add_residue(run=self.run,
res_index=self.res_index, ri_labels=self.ri_labels,
remap_table=self.remap_table, frq_labels=self.frq_labels, frq=self.frq,
values=values, errors=errors, sim=sim)
- def read_columnar_results(self, run, file_data, print_flag=1):
+ def read_columnar_results(self, run, file_data, verbosity=1):
"""Function for reading the results file."""
# Arguments.
@@ -3438,7 +3438,7 @@
# PDB.
if not pdb:
- if self.read_columnar_pdb(print_flag):
+ if self.read_columnar_pdb(verbosity):
pdb = 1
# XH vector, heteronucleus, and proton.
r4576 - /1.3/specific_fns/model_free/model_free.py