From aa8f9f68a809aef2c8bb4de32e25ae643ec92a08 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Fri, 27 Jun 2014 10:02:17 +0100
Subject: [PATCH] Fixed some bugs in documentation
There are now fewer warnings when Doxygen runs
---
CHANGES/Unreleased.txt | 4 ++--
.../ClassicalMultiDimensionalScaling.cpp | 2 +-
src/colvar/RMSD.cpp | 3 +--
user-doc/Colvar.txt | 2 +-
user-doc/Group.txt | 16 ++++++++--------
user-doc/Syntax.txt | 2 +-
6 files changed, 14 insertions(+), 15 deletions(-)
diff --git a/CHANGES/Unreleased.txt b/CHANGES/Unreleased.txt
index fb014aec7..ffda91957 100644
--- a/CHANGES/Unreleased.txt
+++ b/CHANGES/Unreleased.txt
@@ -12,8 +12,8 @@ Changes from version 2.0 which are relevant for users:
enabled or disabled. An internal version of lapack and blas will be used
if these libraries are not installed.
- The command SPHERE has been replaced by \ref UWALLS
-- Labels of quantities calaculated by BIASVALUE have changed from <label>.bias.<argname> to <label>.<argname>_bias, which is more consistent with steered MD
-- Labels of quantities calculated by ABMD have change from <label>.min_<argname> to <label>.<argname>_min, which is more consistent with steered MD
+- Labels of quantities calaculated by BIASVALUE have changed from <i>label</i>.bias.<i>argname</i> to <i>label</i>.<i>argname</i>_bias, which is more consistent with steered MD
+- Labels of quantities calculated by ABMD have change from <i>label</i>.min_<i>argname</i> to <i>label</i>.<i>argname</i>_min, which is more consistent with steered MD
- New actions:
- \ref SPRINT topological collective variables.
- \ref CH3SHIFTS collective variable.
diff --git a/src/analysis/ClassicalMultiDimensionalScaling.cpp b/src/analysis/ClassicalMultiDimensionalScaling.cpp
index c2066a136..27f4dfb81 100644
--- a/src/analysis/ClassicalMultiDimensionalScaling.cpp
+++ b/src/analysis/ClassicalMultiDimensionalScaling.cpp
@@ -79,7 +79,7 @@ D_{ij}^2 = \sum_{\alpha} (X^i_\alpha - X^j_\alpha)^2 = \sum_\alpha (X^i_\alpha)^
\f]
We can use this expression and matrix algebra to calculate multiple distances at once. For instance if we have three points,
-$\mathbf{X}$, we can write distances between them as:
+\f$\mathbf{X}\f$, we can write distances between them as:
\f{eqnarray*}{
D^2(\mathbf{X}) &=& \left[ \begin{array}{ccc}
diff --git a/src/colvar/RMSD.cpp b/src/colvar/RMSD.cpp
index a69a1d4c3..e05aa68c4 100644
--- a/src/colvar/RMSD.cpp
+++ b/src/colvar/RMSD.cpp
@@ -99,8 +99,7 @@ Here we discuss the switch we implemented so far.
you are working with natural units. If you are working with natural units then the coordinates
should be in your natural length unit. For more details on the PDB file format visit http://www.wwpdb.org/docs.html
.
- - If you use TYPE=OPTIMAL you just the root mean square deviation after reset of the geometric center
- and performing an optimal alignment that reads:
+ - If you use TYPE=OPTIMAL you just the root mean square deviation after reset of the geometric center and performing an optimal alignment that reads:
\f[
d(X,X_r) = \sqrt{ \sum_i \sum_\alpha^{x,y,z} \frac{w_i}{\sum_j w_j}[ X_{i,\alpha}-com_\alpha(X)- \sum_\beta M(X,X',w')_{\alpha,\beta}({X'}_{i,\beta}-com_\beta(X')) ]^2 }
\f]
diff --git a/user-doc/Colvar.txt b/user-doc/Colvar.txt
index e8fe24bb8..4a4987085 100644
--- a/user-doc/Colvar.txt
+++ b/user-doc/Colvar.txt
@@ -15,7 +15,7 @@ set of atomic positions and output one or multiple scalar CV values. Informatio
\ref Colvar while information as to how sets of atoms can be selected
can be found in the pages on \ref Group. Please be aware that PLUMED contains implementations of many other collective variables
but that the input for these variables may be less transparent when it is first encourntered.
-In particular, the page on \dists describes the various ways that you can calculate the distance from a particular reference
+In particular, the page on \ref dists describes the various ways that you can calculate the distance from a particular reference
configuration. So you will find instructions on how to calculate the RMSD distance from the folded state of a protein here.
Meanwhile, the page on \ref Function describes the various functions of collective variables that can be used in the
code. This is a very powerful feature of PLUMED as you can use the \ref Function commands to calculate any function or
diff --git a/user-doc/Group.txt b/user-doc/Group.txt
index c64dcb8cd..978613bde 100644
--- a/user-doc/Group.txt
+++ b/user-doc/Group.txt
@@ -38,17 +38,17 @@ following special groups are currently available in PLUMED:
<table align=center frame=void width=95%% cellpadding=5%%>
<tr> <td width=10%> <b> Symbol </b> </td> <td> <b> Topology type </b> </td> <td> <b> Despription </b> </td> </tr>
-<tr> <td> \@phi-# </td> <td> protein </td> <td>
-The torsional angle defined by the C, CA, N and C atoms of the protein backbone in the #th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
+<tr> <td> \@phi-\# </td> <td> protein </td> <td>
+The torsional angle defined by the C, CA, N and C atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
-<tr> <td> \@psi-# </td> <td> protein </td> <td>
-The torsional angle defined by the N, C, CA and N atoms of the protein backbone in the #th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
+<tr> <td> \@psi-\# </td> <td> protein </td> <td>
+The torsional angle defined by the N, C, CA and N atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
-<tr> <td> \@omega-# </td> <td> protein </td> <td>
-The torsional angle defined by the CA, N, C and CA atoms of the protein backbone in the #th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
+<tr> <td> \@omega-\# </td> <td> protein </td> <td>
+The torsional angle defined by the CA, N, C and CA atoms of the protein backbone in the \#th residue. See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
-<tr> <td> \@chi1-# </td> <td> protein </td> <td>
-The first torsional angle of the sidechain of the #th residue. Be aware that this angle is not defined for GLY or ALA residues.
+<tr> <td> \@chi1-\# </td> <td> protein </td> <td>
+The first torsional angle of the sidechain of the \#th residue. Be aware that this angle is not defined for GLY or ALA residues.
See http://en.wikipedia.org/wiki/Ramachandran_plot
</td> </tr>
</table>
diff --git a/user-doc/Syntax.txt b/user-doc/Syntax.txt
index 5de6adfaf..75a40541c 100644
--- a/user-doc/Syntax.txt
+++ b/user-doc/Syntax.txt
@@ -39,7 +39,7 @@ PRINT ARG=d1 FILE=colvar STRIDE=10
then PLUMED will print out the value of the distance between atoms 1 and 2 every 10 steps to the file colvar as you have told
PLUMED to take the value calculated by the action d1 and to print it. You can use any character string to label your actions
-as long as it does not begin with the symbol @. Strings beginning with @ are used by within PLUMED to reference special,
+as long as it does not begin with the symbol \@. Strings beginning with \@ are used by within PLUMED to reference special,
code-generated groups of atoms and to give labels to any Actions for which the user does not provide a label in the input.
Notice that if a word followed by a column is added at the beginning of the line (e.g. pippo:), PLUMED automatically
--
GitLab