simulariumio.mem3dg package

Submodules

simulariumio.mem3dg.mem3dg_converter module

class simulariumio.mem3dg.mem3dg_converter.Mem3dgConverter(input_data: Mem3dgData)[source]

Bases: TrajectoryConverter

Parameters:
input_dataMem3dgData

An object containing info for reading Mem3DG simulation trajectory output

write_to_obj(filepath, data, frame)[source]

simulariumio.mem3dg.mem3dg_data module

class simulariumio.mem3dg.mem3dg_data.Mem3dgData(input_file_path: str, output_obj_file_path: str | None = None, meta_data: MetaData | None = None, agent_name: str | None = None, agent_color: str | None = None, time_units: UnitData | None = None, spatial_units: UnitData | None = None, plots: List[Dict[str, Any]] | None = None)[source]

Bases: object

Parameters:
input_file_pathstr

The path to the .nc file output by Mem3DG for this trajectory.

output_obj_file_pathstr (optional)

The path to the directory where output .obj files will be saved to. If nothing is provided, the output .obj files will be saved to the current directory.

meta_dataMetaData

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

agent_name: str (optional)

This converter generates it’s own DisplayData, but the agent name can optionally be overridden here. This will change the agent name that is displayed on the side column in simularium

agent_color: string (optional)

This converter generates it’s own DisplayData, but the agent color can optionally be overridden here with a hex value for the color to display, e.g “#FFFFFF” Default: Use default colors from Simularium Viewer

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

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

An object containing plot data already in Simularium format

agent_color: str
agent_name: str
input_file_path: str
meta_data: MetaData
output_obj_file_path: str
plots: List[Dict[str, Any]]
spatial_units: UnitData
time_units: UnitData

Module contents