Author: bugman
Date: Tue Oct 7 01:15:04 2008
New Revision: 7548
URL: http://svn.gna.org/viewcvs/relax?rev=7548&view=rev
Log:
A number of epydoc docstring fixes.
Modified:
1.3/generic_fns/palmer.py
1.3/maths_fns/correlation_time.py
1.3/relax
1.3/specific_fns/n_state_model.py
Modified: 1.3/generic_fns/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/palmer.py?rev=7548&r1=7547&r2=7548&view=diff
==============================================================================
--- 1.3/generic_fns/palmer.py (original)
+++ 1.3/generic_fns/palmer.py Tue Oct 7 01:15:04 2008
@@ -47,11 +47,11 @@
"""Function for creating the Modelfree4 input files.
The following files are created:
- dir/mfin
- dir/mfdata
- dir/mfpar
- dir/mfmodel
- dir/run.sh
+ - dir/mfin
+ - dir/mfdata
+ - dir/mfpar
+ - dir/mfmodel
+ - dir/run.sh
"""
# Test if the current pipe exists.
Modified: 1.3/maths_fns/correlation_time.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/maths_fns/correlation_time.py?rev=7548&r1=7547&r2=7548&view=diff
==============================================================================
--- 1.3/maths_fns/correlation_time.py (original)
+++ 1.3/maths_fns/correlation_time.py Tue Oct 7 01:15:04 2008
@@ -36,7 +36,7 @@
def calc_sphere_ti(data, diff_data):
"""Diffusional correlation times.
- The correlation time is
+ The correlation time is::
t0 = tm.
"""
@@ -51,7 +51,7 @@
def calc_sphere_dti(data, diff_data):
"""Partial derivatives of the diffusional correlation times.
- The tm partial derivatives are
+ The tm partial derivatives are::
dt0
--- = 1.
@@ -75,7 +75,7 @@
def calc_spheroid_ti(data, diff_data):
"""Diffusional correlation times.
- The equations for the parameters {Diso, Da} are
+ The equations for the parameters {Diso, Da} are::
t-1 = (6Diso - 2Da)**-1,
@@ -130,7 +130,9 @@
"""Diffusional correlation time gradients.
tm partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~
+ ======================
+
+ The equations are::
dt-1 dDiso
---- = -6 ----- (6Diso - 2Da)**-2,
@@ -145,13 +147,13 @@
dtm dtm
- As
+ As::
dDiso
----- = -1/6 * tm**-2,
dtm
- the equations simplify to
+ the equations simplify to::
dt-1
---- = tm**-2 (6Diso - 2Da)**-2,
@@ -167,7 +169,9 @@
Da partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~
+ ======================
+
+ The equations are::
dt-1
---- = 2(6Diso - 2Da)**-2,
@@ -215,7 +219,9 @@
"""Diffusional correlation time Hessians.
tm-tm partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-1 / dDiso \ 2 d2Diso
----- = 72 | ----- | (6Diso - 2Da)**-3 - 6 ------ (6Diso -
2Da)**-2,
@@ -230,19 +236,19 @@
dtm2 \ dtm / dtm2
- As
+ As::
d2Diso
------ = 1/3 * tm**-3,
dtm2
- and
+ and::
dDiso
----- = -1/6 * tm**-2,
dtm
- the equations simplify to
+ the equations simplify to::
d2t-1
----- = 2tm**-4 (6Diso - 2Da)**-3 - 2tm**-3 (6Diso - 2Da)**-2,
@@ -258,7 +264,9 @@
tm-Da partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-1 dDiso
------- = -24 ----- (6Diso - 2Da)**-3,
@@ -272,13 +280,13 @@
------- = 24 ----- (6Diso + 2Da)**-3.
dtm.dDa dtm
- As
+ As::
dDiso
----- = -1/6 * tm**-2,
dtm
- the equations simplify to
+ the equations simplify to::
d2t-1
------- = 4tm**-2 (6Diso - 2Da)**-3,
@@ -295,7 +303,9 @@
Da-Da partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-1
----- = 8 (6Diso - 2Da)**-3,
@@ -359,7 +369,7 @@
def calc_ellipsoid_ti(data, diff_data):
"""Diffusional correlation times.
- The equations for the parameters {Diso, Da, Dr} are:
+ The equations for the parameters {Diso, Da, Dr} are::
t-2 = (6Diso - 2DaR)**-1,
@@ -371,7 +381,7 @@
t2 = (6Diso + 2DaR)**-1,
- where:
+ where::
__________
R = \/1 + 3Dr**2.
@@ -443,7 +453,9 @@
"""Diffusional correlation time gradients.
tm partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~
+ ======================
+
+ The equations are::
dt-2 dDiso
---- = - 6 ----- (6Diso - 2DaR)**-2,
@@ -466,13 +478,13 @@
dtm dtm
- As
+ As::
dDiso
----- = -1/6 * tm**-2,
dtm
- the equations simplify to
+ the equations simplify to::
dt-2
---- = tm**-2 (6Diso - 2DaR)**-2,
@@ -496,7 +508,9 @@
Da partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~
+ ======================
+
+ The equations are::
dt-2
---- = 2R (6Diso - 2DaR)**-2,
@@ -520,7 +534,9 @@
Dr partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~
+ ======================
+
+ The equations are::
dt-2
---- = 6 Da.Dr/R (6Diso - 2DaR)**-2,
@@ -593,6 +609,8 @@
tm-tm partial derivatives
~~~~~~~~~~~~~~~~~~~~~~~~~
+ The equations are::
+
d2t-2 / dDiso \ 2 d2Diso
----- = 72 | ----- | (6Diso - 2DaR)**-3 - 6 ------ (6Diso -
2DaR)**-2,
dtm2 \ dtm / dtm2
@@ -613,19 +631,19 @@
---- = 72 | ----- | (6Diso + 2DaR)**-3 - 6 ------ (6Diso +
2DaR)**-2.
dtm2 \ dtm / dtm2
- As
+ As::
d2Diso
------ = 1/3 * tm**-3,
dtm2
- and
+ and::
dDiso
----- = -1/6 * tm**-2,
dtm
- the equations simplify to
+ the equations simplify to::
d2t-2
----- = 2tm**-4 (6Diso - 2DaR)**-3 - 2tm**-3 (6Diso - 2DaR)**-2,
@@ -650,7 +668,9 @@
tm-Da partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-2 dDiso
------- = -24R ----- (6Diso - 2DaR)**-3,
@@ -672,13 +692,13 @@
------- = 24R ----- (6Diso + 2DaR)**-3.
dtm.dDa dtm
- As
+ As::
dDiso
----- = -1/6 * tm**-2,
dtm
- the equations simplify to
+ the equations simplify to::
d2t-2
------- = 4R tm**-2 (6Diso - 2DaR)**-3,
@@ -702,7 +722,9 @@
tm-Dr partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-2 dDiso
------- = -72 Da.Dr/R ----- (6Diso - 2DaR)**-3,
@@ -724,13 +746,13 @@
------- = 72 Da.Dr/R ----- (6Diso + 2DaR)**-3.
dtm.dDr dtm
- As
+ As::
dDiso
----- = -1/6 * tm**-2,
dtm
- the equations simplify to
+ the equations simplify to::
d2t-2
------- = 12 Da.Dr/R tm**-2 (6Diso - 2DaR)**-3,
@@ -754,7 +776,9 @@
Da-Da partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-2
----- = 8R**2 (6Diso - 2DaR)**-3,
@@ -778,7 +802,9 @@
Da-Dr partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-2
------- = 24Da.Dr (6Diso - 2DaR)**-3 + 6Dr/R (6Diso - 2DaR)**-2,
@@ -802,7 +828,9 @@
Dr-Dr partial derivatives
- ~~~~~~~~~~~~~~~~~~~~~~~~~
+ =========================
+
+ The equations are::
d2t-2
----- = 72(Da.Dr/R)**2 (6Diso - 2DaR)**-3 + 6Da/R**3 (6Diso -
2DaR)**-2,
Modified: 1.3/relax
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax?rev=7548&r1=7547&r2=7548&view=diff
==============================================================================
--- 1.3/relax (original)
+++ 1.3/relax Tue Oct 7 01:15:04 2008
@@ -297,8 +297,8 @@
def get_intro_string(self):
"""Create the program introduction.
- @return: The program introduction string.
- @type return: str
+ @return: The program introduction string.
+ @rtype: str
"""
# The width of the printout.
Modified: 1.3/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/specific_fns/n_state_model.py?rev=7548&r1=7547&r2=7548&view=diff
==============================================================================
--- 1.3/specific_fns/n_state_model.py (original)
+++ 1.3/specific_fns/n_state_model.py Tue Oct 7 01:15:04 2008
@@ -335,7 +335,7 @@
contain the elements 'rdc', 'pcs' or
'tensor'.
@type data_types: list of str
@keyword scaling_matrix: The diagonal scaling matrix.
- @type scaling_matrx: numpy rank-2 square matrix
+ @type scaling_matrix: numpy rank-2 square matrix
@return: The matrices A and b.
@rtype: tuple of len 2 of a numpy rank-2, size
NxM matrix and numpy
rank-1, size N array
r7548 - in /1.3: generic_fns/palmer.py maths_fns/correlation_time.py relax specific_fns/n_state_model.py