r11642 - /branches/bmrb/generic_fns/diffusion_tensor.py -- October 19, 2010 - 20:05

Author: bugman
Date: Tue Oct 19 20:05:32 2010
New Revision: 11642

URL: http://svn.gna.org/viewcvs/relax?rev=11642&view=rev
Log:
The diffusion tensor saveframe is now being created in the BMRB submission 
file.

This saveframe is not complete and contains no tensor information, as bmrblib 
does not support this
yet.


Modified:
    branches/bmrb/generic_fns/diffusion_tensor.py

Modified: branches/bmrb/generic_fns/diffusion_tensor.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/diffusion_tensor.py?rev=11642&r1=11641&r2=11642&view=diff
==============================================================================
--- branches/bmrb/generic_fns/diffusion_tensor.py (original)
+++ branches/bmrb/generic_fns/diffusion_tensor.py Tue Oct 19 20:05:32 2010
@@ -26,17 +26,92 @@
 # Python module imports.
 from copy import deepcopy
 from math import cos, pi, sin
-from numpy import cross, float64, transpose, zeros
+from numpy import cross, float64, int32, ones, transpose, zeros
 from numpy.linalg import eig, norm
 from re import search
+import string
 
 # relax module imports.
 from angles import wrap_angles
 from data.diff_tensor import DiffTensorData
 from generic_fns import pipes
 from generic_fns.angles import fold_spherical_angles
+from generic_fns.mol_res_spin import get_molecule_names, spin_loop
 from maths_fns.rotation_matrix import R_to_euler_zyz
+from physical_constants import element_from_isotope, number_from_isotope
 from relax_errors import RelaxError, RelaxNoTensorError, RelaxStrError, 
RelaxTensorError, RelaxUnknownParamCombError, RelaxUnknownParamError
+
+
+def bmrb_write(star):
+    """Generate the diffusion tensor 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.
+    mol_name_list = []
+    res_num_list = []
+    res_name_list = []
+    atom_name_list = []
+    isotope_list = []
+    element_list = []
+    attached_atom_name_list = []
+    attached_isotope_list = []
+    attached_element_list = []
+
+    # Relax data labels.
+    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):
+        # Skip deselected spins.
+        if not spin.select:
+            continue
+
+        # Check the data for None (not allowed in BMRB!).
+        if res_num == None:
+            raise RelaxError("For the BMRB, the residue of spin '%s' must be 
numbered." % spin_id)
+        if res_name == None:
+            raise RelaxError("For the BMRB, the residue of spin '%s' must be 
named." % spin_id)
+        if spin.name == None:
+            raise RelaxError("For the BMRB, the spin '%s' must be named." % 
spin_id)
+        if spin.heteronuc_type == None:
+            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))
+
+        # The attached atom info.
+        if hasattr(spin, 'attached_atom'):
+            attached_atom_name_list.append(str(spin.attached_atom))
+        else:
+            attached_atom_name_list.append(str(spin.attached_proton))
+        attached_element_list.append(element_from_isotope(spin.proton_type))
+        
attached_isotope_list.append(str(number_from_isotope(spin.proton_type)))
+
+        # Other info.
+        isotope_list.append(int(string.strip(spin.heteronuc_type, 
string.ascii_letters)))
+        element_list.append(spin.element)
+
+    # 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
+
+    # Add the diffusion tensor.
+    star.tensor.add(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)
 
 
 def copy(pipe_from=None, pipe_to=None):