diff --git a/modules/mol/mm/doc/buildingblock.rst b/modules/mol/mm/doc/buildingblock.rst
index 12b89c5c35ac030be9bfb617cf3dce16ad419ad9..c9dbcfd7d936986f5ed18ffa1a3905e852fe6918 100644
--- a/modules/mol/mm/doc/buildingblock.rst
+++ b/modules/mol/mm/doc/buildingblock.rst
@@ -32,6 +32,7 @@ The BuildingBlock Class
:type residue: :class:`ResidueHandle`
:type match_connectivity: :class:`bool`
+ :returns: :class:`bool`
.. method:: Connect(residue, editor)
@@ -39,7 +40,7 @@ The BuildingBlock Class
BuildingBlock.
:param residue: Residue to be connected
- :param editor: Editor associated to the residues entity
+ :param editor: Editor associated to the residue's entity
:type residue: :class:`ResidueHandle`
:type editor: :class:`XCSEditor`
@@ -95,13 +96,13 @@ The BuildingBlock Class
.. method:: RemoveInteractionsToPrev()
Removes all interactions associated to an atom of a previous residues.
- This gets indicated by an atom name prefixed by a *-*
+ This gets indicated in the :class:`BuildingBlock` by an atom name prefixed by a *-*
.. method:: RemoveInteractionsToNext()
Removes all interactions associated to an atom of a next residues.
- This gets indicated by an atom name prefixed by a *+*
+ This gets indicated in the :class:`BuildingBlock` by an atom name prefixed by a *+*
.. method:: AddBond(bond, [,replace_existing = False])
@@ -178,10 +179,12 @@ The BuildingBlock Class
Gets forcefield type from atom with given name
- :param name: Name from atom you want the type from
+ :param name: Name of atom you want the type from
:type name: :class:`str`
+ :returns: :class:`str`
+
:raises: :class:`RuntimeError` when atom can not be found in
BuildingBlock
@@ -189,10 +192,12 @@ The BuildingBlock Class
Gets charge from atom with given name
- :param name: Name from atom you want the charge from
+ :param name: Name of atom you want the charge from
:type name: :class:`str`
+ :returns: :class:`float`
+
:raises: :class:`RuntimeError` when atom can not be found in
BuildingBlock
@@ -201,10 +206,12 @@ The BuildingBlock Class
Gets mass from atom with given name
- :param name: Name from atom you want the mass from
+ :param name: Name of atom you want the mass from
:type name: :class:`str`
+ :returns: :class:`float`
+
:raises: :class:`RuntimeError` when atom can not be found in
BuildingBlock
@@ -260,6 +267,10 @@ The BuildingBlock Class
Block Modifiers
--------------------------------------------------------------------------------
+.. class:: BlockModifier
+
+ Basis class. Block modifiers are used to change building blocks or residues.
+ See :class:`GromacsBlockModifier` for a specific example.
.. class:: GromacsBlockModifier
@@ -376,6 +387,11 @@ Block Modifiers
Hydrogen Constructors
--------------------------------------------------------------------------------
+.. class:: HydrogenConstructor
+
+ Basis class. Hydrogen constructors are used to add hydrogens to residues.
+
+
.. class:: GromacsHydrogenConstructor
The :class:`GromacsHydrogenConstructor` is the Gromacs way of adding
diff --git a/modules/mol/mm/doc/forcefield.rst b/modules/mol/mm/doc/forcefield.rst
index 3dbc9d07921a5886c791c8ed35a0c0e3c0beddf6..9c5754152381c0712e176100ffe0d42a8cbb4f3b 100644
--- a/modules/mol/mm/doc/forcefield.rst
+++ b/modules/mol/mm/doc/forcefield.rst
@@ -7,7 +7,7 @@ The forcefields are a dump for interactions with their parameters, but also
for atom specific information or residue definitions in the form of a
:class:`BuildingBlock`. Objects for modifying residues can be set in form of
:class:`BlockModifier` or :class:`HydrogenConstructor`.
-They're also involved in the naming mess we're observing in the molecular mechanics
+They're also involved in dealing with the naming mess we're observing in the molecular mechanics
community and contain definable renaming rules that can be applied on an
:class:`EntityHandle` for renaming from e.g. PDB standard to the forcefield
specific standard. The standard forcefields in OpenStructure are loaded from
@@ -66,9 +66,9 @@ as they are used in Gromacs.
.. method:: ReadResidueDatabase(basename)
Searches and reads all files belonging the the residue database
- defined by **basename**. With basename aminoacids this function
- searches and reads all files in the base_dir matching aminoacids.x
- where x is .rtp .arn .hdb .n.tdb .c.tdb .vsd .r2b
+ defined by **basename**. With *basename=aminoacids* this function
+ searches and reads all files in the **base_dir** matching *aminoacids.x*
+ where *x* is *.rtp .arn .hdb .n.tdb .c.tdb .vsd .r2b*.
Only the rtp file is mandatory, all others are neglected if not present.
:param basename: Basename of residue database to be loaded
@@ -77,8 +77,8 @@ as they are used in Gromacs.
.. method:: ReadITP(basename)
- Searches and reads the itp file in the **base_dir**. **basename** amazing_ion
- would therefore load the file amazing_ion.itp
+ Searches and reads the itp file in the **base_dir**. *basename=amazing_ion*
+ would therefore load the file *amazing_ion.itp*
:param basename: Basename of itp file to be loaded
@@ -191,7 +191,7 @@ The Forcefield Class
.. method:: AddDihedral(dihedral)
- :param dihedral: Bond to be added
+ :param dihedral: Dihedral to be added
:type dihedral: :class:`Interaction`
@@ -280,7 +280,7 @@ The Forcefield Class
:param factor: Factor with which the 1,4 electrostatic term
should be dampened
- :type factor: :class:`factor`
+ :type factor: :class:`float`
.. method:: SetGenPairs(gen_pairs)
@@ -294,7 +294,7 @@ The Forcefield Class
.. method:: AddResidueRenamingRule(name, ff_main_name, ff_n_ter_name, ff_c_ter_name, ff_two_ter_name)
- :param name: Original name or the residue
+ :param name: Original name of the residue
(e.g. PDB/Gromacs standard)
:param ff_main_name: Forcefield specific residue name
:param ff_n_ter_name: Forcefield specific name if the residue
@@ -314,8 +314,8 @@ The Forcefield Class
.. method:: AddAtomRenamingRule(res_name, old_atom_name, new_atom_name)
- :param res_name: Forcefield specific residue name the
- atom belongs
+ :param res_name: Forcefield specific name of the residue the
+ atom belongs to
:param old_atom_name: Atom name in PDB/Gromacs standard
@@ -582,7 +582,7 @@ The Forcefield Class
:type type: :class:`str`
- :returns: the mass
+ :returns: :class:`float` - the mass
:raises: :class:`RuntimeError` if no mass has been set for this
atom type
@@ -590,13 +590,13 @@ The Forcefield Class
.. method:: GetFudgeLJ()
- :returns: Factor with which the 1,4 Lennard Jones term
- should be dampened
+ :returns: :class:`float` - Factor with which the 1,4 Lennard Jones
+ term should be dampened
.. method:: GetFudgeQQ()
- :returns: Factor with which the 1,4 electrostatic term
- should be dampened
+ :returns: :class:`float` - Factor with which the 1,4
+ electrostatic term should be dampened
.. method:: GetAtomType(res_name, atom_name)
@@ -609,7 +609,7 @@ The Forcefield Class
:type res_name: :class:`str`
:type atom_name: :class:`str`
- :returns: atom type
+ :returns: :class:`str` - atom type
:raises: :class:`RuntimeError` if forcefield has no such
:class:`BuildingBlock` or when atom is not present
diff --git a/modules/mol/mm/doc/integrators.rst b/modules/mol/mm/doc/integrators.rst
index 326a7831eb8d84ac88fb7bdfca2f641145ef47df..1db383bde8ecb7981e90640528e8fe583549ad07 100644
--- a/modules/mol/mm/doc/integrators.rst
+++ b/modules/mol/mm/doc/integrators.rst
@@ -3,9 +3,11 @@ Integrators
.. currentmodule:: ost.mol
-The Integrators are a wrapper around the integrators provided by OpenMM and
-have to be attached to the :class:`Settings` when setting up a simulation.
-It provides a way of making the thing shake.
+.. class:: Integrator
+
+ The :class:`Integrator` are a wrapper around the integrators provided by OpenMM and
+ have to be attached to the :class:`Settings` when setting up a simulation.
+ It provides a way of making the thing shake.
@@ -55,7 +57,7 @@ Langevin Dynamics
.. method:: GetTemperature()
- :returns: :class:`float`
+ :returns: :class:`float` - the temperature in K
.. method:: SetTemperature(temperature)
@@ -64,7 +66,7 @@ Langevin Dynamics
.. method:: GetFriction()
- :returns: :class:`float`
+ :returns: :class:`float` - the friction in 1/ps
.. method:: SetFriction(friction)
@@ -98,7 +100,7 @@ Langevin Dynamics
.. method:: GetTemperature()
- :returns: :class:`float`
+ :returns: :class:`float` - the temperature in K
.. method:: SetTemperature(temperature)
@@ -107,7 +109,7 @@ Langevin Dynamics
.. method:: GetFriction()
- :returns: :class:`float`
+ :returns: :class:`float` - the friction in 1/ps
.. method:: SetFriction(friction)
@@ -151,7 +153,7 @@ Brownian Dynamics
.. method:: GetTemperature()
- :returns: :class:`float`
+ :returns: :class:`float` - the temperature in K
.. method:: SetTemperature(temperature)
@@ -160,7 +162,7 @@ Brownian Dynamics
.. method:: GetFriction()
- :returns: :class:`float`
+ :returns: :class:`float` - the friction in 1/ps
.. method:: SetFriction(friction)
diff --git a/modules/mol/mm/doc/interaction.rst b/modules/mol/mm/doc/interaction.rst
index d0f3abd7ca42b6fa27aeeab29d3ae373a1a8ab39..95d193e1a9e64b9e312590033bc3214d1b198fc9 100644
--- a/modules/mol/mm/doc/interaction.rst
+++ b/modules/mol/mm/doc/interaction.rst
@@ -63,7 +63,6 @@ Interaction Parametrization
* HarmonicImproper, Interacting Particles: 4, Num Parameters: 2
#. :class:`float` angle in radians
- #. :class:`float` force constant in
#. :class:`float` force constant in kJ/mol/radian^2
* CMap, Interacting Particles: 5, Num Parameters: n*n+1
diff --git a/modules/mol/mm/doc/molmm.rst b/modules/mol/mm/doc/molmm.rst
index a6b67ddcfaf5190c12e238b7279c036013b97298..14df01078b3f1ab87318a1a66e7228e08dae1aca 100644
--- a/modules/mol/mm/doc/molmm.rst
+++ b/modules/mol/mm/doc/molmm.rst
@@ -8,11 +8,10 @@ Introduction
The mol.mm module provides a wrapper around the
`OpenMM <http://openmm.org>`_ molecular mechanics library to provide
-basic md capabilities fully embedded into the OpenStructure universe.
+basic molecular dynamics (MD) capabilities fully embedded into the OpenStructure universe.
The heart of every simulation is the :class:`Topology` describing how the
-particles of an :class:`EntityHandle` interact. The :class:`Simulation` finally
-connects the two and allows one to perform energy minimizations or move the
-simulation through time using an :class:`Integrator`.
+particles of an :class:`EntityHandle` interact. The :class:`Simulation` class connects the :class:`EntityHandle` with a :class:`Topology` and allows you to perform energy minimizations
+or move the simulation through time using an :class:`Integrator`.
A :class:`Topology` can either be built from scratch by adding
one interaction after the other or automatically using the
:class:`TopologyCreator`. The process of :class:`Topology` building