r5114 - in /1.3: generic_fns/structure.py specific_fns/n_state_model.py -- February 21, 2008 - 16:22

Author: bugman
Date: Thu Feb 21 16:22:18 2008
New Revision: 5114

URL: http://svn.gna.org/viewcvs/relax?rev=5114&view=rev
Log:
Modified the cone_edge() function to accept the residue name as an argument.


Modified:
    1.3/generic_fns/structure.py
    1.3/specific_fns/n_state_model.py

Modified: 1.3/generic_fns/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure.py?rev=5114&r1=5113&r2=5114&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Thu Feb 21 16:22:18 2008
@@ -304,7 +304,7 @@
         return R
 
 
-def cone_edge(atomic_data=None, res_num=None, apex=None, axis=None, R=None, 
angle=None, length=None, inc=None):
+def cone_edge(atomic_data=None, res_name='CON', res_num=None, apex=None, 
axis=None, R=None, angle=None, length=None, inc=None):
     """Add a residue to the atomic data representing a cone of the given 
angle.
 
     A series of vectors totalling the number of increments and starting at 
the origin are equally
@@ -314,6 +314,8 @@
 
     @param atomic_data:     The dictionary to place the atomic data into.
     @type atomic_data:      dict
+    @param res_name:        The residue name.
+    @type res_name:         str
     @param res_num:         The residue number.
     @type res_num:          int
     @param apex:            The apex of the cone.
@@ -334,7 +336,7 @@
     """
 
     # Add an atom for the cone apex.
-    atom_add(atomic_data=atomic_data, atom_id='Apex', record_name='HETATM', 
atom_name='APX', res_name='CON', res_num=res_num, pos=apex, element='H')
+    atom_add(atomic_data=atomic_data, atom_id='Apex', record_name='HETATM', 
atom_name='APX', res_name=res_name, res_num=res_num, pos=apex, element='H')
 
     # Initialise the rotation matrix, atom number, etc.
     if R == None:
@@ -371,8 +373,8 @@
         # The atom position.
         pos = apex+vector*length
 
-        # Add the vector as a H atom of the CON residue.
-        atom_add(atomic_data=atomic_data, atom_id=atom_id, 
record_name='HETATM', atom_name='H'+`atom_num`, res_name='CON', 
res_num=res_num, pos=pos, element='H')
+        # Add the vector as a H atom of the cone residue.
+        atom_add(atomic_data=atomic_data, atom_id=atom_id, 
record_name='HETATM', atom_name='H'+`atom_num`, res_name=res_name, 
res_num=res_num, pos=pos, element='H')
 
         # Connect across the radial array (to generate the circular cone 
edge).
         if i != 0:

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=5114&r1=5113&r2=5114&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Thu Feb 21 16:22:18 2008
@@ -235,7 +235,7 @@
             angle = cdp.theta_diff_in_cone
         elif cone_type == 'diff on cone':
             angle = cdp.theta_diff_on_cone
-        generic_fns.structure.cone_edge(atomic_data=atomic_data, res_num=3, 
apex=cdp.pivot_point, R=R, angle=angle, length=norm(cdp.pivot_CoM), inc=inc)
+        generic_fns.structure.cone_edge(atomic_data=atomic_data, 
res_name='CON', res_num=3, apex=cdp.pivot_point, R=R, angle=angle, 
length=norm(cdp.pivot_CoM), inc=inc)
 
         # Generate the cone cap, and stitch it to the cone edge.
         if cone_type == 'diff in cone':