r8600 - /branches/multi_structure/generic_fns/structure/geometric.py -- January 22, 2009 - 16:12

Author: bugman
Date: Thu Jan 22 16:12:58 2009
New Revision: 8600

URL: http://svn.gna.org/viewcvs/relax?rev=8600&view=rev
Log:
Removed a ton of now dead struct_index args from function calls.


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=8600&r1=8599&r2=8600&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/geometric.py (original)
+++ branches/multi_structure/generic_fns/structure/geometric.py Thu Jan 22 
16:12:58 2009
@@ -93,7 +93,7 @@
     atom_num = mol.atom_num[-1]+1
 
     # Add an atom for the cone apex.
-    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)
+    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')
     origin_atom = atom_num
 
     # Initialise the rotation matrix.
@@ -134,7 +134,7 @@
         pos = apex+vector*length
 
         # Add the vector as a H atom of the cone residue.
-        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)
+        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')
 
         # Connect across the radial array (to generate the circular cone 
edge).
         if i != 0:
@@ -231,7 +231,7 @@
         CoM = centre_of_mass()
 
         # Add the central atom.
-        mol.atom_add(pdb_record='HETATM', atom_num=1, 
atom_name='R'+atom_id_ext, res_name='COM', chain_id=chain_id, 
res_num=res_num, pos=CoM, segment_id=None, element='C', struct_index=None)
+        mol.atom_add(pdb_record='HETATM', atom_num=1, 
atom_name='R'+atom_id_ext, res_name='COM', chain_id=chain_id, 
res_num=res_num, pos=CoM, segment_id=None, element='C')
 
         # Increment the residue number.
         res_num = res_num + 1
@@ -528,7 +528,7 @@
             pos = centre + vector
 
             # Add the vector as a H atom of the TNS residue.
-            mol.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name='H'+`atom_num`, res_name=res_name, chain_id=chain_id, 
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, chain_id=chain_id, 
res_num=res_num, pos=pos, segment_id=None, element='H')
 
             # Connect to the previous atom (to generate the longitudinal 
lines).
             if j > j_min:
@@ -591,19 +591,19 @@
     atom_neg_num = mol.atom_num[-1]+3
 
     # The origin atom.
-    mol.atom_add(pdb_record='HETATM', atom_num=origin_num, atom_name='R', 
res_name=res_name_vect, chain_id=chain_id, res_num=res_num, pos=origin, 
segment_id=None, element='C', struct_index=None)
+    mol.atom_add(pdb_record='HETATM', atom_num=origin_num, atom_name='R', 
res_name=res_name_vect, chain_id=chain_id, res_num=res_num, pos=origin, 
segment_id=None, element='C')
 
     # Create the PDB residue representing the vector.
-    mol.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C', 
struct_index=None)
+    mol.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C')
     mol.atom_connect(index1=atom_num-1, index2=origin_num-1)
     if neg:
-        mol.atom_add(pdb_record='HETATM', atom_num=atom_neg_num, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C', 
struct_index=None)
+        mol.atom_add(pdb_record='HETATM', atom_num=atom_neg_num, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin+vector*scale, segment_id=None, element='C')
         mol.atom_connect(index1=atom_neg_num-1, index2=origin_num-1)
 
     # Add another atom to allow the axis labels to be shifted just outside 
of the vector itself.
-    mol.atom_add(pdb_record='HETATM', atom_num=atom_num+2, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin+label_placement*vector*scale, segment_id=None, 
element='N', struct_index=None)
+    mol.atom_add(pdb_record='HETATM', atom_num=atom_num+2, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin+label_placement*vector*scale, segment_id=None, 
element='N')
     if neg:
-        mol.atom_add(pdb_record='HETATM', atom_num=atom_neg_num+2, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin-label_placement*vector*scale, segment_id=None, 
element='N', struct_index=None)
+        mol.atom_add(pdb_record='HETATM', atom_num=atom_neg_num+2, 
atom_name=atom_name, res_name=res_name_vect, chain_id=chain_id, 
res_num=res_num, pos=origin-label_placement*vector*scale, segment_id=None, 
element='N')
 
     # Print out.
     print "    " + atom_name + " vector (scaled + shifted to origin): " + 
`origin+vector*scale`
@@ -620,10 +620,10 @@
             atom_neg_num = mol.atom_num[-1]+2
 
             # Create the PDB residue representing the vector.
-            mol.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name=atom_name, res_name=res_name_sim, chain_id=chain_id, 
res_num=res_num, pos=origin+sim_vectors[i]*scale, segment_id=None, 
element='C', struct_index=None)
+            mol.atom_add(pdb_record='HETATM', atom_num=atom_num, 
atom_name=atom_name, res_name=res_name_sim, chain_id=chain_id, 
res_num=res_num, pos=origin+sim_vectors[i]*scale, segment_id=None, 
element='C')
             mol.atom_connect(index1=atom_num-1, index2=origin_num-1)
             if neg:
-                mol.atom_add(pdb_record='HETATM', atom_num=atom_num+1, 
atom_name=atom_name, res_name=res_name_sim, chain_id=chain_id, 
res_num=res_num, pos=origin-sim_vectors[i]*scale, segment_id=None, 
element='C', struct_index=None)
+                mol.atom_add(pdb_record='HETATM', atom_num=atom_num+1, 
atom_name=atom_name, res_name=res_name_sim, chain_id=chain_id, 
res_num=res_num, pos=origin-sim_vectors[i]*scale, segment_id=None, 
element='C')
                 mol.atom_connect(index1=atom_neg_num-1, index2=origin_num-1)
 
     # Return the new residue number.