Lipid Flip Flop

Classes

class lipyds.analysis.flipflop.LipidFlipFlop(universe: Union[MDAnalysis.core.groups.AtomGroup, MDAnalysis.core.universe.Universe], select: str = 'resname CHOL', cutoff: float = 25, leaflet_width: float = 8, **kwargs)[source]

Quantify lipid flip-flops between leaflets.

This method uses an interstitial space between leaflets. Transitions between the leaflets to the interstitial space, and vice versa, are not counted as translocations. This avoids overcounting rapid transitions at the inter-leaflet interface that may arise from flaws in the leafletfinder.

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*”

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

  • leaflet_width (float (optional)) – Width or z-distance of each leaflet (ångström) for containing lipids. The interstitial space is defined as the space between the two leaflet widths.

  • **kwargs – Passed to LeafletAnalysisBase

Variables
  • flips (numpy.ndarray of ints (n_frames,)) – Number of translocations from outer leaflet to inner leaflet

  • flops (numpy.ndarray of ints (n_frames,)) – Number of translocations from inner leaflet to outer leaflet

  • translocations (numpy.ndarray of ints (n_frames,)) – Number of total translocations

  • flips_by_attr (dictionary of {id: int}) – Dictionary where the key is the label obtained by group_by_attr and the value is the number of translocations from outer leaflet to inner leaflet

  • flops_by_attr (dictionary of {id: int}) – Dictionary where the key is the label obtained by group_by_attr and the value is the number of translocations from inner leaflet to outer leaflet

  • translocations_by_attr (dictionary of {id: int}) – Dictionary where the key is the label obtained by group_by_attr and the value is the number of translocations