From 3041f2f5933e5e54ecbdc6e66fac28c33fd3d3fb Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Thu, 30 Apr 2015 16:41:29 +0200
Subject: [PATCH] some documentation pimps
---
modules/mol/mm/doc/forcefield.rst | 2 ++
modules/mol/mm/doc/molmm.rst | 13 +++++++++++++
modules/mol/mm/doc/topology.rst | 11 ++++++++++-
3 files changed, 25 insertions(+), 1 deletion(-)
diff --git a/modules/mol/mm/doc/forcefield.rst b/modules/mol/mm/doc/forcefield.rst
index ffb80d522..a5071a311 100644
--- a/modules/mol/mm/doc/forcefield.rst
+++ b/modules/mol/mm/doc/forcefield.rst
@@ -127,6 +127,8 @@ as they are used in GROMACS.
ff = new_reader.GetForcefield()
ff.Save("charmm_forcefield.dat")
+The Forcefield Class
+--------------------------------------------------------------------------------
.. class:: Forcefield
diff --git a/modules/mol/mm/doc/molmm.rst b/modules/mol/mm/doc/molmm.rst
index 772d486ac..999213b0a 100644
--- a/modules/mol/mm/doc/molmm.rst
+++ b/modules/mol/mm/doc/molmm.rst
@@ -78,3 +78,16 @@ You want to create your own :class:`BuildingBlock` to parametrize custom
residues? Or even generate your custom :class:`Forcefield`?
Check out the mm dir in the examples/code_fragments directory.
+Documentation
+--------------------------------------------------------------------------------
+
+.. toctree::
+ interaction
+ buildingblock
+ forcefield
+ settings
+ topology
+ observers
+ integrators
+ simulation
+
diff --git a/modules/mol/mm/doc/topology.rst b/modules/mol/mm/doc/topology.rst
index 6988f1e10..e94997f37 100644
--- a/modules/mol/mm/doc/topology.rst
+++ b/modules/mol/mm/doc/topology.rst
@@ -13,6 +13,9 @@ as soon as a :class:`Simulation` is set up. To make setting up a
to create a :class:`Topology` based on an mm :class:`Settings` object,
that should suffice most needs.
+Automatically Create Topologies
+--------------------------------------------------------------------------------
+
.. class:: TopologyCreator
.. method:: Create(entity, settings)
@@ -41,8 +44,10 @@ that should suffice most needs.
#. Check, whether the residues match with the building blocks
#. Extract bonds/angles etc. based on the flags in the **settings**
+
+ #. Impropers and CMaps get only extracted when they are defined in the :class:`BuildingBlock`
- #. Add Parametrization from forcefield to the Topology
+ #. Add Parametrization from :class:`Forcefield` to the :class:`Topology`. Note, that you can override the :class:`Forcefield` parametrization if you add this particular :class:`Interaction` in a parametrized form in the :class:`Buildingblock`!!!
#. Rename entity back to PDB naming if according flag is set in **settings**
@@ -67,6 +72,10 @@ that should suffice most needs.
:class:`RuntimeError` can be supressed by the
according flag in the :class:`Settings` object.
+
+The Topology Class
+--------------------------------------------------------------------------------
+
.. class:: Topology(masses)
:param masses: :class:`list` of the particles masses
--
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