Author: bugman
Date: Mon Oct 25 10:08:53 2010
New Revision: 11660
URL: http://svn.gna.org/viewcvs/relax?rev=11660&view=rev
Log:
Implemented the reading of model-free and CSA BMRB saveframes from NMR-STAR
files.
Modified:
branches/bmrb/specific_fns/model_free/bmrb.py
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=11660&r1=11659&r2=11660&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Mon Oct 25 10:08:53 2010
@@ -40,6 +40,139 @@
class Bmrb:
"""Class containing methods related to BMRB STAR file reading and
writing."""
+ def _bmrb_model_map(self, model_name=None, bmrb_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
+ """
+
+ # 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."
+
+ # The relax to BMRB model-free model name map.
+ map = {'m0': '',
+ 'm1': 'S2',
+ 'm2': 'S2, te',
+ 'm3': 'S2, Rex',
+ 'm4': 'S2, te, Rex',
+ 'm5': 'S2f, S2, ts',
+ 'm6': 'S2f, tf, S2, ts',
+ 'm7': 'S2f, S2, ts, Rex',
+ 'm8': 'S2f, tf, S2, ts, Rex',
+ 'm9': 'Rex',
+ 'tm0': 'tm',
+ 'tm1': 'tm, S2',
+ 'tm2': 'tm, S2, te',
+ 'tm3': 'tm, S2, Rex',
+ 'tm4': 'tm, S2, te, Rex',
+ 'tm5': 'tm, S2f, S2, ts',
+ 'tm6': 'tm, S2f, tf, S2, ts',
+ 'tm7': 'tm, S2f, S2, ts, Rex',
+ 'tm8': 'tm, S2f, tf, S2, ts, Rex',
+ '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():
+ if item[search_index] == search_text:
+ return item[return_index]
+
+ # Should not be here!
+ if model_name:
+ raise RelaxError("The model-free model '%s' is unknown.")
+ else:
+ warn(RelaxWarning("The BMRB model-free model name '%s' is
unknown."))
+
+
+ def _sf_model_free_read(self, star):
+ """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
+ """
+
+ # Init the list of model-free parameters.
+ mf_params = ['local_tm', 's2', 's2f', 's2s', 'te', 'tf', 'ts',
'rex', 'chi2']
+
+ # Get the entities.
+ for data in star.model_free.loop():
+ # Store the keys.
+ keys = data.keys()
+
+ # Global data.
+ if 'global_chi2' in keys:
+ setattr(cdp, 'chi2', data['global_chi2'])
+
+ # Loop over the spins.
+ for i in range(len(data['data_ids'])):
+ # Generate a spin ID.
+ spin_id =
mol_res_spin.generate_spin_id(res_num=data['res_nums'][i],
spin_name=data['atom_names'][i])
+
+ # Obtain the spin.
+ spin = mol_res_spin.return_spin(spin_id)
+
+ # Loop over and set the model-free parameters.
+ for param in mf_params:
+ # Set the parameter.
+ if param in keys:
+ setattr(spin, param, data[param][i])
+
+ # Set the error.
+ param_err = param + '_err'
+ if param_err in keys:
+ setattr(spin, param_err, data[param_err][i])
+
+ # The model.
+ model = self._bmrb_model_map(bmrb_name=data['model_fit'][i])
+ setattr(spin, 'model', model)
+
+ # The equation and parameters.
+ equation, params = self._model_map(model)
+ setattr(spin, 'equation', equation)
+ setattr(spin, 'params', params)
+
+ # The element.
+ if'atom_types' in keys:
+ setattr(spin, 'element', data['atom_types'][i])
+
+ # Heteronucleus type.
+ if'atom_types' in keys and 'isotope' in keys:
+ setattr(spin, 'heteronuc_type', str(data['isotope'][i])
+ data['atom_types'][i])
+
+
+ def _sf_csa_read(self, star):
+ """Place the CSA data from the saveframe records into the spin
container.
+
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ """
+
+ # Get the entities.
+ for data in star.chem_shift_anisotropy.loop():
+ # Loop over the spins.
+ for i in range(len(data['data_ids'])):
+ # Generate a spin ID.
+ spin_id =
mol_res_spin.generate_spin_id(res_num=data['res_nums'][i],
spin_name=data['atom_names'][i])
+
+ # Obtain the spin.
+ spin = mol_res_spin.return_spin(spin_id)
+
+ # The CSA value (converted from ppm).
+ setattr(spin, 'csa', data['csa'][i] * 1e-6)
+
+
def bmrb_read(self, file_path, version='3.1'):
"""Read the model-free results from a BMRB NMR-STAR v3.1 formatted
file.
@@ -65,6 +198,12 @@
# Read the relaxation data saveframes.
relax_data.bmrb_read(star)
+ # Read the model-free data saveframes.
+ self._sf_model_free_read(star)
+
+ # Read the CSA data saveframes.
+ self._sf_csa_read(star)
+
def bmrb_write(self, file_path, version=None):
"""Write the model-free results to a BMRB NMR-STAR v3.1 formatted
file.
@@ -91,29 +230,6 @@
# Rex frq.
rex_frq = cdp.frq[0]
-
- # The relax to BMRB model-free model name map.
- model_map = {'m0': '',
- 'm1': 'S2',
- 'm2': 'S2, te',
- 'm3': 'S2, Rex',
- 'm4': 'S2, te, Rex',
- 'm5': 'S2f, S2, ts',
- 'm6': 'S2f, tf, S2, ts',
- 'm7': 'S2f, S2, ts, Rex',
- 'm8': 'S2f, tf, S2, ts, Rex',
- 'm9': 'Rex',
- 'tm0': 'tm',
- 'tm1': 'tm, S2',
- 'tm2': 'tm, S2, te',
- 'tm3': 'tm, S2, Rex',
- 'tm4': 'tm, S2, te, Rex',
- 'tm5': 'tm, S2f, S2, ts',
- 'tm6': 'tm, S2f, tf, S2, ts',
- 'tm7': 'tm, S2f, S2, ts, Rex',
- 'tm8': 'tm, S2f, tf, S2, ts, Rex',
- 'tm9': 'tm, Rex'
- }
# Initialise the spin specific data lists.
mol_name_list = []
@@ -223,7 +339,7 @@
chi2_list.append(spin.chi2)
# Model-free model.
- model_list.append(model_map[spin.model])
+ model_list.append(self._bmrb_model_map(model_name=spin.model))
# Convert the molecule names into the entity IDs.
entity_ids = zeros(len(mol_name_list), int32)
r11660 - /branches/bmrb/specific_fns/model_free/bmrb.py