def time_leafletfinder(self, cutoff, sparse, pbc):
"""Benchmark LeafletFinder for test lipid
membrane system.
"""
leaflet.LeafletFinder(universe=self.u,
select=self.headgroup_sel,
cutoff=cutoff,
pbc=pbc,
sparse=sparse)
def find_leaflets(mdsys):
""" Find and leaflets in the simulation using PO4 beads
"""
#print "Current frame: ", mdsys.trajectory.frame
cut = 15
while 1:
lfls = leaflet.LeafletFinder(mdsys, 'name PO4', cutoff=cut, pbc=True)
if len(lfls.groups()) <= 2:
break
else:
cut += 0.5
if len(lfls.groups()) != 2:
raise ValueError("Problem don't have x2 leaflets.")
top_head, bot_head = lfls.groups()
rt = float(len(top_head)) / len(bot_head)
if rt > 1.3 or rt < 0.77:
raise ValueError("Uneven leaflets.")
return top_head, bot_head