"""Membrane area per lipid observable."""
import chex
import jax.numpy as jnp
import lipyphilic as lpp
import MDAnalysis
from typing_extensions import override
from mythos.observables.martini_utils import universe_from_trajectory
from mythos.simulators.io import SimulatorTrajectory
[docs]
@chex.dataclass(frozen=True, kw_only=True)
class AreaPerLipid:
"""Observable for calculating area per lipid from a trajectory.
This observable uses the LiPyphilic package to assign leaflets and compute
area per lipid, so see its documentation for more details on the
lipid_sel arguments: https://lipyphilic.readthedocs.io/en/latest/.
Args:
topology: MDAnalysis Universe topology for the system, should not
contain the trajectory data.
lipid_sel: selection string for lipid tail atoms using MDAnalysis query
(e.g. "name GL1 GL2").
"""
topology: MDAnalysis.Universe
lipid_sel: str
[docs]
@override
def __call__(self, trajectory: SimulatorTrajectory) -> float:
universe = universe_from_trajectory(self.topology, trajectory)
leaflets = lpp.AssignLeaflets(universe=universe, lipid_sel=self.lipid_sel)
leaflets.run()
area_per_lipid = lpp.analysis.AreaPerLipid(
universe=universe, lipid_sel=self.lipid_sel, leaflets=leaflets.leaflets
)
area_per_lipid.run()
return jnp.mean(area_per_lipid.areas, axis=0)