r8599 - /branches/multi_structure/generic_fns/structure/geometric.py -- January 22, 2009 - 16:11

Author: bugman
Date: Thu Jan 22 16:11:57 2009
New Revision: 8599

URL: http://svn.gna.org/viewcvs/relax?rev=8599&view=rev
Log:
cone_edge() now also handles the MolContainer.


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=8599&r1=8598&r2=8599&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/geometric.py (original)
+++ branches/multi_structure/generic_fns/structure/geometric.py Thu Jan 22 
16:11:57 2009
@@ -58,7 +58,7 @@
     return 1.8e-6
 
 
-def cone_edge(structure=None, res_name='CON', res_num=None, apex=None, 
axis=None, R=None, angle=None, length=None, inc=None):
+def cone_edge(mol=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
@@ -66,8 +66,8 @@
     bonded together.  This will generate an object representing the outer 
edge of a cone.
 
 
-    @keyword structure:     The structural data object.
-    @type structure:        instance of class derived from Base_struct_API
+    @keyword mol:           The molecule container.
+    @type mol:              MolContainer instance
     @keyword res_name:      The residue name.
     @type res_name:         str
     @keyword res_num:       The residue number.
@@ -90,10 +90,10 @@
     """
 
     # The atom numbers (and indices).
-    atom_num = structure.structural_data[0].atom_num[-1]+1
+    atom_num = mol.atom_num[-1]+1
 
     # Add an atom for the cone apex.
-    structure.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name='APX', res_name=res_name, res_num=res_num, pos=apex, 
segment_id=None, element='H', struct_index=None)
+    mol.atom_add(pdb_record='HETATM', atom_num=atom_num, atom_name='APX', 
res_name=res_name, res_num=res_num, pos=apex, segment_id=None, element='H', 
struct_index=None)
     origin_atom = atom_num
 
     # Initialise the rotation matrix.
@@ -134,18 +134,18 @@
         pos = apex+vector*length
 
         # Add the vector as a H atom of the cone residue.
-        structure.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name='H'+`atom_num`, res_name=res_name, res_num=res_num, pos=pos, 
segment_id=None, element='H', struct_index=None)
+        mol.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name='H'+`atom_num`, res_name=res_name, res_num=res_num, pos=pos, 
segment_id=None, element='H', struct_index=None)
 
         # Connect across the radial array (to generate the circular cone 
edge).
         if i != 0:
-            structure.atom_connect(index1=atom_num-1, index2=atom_num-2)
+            mol.atom_connect(index1=atom_num-1, index2=atom_num-2)
 
         # Connect the last radial array to the first (to zip up the circle).
         if i == inc-1:
-            structure.atom_connect(index1=atom_num-1, index2=origin_atom)
+            mol.atom_connect(index1=atom_num-1, index2=origin_atom)
 
         # Join the atom to the cone apex.
-        structure.atom_connect(index1=origin_atom-1, index2=atom_num-1)
+        mol.atom_connect(index1=origin_atom-1, index2=atom_num-1)
 
 
 def create_diff_tensor_pdb(scale=1.8e-6, file=None, dir=None, force=False):