r9803 - /branches/bmrb/generic_fns/relax_data.py -- October 27, 2009 - 15:52

Author: bugman
Date: Tue Oct 27 15:52:18 2009
New Revision: 9803

URL: http://svn.gna.org/viewcvs/relax?rev=9803&view=rev
Log:
Molecule names are converted to entity IDs and vice versa for BMRB writing 
and reading.


Modified:
    branches/bmrb/generic_fns/relax_data.py

Modified: branches/bmrb/generic_fns/relax_data.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/relax_data.py?rev=9803&r1=9802&r2=9803&view=diff
==============================================================================
--- branches/bmrb/generic_fns/relax_data.py (original)
+++ branches/bmrb/generic_fns/relax_data.py Tue Oct 27 15:52:18 2009
@@ -25,7 +25,7 @@
 
 # Python module imports.
 from copy import deepcopy
-from numpy import ones
+from numpy import int32, ones, zeros
 import string
 import sys
 from warnings import warn
@@ -33,7 +33,7 @@
 # relax module imports.
 from data import Relax_data_store; ds = Relax_data_store()
 from data.exp_info import ExpInfo
-from generic_fns.mol_res_spin import create_spin, exists_mol_res_spin_data, 
generate_spin_id, return_spin, spin_index_loop, spin_loop
+from generic_fns.mol_res_spin import create_spin, exists_mol_res_spin_data, 
generate_spin_id, get_molecule_names, return_spin, spin_index_loop, spin_loop
 from generic_fns import pipes
 from generic_fns import value
 from relax_errors import RelaxError, RelaxNoRiError, RelaxNoSequenceError, 
RelaxNoSpinError, RelaxRiError
@@ -212,7 +212,7 @@
     """
 
     # Get the relaxation data.
-    for data_type, frq, res_nums, res_names, spin_names, val, err in 
star.relaxation.loop():
+    for data_type, frq, entity_ids, res_nums, res_names, spin_names, val, 
err in star.relaxation.loop():
         # Create the labels.
         ri_label = data_type
         frq_label = str(int(frq*1e-6))
@@ -221,8 +221,14 @@
         if test_labels(ri_label, frq_label):
             raise RelaxRiError(ri_label, frq_label)
 
+        # Convert entity IDs to molecule names.
+        mol_names = []
+        names = get_molecule_names()
+        for id in entity_ids:
+            mol_names.append(names[int(id)-1])
+
         # Pack the data.
-        pack_data(ri_label, frq_label, frq, val, err, mol_names=None, 
res_nums=res_nums, res_names=res_names, spin_nums=None, 
spin_names=spin_names, gen_seq=True)
+        pack_data(ri_label, frq_label, frq, val, err, mol_names=mol_names, 
res_nums=res_nums, res_names=res_names, spin_nums=None, 
spin_names=spin_names, gen_seq=True)
 
 
 
@@ -237,6 +243,7 @@
     cdp = pipes.get_pipe()
 
     # Initialise the spin specific data lists.
+    mol_name_list = []
     res_num_list = []
     res_name_list = []
     atom_name_list = []
@@ -273,6 +280,7 @@
             raise RelaxError("For the BMRB, the spin isotope type of '%s' 
must be specified." % spin_id)
 
         # The molecule/residue/spin info.
+        mol_name_list.append(mol_name)
         res_num_list.append(str(res_num))
         res_name_list.append(str(res_name))
         atom_name_list.append(str(spin.name))
@@ -305,6 +313,14 @@
         # Other info.
         isotope_list.append(int(string.strip(spin.heteronuc_type, 
string.ascii_letters)))
 
+    # Convert the molecule names into the entity IDs.
+    entity_ids = zeros(len(mol_name_list), int32)
+    mol_names = get_molecule_names()
+    for i in range(len(mol_name_list)):
+        for j in range(len(mol_names)):
+            if mol_name_list[i] == mol_names[j]:
+                entity_ids[i] = j+1
+
     # Check the temperature control methods.
     if not hasattr(cdp, 'exp_info') or not hasattr(cdp.exp_info, 
'temp_calibration'):
         raise RelaxError("The temperature calibration methods have not been 
specified.")
@@ -328,7 +344,7 @@
             raise RelaxError("The temperature control method for the '%s' 
ri_label and '%s' frq_label have not been specified." % (ri_label, frq_label))
 
         # Add the relaxation data.
-        star.relaxation.add(data_type=ri_label, 
frq=cdp.frq[cdp.remap_table[i]], res_nums=res_num_list, 
res_names=res_name_list, atom_names=atom_name_list, isotope=isotope_list, 
data=relax_data_list[i], errors=relax_error_list[i], 
temp_calibration=temp_calib, temp_control=temp_control)
+        star.relaxation.add(data_type=ri_label, 
frq=cdp.frq[cdp.remap_table[i]], entity_ids=entity_ids, 
res_nums=res_num_list, res_names=res_name_list, atom_names=atom_name_list, 
isotope=isotope_list, data=relax_data_list[i], errors=relax_error_list[i], 
temp_calibration=temp_calib, temp_control=temp_control)
 
 
 def copy(pipe_from=None, pipe_to=None, ri_label=None, frq_label=None):