Author: bugman
Date: Fri Jun 1 16:11:03 2012
New Revision: 16593
URL: http://svn.gna.org/viewcvs/relax?rev=16593&view=rev
Log:
Converted a number of add_verbatim() calls to add_item_list_element() with
items of None.
This allows for proper formatting and indentation of equations. In the
future, a possible
add_equation() method might be added to provide text and LaTeX
representations of equations in the
user function documentation.
Modified:
branches/uf_redesign/user_functions/align_tensor.py
branches/uf_redesign/user_functions/diffusion_tensor.py
branches/uf_redesign/user_functions/palmer.py
branches/uf_redesign/user_functions/spectrum.py
Modified: branches/uf_redesign/user_functions/align_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/align_tensor.py?rev=16593&r1=16592&r2=16593&view=diff
==============================================================================
--- branches/uf_redesign/user_functions/align_tensor.py (original)
+++ branches/uf_redesign/user_functions/align_tensor.py Fri Jun 1 16:11:03
2012
@@ -258,9 +258,9 @@
uf.desc[-1].add_item_list_element("6", "{Pxx, Pyy, Pxy, Pxz, Pyz}
(unitless),")
uf.desc[-1].add_item_list_element("7", "{Pzz, Pxx-yy, Pxy, Pxz, Pyz}
(unitless).")
uf.desc[-1].add_paragraph("Other formats may be added later. The
relationship between the Saupe order matrix S and the alignment tensor A is")
-uf.desc[-1].add_verbatim(" S = 3/2 A.")
+uf.desc[-1].add_item_list_element(None, "S = 3/2 A.")
uf.desc[-1].add_paragraph("The probability matrix P is related to the
alignment tensor A by")
-uf.desc[-1].add_verbatim(" A = P - 1/3 I,")
+uf.desc[-1].add_item_list_element(None, "A = P - 1/3 I,")
uf.desc[-1].add_paragraph("where I is the identity matrix. For the
alignment tensor to be supplied in Hertz, the bond vectors must all be of
equal length.")
# Prompt examples.
uf.desc.append(Desc_container("Prompt examples"))
Modified: branches/uf_redesign/user_functions/diffusion_tensor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/diffusion_tensor.py?rev=16593&r1=16592&r2=16593&view=diff
==============================================================================
--- branches/uf_redesign/user_functions/diffusion_tensor.py (original)
+++ branches/uf_redesign/user_functions/diffusion_tensor.py Fri Jun 1
16:11:03 2012
@@ -176,9 +176,7 @@
uf.desc[-1].add_item_list_element("0", "{tm} (Default),")
uf.desc[-1].add_item_list_element("1", "{Diso},")
uf.desc[-1].add_paragraph("where")
-uf.desc[-1].add_verbatim("""
- 1 / tm = 6Diso.
-""")
+uf.desc[-1].add_item_list_element(None, "1 / tm = 6Diso.")
# The spheroid (axially symmetric diffusion).
uf.desc.append(Desc_container("The spheroid (axially symmetric diffusion)"))
uf.desc[-1].add_paragraph("When two of the three eigenvalues of the
diffusion tensor are equal, the molecule diffuses as a spheroid. Four pieces
of information are required to specify this tensor, the two geometric
parameters, Diso and Da, and the two orientational parameters, the polar
angle theta and the azimuthal angle phi describing the orientation of the
axis of symmetry. The correlation function of the global diffusion is")
@@ -190,17 +188,13 @@
i=-1
""")
uf.desc[-1].add_paragraph("where")
-uf.desc[-1].add_verbatim("""
- c-1 = 1/4 (3 dz^2 - 1)^2,
- c0 = 3 dz^2 (1 - dz^2),
- c1 = 3/4 (dz^2 - 1)^2,
-""")
+uf.desc[-1].add_item_list_element(None, "c-1 = 1/4 (3 dz^2 - 1)^2,")
+uf.desc[-1].add_item_list_element(None, "c0 = 3 dz^2 (1 - dz^2),")
+uf.desc[-1].add_item_list_element(None, "c1 = 3/4 (dz^2 - 1)^2,")
uf.desc[-1].add_paragraph("and")
-uf.desc[-1].add_verbatim("""
- 1 / tau -1 = 6Diso - 2Da,
- 1 / tau 0 = 6Diso - Da,
- 1 / tau 1 = 6Diso + 2Da.
-""")
+uf.desc[-1].add_item_list_element(None, "1 / tau -1 = 6Diso - 2Da,")
+uf.desc[-1].add_item_list_element(None, "1 / tau 0 = 6Diso - Da,")
+uf.desc[-1].add_item_list_element(None, "1 / tau 1 = 6Diso + 2Da.")
uf.desc[-1].add_paragraph("The direction cosine dz is defined as the cosine
of the angle alpha between the XH bond vector and the unique axis of the
diffusion tensor.")
uf.desc[-1].add_paragraph("To select axially symmetric anisotropic
diffusion, the parameters argument should be a tuple of floating point
numbers of length four. A tuple is a type of data structure enclosed in
round brackets, the elements of which are separated by commas. Alternative
sets of parameters, 'param_types', are")
uf.desc[-1].add_item_list_element("0", "{tm, Da, theta, phi} (Default),")
@@ -209,21 +203,15 @@
uf.desc[-1].add_item_list_element("3", "{Dpar, Dper, theta, phi},")
uf.desc[-1].add_item_list_element("4", "{Diso, Dratio, theta, phi},")
uf.desc[-1].add_paragraph("where")
-uf.desc[-1].add_verbatim("""
- tm = 1 / 6Diso,
- Diso = 1/3 (Dpar + 2Dper),
- Da = Dpar - Dper,
- Dratio = Dpar / Dper.
-""")
+uf.desc[-1].add_item_list_element(None, "tm = 1 / 6Diso,")
+uf.desc[-1].add_item_list_element(None, "Diso = 1/3 (Dpar + 2Dper),")
+uf.desc[-1].add_item_list_element(None, "Da = Dpar - Dper,")
+uf.desc[-1].add_item_list_element(None, "Dratio = Dpar / Dper.")
uf.desc[-1].add_paragraph("The spherical angles {theta, phi} orienting the
unique axis of the diffusion tensor within the PDB frame are defined between")
-uf.desc[-1].add_verbatim("""
- 0 <= theta <= pi,
- 0 <= phi <= 2pi,
-""")
+uf.desc[-1].add_item_list_element(None, "0 <= theta <= pi,")
+uf.desc[-1].add_item_list_element(None, "0 <= phi <= 2pi,")
uf.desc[-1].add_paragraph("while the angle alpha which is the angle between
this axis and the given XH bond vector is defined between")
-uf.desc[-1].add_verbatim("""
- 0 <= alpha <= 2pi.
-""")
+uf.desc[-1].add_item_list_element(None, "0 <= alpha <= 2pi.")
uf.desc[-1].add_paragraph("The 'spheroid_type' argument should be 'oblate',
'prolate', or None. The argument will be ignored if the diffusion tensor is
not axially symmetric. If 'oblate' is given, then the constraint Da <= 0 is
used while if 'prolate' is given, then the constraint Da >= 0 is used. If
nothing is supplied, then Da will be allowed to have any values. To prevent
minimisation of diffusion tensor parameters in a space with two minima, it is
recommended to specify which tensor is to be minimised, thereby partitioning
the two minima into the two subspaces along the boundary Da = 0.")
# The ellipsoid (rhombic diffusion).
uf.desc.append(Desc_container("The ellipsoid (rhombic diffusion)"))
@@ -236,30 +224,22 @@
i=-2
""")
uf.desc[-1].add_paragraph("where the weights on the exponentials are")
-uf.desc[-1].add_verbatim("""
- c-2 = 1/4 (d + e),
- c-1 = 3 dy^2 dz^2,
- c0 = 3 dx^2 dz^2,
- c1 = 3 dx^2 dy^2,
- c2 = 1/4 (d + e).
-""")
+uf.desc[-1].add_item_list_element(None, "c-2 = 1/4 (d + e),")
+uf.desc[-1].add_item_list_element(None, "c-1 = 3 dy^2 dz^2,")
+uf.desc[-1].add_item_list_element(None, "c0 = 3 dx^2 dz^2,")
+uf.desc[-1].add_item_list_element(None, "c1 = 3 dx^2 dy^2,")
+uf.desc[-1].add_item_list_element(None, "c2 = 1/4 (d + e).")
uf.desc[-1].add_paragraph("Let")
-uf.desc[-1].add_verbatim("""
- R = sqrt(1 + 3Dr),
-""")
+uf.desc[-1].add_item_list_element(None, "R = sqrt(1 + 3Dr),")
uf.desc[-1].add_paragraph("then")
-uf.desc[-1].add_verbatim("""
- d = 3 (dx^4 + dy^4 + dz^4) - 1,
- e = - 1 / R ((1 + 3Dr)(dx^4 + 2dy^2 dz^2) + (1 - 3Dr)(dy^4 + 2dx^2 dz^2)
- 2(dz^4 + 2dx^2 dy^2)).
-""")
+uf.desc[-1].add_item_list_element(None, "d = 3 (dx^4 + dy^4 + dz^4) - 1,")
+uf.desc[-1].add_item_list_element(None, "e = - 1 / R ((1 + 3Dr)(dx^4 + 2dy^2
dz^2) + (1 - 3Dr)(dy^4 + 2dx^2 dz^2) - 2(dz^4 + 2dx^2 dy^2)).")
uf.desc[-1].add_paragraph("The correlation times are")
-uf.desc[-1].add_verbatim("""
- 1 / tau -2 = 6Diso - 2Da . R,
- 1 / tau -1 = 6Diso - Da (1 + 3Dr),
- 1 / tau 0 = 6Diso - Da (1 - 3Dr),
- 1 / tau 1 = 6Diso + 2Da,
- 1 / tau 1 = 6Diso + 2Da . R.
-""")
+uf.desc[-1].add_item_list_element(None, "1 / tau -2 = 6Diso - 2Da . R,")
+uf.desc[-1].add_item_list_element(None, "1 / tau -1 = 6Diso - Da (1 + 3Dr),")
+uf.desc[-1].add_item_list_element(None, "1 / tau 0 = 6Diso - Da (1 - 3Dr),")
+uf.desc[-1].add_item_list_element(None, "1 / tau 1 = 6Diso + 2Da,")
+uf.desc[-1].add_item_list_element(None, "1 / tau 1 = 6Diso + 2Da . R.")
uf.desc[-1].add_paragraph("The three direction cosines dx, dy, and dz are
the coordinates of a unit vector parallel to the XH bond vector. Hence the
unit vector is [dx, dy, dz].")
uf.desc[-1].add_paragraph("To select fully anisotropic diffusion, the
parameters argument should be a tuple of length six. A tuple is a type of
data structure enclosed in round brackets, the elements of which are
separated by commas. Alternative sets of parameters, 'param_types', are")
uf.desc[-1].add_item_list_element("0", "{tm, Da, Dr, alpha, beta, gamma}
(Default),")
@@ -267,23 +247,17 @@
uf.desc[-1].add_item_list_element("2", "{Dx, Dy, Dz, alpha, beta, gamma},")
uf.desc[-1].add_item_list_element("3", "{Dxx, Dyy, Dzz, Dxy, Dxz, Dyz},")
uf.desc[-1].add_paragraph("where")
-uf.desc[-1].add_verbatim("""
- tm = 1 / 6Diso,
- Diso = 1/3 (Dx + Dy + Dz),
- Da = Dz - (Dx + Dy)/2,
- Dr = (Dy - Dx)/2Da.
-""")
+uf.desc[-1].add_item_list_element(None, "tm = 1 / 6Diso,")
+uf.desc[-1].add_item_list_element(None, "Diso = 1/3 (Dx + Dy + Dz),")
+uf.desc[-1].add_item_list_element(None, "Da = Dz - (Dx + Dy)/2,")
+uf.desc[-1].add_item_list_element(None, "Dr = (Dy - Dx)/2Da.")
uf.desc[-1].add_paragraph("The angles alpha, beta, and gamma are the Euler
angles describing the diffusion tensor within the PDB frame. These angles
are defined using the z-y-z axis rotation notation where alpha is the initial
rotation angle around the z-axis, beta is the rotation angle around the
y-axis, and gamma is the final rotation around the z-axis again. The angles
are defined between")
-uf.desc[-1].add_verbatim("""
- 0 <= alpha <= 2pi,
- 0 <= beta <= pi,
- 0 <= gamma <= 2pi.
-""")
+uf.desc[-1].add_item_list_element(None, "0 <= alpha <= 2pi,")
+uf.desc[-1].add_item_list_element(None, "0 <= beta <= pi,")
+uf.desc[-1].add_item_list_element(None, "0 <= gamma <= 2pi.")
uf.desc[-1].add_paragraph("Within the PDB frame, the XH bond vector is
described using the spherical angles theta and phi where theta is the polar
angle and phi is the azimuthal angle defined between")
-uf.desc[-1].add_verbatim("""
- 0 <= theta <= pi,
- 0 <= phi <= 2pi.
-""")
+uf.desc[-1].add_item_list_element(None, "0 <= theta <= pi,")
+uf.desc[-1].add_item_list_element(None, "0 <= phi <= 2pi.")
uf.desc[-1].add_paragraph("When param_types is set to 3, then the elements
of the diffusion tensor matrix defined within the PDB frame can be supplied.")
# Units.
uf.desc.append(Desc_container("Units"))
Modified: branches/uf_redesign/user_functions/palmer.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/palmer.py?rev=16593&r1=16592&r2=16593&view=diff
==============================================================================
--- branches/uf_redesign/user_functions/palmer.py (original)
+++ branches/uf_redesign/user_functions/palmer.py Fri Jun 1 16:11:03 2012
@@ -142,7 +142,7 @@
uf.desc[-1].add_list_element("'dir/mfmodel'")
uf.desc[-1].add_list_element("'dir/run.sh'")
uf.desc[-1].add_paragraph("The file 'dir/run.sh' contains the single
command,")
-uf.desc[-1].add_verbatim("'modelfree4 -i mfin -d mfdata -p mfpar -m mfmodel
-o mfout -e out',")
+uf.desc[-1].add_item_list_element(None, "'modelfree4 -i mfin -d mfdata -p
mfpar -m mfmodel -o mfout -e out',")
uf.desc[-1].add_paragraph("which can be used to execute modelfree4.")
uf.desc[-1].add_paragraph("If you would like to use a different Modelfree
executable file, change the keyword argument 'binary' to the appropriate file
name. If the file is not located within the environment's path, include the
full path in front of the binary file name.")
uf.backend = palmer.create
Modified: branches/uf_redesign/user_functions/spectrum.py
URL:
http://svn.gna.org/viewcvs/relax/branches/uf_redesign/user_functions/spectrum.py?rev=16593&r1=16592&r2=16593&view=diff
==============================================================================
--- branches/uf_redesign/user_functions/spectrum.py (original)
+++ branches/uf_redesign/user_functions/spectrum.py Fri Jun 1 16:11:03 2012
@@ -126,7 +126,7 @@
# Peak heights with partially replicated spectra.
uf.desc.append(Desc_container("Peak heights with partially replicated
spectra"))
uf.desc[-1].add_paragraph("When spectra are replicated, the variance for a
single spin at a single replicated spectra set is calculated by the formula")
-uf.desc[-1].add_verbatim(" sigma^2 = sum({Ii - Iav}^2) / (n - 1),")
+uf.desc[-1].add_item_list_element(None, "sigma^2 = sum({Ii - Iav}^2) / (n -
1),")
uf.desc[-1].add_paragraph("where sigma^2 is the variance, sigma is the
standard deviation, n is the size of the replicated spectra set with i being
the corresponding index, Ii is the peak intensity for spectrum i, and Iav is
the mean over all spectra i.e. the sum of all peak intensities divided by n.")
uf.desc[-1].add_paragraph("As the value of n in the above equation is always
very low since normally only a couple of spectra are collected per replicated
spectra set, the variance of all spins is averaged for a single replicated
spectra set. Although this results in all spins having the same error, the
accuracy of the error estimate is significantly improved.")
uf.desc[-1].add_paragraph("If there are in addition to the replicated
spectra loaded peak intensities which only consist of a single spectrum, i.e.
not all spectra are replicated, then the variances of replicated replicated
spectra sets will be averaged. This will be used for the entire experiment
so that there will be only a single error value for all spins and for all
spectra.")
@@ -136,9 +136,9 @@
# Peak volumes with baseplane noise RMSD.
uf.desc.append(Desc_container("Peak volumes with baseplane noise RMSD"))
uf.desc[-1].add_paragraph("The method of error analysis when no spectra have
been replicated and peak volumes are used is highly dependent on the
integration method. Many methods simply sum the number of points within a
fixed region, either a box or oval object. The number of points used, N,
must be specified by another user function in this class. Then the error is
simply given by the sum of variances:")
-uf.desc[-1].add_verbatim(" sigma_vol^2 = sigma_i^2 * N,")
+uf.desc[-1].add_item_list_element(None, "sigma_vol^2 = sigma_i^2 * N,")
uf.desc[-1].add_paragraph("where sigma_vol is the standard deviation of the
volume, sigma_i is the standard deviation of a single point assumed to be
equal to the RMSD of the baseplane noise, and N is the total number of points
used in the summation integration method. For a box integration method, this
converts to the Nicholson, Kay, Baldisseri, Arango, Young, Bax, and Torchia
(1992) Biochemistry, 31: 5253-5263 equation:")
-uf.desc[-1].add_verbatim(" sigma_vol = sigma_i * sqrt(n*m),")
+uf.desc[-1].add_item_list_element(None, "sigma_vol = sigma_i * sqrt(n*m),")
uf.desc[-1].add_paragraph("where n and m are the dimensions of the box.
Note that a number of programs, for example peakint
(http://hugin.ethz.ch/wuthrich/software/xeasy/xeasy_m15.html) does not use
all points within the box. And if the number N can not be determined, this
category of error analysis is not possible.")
uf.desc[-1].add_paragraph("Also note that non-point summation methods, for
example when line shape fitting is used to determine peak volumes, the
equations above cannot be used. Hence again this category of error analysis
cannot be used. This is the case for one of the three integration methods
used by Sparky
(http://www.cgl.ucsf.edu/home/sparky/manual/peaks.html#Integration). And if
fancy techniques are used, for example as Cara does to deconvolute
overlapping peaks (http://www.cara.ethz.ch/Wiki/Integration), this again
makes this error analysis impossible.")
# Peak volumes with partially replicated spectra.
r16593 - in /branches/uf_redesign/user_functions: align_tensor.py diffusion_tensor.py palmer.py spectrum.py