r5066 - in /branches/N_state_model: ./ generic_fns/structure.py -- February 21, 2008 - 09:19

Author: bugman
Date: Thu Feb 21 09:19:33 2008
New Revision: 5066

URL: http://svn.gna.org/viewcvs/relax?rev=5066&view=rev
Log:
Merged revisions 5065 via svnmerge from 
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3

........
  r5065 | bugman | 2008-02-21 09:18:42 +0100 (Thu, 21 Feb 2008) | 3 lines
  
  Completed the cone_pdb() function.
........

Modified:
    branches/N_state_model/   (props changed)
    branches/N_state_model/generic_fns/structure.py

Propchange: branches/N_state_model/
------------------------------------------------------------------------------
Binary property 'svnmerge-integrated' - no diff available.

Modified: branches/N_state_model/generic_fns/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/branches/N_state_model/generic_fns/structure.py?rev=5066&r1=5065&r2=5066&view=diff
==============================================================================
--- branches/N_state_model/generic_fns/structure.py (original)
+++ branches/N_state_model/generic_fns/structure.py Thu Feb 21 09:19:33 2008
@@ -22,7 +22,7 @@
 
 # Python module imports.
 from math import sqrt, cos, pi, sin
-from numpy import arccos, dot, float64, zeros
+from numpy import arccos, array, dot, float64, zeros
 from os import F_OK, access
 from re import compile, match
 import Scientific.IO.PDB
@@ -329,8 +329,9 @@
     @type inc:              int
     """
 
-    # Initialise the rotation matrix.
+    # Initialise the rotation matrix, atom number, etc.
     R = zeros((3,3), float64)
+    atom_num = 1
 
     # Get the rotation matrix.
     R_2vect(R, array([0,0,1], float64), axis)
@@ -355,8 +356,19 @@
         # Rotate the vector.
         vector = dot(R, vector)
 
+        # The atom id.
+        atom_id = 'T' + `i`
+
         # 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')
+
+        # Connect across the radial arrays (to generate the latitudinal 
lines).
+        if i != 0:
+            neighbour_id = 'T' + `i-1`
+            atom_connect(atomic_data=atomic_data, atom_id=atom_id, 
bonded_id=neighbour_id)
+
+        # Increment the atom number.
+        atom_num = atom_num + 1
 
 
 def create_diff_tensor_pdb(scale=1.8e-6, file=None, dir=None, force=False):