r8594 - /branches/multi_structure/generic_fns/structure/geometric.py -- January 22, 2009 - 15:48

Author: bugman
Date: Thu Jan 22 15:48:45 2009
New Revision: 8594

URL: http://svn.gna.org/viewcvs/relax?rev=8594&view=rev
Log:
Modified create_diff_tensor_pdb() for the new structural data design.


Modified:
    branches/multi_structure/generic_fns/structure/geometric.py

Modified: branches/multi_structure/generic_fns/structure/geometric.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/geometric.py?rev=8594&r1=8593&r2=8594&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/geometric.py (original)
+++ branches/multi_structure/generic_fns/structure/geometric.py Thu Jan 22 
15:48:45 2009
@@ -183,6 +183,9 @@
     # Add a structure.
     structure.add_molecule(name='diff_tensor')
 
+    # Alias the single molecule from the single model.
+    mol = structure.structural_data[0].mol[0]
+
     # Loop over the pipes.
     for pipe_index in xrange(len(pipe_list)):
         # Get the pipe container.
@@ -228,7 +231,7 @@
         CoM = centre_of_mass()
 
         # Add the central atom.
-        structure.atom_add(pdb_record='HETATM', atom_num=1, 
atom_name='R'+atom_id_ext, res_name='COM', chain_id=chain_id, 
res_num=res_num, pos=CoM, segment_id=None, element='C', struct_index=None)
+        mol.atom_add(pdb_record='HETATM', atom_num=1, 
atom_name='R'+atom_id_ext, res_name='COM', chain_id=chain_id, 
res_num=res_num, pos=CoM, segment_id=None, element='C', struct_index=None)
 
         # Increment the residue number.
         res_num = res_num + 1
@@ -241,7 +244,7 @@
         print "\nGenerating the geometric object."
 
         # The distribution.
-        generate_vector_dist(structure=structure, res_name='TNS', 
res_num=res_num, chain_id=chain_id, centre=CoM, R=pipe.diff_tensor.rotation, 
warp=pipe.diff_tensor.tensor, scale=scale, inc=20)
+        generate_vector_dist(molecule=mol, res_name='TNS', res_num=res_num, 
chain_id=chain_id, centre=CoM, R=pipe.diff_tensor.rotation, 
warp=pipe.diff_tensor.tensor, scale=scale, inc=20)
 
         # Increment the residue number.
         res_num = res_num + 1
@@ -263,7 +266,7 @@
                 sim_vectors = None
                 
             # Generate the axes representation.
-            res_num = generate_vector_residues(structure=structure, 
vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
+            res_num = generate_vector_residues(molecule=mol, 
vector=pipe.diff_tensor.Dpar*pipe.diff_tensor.Dpar_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
 
 
         # Create the three axes of the ellipsoid.
@@ -283,9 +286,9 @@
                 sim_Dz_vectors = None
                 
             # Generate the axes representation.
-            res_num = generate_vector_residues(structure=structure, 
vector=pipe.diff_tensor.Dx*pipe.diff_tensor.Dx_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_Dx_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
-            res_num = generate_vector_residues(structure=structure, 
vector=pipe.diff_tensor.Dy*pipe.diff_tensor.Dy_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_Dy_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
-            res_num = generate_vector_residues(structure=structure, 
vector=pipe.diff_tensor.Dz*pipe.diff_tensor.Dz_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_Dz_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
+            res_num = generate_vector_residues(molecule=mol, 
vector=pipe.diff_tensor.Dx*pipe.diff_tensor.Dx_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_Dx_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
+            res_num = generate_vector_residues(molecule=mol, 
vector=pipe.diff_tensor.Dy*pipe.diff_tensor.Dy_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_Dy_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
+            res_num = generate_vector_residues(molecule=mol, 
vector=pipe.diff_tensor.Dz*pipe.diff_tensor.Dz_unit, atom_name='Dpar', 
res_name_vect='AXS', sim_vectors=sim_Dz_vectors, chain_id=chain_id, 
res_num=res_num, origin=CoM, scale=scale, neg=True)
 
 
     # Create the PDB file.