Lipid APL

Classes

class lipyds.analysis.apl.AreaPerLipid(universe: AtomGroup | Universe, select: str | None = 'not protein', select_other: str | None = 'protein', leafletfinder: LeafletFinder | None = None, leaflet_kwargs: Dict[str, Any] = {}, group_by_attr: str = 'resnames', pbc: bool = True, update_leaflet_step: int = 1, normal_axis=[0, 0, 1], cutoff_other: float = 5, cutoff: float = 15, **kwargs)[source]

Calculate the area of each lipid by projecting it onto a plane with neighboring coordinates and creating a Voronoi diagram.

Parameters:

  • universe (AtomGroup or Universe) – Universe or AtomGroup to operate on.

  • select (str (optional)) – A Universe.select_atoms() selection string for atoms that define the lipid head groups, e.g. “name PO4” or “name P*”

  • select_other (str (optional)) – A Universe.select_atoms() selection string for atoms that should be incorporated in the area calculation but that you do not want to calculat areas for.

  • cutoff (float (optional)) – Cutoff distance (ångström) to look for neighbors

  • cutoff_other (float (optional)) – Cutoff distance (ångström) to look for neighbors in the other selection. This is generally shorter than cutoff – e.g. you may look for only lipid headgroups in select, but all protein atoms in select_other.

  • **kwargs – Passed to BilayerAnalysisBase