smoldynutils 0.1.0

A small collection of utility tools to process the output of Smoldyn simulations.

smoldynutils

Utilities for parsing, analyzing, and visualizing Smoldyn simulation outputs.

Installation

From GitHub with poetry:

git clone https://github.com/rgrosseholz/smoldynutils.git
cd smoldynutils
poetry install
poetry shell

Or via pip:

pip install smoldynutils

Quickstart

from smoldynutils.parser import SmoldynParser

parser = SmoldynParser(delimiter=",")
trajectories = parser.parse_fixed_grid("molpos_output.txt")

for traj in trajectories:
    print(traj.positions)

Authors

Fabian Ormersbach, Maastricht Centre for Systems Biology and Bioinformatics, Maastricht University
Ruth Grosseholz, Maastricht Centre for Systems Biology and Bioinformatics, Maastricht University

License

This project is licensed under the MIT License. See LICENSE.md for details.