all_lipids = loos.selectAtoms(system, all_lipid_selection)
# NOTE: target_lipids must be a subset of all_lipids
target_lipids = loos.selectAtoms(all_lipids, target_lipid_selection)
slicer = ZSliceSelector(zmin, zmax)
# TODO: this should probably be a command line option
# Note: normally, this small a padding might be a problem for Voronoi
# decomposition with 1 atom/lipid. However, we're not using the areas
# (which is what gets screwed up by lack of padding), and 15 ought
# to be big enough to make sure we've got 1 layer of lipid around
# the protein.
padding = 15.
protein_centroid = loos.AtomicGroup()
protein_centroid.append(loos.Atom())
# set up space to hold the neigbor time series
neighbor_timeseries = numpy.zeros(
[len(target_lipids), len(traj)], numpy.float)
for frame in traj:
# Use the centroid of the protein slice to represent the protein
protein_slice = slicer(protein)
centroid = protein_slice.centroid()
protein_centroid[0].coords(centroid)
# We assume you're using 1 atom/lipid.
# Applying slice operation here allows you to be sloppy
# with your selections.
all_lipids_slice = slicer(all_lipids)
except OSError as inst:
print 'Error creating output directory %s : ' % output_directory
print inst
sys.exit(1)
if not os.access(output_directory, os.W_OK):
print "Error: no permission to write to output directory ", output_directory
sys.exit(1)
helices = []
helix_centroids = loos.AtomicGroup()
for h in args.helix_ranges:
first, last = h.split(":")
helix_string = '(resid >= ' + first + ') ' + '&& (resid <= ' + last + ')'
helix = loos.selectAtoms(protein, helix_string)
helices.append(helix)
helix_centroids.append(loos.Atom())
target = loos.selectAtoms(system, args.target_string)
target = loos.selectAtoms(target, "!hydrogen")
chains = target.splitByResidue()
if (args.zmin > args.zmax):
tmp = args.zmax
args.zmax = args.zmin
args.zmin = tmp
slicers = []
block_size = (args.zmax - args.zmin) / args.zblocks
for i in range(args.zblocks):
z1 = args.zmin + i * block_size
sys.stderr.write("Finished bump-checking water against lipid\n")
sys.stderr.write("Current # water molecules: %d\n" %
(len(water.full_system) / 3))
sys.stderr.write("Adding salt\n")
# regenerate the list of oxygens
water_oxygens = loos.selectAtoms(water.full_system, 'name =~ "^O"')
water_residues = water.full_system.splitByResidue()
# now replace waters with salt
salts = []
for salt in config.salt:
ions = loos.AtomicGroup()
for i in range(salt.numres):
a = loos.Atom()
a.resname(salt.resname)
a.segid(salt.segname)
a.name(salt.atomname)
a.resid(i + 1)
# pick a water oxygen at random, replace it with salt
ox = random.choice(water_oxygens)
a.coords(ox.coords())
ions.append(a)
# remove this water
for w in water_residues:
if ox in w:
water.full_system.remove(w)
water_oxygens.remove(ox)
selections = sys.argv[4:]
system = loos.createSystem(system_filename)
traj = loos.pyloos.Trajectory(traj_filename, system)
helices = []
for s in selections:
helices.append(loos.selectAtoms(system, s))
# Make a fake atomicgroup to hold the placeholder atoms
new_group = loos.AtomicGroup()
resnum = 1
for i in range(len(helices)):
a = loos.Atom()
b = loos.Atom()
c = loos.Atom()
a.resid(resnum)
b.resid(resnum)
c.resid(resnum)
a.name("CENT")
b.name("PLUS")
c.name("MIN")
new_group.append(a)
new_group.append(b)
new_group.append(c)
resnum+=1
