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Commit bd8e29ac authored by BIOPZ-Johner Niklaus's avatar BIOPZ-Johner Niklaus
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And more MM documentation corrections.

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...@@ -7,7 +7,7 @@ Integrators ...@@ -7,7 +7,7 @@ Integrators
The :class:`Integrator` are a wrapper around the integrators provided by OpenMM and 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. 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.
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...@@ -33,8 +33,8 @@ mapped back to the attached structure at any time. ...@@ -33,8 +33,8 @@ mapped back to the attached structure at any time.
.. class:: Simulation(topology,entity,settings) .. class:: Simulation(topology,entity,settings)
Second constructor that takes a :class:`Topology` and a consistent Second constructor that takes a :class:`Topology`, a consistent
:class:`ost.mol.EntityHandle` as an input. :class:`ost.mol.EntityHandle` and a :class:`Settings` as input.
:param topology: Topology to initialize the :class:`Simulation` :param topology: Topology to initialize the :class:`Simulation`
:param entity: Entity that is consistent with :param entity: Entity that is consistent with
...@@ -140,7 +140,7 @@ mapped back to the attached structure at any time. ...@@ -140,7 +140,7 @@ mapped back to the attached structure at any time.
.. method:: GetForces() .. 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) .. method:: SetVelocities(velocities)
...@@ -153,17 +153,17 @@ mapped back to the attached structure at any time. ...@@ -153,17 +153,17 @@ mapped back to the attached structure at any time.
.. method:: GetEnergy() .. 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 simulation state
.. method:: GetPotentialEnergy() .. 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 state
.. method:: GetKineticEnergy() .. 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 state
.. method:: GetTopology() .. method:: GetTopology()
...@@ -172,7 +172,7 @@ mapped back to the attached structure at any time. ...@@ -172,7 +172,7 @@ mapped back to the attached structure at any time.
.. method:: GetPeriodicBoxExtents() .. 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) .. method:: SetPeriodicBoxExtents(vec)
...@@ -359,7 +359,7 @@ mapped back to the attached structure at any time. ...@@ -359,7 +359,7 @@ mapped back to the attached structure at any time.
:param z_scale: New z-scale :param z_scale: New z-scale
:type index: :class:`int` :type index: :class:`int`
:type ref_position :class:`ost.geom.Vec3` :type ref_position: :class:`ost.geom.Vec3`
:type force_constant: :class:`float` :type force_constant: :class:`float`
:type x_scale: :class:`float` :type x_scale: :class:`float`
:type y_scale: :class:`float` :type y_scale: :class:`float`
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