simulariumio.springsalad package

Submodules

simulariumio.springsalad.springsalad_converter module

class simulariumio.springsalad.springsalad_converter.SpringsaladConverter(input_data: SpringsaladData, progress_callback: Callable[[float], None] | None = None, callback_interval: float = 10)[source]

Bases: TrajectoryConverter

This object reads simulation trajectory outputs from SpringSaLaD (https://vcell.org/ssalad) and plot data and writes them in the JSON format used by the Simularium viewer

Parameters:
input_dataSpringsaladData

An object containing info for reading SpringSaLaD 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

simulariumio.springsalad.springsalad_data module

class simulariumio.springsalad.springsalad_data.SpringsaladData(sim_view_txt_file: InputFileData, meta_data: MetaData | None = None, display_data: Dict[str, DisplayData] | None = None, draw_bonds: bool = True, plots: List[Dict[str, Any]] | None = None)[source]

Bases: object

This object holds simulation trajectory outputs from SpringSaLaD (https://vcell.org/ssalad) and plot data

Parameters:
sim_view_txt_file: InputFileData

A InputFileData object containing a string path or string contents of the txt file named “[model name]_SIM_VIEW_[run name].txt”

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 particle type name from SpringSaLaD data mapped to display names and rendering info for that type, Default: for names, use names from sim view txt file,

for radius, use value from SpringSaLaD, for rendering, use default representations and colors

draw_bonds: bool (optional)

Draw lines connecting bonded particles? Default: True

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

An object containing plot data already in Simularium format

display_data: Dict[str, DisplayData]
draw_bonds: bool
meta_data: MetaData
plots: List[Dict[str, Any]]
sim_view_txt_file: InputFileData

Module contents