Author: bugman
Date: Wed Jan 27 13:32:04 2010
New Revision: 10433
URL: http://svn.gna.org/viewcvs/relax?rev=10433&view=rev
Log:
Epydoc fixes throughout the 'data' package.
Modified:
1.3/data/__init__.py
1.3/data/align_tensor.py
1.3/data/diff_tensor.py
1.3/data/relax_xml.py
Modified: 1.3/data/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/__init__.py?rev=10433&r1=10432&r2=10433&view=diff
==============================================================================
--- 1.3/data/__init__.py (original)
+++ 1.3/data/__init__.py Wed Jan 27 13:32:04 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2004, 2006-2009 Edward d'Auvergne
#
+# Copyright (C) 2003-2004, 2006-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -149,8 +149,10 @@
statement 'D[pipe] = PipeContainer()', where D is the relax data
storage object and pipe is
the name of the data pipe.
- @param pipe: The name of the new data pipe.
- @type pipe: str
+ @param pipe_name: The name of the new data pipe.
+ @type pipe_name: str
+ @param pipe_type: The data pipe type.
+ @type pipe_type: str
"""
# Test if the pipe already exists.
Modified: 1.3/data/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/align_tensor.py?rev=10433&r1=10432&r2=10433&view=diff
==============================================================================
--- 1.3/data/align_tensor.py (original)
+++ 1.3/data/align_tensor.py Wed Jan 27 13:32:04 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2004, 2006-2009 Edward d'Auvergne
#
+# Copyright (C) 2003-2004, 2006-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -362,9 +362,7 @@
The diagonalised alignment tensor is calculated by eigenvalue
decomposition.
- @param rotation: The rotation matrix.
- @type rotation: numpy array ((3, 3), float64)
- @param tensor: The full alignment tensor.
+ @param tensor: The full alignment tensor in its eigenframe.
@type tensor: numpy array ((3, 3), float64)
@return: The diagonalised alignment tensor.
@rtype: numpy array ((3, 3), float64)
@@ -596,9 +594,7 @@
The diagonalised alignment tensor is calculated by eigenvalue
decomposition.
- @param rotation: The rotation matrix.
- @type rotation: numpy array ((3, 3), float64)
- @param tensor: The full alignment tensor.
+ @param tensor: The full alignment tensor in its eigenframe.
@type tensor: numpy array ((3, 3), float64)
@return: The diagonalised alignment tensor.
@rtype: numpy array ((3, 3), float64)
@@ -634,7 +630,7 @@
def calc_Pxx(Axx):
"""Function for calculating the Pxx value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Pxx = Axx + 1/3.
Modified: 1.3/data/diff_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/diff_tensor.py?rev=10433&r1=10432&r2=10433&view=diff
==============================================================================
--- 1.3/data/diff_tensor.py (original)
+++ 1.3/data/diff_tensor.py Wed Jan 27 13:32:04 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2004, 2006-2009 Edward d'Auvergne
#
+# Copyright (C) 2003-2004, 2006-2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -37,7 +37,7 @@
def calc_Diso(tm):
"""Function for calculating the Diso value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Diso = 1 / (6tm).
@@ -54,7 +54,7 @@
def calc_Dpar(Diso, Da):
"""Function for calculating the Dpar value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Dpar = Diso + 2/3 Da.
@@ -73,7 +73,7 @@
def calc_Dpar_unit(theta, phi):
"""Function for calculating the Dpar unit vector.
- The unit vector parallel to the unique axis of the diffusion tensor is
+ The unit vector parallel to the unique axis of the diffusion tensor is::
| sin(theta) * cos(phi) |
Dpar_unit = | sin(theta) * sin(phi) |.
@@ -102,7 +102,7 @@
def calc_Dper(Diso, Da):
"""Function for calculating the Dper value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Dper = Diso - 1/3 Da.
@@ -121,7 +121,7 @@
def calc_Dratio(Dpar, Dper):
"""Function for calculating the Dratio value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Dratio = Dpar / Dper.
@@ -140,7 +140,7 @@
def calc_Dx(Diso, Da, Dr):
"""Function for calculating the Dx value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Dx = Diso - 1/3 Da(1 + 3Dr).
@@ -161,7 +161,7 @@
def calc_Dx_unit(alpha, beta, gamma):
"""Function for calculating the Dx unit vector.
- The unit Dx vector is
+ 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) |.
@@ -192,7 +192,7 @@
def calc_Dy(Diso, Da, Dr):
"""Function for calculating the Dy value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Dy = Diso - 1/3 Da(1 - 3Dr),
@@ -213,7 +213,7 @@
def calc_Dy_unit(alpha, beta, gamma):
"""Function for calculating the Dy unit vector.
- The unit Dy vector is
+ 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) |.
@@ -244,7 +244,7 @@
def calc_Dz(Diso, Da):
"""Function for calculating the Dz value.
- The equation for calculating the parameter is
+ The equation for calculating the parameter is::
Dz = Diso + 2/3 Da.
@@ -263,7 +263,7 @@
def calc_Dz_unit(beta, gamma):
"""Function for calculating the Dz unit vector.
- The unit Dz vector is
+ The unit Dz vector is::
| -sin(beta) * cos(gamma) |
Dz_unit = | sin(beta) * sin(gamma) |.
@@ -296,7 +296,7 @@
===================
As the orientation of the diffusion tensor within the structural frame
is undefined when the
- molecule diffuses as a sphere, the rotation matrix is simply the
identity matrix
+ molecule diffuses as a sphere, the rotation matrix is simply the
identity matrix::
| 1 0 0 |
R = | 0 1 0 |.
@@ -307,7 +307,7 @@
====================
The rotation matrix required to shift from the diffusion tensor frame to
the structural
- frame is equal to
+ frame is equal to::
| cos(theta) * cos(phi) -sin(phi) sin(theta) * cos(phi) |
R = | cos(theta) * sin(phi) cos(phi) sin(theta) * sin(phi) |.
@@ -318,7 +318,7 @@
=====================
The rotation matrix required to shift from the diffusion tensor frame to
the structural
- frame is equal to
+ frame is equal to::
R = | Dx_unit Dy_unit Dz_unit |,
@@ -326,8 +326,8 @@
= | Dx_unit[1] Dy_unit[1] Dz_unit[1] |.
| Dx_unit[2] Dy_unit[2] Dz_unit[2] |
- @param *args: All the function arguments.
- @type *args: tuple
+ @param args: All the function arguments.
+ @type args: tuple
@param theta: The azimuthal angle in radians.
@type theta: float
@param phi: The polar angle in radians.
@@ -400,7 +400,7 @@
"""Function for calculating the diffusion tensor (in the structural
frame).
The diffusion tensor is calculated using the diagonalised tensor and the
rotation matrix
- through the equation
+ through the equation::
R . tensor_diag . R^T.
@@ -419,26 +419,26 @@
def calc_tensor_diag(diff_type, *args):
"""Function for calculating the diagonalised diffusion tensor.
- The diagonalised spherical diffusion tensor is defined as
+ The diagonalised spherical diffusion tensor is defined as::
| Diso 0 0 |
tensor = | 0 Diso 0 |.
| 0 0 Diso |
- The diagonalised spheroidal tensor is defined as
+ The diagonalised spheroidal tensor is defined as::
| Dper 0 0 |
tensor = | 0 Dper 0 |.
| 0 0 Dpar |
- The diagonalised ellipsoidal diffusion tensor is defined as
+ The diagonalised ellipsoidal diffusion tensor is defined as::
| Dx 0 0 |
tensor = | 0 Dy 0 |.
| 0 0 Dz |
- @param *args: All the arguments.
- @type *args: tuple
+ @param args: All the arguments.
+ @type args: tuple
@param Diso: The Diso parameter of the sphere.
@type Diso: float
@param Dpar: The Dpar parameter of the spheroid.
@@ -613,7 +613,7 @@
def __setattr__(self, name, value):
"""Function for calculating the parameters, unit vectors, and
tensors on the fly.
- The equations for the parameters Dper, Dpar, and Dratio are
+ The equations for the parameters Dper, Dpar, and Dratio are::
Dratio = Dpar / Dper.
"""
Modified: 1.3/data/relax_xml.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/data/relax_xml.py?rev=10433&r1=10432&r2=10433&view=diff
==============================================================================
--- 1.3/data/relax_xml.py (original)
+++ 1.3/data/relax_xml.py Wed Jan 27 13:32:04 2010
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2008 Edward d'Auvergne
#
+# Copyright (C) 2008, 2010 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -95,7 +95,7 @@
@param elem: The element to extract all python objects from.
@type elem: xml.dom.minidom.Element instance
@keyword base_object: The python class instance to place the objects
into.
- @type base_bject: instance
+ @type base_object: instance
@keyword set_fn: A function used to replace setattr for placing
the object into the base
object.
@type set_fn: function
r10433 - in /1.3/data: __init__.py align_tensor.py diff_tensor.py relax_xml.py