/simulate_singlemolecules

Simulate single molecule trajectories

Primary LanguagePythonMIT LicenseMIT

simulate_singlemolecules

Simulate single molecule trajectories

Install

git clone https://github.com/ckinzthompson/simulate_singlemolecules.git
cd biasd
pip install ./

Functions

  • steady_state(Q): Calculates the steady state probabilities from a Q matrix.
  • simulate_single(rates, emissions, noise, nframes, dt): Simulates a single trajectory with given rates, emissions, and noise.
  • simulate_ensemble(rates, emissions, noise, nframes, dt, nmol): Simulates an ensemble of trajectories.
  • simulate_fret(rates, emissions, noise, nframes, dt, nmol, nphotons): Simulates FRET signals for an ensemble of molecules.

Testing/Development

pip install -e ".[test]"
pytest