r7216 - in /1.3/generic_fns/structure: geometric.py mass.py -- August 21, 2008 - 15:13

Author: bugman
Date: Thu Aug 21 14:55:19 2008
New Revision: 7216

URL: http://svn.gna.org/viewcvs/relax?rev=7216&view=rev
Log:
Fixes for the cone_edge() function for the structural API changes.


Modified:
    1.3/generic_fns/structure/geometric.py
    1.3/generic_fns/structure/mass.py

Modified: 1.3/generic_fns/structure/geometric.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=7216&r1=7215&r2=7216&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Thu Aug 21 14:55:19 2008
@@ -89,8 +89,11 @@
     @type inc:              int
     """
 
+    # The atom numbers (and indices).
+    atom_num = structure.structural_data[0].atom_num[-1]+1
+    
     # Add an atom for the cone apex.
-    structure.atom_add(pdb_record='HETATM', atom_num=apex, atom_name='APX', 
res_name=res_name, res_num=res_num, pos=apex, segment_id=None, element='H', 
struct_index=None)
+    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)
 
     # Initialise the rotation matrix, atom number, etc.
     if R == None:
@@ -103,6 +106,9 @@
 
     # Loop over each vector.
     for i in xrange(inc):
+        # Increment the atom number.
+        atom_num = atom_num + 1
+
         # The azimuthal angle theta.
         theta = 2.0 * pi * float(i) / float(inc)
 
@@ -128,7 +134,7 @@
         pos = apex+vector*length
 
         # Add the vector as a H atom of the cone residue.
-        structure.atom_add(pdb_record='HETATM', atom_num=atom_id, 
atom_name='H'+`atom_num`, res_name=res_name, res_num=res_num, pos=pos, 
segment_id=None, element='H', struct_index=None)
+        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)
 
         # Connect across the radial array (to generate the circular cone 
edge).
         if i != 0:

Modified: 1.3/generic_fns/structure/mass.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/mass.py?rev=7216&r1=7215&r2=7216&view=diff
==============================================================================
--- 1.3/generic_fns/structure/mass.py (original)
+++ 1.3/generic_fns/structure/mass.py Thu Aug 21 14:55:19 2008
@@ -60,6 +60,7 @@
 
     # Loop over all atoms.
     for mol_name, res_num, res_name, atom_num, atom_name, element, pos in 
cdp.structure.atom_loop(mol_name_flag=True, res_num_flag=True, 
res_name_flag=True, atom_num_flag=True, atom_name_flag=True, 
element_flag=True, pos_flag=True):
+        print mol_name, res_num, res_name, atom_num, atom_name, element, pos
         # Get the corresponding molecule container.
         if mol_name == None:
             mol_cont = cdp.mol[0]