openfe_analysis

Quickstart

A package for the analysis of simulations performed using OpenFE (more specifically .nc files created by OpenMMTools MultiStateReporter). This package provides a MDAnalysis Reader to start to explore your trajectory data:

import MDAnalysis as mda
from openfe_analysis import FEReader

# a "simulation.nc" file contains multiple replicas, so we must choose which of these we load
# provide either a state (following a single lambda state) or replica (following a particular replica) id (typically 0-10)
u = mda.Universe('hybrid_system.pdb', 'simulation.nc', format=FEReader, state=0)

For example to convert your trajectory to a different format for visualisation:

import MDAnalysis as mda
from openfe_analysis import FEReader

with mda.Writer('out.xtc', n_atoms=len(u.atoms)) as w:
    for ts in u.trajectory:
        w.write(u.atoms)

Installation

Installation is done via the conda package manager, simply:

conda install -c conda-forge openfe-analysis

For further guidance on using the conda package manager, please consult our installation guide