simulariumio.md package

Submodules

simulariumio.md.md_converter module

class simulariumio.md.md_converter.MdConverter(input_data: MdData, progress_callback: Callable[[float], None] | None = None, callback_interval: float = 10, draw_bonds: bool = False)[source]

Bases: TrajectoryConverter

This object reads simulation trajectory outputs from molecular dynamics models and plot data and writes them in the format used by the Simularium viewer

Parameters:
input_dataMdData

An object containing info for reading MD simulation trajectory outputs and plot data

progress_callbackCallable[[float], None] (optional)

Callback function that accepts 1 float argument and returns None which will be called at a given progress interval, determined by callback_interval requested, providing the current percent progress Default: None

callback_intervalfloat (optional)

If a progress_callback was provided, the period between updates to be sent to the callback, in seconds Default: 10

draw_bonds: bool (optional)

Default: False

simulariumio.md.md_data module

class simulariumio.md.md_data.MdData(md_universe: Universe, nth_timestep_to_read: int = 1, meta_data: MetaData | None = None, display_data: Dict[str, DisplayData] | None = None, time_units: UnitData | None = None, spatial_units: UnitData | None = None, draw_bonds: bool = False, plots: List[Dict[str, Any]] | None = None)[source]

Bases: object

This object holds simulation trajectory outputs from molecular dynamics models

Parameters:
timestepfloat

A float amount of time in seconds that passes each step

md_universe: Universe

A MDAnalysis Universe object containing MD trajectory data. See MDAnalysis package documentation for how to create one (https://docs.mdanalysis.org/stable/documentation_pages/core/universe.html)

nth_timestep_to_read: int (optional)

Visualize every Nth timestep e.g. if 10, only every 10th timestep will be visualized Default: 1

meta_dataMetaData (optional)

An object containing metadata for the trajectory including box size, scale factor, and camera defaults

display_data: Dict[str, DisplayData] (optional)

The element abbreviation mapped to display name and rendering info for that type, Default: for names, use element abbreviation,

for radius, use 1.0, for rendering, use colors from Jmol and default representations

time_units: UnitData (optional)

multiplier and unit name for time values Default: 1.0 second

spatial_units: UnitData (optional)

multiplier and unit name for spatial values (including positions, radii, and box size) Default: 1.0 meter

draw_bonds: bool (optional)

Draw bonds between atoms? Default: False

plotsList[Dict[str, Any]] (optional)

An object containing plot data already in Simularium format

display_data: Dict[str, DisplayData]
draw_bonds: bool
md_universe: Universe
meta_data: MetaData
nth_timestep_to_read: int
plots: List[Dict[str, Any]]
spatial_units: UnitData
time_units: UnitData

Module contents