Process ReaDDy no compression simulations

Notebook contains steps for post processing of ReaDDy simulations for a baseline single actin fiber with no compression.

This notebook provides an example of processing a simulation series for a single condition with multiple replicates. For an example of processing a simulation series with multiple conditions, each of which have multiple replicates, see process_readdy_compression_simulations.py.

if __name__ != "__main__":
    raise ImportError("This module is a notebook and is not meant to be imported")

from pathlib import Path

from subcell_pipeline.simulation.readdy.parser import parse_readdy_simulation_data

Define simulation conditions

Defines the ACTIN_NO_COMPRESSION simulation series, which simulates a single actin fiber with a free barbed end across five replicates.

# Name of the simulation series
series_name: str = "ACTIN_NO_COMPRESSION"

# S3 bucket for input and output files
bucket: str = "s3://readdy-working-bucket"

# Number of simulation replicates
n_replicates: int = 5

# Number of timepoints
n_timepoints = 200

# Number of monomer points per fiber
n_monomer_points = 200

# Temporary path to save downloaded trajectories
temp_path: Path = Path(__file__).parents[3] / "aws_downloads"
temp_path.mkdir(parents=True, exist_ok=True)

Parse simulation data

Iterate through all replicates to load simulation output files and parse them into a tidy data format. If the parsed file for a given replicate already exists, parsing is skipped.

  • Input: (series_name)/outputs/(series_name)_(index + 1).h5

  • Input: (series_name)/data/(series_name)_(index + 1).pkl

  • Output: (series_name)/samples/(series_name)_(index + 1).csv

parse_readdy_simulation_data(
    bucket,
    series_name,
    [""],
    n_replicates,
    n_timepoints,
    n_monomer_points,
    compression=False,
    temp_path=str(temp_path),
)