Author: bugman
Date: Mon Feb 7 15:05:54 2011
New Revision: 12515
URL: http://svn.gna.org/viewcvs/relax?rev=12515&view=rev
Log:
The sample conditions label is now being used to select the correct BMRB
saveframes to read.
Modified:
branches/bmrb/generic_fns/relax_data.py
branches/bmrb/specific_fns/model_free/bmrb.py
Modified: branches/bmrb/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=12515&r1=12514&r2=12515&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Mon Feb 7 15:05:54 2011
@@ -233,17 +233,23 @@
update_data_structures_spin(spin, ri_label, frq_label, frq, value)
-def bmrb_read(star):
+def bmrb_read(star, sample_conditions=None):
"""Read the relaxation data from the NMR-STAR dictionary object.
- @param star: The NMR-STAR dictionary object.
- @type star: NMR_STAR instance
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ @keyword sample_conditions: The sample condition label to read. Only
one sample condition can be read per data pipe.
+ @type sample_conditions: None or str
"""
# Get the relaxation data.
for data in star.relaxation.loop():
# Store the keys.
keys = data.keys()
+
+ # Sample conditions do not match (remove the $ sign).
+ if 'sample_cond_list_label' in keys and
string.replace(data['sample_cond_list_label'], '$', '') != sample_conditions:
+ continue
# Create the labels.
ri_label = data['data_type']
Modified: branches/bmrb/specific_fns/model_free/bmrb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/bmrb.py?rev=12515&r1=12514&r2=12515&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Mon Feb 7 15:05:54 2011
@@ -112,11 +112,13 @@
warn(RelaxWarning("The BMRB model-free model name '%s' is
unknown." % model_name))
- def _sf_model_free_read(self, star):
+ def _sf_model_free_read(self, star, sample_conditions=None):
"""Fill the spin containers with the model-free data from the
saveframe records.
- @param star: The NMR-STAR dictionary object.
- @type star: NMR_STAR instance
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ @keyword sample_conditions: The sample condition label to read.
Only one sample condition can be read per data pipe.
+ @type sample_conditions: None or str
"""
# The list of model-free parameters (both bmrblib names and relax
names).
@@ -127,6 +129,10 @@
for data in star.model_free.loop():
# Store the keys.
keys = data.keys()
+
+ # Sample conditions do not match (remove the $ sign).
+ if 'sample_cond_list_label' in keys and
string.replace(data['sample_cond_list_label'], '$', '') != sample_conditions:
+ continue
# Global data.
if 'global_chi2' in keys:
@@ -195,19 +201,27 @@
# The value.
value = data[mf_bmrb_key[j]][i]
+ # The parameter.
+ param = mf_params[j]
+
+ # Change the parameter name of te to ts.
+ if param == 'te':
+ if data['s2s'] and data['s2s'][i] != None:
+ param = 'ts'
+
# Parameter scaling.
if value != None:
- if mf_params[j] == 'te':
+ if param == 'te':
value = value * te_scale
- elif mf_params[j] == 'tf':
+ elif param == 'tf':
value = value * tf_scale
- elif mf_params[j] == 'ts':
+ elif param == 'ts':
value = value * ts_scale
- elif mf_params[j] == 'rex':
+ elif param == 'rex':
value = value * rex_scale
# Set the parameter.
- setattr(spin, mf_params[j], value)
+ setattr(spin, param, value)
# The error.
mf_bmrb_key_err = mf_bmrb_key[j] + '_err'
@@ -215,17 +229,17 @@
# Error scaling.
if error != None:
- if mf_params[j] == 'te':
+ if param == 'te':
error = error * te_scale
- elif mf_params[j] == 'tf':
+ elif param == 'tf':
error = error * tf_scale
- elif mf_params[j] == 'ts':
+ elif param == 'ts':
error = error * ts_scale
- elif mf_params[j] == 'rex':
+ elif param == 'rex':
error = error * rex_scale
# Set the error.
- mf_param_err = mf_params[j] + '_err'
+ mf_param_err = param + '_err'
if mf_bmrb_key_err in keys and data[mf_bmrb_key_err] !=
None:
setattr(spin, mf_param_err, error)
@@ -289,6 +303,7 @@
@type sample_conditions: None or str
"""
+ print sample_conditions
# Initialise the NMR-STAR data object.
star = bmrblib.create_nmr_star('relax_model_free_results',
file_path, version)
@@ -309,10 +324,10 @@
mol_res_spin.bmrb_read(star)
# Read the relaxation data saveframes.
- relax_data.bmrb_read(star)
+ relax_data.bmrb_read(star, sample_conditions=sample_conditions)
# Read the model-free data saveframes.
- self._sf_model_free_read(star)
+ self._sf_model_free_read(star, sample_conditions=sample_conditions)
# Read the CSA data saveframes.
self._sf_csa_read(star)
r12515 - in /branches/bmrb: generic_fns/relax_data.py specific_fns/model_free/bmrb.py