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 an index for the state or replica to extract.
# The `index_method` then determines whether `index` refers to a Hamiltonian ``state`` (following a single lambda state)
# or a ``replica`` (following a particular replica).
u = mda.Universe('hybrid_system.pdb', 'simulation.nc', format=FEReader, index=0, index_method='state')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 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