ionerdss.analysis package

Subpackages

Module contents

ionerdss.analysis: A modular library for analyzing biophysical simulations.

class ionerdss.analysis.Analyzer(root_dir: str | Path)[source]

Bases: object

Main analysis controller.

Usage:

analyzer = Analyzer(“./my_data”) analyzer.plot.free_energy()

compute_free_energy(sim: Simulation, temperature: float = 1.0) → DataFrame[source]

Computes free energy for a simulation from transition matrix file.

compute_size_distribution(sim: Simulation) → DataFrame[source]

Computes size distribution for a simulation from transition matrix file.

get_simulation(index_or_id: int | str) → Simulation[source]

Retrieves a simulation by index or ID.

load_simulations(simulations: List[int | str] | None = None, time_frame: Tuple[float, float] | None = None) → List[Simulation][source]

Compatibility method to retrieve simulations.

class ionerdss.analysis.LegacyPlotInterface(analyzer)[source]

Bases: object

Legacy compatibility bridge for existing plot_figure interface.

plot_figure(figure_type: str, **kwargs)[source]

Legacy plot_figure method with full backward compatibility.

class ionerdss.analysis.SimulationData(transitions: List[TransitionData], lifetimes: List[LifetimeData], copy_numbers: DataFrame | None = None, complex_histograms: List[Dict[str, Any]] | None = None, hist_times: ndarray | None = None, hist_comps: List[Dict[str, Any]] | None = None, hist_matrix: csc_array | None = None, df_free_energy: DataFrame | None = None, df_size_dist: DataFrame | None = None)[source]

Bases: object

aggregated data for a single simulation.

complex_histograms: List[Dict[str, Any]] | None = None
copy_numbers: DataFrame | None = None
df_free_energy: DataFrame | None = None
df_size_dist: DataFrame | None = None
hist_comps: List[Dict[str, Any]] | None = None
hist_matrix: csc_array | None = None
hist_times: ndarray | None = None
lifetimes: List[LifetimeData]
transitions: List[TransitionData]
class ionerdss.analysis.SimulationMetadata(id: str, path: Path, box_size: List[float] | None = None, volume: float | None = None, params: Dict[str, Any] | None = None)[source]

Bases: object

Metadata associated with a simulation.

box_size: List[float] | None = None
id: str
params: Dict[str, Any] | None = None
path: Path
volume: float | None = None