r10961 - /1.3/generic_fns/structure/geometric.py -- March 10, 2010 - 10:07

Author: bugman
Date: Wed Mar 10 10:07:35 2010
New Revision: 10961

URL: http://svn.gna.org/viewcvs/relax?rev=10961&view=rev
Log:
Modified stitch_cone_to_edge() to use the new cone limits function.


Modified:
    1.3/generic_fns/structure/geometric.py

Modified: 1.3/generic_fns/structure/geometric.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/geometric.py?rev=10961&r1=10960&r2=10961&view=diff
==============================================================================
--- 1.3/generic_fns/structure/geometric.py (original)
+++ 1.3/generic_fns/structure/geometric.py Wed Mar 10 10:07:35 2010
@@ -720,7 +720,7 @@
             return names[i] + repr(atom_num - lims[i])
 
 
-def stitch_cone_to_edge(mol=None, cone_start=None, edge_start=None, 
max_angle=None, inc=None, debug=False):
+def stitch_cone_to_edge(mol=None, cone_start=None, edge_start=None, 
limit_check=None, inc=None, debug=False):
     """Function for stitching the cone dome to its edge, in the PDB 
representations.
 
     @keyword mol:           The molecule container.
@@ -729,34 +729,44 @@
     @type cone_start:       int
     @keyword edge_start:    The starting atom number of the cone edge 
residue.
     @type edge_start:       int
-    @keyword max_angle:     The maximal polar angle, in rad, after which all 
vectors are skipped.
-    @type max_angle:        float
-    @keyword inc:           The number of increments or number of vectors 
used to generate the outer
-                            edge of the cone.
+    @keyword limit_check:   A function with determines the limits of the 
distribution.  It should accept two arguments, the polar angle phi and the 
azimuthal angle theta, and return True if the point is in the limits or False 
if outside.
+    @type limit_check:      function
+    @keyword inc:           The number of increments or number of vectors 
used to generate the outer edge of the cone.
     @type inc:              int
     """
 
     # Get the polar and azimuthal angles for the distribution.
     phi, theta = angles_uniform(inc)
 
-    # Loop over the angles and find the minimum latitudinal index.
-    for j_min in xrange(len(phi)):
-        if phi[j_min] < max_angle:
-            break
-
-    # The number of j increments.
-    num_j = inc/2+2 - j_min
-
-    # Loop over the radial array of vectors (change in longitude).
-    for i in range(inc):
+    # Find the cone edge atoms of the first and last longitudes.
+    edge_index = zeros(len(theta), int)
+    for i in range(len(theta)):
+        for j in range(len(phi)):
+            if limit_check(phi[j], theta[i]):
+                edge_index[i] = j
+                break
+
+    # Debugging.
+    if debug:
+        print("\nCone start: %s" % cone_start)
+        print("Edge start: %s" % edge_start)
+        print("Edge indices: %s" % edge_index)
+
+    # Move around the azimuth.
+    dome_edge = cone_start
+    for j in range(len(theta)):
         # Cone edge atom.
-        edge_atom = edge_start + i
-
-        # Dome edge atom.
-        dome_edge = cone_start + i*num_j
+        edge_atom = edge_start + j
+
+        # Debugging.
+        if debug:
+            print("Stitching %s to %s" % (get_proton_name(edge_atom), 
get_proton_name(dome_edge)))
 
         # Connect the two atoms (to stitch up the 2 objects).
         mol.atom_connect(index1=dome_edge-1, index2=edge_atom-1)
+
+        # Update the dome edge atom.
+        dome_edge = dome_edge + (len(phi) - edge_index[j])
 
 
 def uniform_vect_dist_spherical_angles(inc=20):