From efb579cb7d3a6be9cd31feed3b53a302081573e5 Mon Sep 17 00:00:00 2001
From: Gabriel Studer <gabriel.studer@unibas.ch>
Date: Wed, 29 Apr 2015 16:32:49 +0200
Subject: [PATCH] also document the init parameters
---
modules/mol/mm/doc/integrators.rst | 35 +++++++++++++++++++++++----
modules/mol/mm/doc/interaction.rst | 4 +++-
modules/mol/mm/doc/simulation.rst | 38 ++++++++++++++++++++++++++++--
modules/mol/mm/doc/topology.rst | 3 ++-
4 files changed, 71 insertions(+), 9 deletions(-)
diff --git a/modules/mol/mm/doc/integrators.rst b/modules/mol/mm/doc/integrators.rst
index 641b5e168..011def6a7 100644
--- a/modules/mol/mm/doc/integrators.rst
+++ b/modules/mol/mm/doc/integrators.rst
@@ -7,16 +7,25 @@ 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
to provide a way of making the thing shake.
-.. class:: VerletIntegrator
+.. class:: VerletIntegrator(step_size)
Implementation of Verlet dynamics
+ :param step_size: :class:`float` defining timestep in ps.
-.. class:: BrownianIntegrator
+
+.. class:: BrownianIntegrator(temperature, friction_coeff, step_size)
Implementation of Brownian dynamics
+ :param temperature: :class:`float` temperature of heat bath in K
+
+ :param friction_coeff: :class:`float` friction coefficient coupling the
+ system to the heat bath in 1/ps
+
+ :param step_size: :class:`float` defining timestep in ps.
+
.. method:: GetTemperature()
:returns: :class:`float`
@@ -44,10 +53,17 @@ to provide a way of making the thing shake.
-.. class:: LangevinIntegrator
+.. class:: LangevinIntegrator(temperature, friction_coeff, step_size)
Implementation of the Langevin dynamics
+ :param temperature: :class:`float` temperature of heat bath in K
+
+ :param friction_coeff: :class:`float` friction coefficient coupling the
+ system to the heat bath in 1/ps
+
+ :param step_size: :class:`float` defining timestep in ps.
+
.. method:: GetTemperature()
:returns: :class:`float`
@@ -74,10 +90,12 @@ to provide a way of making the thing shake.
-.. class:: VariableVerletIntegrator
+.. class:: VariableVerletIntegrator(error_tol)
Implementation of Verlet dynamics with variable time steps
+ :param error_tol: :class:`float` error tolerance
+
.. method:: GetErrorTolerance()
:returns: :class:`float`
@@ -88,10 +106,17 @@ to provide a way of making the thing shake.
-.. class:: VariableLangevinIntegrator
+.. class:: VariableLangevinIntegrator(temperature, friction_coeff, error_tol)
Implementation of Langevin dynamics with variable time steps
+ :param temperature: :class:`float` temperature of heat bath in K
+
+ :param friction_coeff: :class:`float` friction coefficient coupling the
+ system to the heat bath in 1/ps
+
+ :param error_tol: :class:`float` error_tolerance.
+
.. method:: GetTemperature()
:returns: :class:`float`
diff --git a/modules/mol/mm/doc/interaction.rst b/modules/mol/mm/doc/interaction.rst
index b2bd0439f..b25b9d01e 100644
--- a/modules/mol/mm/doc/interaction.rst
+++ b/modules/mol/mm/doc/interaction.rst
@@ -29,7 +29,9 @@ a harmonic angle)
--------------------------------------------------------------------------------
-.. class:: Interaction
+.. class:: Interaction(func_type)
+
+ :param func_type: :class:`FuncType` defining a particular interaction
..method:: SetTypes(types)
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
index 3de0804fb..0a7176133 100644
--- a/modules/mol/mm/doc/simulation.rst
+++ b/modules/mol/mm/doc/simulation.rst
@@ -3,11 +3,45 @@ Simulation
.. currentmodule:: ost.mol
+The simulation finally connects a :class:`Topology` with an
+:class:`ost.mol.EntityHandle`. While applying minimization or
+MD tasks, the current positions of the simulation object can be
+mapped back to the attached structure at any time.
-.. class:: Simulation
- The :class:`mm.Simulation` class is used to run a simulation.
+.. class:: Simulation(entity, settings)
+
+ first constructor, that takes an :class:`ost.mol.EntityHandle` as an input
+ and automatically constructs an internal :class:`Topology` according
+ to the provided **settings**. Be aware, that the **entity** will be altered
+ depending on hydrogen/termini definitions in the :class:`Forcefield` attached
+ to the **settings**
+
+ :param entity: :class:`ost.mol.EntityHandle` from which a default
+ :class:`Topology` will be created according to the
+ **settings**
+
+ :param settings: :class:`Settings` to control the parametrization of
+ the :class:`Simulation` and the buildup of the
+ internal :class:`Topology`
+
+ :raises: :class:`RuntimeError` when construction of
+ :class:`Topology` fails
+
+.. class:: Simulation(topology,entity,settings)
+
+ second constructor, that takes a :class:`Topology` and a consistent
+ :class:`ost.mol.EntityHandle` as an input.
+
+ :param topology: :class:`Topology` to initialize the :class:`Simulation`
+
+ :param entity: :class:`ost.mol.EntityHandle` that is consistent with
+ the provided **topology**
+
+ :param settings: :class:`Settings` to control the parametrization of
+ the :class:`Simulation`
+
.. method:: Save(filename)
diff --git a/modules/mol/mm/doc/topology.rst b/modules/mol/mm/doc/topology.rst
index 5fb169e76..2a4f63604 100644
--- a/modules/mol/mm/doc/topology.rst
+++ b/modules/mol/mm/doc/topology.rst
@@ -43,8 +43,9 @@ that should suffice most needs.
:class:`RuntimeError` can be supressed by the
according flag in the :class:`Settings` object.
-.. class:: Topology
+.. class:: Topology(masses)
+ :param masses: :class:`list` of the particles masses
.. method:: Save(filename)
--
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