Author: bugman
Date: Thu Mar 5 10:00:43 2009
New Revision: 8904
URL: http://svn.gna.org/viewcvs/relax?rev=8904&view=rev
Log:
Shifted the relaxation data saveframe generation code into
generic_fns.relax_data.bmrb_write().
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=8904&r1=8903&r2=8904&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Thu Mar 5 10:00:43 2009
@@ -203,6 +203,52 @@
# Update all data structures.
update_data_structures_spin(spin, ri_label, frq_label, frq, value)
+
+
+def bmrb_write(star):
+ """Generate the relaxation data saveframes for the NMR-STAR dictionary
object.
+
+ @param star: The NMR-STAR dictionary object.
+ @type star: NMR_STAR instance
+ """
+
+ # Get the current data pipe.
+ cdp = pipes.get_pipe()
+
+ # Initialise the spin specific data lists.
+ res_num_list = []
+ res_name_list = []
+ atom_name_list = []
+ relax_data_list = []
+ relax_error_list = []
+ for i in range(cdp.num_ri):
+ relax_data_list.append([])
+ relax_error_list.append([])
+
+ # Store the spin specific data in lists for later use.
+ for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # The molecule/R1residue/spin info.
+ res_num_list.append(str(res_num))
+ res_name_list.append(str(res_name))
+ atom_name_list.append(str(spin.name))
+
+ # The relaxation data.
+ for i in range(cdp.num_ri):
+ relax_data_list[i].append(str(spin.relax_data[i]))
+ relax_error_list[i].append(str(spin.relax_error[i]))
+
+ # Add the relaxation data.
+ for i in range(cdp.num_ri):
+ if cdp.ri_labels[i] == 'R1':
+
star.heteronucl_T1_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
data=relax_data_list[i], errors=relax_error_list[i])
+ elif cdp.ri_labels[i] == 'R2':
+
star.heteronucl_T2_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
data=relax_data_list[i], errors=relax_error_list[i])
+ elif cdp.ri_labels[i] == 'NOE':
+ star.heteronucl_NOEs.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
data=relax_data_list[i], errors=relax_error_list[i])
def copy(pipe_from=None, pipe_to=None, ri_label=None, frq_label=None):
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=8904&r1=8903&r2=8904&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/bmrb.py (original)
+++ branches/bmrb/specific_fns/model_free/bmrb.py Thu Mar 5 10:00:43 2009
@@ -22,7 +22,7 @@
# relax module imports.
from bmrblib.nmr_star_dict_v3_1 import NMR_STAR_v3_1
-from generic_fns import mol_res_spin
+from generic_fns import mol_res_spin, relax_data
from generic_fns.mol_res_spin import spin_loop
from generic_fns.pipes import get_pipe
@@ -60,40 +60,8 @@
# Generate the entity saveframe.
mol_res_spin.bmrb_write_entity(star)
- # Initialise the spin specific data lists.
- res_num_list = []
- res_name_list = []
- atom_name_list = []
- relax_data_list = []
- relax_error_list = []
- for i in range(cdp.num_ri):
- relax_data_list.append([])
- relax_error_list.append([])
-
- # Store the spin specific data in lists for later use.
- for spin, mol_name, res_num, res_name in spin_loop(full_info=True):
- # Skip deselected spins.
- if not spin.select:
- continue
-
- # The molecule/R1residue/spin info.
- res_num_list.append(str(res_num))
- res_name_list.append(str(res_name))
- atom_name_list.append(str(spin.name))
-
- # The relaxation data.
- for i in range(cdp.num_ri):
- relax_data_list[i].append(str(spin.relax_data[i]))
- relax_error_list[i].append(str(spin.relax_error[i]))
-
- # Add the relaxation data.
- for i in range(cdp.num_ri):
- if cdp.ri_labels[i] == 'R1':
-
star.heteronucl_T1_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
data=relax_data_list[i], errors=relax_error_list[i])
- elif cdp.ri_labels[i] == 'R2':
-
star.heteronucl_T2_relaxation.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
data=relax_data_list[i], errors=relax_error_list[i])
- elif cdp.ri_labels[i] == 'NOE':
- star.heteronucl_NOEs.add(frq=cdp.frq[cdp.remap_table[i]],
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list,
data=relax_data_list[i], errors=relax_error_list[i])
+ # Generate the relaxation data saveframes.
+ relax_data.bmrb_write(star)
# Write the contents to the STAR formatted file.
star.write()
r8904 - in /branches/bmrb: generic_fns/relax_data.py specific_fns/model_free/bmrb.py