Author: bugman
Date: Sun Oct 29 04:00:54 2006
New Revision: 2684
URL: http://svn.gna.org/viewcvs/relax?rev=2684&view=rev
Log:
Created the geometric representation of the diffusion tensor in the tensor
PDB file.
The lengths of the uniformly distributed vectors have been extended and
scaled to the shape of the
geometric object. Each atom has been connected to the previous atom in its
radial array (generating
longitudinal lines) and the atoms of each radial array have been joined to
the equivalent atoms of
the previous array (generating latitudinal lines). To zip up a gap in the
geometric object where
the latitudinal lines are not continuous ellipses, the atoms of the last
radial array have been
joined to the first radial array.
Modified:
branches/tensor_pdb/generic_fns/pdb.py
Modified: branches/tensor_pdb/generic_fns/pdb.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/generic_fns/pdb.py?rev=2684&r1=2683&r2=2684&view=diff
==============================================================================
--- branches/tensor_pdb/generic_fns/pdb.py (original)
+++ branches/tensor_pdb/generic_fns/pdb.py Sun Oct 29 04:00:54 2006
@@ -21,7 +21,7 @@
###############################################################################
from math import sqrt, cos, pi, sin
-from Numeric import Float64, arccos, dot, zeros
+from Numeric import Float64, arccos, dot, transpose, zeros
from os import F_OK, access
from re import compile
import Scientific.IO.PDB
@@ -280,12 +280,55 @@
print
- # Uniform vector distribution.
- ##############################
-
- vectors = self.uniform_vect_dist_spherical_angles()
- for i in xrange(len(vectors)):
- self.atom_add(atom_id='H'+`i`, element='H', pos=vectors[i])
+ # Vector distribution.
+ ######################
+
+ # Print out.
+ print "Creating the vector distribution."
+
+ # Increment value.
+ inc = 20
+
+ # Get the uniform vector distribution.
+ vectors = self.uniform_vect_dist_spherical_angles(inc=20)
+
+ # Loop over the radial array of vectors (loop over the azimauthal
angle distribution of theta).
+ for i in range(inc):
+ # Loop over the vectors of the radial array (loop over the polar
angle distribution of phi).
+ for j in range(inc/2+1):
+ # Index.
+ index = i + j*inc
+
+ # Atom id.
+ atom_id = 'T' + `i` + 'P' + `j`
+
+ # Tranform from the structural into the diffusion frame.
+ vector =
dot(transpose(self.relax.data.diff[self.run].tensor), vectors[index])
+
+ # Scale the vector.
+ vector = vector * scale
+
+ # Position relative to the center of mass.
+ pos = R + vector
+
+ # Add the vector as a H atom.
+ self.atom_add(atom_id=atom_id, element='H', pos=pos)
+
+ # Connect to the previous atom.
+ if j != 0:
+ prev_id = 'T' + `i` + 'P' + `j-1`
+ self.atom_connect(atom_id=atom_id, bonded_id=prev_id)
+
+ # Connect across the radial arrays.
+ if i != 0:
+ neighbour_id = 'T' + `i-1` + 'P' + `j`
+ self.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
+
+ # Connect the last radial array to the first.
+ if i == inc-1:
+ neighbour_id = 'T' + `0` + 'P' + `j`
+ self.atom_connect(atom_id=atom_id,
bonded_id=neighbour_id)
+
# Create the PDB file.
@@ -630,7 +673,7 @@
# Replace the temporary vector list with the normalised average
vector.
data.xh_vect = ave_vector / sqrt(dot(ave_vector, ave_vector))
-
+
def uniform_vect_dist_spherical_angles(self, inc=20):
"""Uniform distribution of vectors on a sphere using uniform
spherical angles.
r2684 - /branches/tensor_pdb/generic_fns/pdb.py