Author: bugman
Date: Thu Mar 17 12:51:13 2011
New Revision: 12808
URL: http://svn.gna.org/viewcvs/relax?rev=12808&view=rev
Log:
Split the _bmrb_model_map() method into two as it was not functioning
correctly as was too complex.
The two new methods are _from_bmrb_name() and _to_bmrb_name().
Modified:
1.3/specific_fns/model_free/bmrb.py
Modified: 1.3/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/model_free/bmrb.py?rev=12808&r1=12807&r2=12808&view=diff
==============================================================================
--- 1.3/specific_fns/model_free/bmrb.py (original)
+++ 1.3/specific_fns/model_free/bmrb.py Thu Mar 17 12:51:13 2011
@@ -41,20 +41,66 @@
class Bmrb:
"""Class containing methods related to BMRB STAR file reading and
writing."""
- def _bmrb_model_map(self, model_name=None, bmrb_name=None):
+ def _from_bmrb_model(self, name=None):
"""The model-free model name to BMRB name mapping.
- @return: Either the bmrb_name or model_name corresponding to the
given model_name or bmrb_name respectively. Both args cannot be given.
- @rtype: str
+ @keyword name: The BMRB model name.
+ @type name: str
+ @return: The corresponding model-free model name.
+ @rtype: str
"""
- # Check.
- if model_name != None and bmrb_name != None:
- raise RelaxError, "Either the model_name or bmrb_name args can
be supplied, but not both together."
-
# Conversion of Modelfree4 (and relax) model numbers.
- if bmrb_name in ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']:
- return 'm' + bmrb_name
+ if name in ['0', '1', '2', '3', '4', '5', '6', '7', '8', '9']:
+ return 'm' + name
+
+ # The BMRB to model-free model name map.
+ map = {'': 'm0',
+ 'S2': 'm1',
+ 'S2, te': 'm2',
+ 'S2, Rex': 'm3',
+ 'S2, te, Rex': 'm4',
+ 'S2, te, S2f': 'm5',
+ 'S2f, S2, ts': 'm5',
+ 'S2f, tf, S2, ts': 'm6',
+ 'S2f, S2, ts, Rex': 'm7',
+ 'S2f, tf, S2, ts, Rex': 'm8',
+ 'Rex': 'm9',
+ 'tm': 'tm0',
+ 'tm, S2': 'tm1',
+ 'tm, S2, te': 'tm2',
+ 'tm, S2, Rex': 'tm3',
+ 'tm, S2, te, Rex': 'tm4',
+ 'tm, S2f, S2, ts': 'tm5',
+ 'tm, S2f, tf, S2, ts': 'tm6',
+ 'tm, S2f, S2, ts, Rex': 'tm7',
+ 'tm, S2f, tf, S2, ts, Rex': 'tm8',
+ 'tm, Rex': 'tm9'
+ }
+
+ # Loop over the dictionary.
+ for item in map.items():
+ # Normal match.
+ if item[0] == name:
+ return item[1]
+
+ # No whitespace.
+ if string.replace(item[0], ' ', '') == name:
+ return item[1]
+
+ # Should not be here!
+ if name:
+ raise RelaxError("The BMRB model-free model '%s' is unknown." %
model_name)
+
+
+ def _to_bmrb_model(self, name=None):
+ """Convert the model-free model name to the BMRB name.
+
+ @keyword name: The model-free model name.
+ @type name: str
+ @return: The corresponding BMRB model name.
+ @rtype: str
+ """
# The relax to BMRB model-free model name map.
map = {'m0': '',
@@ -62,7 +108,6 @@
'm2': 'S2, te',
'm3': 'S2, Rex',
'm4': 'S2, te, Rex',
- 'm5': 'S2, te, S2f', # This non-standard naming
(incorrect) must go before the correct m5.
'm5': 'S2f, S2, ts',
'm6': 'S2f, tf, S2, ts',
'm7': 'S2f, S2, ts, Rex',
@@ -80,36 +125,12 @@
'tm9': 'tm, Rex'
}
- # Indicies.
- if model_name:
- search_text = model_name
- search_index = 0
- return_index = 1
- else:
- search_text = bmrb_name
- search_index = 1
- return_index = 0
-
- # Loop over the dictionary.
- for item in map.items():
- # Normal match.
- if item[search_index] == search_text:
- return item[return_index]
-
- # No whitespace.
- if string.replace(item[search_index], ' ', '') == search_text:
- return item[return_index]
-
- # The bmrb name is the relax name!
- for item in map.items():
- if item[0] == bmrb_name:
- return bmrb_name
-
- # Should not be here!
- if model_name:
+ # No match.
+ if name not in map.keys():
raise RelaxError("The model-free model '%s' is unknown." %
model_name)
- else:
- warn(RelaxWarning("The BMRB model-free model name '%s' is
unknown." % model_name))
+
+ # Return the BMRB model name.
+ return map[name]
def _sf_model_free_read(self, star, sample_conditions=None):
@@ -258,7 +279,7 @@
# The model.
if data['model_fit'] != None and data['model_fit'][i] !=
None:
- model =
self._bmrb_model_map(bmrb_name=data['model_fit'][i])
+ model = self._from_bmrb_model(data['model_fit'][i])
setattr(spin, 'model', model)
# The equation and parameters.
@@ -476,7 +497,7 @@
chi2_list.append(spin.chi2)
# Model-free model.
- model_list.append(self._bmrb_model_map(model_name=spin.model))
+ model_list.append(self._to_bmrb_model(spin.model))
# Convert the molecule names into the entity IDs.
entity_ids = zeros(len(mol_name_list), int32)
r12808 - /1.3/specific_fns/model_free/bmrb.py