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schwede
openstructure
Commits
bd8e29ac
Commit
bd8e29ac
authored
10 years ago
by
BIOPZ-Johner Niklaus
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And more MM documentation corrections.
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15864a24
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modules/mol/mm/doc/integrators.rst
+1
-1
1 addition, 1 deletion
modules/mol/mm/doc/integrators.rst
modules/mol/mm/doc/simulation.rst
+8
-8
8 additions, 8 deletions
modules/mol/mm/doc/simulation.rst
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9 additions
and
9 deletions
modules/mol/mm/doc/integrators.rst
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−
1
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bd8e29ac
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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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modules/mol/mm/doc/simulation.rst
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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` a
s
a
n
input.
:class:`ost.mol.EntityHandle` a
nd a :class:`Settings`
a
s
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
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@@ -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 force
s
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
m
in 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.Vec3
List
` 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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