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Commit 9de283d4 authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Minor doc fixes.

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modules/mol/mm/doc/settings.rst
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......@@ -12,136 +12,136 @@ of the :class:`Simulation` object.
.. attribute:: add_bonds
Flag, whether bonds should be parametrized
in :class:`TopologyCreator`. default: True
in :class:`TopologyCreator`. Default: True
.. attribute:: add_angles
Flag, whether angles should be parametrized
in :class:`TopologyCreator`. default: True
in :class:`TopologyCreator`. Default: True
.. attribute:: add_dihedrals
Flag, whether dihedrals should be parametrized
in :class:`TopologyCreator`. default: True
in :class:`TopologyCreator`. Default: True
.. attribute:: add_impropers
Flag, whether impropers should be parametrized
in :class:`TopologyCreator`. default: True
in :class:`TopologyCreator`. Default: True
.. attribute:: add_cmaps
Flag, whether cmaps should be parametrized
in :class:`TopologyCreator`. default: True
in :class:`TopologyCreator`. Default: True
.. attribute:: add_exclusions
Flag, whether exclusions should be parametrized
in :class:`TopologyCreator`. default: True
in :class:`TopologyCreator`. Default: True
.. attribute:: add_nonbonded
Flag, whether nonbonded interactions should be parametrized
in :class:`TopologyCreator`. default: True
in :class:`TopologyCreator`. Default: True
.. attribute:: add_gbsa
Flag, whether GBSA interactions should be parametrized
in :class:`TopologyCreator`. default: False
in :class:`TopologyCreator`. Default: False
.. attribute:: constrain_hbonds
Flag, whether bonds involving hydrogens should be constrained
in :class:`TopologyCreator`. default: False
in :class:`TopologyCreator`. Default: False
.. attribute:: constrain_bonds
Flag, whether all bonds should be constrained in
:class:`TopologyCreator`. default: False
:class:`TopologyCreator`. Default: False
.. attribute:: rigid_water
Flag, whether water molecules should be made rigid in
:class:`TopologyCreator`. This is achieved by adding
a distance constraint on the O-H bonds and an additional
one between the two hydrogens. default: False
one between the two hydrogens. Default: False
.. attribute:: strict_interactions
Makes sure that an error is thrown when a particular interaction cannot
be parametrized with the given forcefield in the :class:`TopologyCreator`.
By setting it to False, these cases just get ignored. default: True
By setting it to False, these cases just get ignored. Default: True
.. attribute:: ideal_bond_length_constraints
Flag, whether the ideal bond length from the :class:`Forcefield` should be
taken for distance constraints in the :class:`TopologyCreator`.
The actual distances from the :class:`EntityHandle` get taken otherwise.
default: True
taken for distance constraints in the :class:`TopologyCreator`. The actual
distances from the :class:`~ost.mol.EntityHandle` get taken otherwise.
Default: True
.. attribute:: fix_heavy_atoms
Flag, whether all heavy atom positions (non hydrogens) should be fixed in
space in the :class:`TopologyCreator`. default: False
space in the :class:`TopologyCreator`. Default: False
.. attribute:: kill_electrostatics
Flag, whether all charges should just be set to zero in the
:class:`TopologyCreator`. default: False
:class:`TopologyCreator`. Default: False
.. attribute:: generate_disulfid_bonds
Flag, whether disulfid bonds based on a simple geometric criterion
(SG-SG dist < 2.5A) should be built in :class:`TopologyCreator`.
default: True
Default: True
.. attribute:: nonbonded_method
Nonbonded method set up at the creation of the :class:`Simulation`.
Must be one of mm.NoCutoff, mm.CutoffNonPeriodic, mm.CutoffPeriodic
mm.Ewald or mm.PME. default: mm.NoCutoff
mm.Ewald or mm.PME. Default: mm.NoCutoff
.. attribute:: nonbonded_cutoff
Nonbonded cutoff set when simulation is set up. default: 10.0
Nonbonded cutoff set when simulation is set up. Default: 10.0
.. attribute:: remove_cmm_motion
Whether a center of mass remover object should be attached to the
:class:`Simulation`. default: True
:class:`Simulation`. Default: True
.. attribute:: cmm_frequency
Frequency regarding simulation steps when the cmm remover should be applied.
default: 1
Default: 1
.. attribute:: periodic_box_extent
:class:`ost.geom.Vec3` describing the X,Y and Z extents of the rectangular
simulation_box defined when setting up the :class:`Simulation`.
default: (0,0,0)
Default: (0,0,0)
.. attribute:: init_temperature
Initial simulation velocities get set according to a Boltzman distribution
controlled by init_temperature(Kelvin). default: 0.0
controlled by init_temperature(Kelvin). Default: 0.0
.. attribute:: forcefield
:class:`Forcefield` that is used in :class:`TopologyCreator`. default: None
:class:`Forcefield` that is used in :class:`TopologyCreator`. Default: None
.. attribute:: termini_exceptions
Use termini other than the defaults set in the :class:`Forcefield` when
using :class:`TopologyCreator`. Has to be a :class:`TerminiExceptions`
object. default: None
object. Default: None
.. attribute:: platform
Platform used by OpenMM to do the calculations. Must be one of mm.Reference,
mm.CPU, mm.CUDA or mm.OpenCL. If anything else than the reference platform
is used, the attribute openmm_plugin_directory has to be set accordingly.
default: mm.Reference
Default: mm.Reference
.. attribute:: reference_properties
......@@ -166,66 +166,66 @@ of the :class:`Simulation` object.
.. attribute:: add_thermostat
Flag, whether an Andersen thermostat should be attached when settings up
the :class:`Simulation`. default: False
the :class:`Simulation`. Default: False
.. attribute:: thermostat_temperature
Temperature for the Andersen thermostat in K. default: NaN
Temperature for the Andersen thermostat in K. Default: NaN
.. attribute:: thermostat_collision_frequency
Collision frequency of the Andersen thermostat in 1/ps. default: NaN
Collision frequency of the Andersen thermostat in 1/ps. Default: NaN
.. attribute:: add_barostat
Flag, whether an MonteCarlo barostat should be attached when setting up
the :class:`Simulation`. default: False
the :class:`Simulation`. Default: False
.. attribute:: barostat_temperature
Temperature for the MonteCarlo Barostat in K. default: NaN
Temperature for the MonteCarlo Barostat in K. Default: NaN
.. attribute:: barostat_pressure
Pressure for the MonteCarlo Barostat in bar. default: NaN
Pressure for the MonteCarlo Barostat in bar. Default: NaN
.. attribute:: barostat_frequency
Frequency of the MonteCarlo Barostat. default: 25
Frequency of the MonteCarlo Barostat. Default: 25
.. attribute:: integrator
Integrator to move the simulation forward in time. OpenMM offers following
Integrators: :class:`VerletIntegrator`, :class:`BrownianIntegrator`,
:class:`LangevinIntegrator`, :class:`VariableVerletIntegrator` and
:class:`VariableLangevinIntegrator`. default: None
:class:`VariableLangevinIntegrator`. Default: None
.. attribute:: solvent_dielectric
Solvent dielectric constant. This is used for the GBSA force when the
:class:`Simulation` gets set up. default: 78.3
:class:`Simulation` gets set up. Default: 78.3
.. attribute:: solute_dielectric
Solute dielectric constant. This is used for the GBSA force when the
:class:`Simulation` gets set up. default: 1.0
:class:`Simulation` gets set up. Default: 1.0
.. attribute:: reaction_field_dielecric
Sets the reaction field dielectric for the Nonbonded Force when setting
up the :class:`Simulation`. default: 78.3
up the :class:`Simulation`. Default: 78.3
.. attribute:: use_dispersion_correction
Flag, whether the dispersion correction should be used when setting
up the Nonbonded Force in the :class:`Simulation`. default: True
up the Nonbonded Force in the :class:`Simulation`. Default: True
.. attribute:: keep_ff_specific_naming
When running through the :class:`TopologyCreator`, the given entity gets
renamed to the forcefield specific naming. If set to true, the naming
stays like that, if not the entity gets renamed to PDB standard.
default: True
Default: True
.. attribute:: openmm_plugin_directory
......
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