r5060 - /1.3/generic_fns/structure.py -- February 20, 2008 - 18:54

Author: bugman
Date: Wed Feb 20 18:54:37 2008
New Revision: 5060

URL: http://svn.gna.org/viewcvs/relax?rev=5060&view=rev
Log:
Started writing the generic_fns.structure.cone_edge() function.

This function generates a geometric shape constructed from atoms to be 
embedded into a PDB file,
representing the outer edge of the cone.


Modified:
    1.3/generic_fns/structure.py

Modified: 1.3/generic_fns/structure.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure.py?rev=5060&r1=5059&r2=5060&view=diff
==============================================================================
--- 1.3/generic_fns/structure.py (original)
+++ 1.3/generic_fns/structure.py Wed Feb 20 18:54:37 2008
@@ -301,6 +301,53 @@
         return R,M
     else:
         return R
+
+
+def cone_edge(atomic_data=None, apex=None, axis=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
+    spaced around the cone axis.  The atoms representing neighbouring 
vectors will be directly
+    bonded together.  This will generate an object representing the outer 
edge of a cone.
+
+
+    @param atomic_data:     The dictionary to place the atomic data into.
+    @type atomic_data:      dict
+    @param apex:            The apex of the cone.
+    @type apex:             numpy array, len 3
+    @param axis:            The central axis of the cone.
+    @type axis:             numpy array, len 3
+    @param angle:           The cone angle in radians.
+    @type angle:            float
+    @param length:          The cone length in meters.
+    @type length:           float
+    @param inc:             The number of increments or number of vectors 
used to generate the outer
+                            edge of the cone.
+    @type inc:              int
+    """
+
+    # Initialise the rotation matrix.
+    R = zeros((3,3), float64)
+
+    # Get the rotation matrix.
+    R_2vect(R, array([0,0,1], float64), axis)
+
+    # Loop over each vector.
+    for i in xrange(inc):
+        # The azimuthal angle theta.
+        theta = 2.0 * pi * float(i) / float(inc)
+
+        # X coordinate.
+        x = cos(theta) * sin(angle)
+
+        # Y coordinate.
+        y = sin(theta)* sin(angle)
+
+        # Z coordinate.
+        z = cos(angle)
+
+        # The vector in the unrotated frame.
+        vector = array([x, y, z], float64)
 
 
 def create_diff_tensor_pdb(scale=1.8e-6, file=None, dir=None, force=False):