def time_optimize_cutoff(self, sparse, pbc):
"""Benchmark optimize_cutoff for test lipid
membrane system using default network distance
range.
"""
leaflet.optimize_cutoff(universe=self.u,
select=self.headgroup_sel,
pbc=pbc,
sparse=sparse)
def test_optimize_cutoff(universe, lipid_heads):
cutoff, N = optimize_cutoff(universe, lipid_heads, pbc=True)
assert N == 2
assert_almost_equal(cutoff, 10.5, decimal=4)
for i in list(lipidTypeDic.values()):
defFlipFlopHeadgroups += i.getNoneLeafletSelection(syst)
#LOGGER.info('FlipFlopHeadgroups = {}'.format(defFlipFlopHeadgroups))
# --------------------------------------------------------------------------
# Define top/bottom leaflets
# Get beads that define the bilayer leaflets
# (not in bilayer middle, but closly packed, use linker + first tail bead of lipids that do not flip-flop)
defHeadgroups = MDAnalysis.core.groups.AtomGroup([], syst)
for i in list(lipidTypeDic.values()):
defHeadgroups += i.getLeafletSelection(syst)
# get leaflets
rcutoff, n = optimize_cutoff(syst, defHeadgroups)
lfls = LeafletFinder(syst, defHeadgroups, cutoff=rcutoff, pbc=True)
grps = lfls.groups()
if len(grps) == 2:
LOGGER.info('Found {} leaflet groups'.format(len(grps)))
# check if they're even
top_head = grps[0]
bot_head = grps[1]
rt = float(len(top_head)) / len(bot_head)
if rt > 1.3 or rt < 0.77:
raise ValueError('Found uneven leaflets. top = {}, bot = {}'.format(
len(top_head), len(bot_head)))
def test_optimize_cutoff(self):
from MDAnalysis.analysis.leaflet import optimize_cutoff
cutoff, N = optimize_cutoff(self.universe, self.lipid_heads, pbc=True)
assert_equal(N, 2)
assert_almost_equal(cutoff, 10.5, decimal=4)
structure = args[0]
except IndexError:
raise ValueError("Need structure file (pdb, gro, ...) as input")
if not os.path.exists(structure):
raise IOError(errno.ENOENT, "Structure file not found", structure)
if not options.topology:
options.topology = structure
u = MDAnalysis.Universe(options.topology, structure)
if options.optimize:
print "# Finding best cutoff (--optimize)..."
try:
cutoff, N = optimize_cutoff(u, options.selection, pbc=options.pbc,
max_imbalance=options.max_imbalance)
except:
raise RuntimeError("Failed cutoff optimization, try without --optimize")
print "# Optimized cutoff=%(cutoff).1f A, finding %(N)d disconnected groups" % vars()
else:
cutoff = options.cutoff
print "# Using fixed cutoff=%(cutoff).1f A" % vars()
LF = LeafletFinder(u, options.selection, cutoff=cutoff, pbc=options.pbc)
p = get_membrane_parameters(u, LF)
# show results
print "#" + 60 * "="
print "thickness tmem = %(thickness).2f A" % p
print "center zmem = %(zmem).2f A" % p
print "#" + 60 * "="
except IndexError:
raise ValueError("Need structure file (pdb, gro, ...) as input")
if not os.path.exists(structure):
raise IOError(errno.ENOENT, "PQR file not found", structure)
if not options.topology:
options.topology = structure
u = MDAnalysis.Universe(options.topology, structure)
if options.optimize:
print "# Finding best cutoff (--optimize)..."
try:
cutoff, N = optimize_cutoff(u,
options.selection,
pbc=options.pbc,
max_imbalance=options.max_imbalance)
except:
raise RuntimeError(
"Failed cutoff optimization, try without --optimize")
print "# Optimized cutoff={cutoff:.1f} A, finding {N:d} disconnected groups".format(
**vars())
else:
cutoff = options.cutoff
print "# Using fixed cutoff={cutoff:.1f} A".format(**vars())
LF = LeafletFinder(u, options.selection, cutoff=cutoff, pbc=options.pbc)
print "# group sizes = {0!r} ".format(LF.sizes())
# two leaflets
def estimate_bilayerDist(self):
try:
self.bilayerDist = optimize_cutoff(self.universe, self.phosphates)
except IndexError:
print "Unable to determine cutoff value. Skipping sample %s" % self.name