r22044 - /trunk/lib/structure/represent/rotor.py -- January 24, 2014 - 11:50

Author: bugman
Date: Fri Jan 24 11:50:00 2014
New Revision: 22044

URL: http://svn.gna.org/viewcvs/relax?rev=22044&view=rev
Log:
More improvements for handling multiple rotors in the 
lib.structure.represent.rotor.rotor_pdb() function.

The atom numbering is now better handled.


Modified:
    trunk/lib/structure/represent/rotor.py

Modified: trunk/lib/structure/represent/rotor.py
URL: 
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/represent/rotor.py?rev=22044&r1=22043&r2=22044&view=diff
==============================================================================
--- trunk/lib/structure/represent/rotor.py (original)
+++ trunk/lib/structure/represent/rotor.py Fri Jan 24 11:50:00 2014
@@ -68,31 +68,34 @@
     # Add a structure (handling up to 3 rotors).
     if structure.has_molecule(name='rotor') and 
structure.has_molecule(name='rotor2'):
         structure.add_molecule(name='rotor3')
+        mol_name = 'rotor3'
     elif structure.has_molecule(name='rotor'):
         structure.add_molecule(name='rotor2')
+        mol_name = 'rotor2'
     else:
         structure.add_molecule(name='rotor')
+        mol_name = 'rotor'
 
     # Loop over the models.
     for model in structure.model_loop(model):
         # Alias the single molecule from the single model.
-        mol = structure.get_molecule('rotor', model=model.num)
+        mol = structure.get_molecule(mol_name, model=model.num)
 
         # The central point.
         mid_point = closest_point_ax(line_pt=axis_pt, axis=axis, 
point=centre)
-        mol.atom_add(pdb_record='HETATM', atom_num=1, atom_name='CTR', 
res_name='AX', res_num=1, pos=mid_point, element='PT')
+        pos_index = mol.atom_add(pdb_record='HETATM', atom_name='CTR', 
res_name='AX', res_num=1, pos=mid_point, element='PT')
 
         # Centre of the propellers.
         prop1 = mid_point + axis_norm * span
-        prop1_index = 1
-        mol.atom_add(pdb_record='HETATM', atom_num=2, atom_name='PRP', 
res_name='PRC', res_num=2, pos=prop1, element='O')
-        mol.atom_connect(index1=0, index2=prop1_index)
+        prop1_index = pos_index + 1
+        mol.atom_add(pdb_record='HETATM', atom_name='PRP', res_name='PRC', 
res_num=2, pos=prop1, element='O')
+        mol.atom_connect(index1=pos_index, index2=prop1_index)
 
         # Centre of the propellers.
         prop2 = mid_point - axis_norm * span
-        prop2_index = 2
-        mol.atom_add(pdb_record='HETATM', atom_num=3, atom_name='PRP', 
res_name='PRC', res_num=3, pos=prop2, element='O')
-        mol.atom_connect(index1=0, index2=prop2_index)
+        prop2_index = pos_index + 2
+        mol.atom_add(pdb_record='HETATM', atom_name='PRP', res_name='PRC', 
res_num=3, pos=prop2, element='O')
+        mol.atom_connect(index1=pos_index, index2=prop2_index)
 
         # Create the rotor propellers.
         rotor_propellers(mol=mol, rotor_angle=rotor_angle, centre=prop1, 
axis=axis, blade_length=blade_length, staggered=staggered)