Author: bugman
Date: Sun Oct 29 03:29:50 2006
New Revision: 2677
URL: http://svn.gna.org/viewcvs/relax?rev=2677&view=rev
Log:
The diffusion tensor data structure now returns unit vectors parallel to the
tensor axes.
The 'self.__getattr__()' function has been expanded. The docstring now
describes all the equations
used in the calculation of the parameters Diso, Dper, Dpar, Dratio, Dx, Dy,
and Dz. It also
describes how the unit vectors parallel to Dpar, Dx, Dy, and Dz are related
to the spherical or
Euler angles.
Dper, Dpar, and Dratio are now only calculated if the diffusion tensor is
spheroidal and Dx, Dy, and
Dz are only calculated if the diffusion is ellipsoidal.
The Dpar, Dx, Dy, and Dz unit vectors are calculated and a Numeric array is
returned.
Modified:
branches/tensor_pdb/data.py
Modified: branches/tensor_pdb/data.py
URL:
http://svn.gna.org/viewcvs/relax/branches/tensor_pdb/data.py?rev=2677&r1=2676&r2=2677&view=diff
==============================================================================
--- branches/tensor_pdb/data.py (original)
+++ branches/tensor_pdb/data.py Sun Oct 29 03:29:50 2006
@@ -21,7 +21,8 @@
###############################################################################
-from math import pi
+from Numeric import Float64, zeros
+from math import cos, pi, sin
from re import match
from types import DictType, ListType
@@ -64,7 +65,6 @@
self.g_count = {}
self.h_count = {}
self.warning = {}
-
def __repr__(self):
@@ -150,7 +150,7 @@
def add_item(self, key):
"""Function for adding an empty container to the dictionary.
-
+
This overwrites the function from the parent class SpecificData.
"""
@@ -164,7 +164,64 @@
def __getattr__(self, name):
- """Function for calculating the parameters on the fly."""
+ """Function for calculating the parameters and unit vectors on the
fly.
+
+ All tensor types
+ ================
+
+ The equation for calculating Diso is
+
+ Diso = 1 / (6tm).
+
+
+ Spheroidal diffusion
+ ====================
+
+ The equations for the parameters Dper, Dpar, and Dratio are
+
+ Dper = Diso - 1/3 Da,
+
+ Dpar = Diso + 2/3 Da,
+
+ Dratio = Dpar / Dper.
+
+ The unit vector parallel to the unique axis of the diffusion tensor
is
+
+ | sin(theta) * cos(phi) |
+ Dpar_unit = | sin(theta) * sin(phi) |.
+ | cos(theta) |
+
+
+ Ellipsoidal diffusion
+ =====================
+
+ The equations for the parameters Dx, Dy, and Dz are
+
+ Dx = Diso - 1/3 Da(1 + 3Dr),
+
+ Dy = Diso - 1/3 Da(1 - 3Dr),
+
+ Dz = Diso + 2/3 Da.
+
+ The unit Dx vector is
+
+ | -sin(alpha) * sin(gamma) + cos(alpha) * cos(beta)
* cos(gamma) |
+ Dx_unit = | -sin(alpha) * cos(gamma) - cos(alpha) * cos(beta)
* sin(gamma) |,
+ | cos(alpha) * sin(beta)
|
+
+ the unit Dy vector is
+
+ | cos(alpha) * sin(gamma) + sin(alpha) * cos(beta) *
cos(gamma) |
+ Dy_unit = | cos(alpha) * cos(gamma) - sin(alpha) * cos(beta) *
sin(gamma) |,
+ | sin(alpha) * sin(beta)
|
+
+ and the unit Dz vector is
+
+ | -sin(beta) * cos(gamma) |
+ Dz_unit = | sin(beta) * sin(gamma) |.
+ | cos(beta) |
+
+ """
# All tensor types.
###################
@@ -177,33 +234,85 @@
# Spheroidal diffusion.
#######################
- # Dper = Diso - 1/3Da.
- if name == 'Dper':
+ # Dper.
+ if name == 'Dper' and self.type == 'spheroid':
return self.Diso - 1.0/3.0 * self.Da
- # Dpar = Diso + 2/3Da.
- if name == 'Dpar':
+ # Dpar.
+ if name == 'Dpar' and self.type == 'spheroid':
return self.Diso + 2.0/3.0 * self.Da
- # Dratio = Dpar / Dper.
- if name == 'Dratio':
+ # Dratio.
+ if name == 'Dratio' and self.type == 'spheroid':
return self.Dpar / self.Dper
-
+ # Dpar unit vector.
+ if name == 'Dpar_unit' and self.type == 'spheroid':
+ # Initilise the vector.
+ Dpar_unit = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dpar_unit[0] = sin(self.theta) * cos(self.phi)
+ Dpar_unit[1] = sin(self.theta) * sin(self.phi)
+ Dpar_unit[2] = cos(self.theta)
+
+ # Return the unit vector.
+ return Dpar_unit
+
+
# Ellipsoidal diffusion.
########################
- # Dx = Diso - 1/3Da(1 + 3Dr).
- if name == 'Dx':
+ # Dx.
+ if name == 'Dx' and self.type == 'ellipsoid':
return self.Diso - 1.0/3.0 * self.Da * (1.0 + 3.0*self.Dr)
- # Dy = Diso - 1/3Da(1 - 3Dr).
- if name == 'Dy':
+ # Dy.
+ if name == 'Dy' and self.type == 'ellipsoid':
return self.Diso - 1.0/3.0 * self.Da * (1.0 - 3.0*self.Dr)
- # Dz = Diso + 2/3Da.
- if name == 'Dz':
+ # Dz.
+ if name == 'Dz' and self.type == 'ellipsoid':
return self.Diso + 2.0/3.0 * self.Da
+
+ # Dx unit vector.
+ if name == 'Dx_unit' and self.type == 'ellipsoid':
+ # Initilise the vector.
+ Dx_unit = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dx_unit[0] = -sin(self.alpha) * sin(self.gamma) +
cos(self.alpha) * cos(self.beta) * cos(self.gamma)
+ Dx_unit[1] = -sin(self.alpha) * cos(self.gamma) -
cos(self.alpha) * cos(self.beta) * sin(self.gamma)
+ Dx_unit[2] = cos(self.alpha) * sin(self.beta)
+
+ # Return the unit vector.
+ return Dx_unit
+
+ # Dy unit vector.
+ if name == 'Dy_unit' and self.type == 'ellipsoid':
+ # Initilise the vector.
+ Dy_unit = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dy_unit[0] = cos(self.alpha) * sin(self.gamma) +
sin(self.alpha) * cos(self.beta) * cos(self.gamma)
+ Dy_unit[1] = cos(self.alpha) * cos(self.gamma) -
sin(self.alpha) * cos(self.beta) * sin(self.gamma)
+ Dy_unit[2] = sin(self.alpha) * sin(self.beta)
+
+ # Return the unit vector.
+ return Dy_unit
+
+ # Dz unit vector.
+ if name == 'Dz_unit' and self.type == 'ellipsoid':
+ # Initilise the vector.
+ Dz_unit = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dz_unit[0] = -sin(self.beta) * cos(self.gamma)
+ Dz_unit[1] = sin(self.beta) * sin(self.gamma)
+ Dz_unit[2] = cos(self.beta)
+
+ # Return the unit vector.
+ return Dz_unit
# The attribute asked for does not exist.
r2677 - /branches/tensor_pdb/data.py