Author: bugman
Date: Wed Jan 9 18:21:28 2008
New Revision: 4574
URL: http://svn.gna.org/viewcvs/relax?rev=4574&view=rev
Log:
Merged revisions 4567-4572 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r4567 | semor | 2008-01-09 17:51:14 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all instances of the 'print_flag' arg to 'verbosity' in the prompt
for tab_completion.
........
r4569 | semor | 2008-01-09 17:54:26 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed 1 instance of the 'print_flag' arg to 'verbosity' in the OpenDX
code for 3D isosurfaces.
........
r4571 | semor | 2008-01-09 18:02:54 +0100 (Wed, 09 Jan 2008) | 3 lines
Changed all instances of the 'print_flag' arg to 'verbosity' in the generic
directory.
........
r4572 | bugman | 2008-01-09 18:13:20 +0100 (Wed, 09 Jan 2008) | 3 lines
Updated the RelaxNoTensorError class to allow for the tensor label to be
printed in the traceback.
........
Modified:
branches/N_state_model/ (props changed)
branches/N_state_model/dx/isosurface_3D.py
branches/N_state_model/generic_fns/dasha.py
branches/N_state_model/generic_fns/palmer.py
branches/N_state_model/generic_fns/results.py
branches/N_state_model/generic_fns/structure.py
branches/N_state_model/prompt/tab_completion.py
branches/N_state_model/relax_errors.py
Propchange: branches/N_state_model/
------------------------------------------------------------------------------
Binary property 'svnmerge-integrated' - no diff available.
Modified: branches/N_state_model/dx/isosurface_3D.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/dx/isosurface_3D.py?rev=4574&r1=4573&r2=4574&view=diff
==============================================================================
--- branches/N_state_model/dx/isosurface_3D.py (original)
+++ branches/N_state_model/dx/isosurface_3D.py Wed Jan 9 18:21:28 2008
@@ -103,7 +103,7 @@
self.relax.generic.value.set(run=self.run, value=values,
param=self.params, res_num=self.res_num, force=1)
# Calculate the function values.
- self.calculate(run=self.run, res_num=self.res_num,
print_flag=0)
+ self.calculate(run=self.run, res_num=self.res_num,
verbosity=0)
# Get the minimisation statistics for the model.
k, n, chi2 = self.model_stats(run=self.run,
instance=self.index)
Modified: branches/N_state_model/generic_fns/dasha.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/dasha.py?rev=4574&r1=4573&r2=4574&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/dasha.py (original)
+++ branches/N_state_model/generic_fns/dasha.py Wed Jan 9 18:21:28 2008
@@ -80,7 +80,7 @@
# Directory creation.
if self.dir == None:
self.dir = self.run
- self.relax.IO.mkdir(self.dir, print_flag=0)
+ self.relax.IO.mkdir(self.dir, verbosity=0)
# Number of field strengths and values.
self.num_frq = 0
Modified: branches/N_state_model/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/palmer.py?rev=4574&r1=4573&r2=4574&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/palmer.py (original)
+++ branches/N_state_model/generic_fns/palmer.py Wed Jan 9 18:21:28 2008
@@ -78,7 +78,7 @@
# Directory creation.
if dir == None:
dir = run
- self.relax.IO.mkdir(dir, print_flag=0)
+ self.relax.IO.mkdir(dir, verbosity=0)
# Place the arguments into 'self'.
self.run = run
Modified: branches/N_state_model/generic_fns/results.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/results.py?rev=4574&r1=4573&r2=4574&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/results.py (original)
+++ branches/N_state_model/generic_fns/results.py Wed Jan 9 18:21:28 2008
@@ -87,7 +87,7 @@
self.write_function(sys.stdout, run)
- def read(self, run=None, file='results', directory=None, file_data=None,
format='columnar', print_flag=1):
+ def read(self, run=None, file='results', directory=None, file_data=None,
format='columnar', verbosity=1):
"""Function for reading the data out of a file."""
# Test if the run exists.
@@ -138,10 +138,10 @@
raise RelaxFileEmptyError
# Read the results.
- self.read_function(run, file_data, print_flag)
+ self.read_function(run, file_data, verbosity)
- def write(self, run=None, file="results", directory=None, force=0,
format='columnar', compress_type=1, print_flag=1):
+ def write(self, run=None, file="results", directory=None, force=0,
format='columnar', compress_type=1, verbosity=1):
"""Create the results file."""
# Test if the run exists.
@@ -169,7 +169,7 @@
raise RelaxError, "The " + format + " format is not currently
supported for " + self.relax.specific_setup.get_string(function_type) + "."
# Open the file for writing.
- results_file = self.relax.IO.open_write_file(file_name=file,
dir=directory, force=force, compress_type=compress_type,
print_flag=print_flag)
+ results_file = self.relax.IO.open_write_file(file_name=file,
dir=directory, force=force, compress_type=compress_type, verbosity=verbosity)
# Write the results.
self.write_function(results_file, run)
Modified: branches/N_state_model/generic_fns/structure.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/structure.py?rev=4574&r1=4573&r2=4574&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/structure.py (original)
+++ branches/N_state_model/generic_fns/structure.py Wed Jan 9 18:21:28 2008
@@ -46,7 +46,7 @@
self.relax = relax
# Print flag.
- self.print_flag = 1
+ self.verbosity = 1
def atom_add(self, atom_id=None, record_name='', atom_name='',
res_name='', chain_id='', res_num=None, pos=[None, None, None],
segment_id='', element=''):
@@ -827,7 +827,7 @@
relax_data_store.pdb[self.run].structures =
relax_data_store.pdb[run].structures
# Print out.
- if self.print_flag:
+ if self.verbosity:
print "Using the structures from the run " + `run` + "."
for i in
xrange(len(relax_data_store.pdb[self.run].structures)):
print relax_data_store.pdb[self.run].structures[i]
@@ -841,7 +841,7 @@
# Load the structure i from the PDB file.
if type(self.model) == int:
# Print out.
- if self.print_flag:
+ if self.verbosity:
print "Loading structure " + `self.model` + " from the PDB
file."
# Load the structure into 'str'.
@@ -852,7 +852,7 @@
raise RelaxPdbLoadError, self.file_path
# Print the PDB info.
- if self.print_flag:
+ if self.verbosity:
print str
# Place the structure in 'relax_data_store.pdb[self.run]'.
@@ -862,7 +862,7 @@
# Load all structures.
else:
# Print out.
- if self.print_flag:
+ if self.verbosity:
print "Loading all structures from the PDB file."
# First model.
@@ -885,7 +885,7 @@
break
# Print the PDB info.
- if self.print_flag:
+ if self.verbosity:
print str
# Place the structure in 'relax_data_store.pdb[self.run]'.
@@ -895,7 +895,7 @@
i = i + 1
- def read_pdb(self, run=None, file=None, dir=None, model=None,
load_seq=1, fail=1, print_flag=1):
+ def read_pdb(self, run=None, file=None, dir=None, model=None,
load_seq=1, fail=1, verbosity=1):
"""The pdb loading function."""
# Arguments.
@@ -905,7 +905,7 @@
self.model = model
self.load_seq = load_seq
self.fail = fail
- self.print_flag = print_flag
+ self.verbosity = verbosity
# Tests.
########
@@ -1004,7 +1004,7 @@
num_str = len(relax_data_store.pdb[self.run].structures)
# Print out.
- if self.print_flag:
+ if self.verbosity:
if num_str > 1:
print "\nCalculating and averaging the unit XH vectors from
all structures."
else:
Modified: branches/N_state_model/prompt/tab_completion.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/prompt/tab_completion.py?rev=4574&r1=4573&r2=4574&view=diff
==============================================================================
--- branches/N_state_model/prompt/tab_completion.py (original)
+++ branches/N_state_model/prompt/tab_completion.py Wed Jan 9 18:21:28 2008
@@ -25,11 +25,11 @@
class Tab_completion:
- def __init__(self, name_space={}, print_flag=0):
+ def __init__(self, name_space={}, verbosity=0):
"""Function for tab completion."""
self.name_space = name_space
- self.print_flag = print_flag
+ self.verbosity = verbosity
def create_list(self):
@@ -71,7 +71,7 @@
if match(list[-1], name):
self.options.append(module + '.' + name)
- if self.print_flag:
+ if self.verbosity:
print "List: " + `list`
print "Module: " + `module`
print "self.list: " + `self.list`
@@ -86,24 +86,24 @@
# Create a list of all possible options.
# Find a list of options by matching the input with self.list
- if self.print_flag:
+ if self.verbosity:
print "\nInput: " + `self.input`
if not "." in self.input:
- if self.print_flag:
+ if self.verbosity:
print "Creating list."
self.create_list()
- if self.print_flag:
+ if self.verbosity:
print "\tOk."
else:
- if self.print_flag:
+ if self.verbosity:
print "Creating sublist."
self.create_sublist()
- if self.print_flag:
+ if self.verbosity:
print "\tOk."
# Return the options if self.options[state] exists, or return None
otherwise.
- if self.print_flag:
+ if self.verbosity:
print "Returning options."
if self.state < len(self.options):
return self.options[self.state]
Modified: branches/N_state_model/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/N_state_model/relax_errors.py?rev=4574&r1=4573&r2=4574&view=diff
==============================================================================
--- branches/N_state_model/relax_errors.py (original)
+++ branches/N_state_model/relax_errors.py Wed Jan 9 18:21:28 2008
@@ -503,8 +503,11 @@
# No tensor data exists.
class RelaxNoTensorError(BaseError):
- def __init__(self, tensor_type):
- self.text = "No " + tensor_type + " tensor data exists."
+ def __init__(self, tensor_type, tensor_label=None):
+ if not tensor_label:
+ self.text = "No " + tensor_type + " tensor data exists."
+ else:
+ self.text = "No " + tensor_type + " tensor data exists for the
tensor " + `tensor_label` + "."
if Debug:
self.save_state()
r4574 - in /branches/N_state_model: ./ dx/ generic_fns/ prompt/