r5372 - /1.3/specific_fns/n_state_model.py -- April 07, 2008 - 17:01

Author: bugman
Date: Mon Apr  7 17:01:24 2008
New Revision: 5372

URL: http://svn.gna.org/viewcvs/relax?rev=5372&view=rev
Log:
Updated the cone_pdb() method to use the internal PDB structural object.


Modified:
    1.3/specific_fns/n_state_model.py

Modified: 1.3/specific_fns/n_state_model.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=5372&r1=5371&r2=5372&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Mon Apr  7 17:01:24 2008
@@ -31,6 +31,7 @@
 from float import isNaN, isInf
 import generic_fns
 import generic_fns.structure.mass
+from generic_fns.structure.internal_pdb import Internal_PDB
 from maths_fns.n_state_model import N_state_opt
 from maths_fns.rotation_matrix import R_2vect, R_euler_zyz
 from minfx.generic import generic_minimise
@@ -220,8 +221,11 @@
         R = zeros((3,3), float64)
         R_2vect(R, array([0,0,1], float64), 
cdp.ave_pivot_CoM/norm(cdp.ave_pivot_CoM))
 
+        # Create the structural object.
+        structure = Internal_PDB()
+
         # Add the pivot point.
-        generic_fns.structure.atom_add(atomic_data=atomic_data, atom_id='R', 
record_name='HETATM', atom_name='R', res_name='PIV', res_num=1, 
pos=cdp.pivot_point, element='C')
+        structure.atom_add(atom_id='R', record_name='HETATM', atom_name='R', 
res_name='PIV', res_num=1, pos=cdp.pivot_point, element='C')
 
         # Generate the average pivot-CoM vectors.
         print "\nGenerating the average pivot-CoM vectors."
@@ -245,12 +249,12 @@
             
generic_fns.structure.stitch_cap_to_cone(atomic_data=atomic_data, 
max_angle=angle, inc=inc)
 
         # Terminate the chain.
-        generic_fns.structure.terminate(atomic_data=atomic_data, 
res_num=res_num)
+        structure.terminate(res_num=res_num)
 
         # Create the PDB file.
         print "\nGenerating the PDB file."
         pdb_file = open_write_file(file, dir, force=force)
-        generic_fns.structure.write_pdb_file(atomic_data, pdb_file)
+        structure.write_pdb_file(pdb_file)
         pdb_file.close()