From bd8e29ac182eb5de4166a7d79a5c9b2d962cdbb8 Mon Sep 17 00:00:00 2001
From: Niklaus Johner <niklaus.johner@unibas.ch>
Date: Fri, 15 May 2015 09:11:01 +0200
Subject: [PATCH] And more MM documentation corrections.
---
modules/mol/mm/doc/integrators.rst | 2 +-
modules/mol/mm/doc/simulation.rst | 16 ++++++++--------
2 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/modules/mol/mm/doc/integrators.rst b/modules/mol/mm/doc/integrators.rst
index 1db383bde..ed94d8695 100644
--- a/modules/mol/mm/doc/integrators.rst
+++ b/modules/mol/mm/doc/integrators.rst
@@ -7,7 +7,7 @@ Integrators
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.
+ They define the algorithm used to integrate the equations of motion of the system.
diff --git a/modules/mol/mm/doc/simulation.rst b/modules/mol/mm/doc/simulation.rst
index f8e661932..217c1cc7d 100644
--- a/modules/mol/mm/doc/simulation.rst
+++ b/modules/mol/mm/doc/simulation.rst
@@ -33,8 +33,8 @@ mapped back to the attached structure at any time.
.. class:: Simulation(topology,entity,settings)
- Second constructor that takes a :class:`Topology` and a consistent
- :class:`ost.mol.EntityHandle` as an input.
+ Second constructor that takes a :class:`Topology`, a consistent
+ :class:`ost.mol.EntityHandle` and a :class:`Settings` as input.
:param topology: Topology to initialize the :class:`Simulation`
:param entity: Entity that is consistent with
@@ -140,7 +140,7 @@ mapped back to the attached structure at any time.
.. method:: GetForces()
- :returns: A :class:`~ost.geom.Vec3List` of all the resulting force for each the atom in the Entity.
+ :returns: A :class:`~ost.geom.Vec3List` of all the resulting forces for each atom in the Entity.
.. method:: SetVelocities(velocities)
@@ -153,17 +153,17 @@ mapped back to the attached structure at any time.
.. method:: GetEnergy()
- :returns: :class:`float` Potential + Kinetic energy min kJ/mol of current
+ :returns: :class:`float` *Potential + Kinetic* energy in kJ/mol of current
simulation state
.. method:: GetPotentialEnergy()
- :returns: :class:`float` Potential energy in kJ/mol of current simulation
+ :returns: :class:`float` *Potential* energy in kJ/mol of current simulation
state
.. method:: GetKineticEnergy()
- :returns: :class:`float` Kinetic energy in kJ/mol of current simulation
+ :returns: :class:`float` *Kinetic* energy in kJ/mol of current simulation
state
.. method:: GetTopology()
@@ -172,7 +172,7 @@ mapped back to the attached structure at any time.
.. method:: GetPeriodicBoxExtents()
- :returns: :class:`~ost.geom.Vec3List` Extents of the periodic box
+ :returns: :class:`~ost.geom.Vec3` Extents of the periodic box
.. method:: SetPeriodicBoxExtents(vec)
@@ -359,7 +359,7 @@ mapped back to the attached structure at any time.
:param z_scale: New z-scale
:type index: :class:`int`
- :type ref_position :class:`ost.geom.Vec3`
+ :type ref_position: :class:`ost.geom.Vec3`
:type force_constant: :class:`float`
:type x_scale: :class:`float`
:type y_scale: :class:`float`
--
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