Lipid Flip Flop
Classes
- class lipyds.analysis.flipflop.LipidFlipFlop(universe: AtomGroup | Universe, select: str = 'name ROH', 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
orAtomGroup
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 leafletflops_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 leaflettranslocations_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