Author: bugman
Date: Wed Mar 2 11:29:47 2011
New Revision: 12700
URL: http://svn.gna.org/viewcvs/relax?rev=12700&view=rev
Log:
Updated the relaxation data bmrb_write() method for the new relax data ID
string design.
Modified:
branches/relax_data/generic_fns/relax_data.py
Modified: branches/relax_data/generic_fns/relax_data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/relax_data/generic_fns/relax_data.py?rev=12700&r1=12699&r2=12700&view=diff
==============================================================================
--- branches/relax_data/generic_fns/relax_data.py (original)
+++ branches/relax_data/generic_fns/relax_data.py Wed Mar 2 11:29:47 2011
@@ -198,19 +198,17 @@
attached_atom_name_list = []
attached_isotope_list = []
attached_element_list = []
- relax_data_list = []
- relax_error_list = []
+ ri_data_list = []
+ ri_data_err_list = []
for i in range(cdp.num_ri):
- relax_data_list.append([])
- relax_error_list.append([])
+ ri_data_list.append([])
+ ri_data_err_list.append([])
# Relax data labels.
- labels = []
+ labels = cdp.ri_ids
exp_label = []
spectro_ids = []
spectro_labels = []
- for i in range(cdp.num_ri):
- labels.append(cdp.ri_labels[i] + '_' +
cdp.frq_labels[cdp.remap_table[i]])
# Store the spin specific data in lists for later use.
for spin, mol_name, res_num, res_name, spin_id in
spin_loop(full_info=True, return_id=True):
@@ -219,7 +217,7 @@
continue
# Skip spins with no relaxation data.
- if not hasattr(spin, 'relax_data'):
+ if not hasattr(spin, 'ri_data'):
continue
# Check the data for None (not allowed in BMRB!).
@@ -248,28 +246,14 @@
# The relaxation data.
used_index = -ones(spin.num_ri)
- for i in range(len(spin.ri_labels)):
- # Labels.
- label = spin.ri_labels[i] + '_' +
spin.frq_labels[spin.remap_table[i]]
-
- # Find the global index.
- index = None
- for j in range(cdp.num_ri):
- if label == labels[j] and j not in used_index:
- index = j
- used_index[i] = j
- break
-
+ for i in range(len(cdp.ri_ids)):
# Data exists.
- if index != None:
- relax_data_list[index].append(str(spin.relax_data[i]))
- relax_error_list[index].append(str(spin.relax_error[i]))
-
- # No relaxation data.
- for i in range(cdp.num_ri):
- if i not in used_index:
- relax_data_list[i].append(None)
- relax_error_list[i].append(None)
+ if cdp.ri_ids[i] in spin.ri_data.keys():
+ ri_data_list[i].append(str(spin.ri_data[i]))
+ ri_data_err_list[i].append(str(spin.ri_data_err[i]))
+ else:
+ ri_data_list[i].append(None)
+ ri_data_err_list[i].append(None)
# Other info.
isotope_list.append(int(string.strip(spin.heteronuc_type,
string.ascii_letters)))
@@ -296,34 +280,34 @@
# Loop over the relaxation data.
for i in range(cdp.num_ri):
# Alias.
- ri_label = cdp.ri_labels[i]
- frq_label = cdp.frq_labels[cdp.remap_table[i]]
+ ri_id = cdp.ri_ids[i]
+ ri_type = cdp.ri_type[ri_id]
# Convert to MHz.
- frq = cdp.frq[cdp.remap_table[i]] * 1e-6
+ frq = cdp.frq[ri_id] * 1e-6
# Get the temperature control methods.
- temp_calib = cdp.exp_info.get_temp_calibration(ri_label, frq_label)
- temp_control = cdp.exp_info.get_temp_control(ri_label, frq_label)
+ temp_calib = cdp.exp_info.temp_calibration[ri_id]
+ temp_control = cdp.exp_info.temp_control[ri_id]
# Get the peak intensity type.
- peak_intensity_type = cdp.exp_info.get_peak_intensity_type(ri_label,
frq_label)
+ peak_intensity_type = cdp.exp_info.peak_intensity_type[ri_id]
# Check.
if not temp_calib:
- raise RelaxError("The temperature calibration method for the
'%s' ri_label and '%s' frq_label have not been specified." % (ri_label,
frq_label))
+ raise RelaxError("The temperature calibration method for the
'%s' relaxation data ID string has not been specified." % ri_id)
if not temp_control:
- raise RelaxError("The temperature control method for the '%s'
ri_label and '%s' frq_label have not been specified." % (ri_label, frq_label))
+ raise RelaxError("The temperature control method for the '%s'
relaxation data ID string has not been specified." % ri_id)
# Add the relaxation data.
- star.relaxation.add(data_type=ri_label, frq=frq,
entity_ids=entity_ids, res_nums=res_num_list, res_names=res_name_list,
atom_names=atom_name_list, atom_types=element_list, isotope=isotope_list,
entity_ids_2=entity_ids, res_nums_2=res_num_list, res_names_2=res_name_list,
atom_names_2=attached_atom_name_list, atom_types_2=attached_element_list,
isotope_2=attached_isotope_list, data=relax_data_list[i],
errors=relax_error_list[i], temp_calibration=temp_calib,
temp_control=temp_control, peak_intensity_type=peak_intensity_type)
+ star.relaxation.add(data_type=ri_type, frq=frq,
entity_ids=entity_ids, res_nums=res_num_list, res_names=res_name_list,
atom_names=atom_name_list, atom_types=element_list, isotope=isotope_list,
entity_ids_2=entity_ids, res_nums_2=res_num_list, res_names_2=res_name_list,
atom_names_2=attached_atom_name_list, atom_types_2=attached_element_list,
isotope_2=attached_isotope_list, data=ri_data_list[i],
errors=ri_data_err_list[i], temp_calibration=temp_calib,
temp_control=temp_control, peak_intensity_type=peak_intensity_type)
# The experimental label.
- if ri_label == 'NOE':
+ if ri_type == 'NOE':
exp_name = 'steady-state NOE'
else:
- exp_name = ri_label
- exp_label.append("%s MHz %s" % (frq_label, exp_name))
+ exp_name = ri_type
+ exp_label.append("%s MHz %s" % (frq, exp_name))
# Spectrometer info.
spectro_ids.append(cdp.remap_table[i] + 1)
r12700 - /branches/relax_data/generic_fns/relax_data.py