separated .rst documentation of dihedral PCA and hydrogen-bonds

The section of the reference manual on hydrogen-bonds was included
in dihedral-pca.rst. This hindered insertion of a section on an
analysis method related to PCA right after the dihedral PCA section.

Change-Id: I4d7c88624a12fc516cb63465098060fc871cc987

diff --git a/docs/CMakeLists.txt b/docs/CMakeLists.txt
index 55a43089e8503e9d50164baf2c78c38d2b33ef4c..8ad2e04f5a0fa9e773899a049354432bb002a513 100644 (file)
--- a/docs/CMakeLists.txt
+++ b/docs/CMakeLists.txt
@@ -245,6 +245,7 @@ if (SPHINX_FOUND)
         reference-manual/analysis/rmsd.rst
         reference-manual/analysis/covariance-analysis.rst
         reference-manual/analysis/dihedral-pca.rst
+        reference-manual/analysis/hydrogen-bonds.rst
         reference-manual/analysis/protein-related.rst
         reference-manual/analysis/interface-related.rst)
     # The image files have also been ordered by the respective

diff --git a/docs/reference-manual/analysis.rst b/docs/reference-manual/analysis.rst
index 4c698f9bdc7ce7057a8b314d5489316c240a6671..d789d3d40daf3d948cb41889eeff8c1633cccee7 100644 (file)
--- a/docs/reference-manual/analysis.rst
+++ b/docs/reference-manual/analysis.rst
@@ -30,6 +30,7 @@ different analysis tools are presented.
    analysis/rmsd
    analysis/covariance-analysis
    analysis/dihedral-pca
+   analysis/hydrogen-bonds
    analysis/protein-related
    analysis/interface-related
 

diff --git a/docs/reference-manual/analysis/dihedral-pca.rst b/docs/reference-manual/analysis/dihedral-pca.rst
index 8c31695026b4a3c9e196d3857335ae78aa2c9634..a49b684dff643496cb05438415c986e03fe97cd8 100644 (file)
--- a/docs/reference-manual/analysis/dihedral-pca.rst
+++ b/docs/reference-manual/analysis/dihedral-pca.rst
@@ -26,91 +26,3 @@ Dihedral principal component analysis
   reference file do not correspond in any way to the information in the
   :ref:`trr` file. Analysis of the results is done using
   :ref:`gmx anaeig <gmx anaeig>`.
-
-Hydrogen bonds
---------------
-
-| :ref:`gmx hbond <gmx hbond>`
-| The program :ref:`gmx hbond <gmx hbond>`
-  analyzes the *hydrogen bonds* (H-bonds) between all possible donors D
-  and acceptors A. To determine if an H-bond exists, a geometrical
-  criterion is used, see also :numref:`Fig. %s <fig-hbond>`:
-
-  .. math:: \begin{array}{rclcl}
-            r       & \leq  & r_{HB}        & = & 0.35~\mbox{nm}    \\
-            \alpha  & \leq  & \alpha_{HB}   & = & 30^o              \\
-            \end{array}
-            :label: eqnhbondgeomtric
-
-.. _fig-hbond:
-
-.. figure:: plots/hbond.*
-   :width: 7.50000cm
-
-   Geometrical Hydrogen bond criterion.
-
-The value of :math:`r_{HB} = 0.35 \mathrm{nm}` corresponds to the first minimum
-of the RDF of SPC water (see also :numref:`Fig. %s <fig-hbondinsert>`).
-
-The program :ref:`gmx hbond <gmx hbond>` analyzes all hydrogen bonds
-existing between two groups of atoms (which must be either identical or
-non-overlapping) or in specified donor-hydrogen-acceptor triplets, in
-the following ways:
-
-.. _fig-hbondinsert:
-
-.. figure:: plots/hbond-insert.*
-    :width: 7.50000cm
-
-    Insertion of water into an H-bond. (1) Normal H-bond between two
-    residues. (2) H-bonding bridge via a water molecule.
-
--  Donor-Acceptor distance (:math:`r`) distribution of all H-bonds
-
--  Hydrogen-Donor-Acceptor angle (:math:`\alpha`) distribution of all
-   H-bonds
-
--  The total number of H-bonds in each time frame
-
--  The number of H-bonds in time between residues, divided into groups
-   :math:`n`-:math:`n`\ +\ :math:`i` where :math:`n` and
-   :math:`n`\ +\ :math:`i` stand for residue numbers and :math:`i` goes
-   from 0 to 6. The group for :math:`i=6` also includes all H-bonds for
-   :math:`i>6`. These groups include the
-   :math:`n`-:math:`n`\ +\ :math:`3`, :math:`n`-:math:`n`\ +\ :math:`4`
-   and :math:`n`-:math:`n`\ +\ :math:`5` H-bonds, which provide a
-   measure for the formation of :math:`\alpha`-helices or
-   :math:`\beta`-turns or strands.
-
--  The lifetime of the H-bonds is calculated from the average over all
-   autocorrelation functions of the existence functions (either 0 or 1)
-   of all H-bonds:
-
-   .. math:: C(\tau) ~=~ \langle s_i(t)~s_i (t + \tau) \rangle
-             :label: eqnhbcorr
-
--  with :math:`s_i(t) = \{0,1\}` for H-bond :math:`i` at time
-   :math:`t`. The integral of :math:`C(\tau)` gives a rough estimate of
-   the average H-bond lifetime :math:`\tau_{HB}`:
-
-   .. math::  \tau_{HB} ~=~ \int_{0}^{\infty} C(\tau) d\tau
-              :label: eqnhblife
-
--  Both the integral and the complete autocorrelation function
-   :math:`C(\tau)` will be output, so that more sophisticated analysis
-   (*e.g.* using multi-exponential fits) can be used to get better
-   estimates for :math:`\tau_{HB}`. A more complete analysis is given in
-   ref. \ :ref:`173 <refSpoel2006b>`; one of the more fancy option is the Luzar
-   and Chandler analysis of hydrogen bond kinetics \ :ref:`174 <refLuzar96b>`, :ref:`175 <refLuzar2000a>`.
-
--  An H-bond existence map can be generated of dimensions
-   *# H-bonds*\ :math:`\times`\ *# frames*. The ordering is identical to
-   the index file (see below), but reversed, meaning that the last
-   triplet in the index file corresponds to the first row of the
-   existence map.
-
--  Index groups are output containing the analyzed groups, all
-   donor-hydrogen atom pairs and acceptor atoms in these groups,
-   donor-hydrogen-acceptor triplets involved in hydrogen bonds between
-   the analyzed groups and all solvent atoms involved in insertion.
-

diff --git a/docs/reference-manual/analysis/hydrogen-bonds.rst b/docs/reference-manual/analysis/hydrogen-bonds.rst
new file mode 100644 (file)
index 0000000..c88f284
--- /dev/null
+++ b/docs/reference-manual/analysis/hydrogen-bonds.rst
@@ -0,0 +1,86 @@
+Hydrogen bonds
+--------------
+
+| :ref:`gmx hbond <gmx hbond>`
+| The program :ref:`gmx hbond <gmx hbond>`
+  analyzes the *hydrogen bonds* (H-bonds) between all possible donors D
+  and acceptors A. To determine if an H-bond exists, a geometrical
+  criterion is used, see also :numref:`Fig. %s <fig-hbond>`:
+
+  .. math:: \begin{array}{rclcl}
+            r       & \leq  & r_{HB}        & = & 0.35~\mbox{nm}    \\
+            \alpha  & \leq  & \alpha_{HB}   & = & 30^o              \\
+            \end{array}
+            :label: eqnhbondgeomtric
+
+.. _fig-hbond:
+
+.. figure:: plots/hbond.*
+   :width: 7.50000cm
+
+   Geometrical Hydrogen bond criterion.
+
+The value of :math:`r_{HB} = 0.35 \mathrm{nm}` corresponds to the first minimum
+of the RDF of SPC water (see also :numref:`Fig. %s <fig-hbondinsert>`).
+
+The program :ref:`gmx hbond <gmx hbond>` analyzes all hydrogen bonds
+existing between two groups of atoms (which must be either identical or
+non-overlapping) or in specified donor-hydrogen-acceptor triplets, in
+the following ways:
+
+.. _fig-hbondinsert:
+
+.. figure:: plots/hbond-insert.*
+    :width: 7.50000cm
+
+    Insertion of water into an H-bond. (1) Normal H-bond between two
+    residues. (2) H-bonding bridge via a water molecule.
+
+-  Donor-Acceptor distance (:math:`r`) distribution of all H-bonds
+
+-  Hydrogen-Donor-Acceptor angle (:math:`\alpha`) distribution of all
+   H-bonds
+
+-  The total number of H-bonds in each time frame
+
+-  The number of H-bonds in time between residues, divided into groups
+   :math:`n`-:math:`n`\ +\ :math:`i` where :math:`n` and
+   :math:`n`\ +\ :math:`i` stand for residue numbers and :math:`i` goes
+   from 0 to 6. The group for :math:`i=6` also includes all H-bonds for
+   :math:`i>6`. These groups include the
+   :math:`n`-:math:`n`\ +\ :math:`3`, :math:`n`-:math:`n`\ +\ :math:`4`
+   and :math:`n`-:math:`n`\ +\ :math:`5` H-bonds, which provide a
+   measure for the formation of :math:`\alpha`-helices or
+   :math:`\beta`-turns or strands.
+
+-  The lifetime of the H-bonds is calculated from the average over all
+   autocorrelation functions of the existence functions (either 0 or 1)
+   of all H-bonds:
+
+   .. math:: C(\tau) ~=~ \langle s_i(t)~s_i (t + \tau) \rangle
+             :label: eqnhbcorr
+
+-  with :math:`s_i(t) = \{0,1\}` for H-bond :math:`i` at time
+   :math:`t`. The integral of :math:`C(\tau)` gives a rough estimate of
+   the average H-bond lifetime :math:`\tau_{HB}`:
+
+   .. math::  \tau_{HB} ~=~ \int_{0}^{\infty} C(\tau) d\tau
+              :label: eqnhblife
+
+-  Both the integral and the complete autocorrelation function
+   :math:`C(\tau)` will be output, so that more sophisticated analysis
+   (*e.g.* using multi-exponential fits) can be used to get better
+   estimates for :math:`\tau_{HB}`. A more complete analysis is given in
+   ref. \ :ref:`173 <refSpoel2006b>`; one of the more fancy option is the Luzar
+   and Chandler analysis of hydrogen bond kinetics \ :ref:`174 <refLuzar96b>`, :ref:`175 <refLuzar2000a>`.
+
+-  An H-bond existence map can be generated of dimensions
+   *# H-bonds*\ :math:`\times`\ *# frames*. The ordering is identical to
+   the index file (see below), but reversed, meaning that the last
+   triplet in the index file corresponds to the first row of the
+   existence map.
+
+-  Index groups are output containing the analyzed groups, all
+   donor-hydrogen atom pairs and acceptor atoms in these groups,
+   donor-hydrogen-acceptor triplets involved in hydrogen bonds between
+   the analyzed groups and all solvent atoms involved in insertion.