Author: bugman
Date: Tue Nov 7 06:32:28 2006
New Revision: 2757
URL: http://svn.gna.org/viewcvs/relax?rev=2757&view=rev
Log:
Added automatically generated MC simulation objects to the diffusion tensor
data structure.
The class implementing the object is called 'DiffAutoSimArrayObject'. The
following functions have
been addded to generate the objects:
self._auto_object_Diso_sim()
self._auto_object_Dpar_sim()
self._auto_object_Dper_sim()
self._auto_object_Dpar_unit_sim()
self._auto_object_Dx_sim()
self._auto_object_Dy_sim()
self._auto_object_Dz_sim()
self._auto_object_Dx_unit_sim()
self._auto_object_Dy_unit_sim()
self._auto_object_Dz_unit_sim()
These are simply copies of the non-simulation functions with the added
argument 'i' for selecting
the simulation.
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=2757&r1=2756&r2=2757&view=diff
==============================================================================
--- branches/tensor_pdb/data.py (original)
+++ branches/tensor_pdb/data.py Tue Nov 7 06:32:28 2006
@@ -177,22 +177,38 @@
# The isotropic diffusion rate.
#self.Diso = DiffAutoFloat(self._auto_object_tensor)
+ self.Diso_sim = DiffAutoSimArrayObject(self._auto_object_Diso_sim,
self)
# Automatically generated objects for spherical diffusion.
##########################################################
+ # Eigenvalue parallel to the unique axis.
+ self.Dpar_sim = DiffAutoSimArrayObject(self._auto_object_Dpar_sim,
self)
+
+ # Eigenvalue perpendicular to the unique axis.
+ self.Dper_sim = DiffAutoSimArrayObject(self._auto_object_Dper_sim,
self)
+
# Unit vector parallel to the axis.
self.Dpar_unit = DiffAutoNumericObject(self._auto_object_Dpar_unit)
+ self.Dpar_unit_sim =
DiffAutoSimArrayObject(self._auto_object_Dpar_unit_sim, self)
# Automatically generated objects for ellipsoidal diffusion.
############################################################
+
+ # Eigenvalues Dx, Dy, and Dz.
+ self.Dx_sim = DiffAutoSimArrayObject(self._auto_object_Dx_sim, self)
+ self.Dy_sim = DiffAutoSimArrayObject(self._auto_object_Dy_sim, self)
+ self.Dz_sim = DiffAutoSimArrayObject(self._auto_object_Dz_sim, self)
# Unit vectors parallel to the axes.
self.Dx_unit = DiffAutoNumericObject(self._auto_object_Dx_unit)
self.Dy_unit = DiffAutoNumericObject(self._auto_object_Dy_unit)
self.Dz_unit = DiffAutoNumericObject(self._auto_object_Dz_unit)
+ self.Dx_unit_sim =
DiffAutoSimArrayObject(self._auto_object_Dx_unit_sim, self)
+ self.Dy_unit_sim =
DiffAutoSimArrayObject(self._auto_object_Dy_unit_sim, self)
+ self.Dz_unit_sim =
DiffAutoSimArrayObject(self._auto_object_Dz_unit_sim, self)
def __getattr__(self, name):
@@ -273,6 +289,29 @@
# The attribute asked for does not exist.
raise AttributeError, name
+
+
+ def _auto_object_Diso_sim(self, i):
+ """Function for automatically calculating the Diso value for
simulation i.
+
+ @return: The Diso value for Monte Carlo simulation i.
+ @rtype: float
+ """
+
+ # Diso value for simulation i.
+ return 1.0 / (6.0 * self.tm_sim[i])
+
+
+ def _auto_object_Dpar_sim(self, i):
+ """Function for automatically calculating the Dpar value for
simulation i.
+
+ @return: The Dpar value for Monte Carlo simulation i.
+ @rtype: float
+ """
+
+ # Dpar value for simulation i (only generate the object if the
diffusion is spheroidal).
+ if self.type == 'spheroid':
+ return self.Diso_sim[i] + 2.0/3.0 * self.Da_sim[i]
def _auto_object_Dpar_unit(self):
@@ -302,6 +341,57 @@
return Dpar_unit
+ def _auto_object_Dpar_unit_sim(self, i):
+ """Function for automatically calculating the Dpar unit vector for
the simulation i.
+
+ 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) |
+
+ @return: The Dpar unit vector for Monte Carlo simulation i.
+ @rtype: array (Float64)
+ """
+
+ # Dpar unit vector for simulation i (only generate the object if the
diffusion is spheroidal).
+ if self.type == 'spheroid':
+ # Initilise the vector.
+ Dpar_unit_i = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dpar_unit_i[0] = sin(self.theta_sim[i]) * cos(self.phi_sim[i])
+ Dpar_unit_i[1] = sin(self.theta_sim[i]) * sin(self.phi_sim[i])
+ Dpar_unit_i[2] = cos(self.theta_sim[i])
+
+ # Return the unit vector.
+ return Dpar_unit_i
+
+
+ def _auto_object_Dper_sim(self, i):
+ """Function for automatically calculating the Dper value for
simulation i.
+
+ @return: The Dper value for Monte Carlo simulation i.
+ @rtype: float
+ """
+
+ # Dper value for simulation i (only generate the object if the
diffusion is spheroidal).
+ if self.type == 'spheroid':
+ return self.Diso_sim[i] - 1.0/3.0 * self.Da_sim[i]
+
+
+ def _auto_object_Dx_sim(self, i):
+ """Function for automatically calculating the Dx value for
simulation i.
+
+ @return: The Dx value for Monte Carlo simulation i.
+ @rtype: float
+ """
+
+ # Dx value for simulation i (only generate the object if the
diffusion is ellipsoidal).
+ if self.type == 'ellipsoid':
+ return self.Diso_sim[i] - 1.0/3.0 * self.Da_sim[i] * (1.0 +
3.0*self.Dr_sim[i])
+
+
def _auto_object_Dx_unit(self):
"""Function for automatically calculating the Dx unit vector.
@@ -329,6 +419,39 @@
return Dx_unit
+ def _auto_object_Dx_unit_sim(self, i):
+ """Function for automatically calculating the Dx unit vector for
simulation i.
+
+ @return: The Dx unit vector for Monte Carlo simulation i.
+ @rtype: array (Float64)
+ """
+
+ # Dx unit vector for simulation i (only generate the object if the
diffusion is ellipsoidal).
+ if self.type == 'ellipsoid':
+ # Initilise the vector.
+ Dx_unit_i = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dx_unit_i[0] = -sin(self.alpha_sim[i]) * sin(self.gamma_sim[i])
+ cos(self.alpha_sim[i]) * cos(self.beta_sim[i]) * cos(self.gamma_sim[i])
+ Dx_unit_i[1] = -sin(self.alpha_sim[i]) * cos(self.gamma_sim[i])
- cos(self.alpha_sim[i]) * cos(self.beta_sim[i]) * sin(self.gamma_sim[i])
+ Dx_unit_i[2] = cos(self.alpha_sim[i]) * sin(self.beta_sim[i])
+
+ # Return the unit vector.
+ return Dx_unit_i
+
+
+ def _auto_object_Dy_sim(self, i):
+ """Function for automatically calculating the Dy value for
simulation i.
+
+ @return: The Dy value for Monte Carlo simulation i.
+ @rtype: float
+ """
+
+ # Dy value for simulation i (only generate the object if the
diffusion is ellipsoidal).
+ if self.type == 'ellipsoid':
+ return self.Diso_sim[i] - 1.0/3.0 * self.Da_sim[i] * (1.0 -
3.0*self.Dr_sim[i])
+
+
def _auto_object_Dy_unit(self):
"""Function for automatically calculating the Dy unit vector.
@@ -356,6 +479,39 @@
return Dy_unit
+ def _auto_object_Dy_unit_sim(self, i):
+ """Function for automatically calculating the Dy unit vector for
simulation i.
+
+ @return: The Dy unit vector for Monte Carlo simulation i.
+ @rtype: array (Float64)
+ """
+
+ # Dy unit vector for simulation i (only generate the object if the
diffusion is ellipsoidal).
+ if self.type == 'ellipsoid':
+ # Initilise the vector.
+ Dy_unit_i = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dy_unit_i[0] = cos(self.alpha_sim[i]) * sin(self.gamma_sim[i])
+ sin(self.alpha_sim[i]) * cos(self.beta_sim[i]) * cos(self.gamma_sim[i])
+ Dy_unit_i[1] = cos(self.alpha_sim[i]) * cos(self.gamma_sim[i])
- sin(self.alpha_sim[i]) * cos(self.beta_sim[i]) * sin(self.gamma_sim[i])
+ Dy_unit_i[2] = sin(self.alpha_sim[i]) * sin(self.beta_sim[i])
+
+ # Return the unit vector.
+ return Dy_unit_i
+
+
+ def _auto_object_Dz_sim(self, i):
+ """Function for automatically calculating the Dz value for
simulation i.
+
+ @return: The Dz value for Monte Carlo simulation i.
+ @rtype: float
+ """
+
+ # Dz value for simulation i (only generate the object if the
diffusion is ellipsoidal).
+ if self.type == 'ellipsoid':
+ return self.Diso_sim[i] - 1.0/3.0 * self.Da_sim[i] * (1.0 -
3.0*self.Dr_sim[i])
+
+
def _auto_object_Dz_unit(self):
"""Function for automatically calculating the Dz unit vector.
@@ -383,6 +539,27 @@
return Dz_unit
+ def _auto_object_Dz_unit_sim(self, i):
+ """Function for automatically calculating the Dz unit vector for
simulation i.
+
+ @return: The Dz unit vector for Monte Carlo simulation i.
+ @rtype: array (Float64)
+ """
+
+ # Dz unit vector for simulation i (only generate the object if the
diffusion is ellipsoidal).
+ if self.type == 'ellipsoid':
+ # Initilise the vector.
+ Dz_unit_i = zeros(3, Float64)
+
+ # Calculate the x, y, and z components.
+ Dz_unit_i[0] = -sin(self.beta_sim[i]) * cos(self.gamma_sim[i])
+ Dz_unit_i[1] = sin(self.beta_sim[i]) * sin(self.gamma_sim[i])
+ Dz_unit_i[2] = cos(self.beta_sim[i])
+
+ # Return the unit vector.
+ return Dz_unit_i
+
+
def _auto_object_rotation(self):
"""Function for automatically calculating the rotation matrix.
@@ -627,6 +804,104 @@
"""
raise RelaxError, "This object cannot be modified!"
+
+
+
+# Automatic array-like objects for the Monte Carlo simulations.
+class DiffAutoSimArrayObject(ListType):
+ def __init__(self, object, diff_data):
+ """Class for implementing an automatically generated array-like
object for the MC sims."""
+
+ # Function which returns the Numeric data structure (to be called at
run-time).
+ self.object = object
+
+ # The local scope of the diffusion tensor data structure.
+ self.diff_data = diff_data
+
+
+ def __add__(self, x):
+ """Disallow addition.
+
+ @raise: RelaxError.
+ """
+
+ raise RelaxError, "Addition is not allowed."
+
+
+ def __getitem__(self, i):
+ """Function for selecting individual elements of the array.
+
+ @return: Element i of the array.
+ @rtype: float
+ """
+
+ return self.object(i)
+
+
+ def __iter__(self):
+ """Function for looping over the array.
+
+ @return: An iterator object for looping over the array.
+ @rtype: iterator object
+ """
+
+ return iter(self.create_array())
+
+
+ def __len__(self):
+ """Function to calculate the length of the array.
+
+ @return: The length of the array.
+ @rtype: int
+ """
+
+ return len(self.diff_data.tm_sim)
+
+
+ def __mul__(self, x):
+ """Disallow multiplication.
+
+ @raise: RelaxError.
+ """
+
+ raise RelaxError, "Multiplication is not allowed."
+
+
+ def __repr__(self):
+ """Function for computing the 'official' string representation of
the array.
+
+ @return: The string representation of the array.
+ @rtype: string
+ """
+
+ return `self.create_array()`
+
+
+ def __setitem__(self, key, value):
+ """Disallow modifications to the array.
+
+ @raise: RelaxError.
+ """
+
+ raise RelaxError, "This object cannot be modified!"
+
+
+ def create_array(self):
+ """Generate the array.
+
+ @return: The array of objects.
+ @rtype: list
+ """
+
+ # Initialise the array.
+ array = []
+
+ # Loop over the elements, appending the structure to the array.
+ for i in xrange(len(self.diff_data.tm_sim)):
+ array.append(self.object(i))
+
+ # Return the array.
+ return array
r2757 - /branches/tensor_pdb/data.py