def generate_mdp(pool):
mdp = read_mdp_file(pool.mdp_fn)
dt = float(mdp['dt'])
gen_vel = mdp['gen_vel']
gen_seed = int(mdp['gen_seed'])
tcoupl = mdp['tcoupl']
pcoupl = mdp['pcoupl']
orig_mdp = open(pool.mdp_fn).read()
orig_mdp = re.sub("\n(?i)nsteps", "\n; zgf_setup_nodes: commented-out the following line\n; nsteps", orig_mdp)
orig_mdp = re.sub("\n(?i)gen_vel", "\n; zgf_setup_nodes: commented-out the following line\n; gen_vel", orig_mdp)
orig_mdp = re.sub("\n(?i)gen_seed", "\n; zgf_setup_nodes: commented-out the following line\n; gen_seed", orig_mdp)
orig_mdp = re.sub("\n(?i)tcoupl", "\n; zgf_setup_nodes: commented-out the following line\n; tcoupl", orig_mdp)
orig_mdp = re.sub("\n(?i)pcoupl(?!type)", "\n; zgf_setup_nodes: commented-out the following line\n; pcoupl", orig_mdp)
for n in pool.where("state == 'created'"):
print("Writing: "+n.mdp_fn)
nsteps = int(n.sampling_length / dt)
f = open(n.mdp_fn, "w")
f.write(orig_mdp)
f.write("\n; zgf_setup_nodes:\n")
f.write("nsteps = %d\n"%nsteps)
# unrestrained (transition) nodes require
# 1. gen_vel = yes
# 2. random gen_seed (-1)
# tcoupl = pcoupl = no
if not(n.has_restraints):
gen_vel = "yes"
gen_seed = -1
tcoupl = "no"
pcoupl = "no"
f.write("gen_vel = "+gen_vel+"\n")
f.write("gen_seed = %d\n"%gen_seed)
f.write("tcoupl = "+tcoupl+"\n")
f.write("pcoupl = "+pcoupl+"\n")
f.close()
def main():
options = options_desc.parse_args(sys.argv)[0]
zgf_cleanup.main()
pool = Pool()
#not_reweightable = "state not in ('refined','converged')"
not_reweightable = "isa_partition and state!='converged'"
if options.ignore_convergence:
not_reweightable = "isa_partition and state not in ('converged','not-converged')"
if pool.where(not_reweightable):
print "Pool can not be reweighted due to the following nodes:"
for bad_guy in pool.where(not_reweightable):
print "Node %s with state %s."%(bad_guy.name, bad_guy.state)
sys.exit("Aborting.")
active_nodes = pool.where("isa_partition")
assert(len(active_nodes) == len(active_nodes.multilock())) # make sure we lock ALL nodes
for n in active_nodes:
check_restraint_energy(n)
# find out about number of energygrps
mdp_file = gromacs.read_mdp_file(pool.mdp_fn)
energygrps = [str(egrp) for egrp in re.findall('[\S]+', mdp_file["energygrps"])]
moi_energies = True
if len(energygrps) < 2:
moi_energies = False # Gromacs energies are named differently when there are less than two energygrps :(
if(options.method == "direct"):
reweight_direct(active_nodes, moi_energies, options.sol_energy, options.save_refpoints)
elif(options.method == "entropy"):
reweight_entropy(active_nodes, moi_energies, options.sol_energy, options.save_refpoints)
elif(options.method == "presampling"):
reweight_presampling(active_nodes, options.presamp_temp, moi_energies, options.sol_energy)
else:
raise(Exception("Method unkown: "+options.method))
weight_sum = np.sum([n.tmp['weight'] for n in active_nodes])
print "Thermodynamic weights calculated by method '%s' (sol-energy=%s):"%(options.method, options.sol_energy)
for n in active_nodes:
n.obs.weight_direct = n.tmp['weight'] / weight_sum
if(options.method == "direct"):
print(" %s with mean_V: %f [kJ/mol], %d refpoints and weight: %f" % (n.name, n.obs.mean_V, n.tmp['n_refpoints'], n.obs.weight_direct))
else:
print(" %s with A: %f [kJ/mol] and weight: %f" % (n.name, n.obs.A, n.obs.weight_direct))
for n in active_nodes:
n.save()
active_nodes.unlock()
def generate_mdp(pool):
mdp = read_mdp_file(pool.mdp_fn)
dt = float(mdp['dt'])
orig_mdp = open(pool.mdp_fn).read()
orig_mdp = re.sub("\nnsteps", "\n; zgf_setup_nodes: commented-out the following line\n; nsteps", orig_mdp)
for n in pool.where("state == 'created'"):
print("Writing: "+n.mdp_fn)
nsteps = int(n.sampling_length / dt)
f = open(n.mdp_fn, "w")
f.write(orig_mdp)
f.write("\n; zgf_setup_nodes:\n")
f.write("nsteps = %d\n"%nsteps)
f.close()
def generate_mdp(pool):
mdp = read_mdp_file(pool.mdp_fn)
dt = float(mdp['dt'])
gen_vel = mdp['gen_vel']
gen_seed = int(mdp['gen_seed'])
tcoupl = mdp['tcoupl']
pcoupl = mdp['pcoupl']
orig_mdp = open(pool.mdp_fn).read()
orig_mdp = re.sub(
"\n(?i)nsteps",
"\n; zgf_setup_nodes: commented-out the following line\n; nsteps",
orig_mdp)
orig_mdp = re.sub(
"\n(?i)gen_vel",
"\n; zgf_setup_nodes: commented-out the following line\n; gen_vel",
orig_mdp)
orig_mdp = re.sub(
"\n(?i)gen_seed",
"\n; zgf_setup_nodes: commented-out the following line\n; gen_seed",
orig_mdp)
orig_mdp = re.sub(
"\n(?i)tcoupl",
"\n; zgf_setup_nodes: commented-out the following line\n; tcoupl",
orig_mdp)
orig_mdp = re.sub(
"\n(?i)pcoupl(?!type)",
"\n; zgf_setup_nodes: commented-out the following line\n; pcoupl",
orig_mdp)
for n in pool.where("state == 'created'"):
print("Writing: " + n.mdp_fn)
nsteps = int(n.sampling_length / dt)
f = open(n.mdp_fn, "w")
f.write(orig_mdp)
f.write("\n; zgf_setup_nodes:\n")
f.write("nsteps = %d\n" % nsteps)
# unrestrained (transition) nodes require
# 1. gen_vel = yes
# 2. random gen_seed (-1)
# tcoupl = pcoupl = no
if not (n.has_restraints):
gen_vel = "yes"
gen_seed = -1
tcoupl = "no"
pcoupl = "no"
f.write("gen_vel = " + gen_vel + "\n")
f.write("gen_seed = %d\n" % gen_seed)
f.write("tcoupl = " + tcoupl + "\n")
f.write("pcoupl = " + pcoupl + "\n")
f.close()
def main():
options = options_desc.parse_args(sys.argv)[0]
if options.common_filename:
options.molecule = options.common_filename + ".pdb"
options.presampling = options.common_filename + ".trr"
options.internals = options.common_filename + ".int"
options.grompp = options.common_filename + ".mdp"
options.topology = options.common_filename + ".top"
options.index = options.common_filename + ".ndx"
print("Options:\n%s\n" % pformat(eval(str(options))))
assert path.exists(options.molecule)
assert path.exists(options.presampling)
assert path.exists(options.internals)
assert path.exists(options.grompp)
assert path.exists(options.topology)
# TODO: what if there is no index-file? (make_ndx)
assert path.exists(options.index)
assert "MOI" in gromacs.read_index_file(options.index), "group MOI should be defined in index file"
# checks e.g. if the mdp-file looks good
mdp_options = gromacs.read_mdp_file(options.grompp)
# options we cannot fix
for ref_t in re.findall("[0-9]+", mdp_options["ref_t"]):
assert int(ref_t) == options.temperature, "temperature in mdp file does not match ZIBgridfree temperature"
# TODO drop options.temperature and get temperature directly from mdp file... ask again if temperature is above 310K
# options we can fix
mdp_options_dirty = False # if set, a new mdp-file will be written
required_mdp_options = {"dihre": "yes", "dihre_fc": "1", "disre": "simple", "disre_fc": "1"}
for (k, v) in required_mdp_options.items():
if mdp_options.has_key(k):
assert mdp_options[k] == v # check, if we would overwrite something
else:
mdp_options[k] = v
mdp_options_dirty = True
if mdp_options.has_key("energygrps"):
assert "MOI" in [
str(egrp) for egrp in re.findall("[\S]+", mdp_options["energygrps"])
], "group MOI should be among energygrps in mdp file"
else:
mdp_options["energygrps"] = "MOI"
mdp_options_dirty = True
a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
if a and not b:
mdp_options["nstenergy"] = mdp_options["nstxout"]
mdp_options_dirty = True
elif b and not a:
mdp_options["nstxout"] = mdp_options["nstenergy"]
mdp_options_dirty = True
elif b and a:
assert mdp_options["nstxout"] == mdp_options["nstenergy"], "nstxout should equal nstenergy"
if int(mdp_options["nsteps"]) > 1e6:
msg = "Number of MD-steps?"
mdp_options["nsteps"] = str(userinput(msg, "int", default=int(mdp_options["nsteps"])))
# create a fixed mdp-file
if mdp_options_dirty:
print("Creating copy of mdp-file and adding missing options.")
out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
f = open(out_fn, "w") # append
f.write("; Generated by zgf_create_pool\n")
for i in mdp_options.items():
f.write("%s = %s\n" % i)
f.write("; EOF\n")
f.close()
options.grompp = out_fn
# check if subsampling is reasonable
if os.path.getsize(options.presampling) > 100e6: # 100MB
print("Presampling trajectory is large")
trr = TrrFile(options.presampling)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
print("Presampling timestep is %.2f ps" % dt)
if dt < 10: # picoseconds
# TODO: maybe calculate subsampling factor individually, or ask?
msg = "Subsample presampling trajectory by a tenth?"
if userinput(msg, "bool"):
out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
cmd = ["trjconv", "-f", options.presampling, "-o", out_fn, "-skip", "10"]
check_call(cmd)
options.presampling = out_fn
# balance linears
if options.balance_linears:
print("Balance Linears")
old_converter = Converter(options.internals)
print("Loading presampling....")
frames = old_converter.read_trajectory(options.presampling)
new_coord_list = []
for c in old_converter:
if not isinstance(c, LinearCoordinate):
new_coord_list.append(c)
continue # we do not work on other Coordinate-Types
# TODO: is this a good way to determine new_weight and new_offset???
new_weight = c.weight / sqrt(2 * frames.var().getcoord(c))
new_offset = c.offset + frames.mean().getcoord(c)
new_coord = LinearCoordinate(*c.atoms, label=c.label, weight=new_weight, offset=new_offset)
new_coord_list.append(new_coord)
new_converter = Converter(coord_list=new_coord_list)
assert old_converter.filename.endswith(".int")
options.internals = old_converter.filename[:-4] + "_balanced.int"
print("Writing balanced Converter to: " + options.internals)
f = open(options.internals, "w")
f.write(new_converter.serialize())
f.close()
assert len(Converter(options.internals)) == len(new_coord_list) # try parsing
# Finally: Create root-node and pool
pool = Pool()
if len(pool) != 0:
print("ERROR: A pool already exists here.")
sys.exit(1)
pool.int_fn = options.internals
pool.mdp_fn = options.grompp
pool.top_fn = options.topology
pool.ndx_fn = options.index
pool.temperature = options.temperature
pool.gr_threshold = options.gr_threshold
pool.gr_chains = options.gr_chains
pool.alpha = None
pool.save() # save pool for the first time...
# ... then we can save the first node...
node0 = Node()
node0.state = "refined"
node0.save() # also creates the node directory ... needed for symlink
os.symlink(os.path.relpath(options.presampling, node0.dir), node0.trr_fn)
os.symlink(os.path.relpath(options.molecule, node0.dir), node0.pdb_fn)
pool.root_name = node0.name
pool.save() # ... now we have to save the pool again.
if not path.exists("analysis"):
os.mkdir("analysis")
def main():
options = options_desc.parse_args(sys.argv)[0]
if(options.common_filename):
options.molecule = options.common_filename+".pdb"
options.presampling = options.common_filename+".trr"
options.internals = options.common_filename+".int"
options.grompp = options.common_filename+".mdp"
options.topology = options.common_filename+".top"
options.index = options.common_filename+".ndx"
print("Options:\n%s\n"%pformat(eval(str(options))))
assert(path.exists(options.molecule))
assert(path.exists(options.presampling))
assert(path.exists(options.internals))
assert(path.exists(options.grompp))
assert(path.exists(options.topology))
#TODO: what if there is no index-file? (make_ndx)
assert(path.exists(options.index))
assert('moi' in gromacs.read_index_file(options.index)), "group 'MOI' should be defined in index file"
# checks e.g. if the mdp-file looks good
mdp_options = gromacs.read_mdp_file(options.grompp)
temperatures = [ref_t for ref_t in re.findall("[0-9]+", mdp_options["ref_t"])]
assert(len(set(temperatures)) == 1), "temperature definition in mdp file is ambiguous"
temperature = temperatures[0]
# get sampling temperature from mdp file
if(int(temperature) > 310):
if not(userinput("Your sampling temperature is set to %s K. Continue?"%temperature, "bool")):
sys.exit("Quit by user.")
# options we can fix
mdp_options_dirty = False #if set, a new mdp-file will be written
# the value of the following options need to be fixed
critical_mdp_options = {"dihre":"yes", "dihre_fc":"1", "disre":"simple", "disre_fc":"1", "gen_temp":temperature}
for (k,v) in critical_mdp_options.items():
if(mdp_options.has_key(k) and mdp_options[k].strip() != v):
print "Error. I do not want to use '%s' for option '%s' ('%s' required). Please fix your mdp file."%(mdp_options[k].strip(),k,v)
sys.exit("Quitting.")
else:
mdp_options[k] = v
mdp_options_dirty = True
# the value of the following options does not matter, but they should be there
noncritical_mdp_options = {"tcoupl":"no", "pcoupl":"no", "gen_vel":"no", "gen_seed":"-1"}
for (k,v) in noncritical_mdp_options.items():
if not(mdp_options.has_key(k)):
mdp_options[k] = v
mdp_options_dirty = True
a = mdp_options.has_key("energygrps") and "moi" not in [str(egrp) for egrp in re.findall('[\S]+', mdp_options["energygrps"])]
b = not(mdp_options.has_key("energygrps"))
if(a or b):
if not(userinput("'MOI' is not defined as an energy group in your mdp file. Maybe you have forgotten to define proper 'energygrps'. Continue?", "bool")):
sys.exit("Quit by user.")
a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
if(a and not b):
mdp_options["nstenergy"] = mdp_options["nstxout"]
mdp_options_dirty = True
elif(b and not a):
mdp_options["nstxout"] = mdp_options["nstenergy"]
mdp_options_dirty = True
elif(b and a):
assert(mdp_options["nstxout"] == mdp_options["nstenergy"]), "nstxout should equal nstenergy"
if(int(mdp_options["nsteps"]) > 1e6):
msg = "Number of MD-steps?"
mdp_options["nsteps"] = str( userinput(msg, "int", default=int(mdp_options["nsteps"])) )
# create a fixed mdp-file
if(mdp_options_dirty):
print("Creating copy of mdp-file and adding missing options.")
out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
f = open(out_fn, "w") # append
f.write("; Generated by zgf_create_pool\n")
for i in sorted(mdp_options.items()):
f.write("%s = %s\n"%i)
f.write("; EOF\n")
f.close()
options.grompp = out_fn
# check if subsampling is reasonable
if(os.path.getsize(options.presampling) > 100e6): # 100MB
print("Presampling trajectory is large")
trr = TrrFile(options.presampling)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
print("Presampling timestep is %.2f ps"%dt)
if(dt < 10): # picoseconds
#TODO: maybe calculate subsampling factor individually, or ask?
msg = "Subsample presampling trajectory by a tenth?"
if(userinput(msg, "bool")):
out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
cmd = ["trjconv", "-f", options.presampling, "-o", out_fn, "-skip", "10"]
check_call(cmd)
options.presampling = out_fn
# balance linears
if(options.balance_linears):
print("Balance Linears")
old_converter = Converter(options.internals)
print("Loading presampling....")
frames = old_converter.read_trajectory(options.presampling)
new_coord_list = []
for c in old_converter:
if(not isinstance(c, LinearCoordinate)):
new_coord_list.append(c)
continue # we do not work on other Coordinate-Types
#TODO: is this a good way to determine new_weight and new_offset???
new_weight = c.weight / sqrt(2*frames.var().getcoord(c))
new_offset = c.offset + frames.mean().getcoord(c)
new_coord = LinearCoordinate(*c.atoms, label=c.label, weight=new_weight, offset=new_offset)
new_coord_list.append(new_coord)
new_converter = Converter(coord_list=new_coord_list)
assert(old_converter.filename.endswith(".int"))
options.internals = old_converter.filename[:-4] + "_balanced.int"
print("Writing balanced Converter to: "+options.internals)
f = open(options.internals, "w")
f.write(new_converter.serialize())
f.close()
assert(len(Converter(options.internals)) == len(new_coord_list)) #try parsing
# Finally: Create root-node and pool
pool = Pool()
if(len(pool) != 0):
print("ERROR: A pool already exists here.")
sys.exit(1)
pool.int_fn = options.internals
pool.mdp_fn = options.grompp
pool.top_fn = options.topology
pool.ndx_fn = options.index
pool.temperature = int(temperature)
pool.gr_threshold = options.gr_threshold
pool.gr_chains = options.gr_chains
pool.alpha = None
pool.save() # save pool for the first time...
# ... then we can save the first node...
node0 = Node()
node0.state = "refined"
node0.save() # also creates the node directory ... needed for symlink
os.symlink(os.path.relpath(options.presampling, node0.dir), node0.trr_fn)
os.symlink(os.path.relpath(options.molecule, node0.dir), node0.pdb_fn)
pool.root_name = node0.name
pool.save() #... now we have to save the pool again.
if(not path.exists("analysis")):
os.mkdir("analysis")
def main():
options = options_desc.parse_args(sys.argv)[0]
if (options.common_filename):
options.molecule = options.common_filename + ".pdb"
options.presampling = options.common_filename + ".trr"
options.internals = options.common_filename + ".int"
options.grompp = options.common_filename + ".mdp"
options.topology = options.common_filename + ".top"
options.index = options.common_filename + ".ndx"
print("Options:\n%s\n" % pformat(eval(str(options))))
assert (path.exists(options.molecule))
assert (path.exists(options.presampling))
assert (path.exists(options.internals))
assert (path.exists(options.grompp))
assert (path.exists(options.topology))
#TODO: what if there is no index-file? (make_ndx)
assert (path.exists(options.index))
assert ('moi' in gromacs.read_index_file(
options.index)), "group 'MOI' should be defined in index file"
# checks e.g. if the mdp-file looks good
mdp_options = gromacs.read_mdp_file(options.grompp)
temperatures = [
ref_t for ref_t in re.findall("[0-9]+", mdp_options["ref_t"])
]
assert (len(set(temperatures)) == 1
), "temperature definition in mdp file is ambiguous"
temperature = temperatures[0]
# get sampling temperature from mdp file
if (int(temperature) > 310):
if not (userinput(
"Your sampling temperature is set to %s K. Continue?" %
temperature, "bool")):
sys.exit("Quit by user.")
# options we can fix
mdp_options_dirty = False #if set, a new mdp-file will be written
# the value of the following options need to be fixed
critical_mdp_options = {
"dihre": "yes",
"dihre_fc": "1",
"disre": "simple",
"disre_fc": "1",
"gen_temp": temperature
}
for (k, v) in critical_mdp_options.items():
if (mdp_options.has_key(k) and mdp_options[k].strip() != v):
print "Error. I do not want to use '%s' for option '%s' ('%s' required). Please fix your mdp file." % (
mdp_options[k].strip(), k, v)
sys.exit("Quitting.")
else:
mdp_options[k] = v
mdp_options_dirty = True
# the value of the following options does not matter, but they should be there
noncritical_mdp_options = {
"tcoupl": "no",
"pcoupl": "no",
"gen_vel": "no",
"gen_seed": "-1"
}
for (k, v) in noncritical_mdp_options.items():
if not (mdp_options.has_key(k)):
mdp_options[k] = v
mdp_options_dirty = True
a = mdp_options.has_key("energygrps") and "moi" not in [
str(egrp) for egrp in re.findall('[\S]+', mdp_options["energygrps"])
]
b = not (mdp_options.has_key("energygrps"))
if (a or b):
if not (userinput(
"'MOI' is not defined as an energy group in your mdp file. Maybe you have forgotten to define proper 'energygrps'. Continue?",
"bool")):
sys.exit("Quit by user.")
a, b = mdp_options.has_key("nstxout"), mdp_options.has_key("nstenergy")
if (a and not b):
mdp_options["nstenergy"] = mdp_options["nstxout"]
mdp_options_dirty = True
elif (b and not a):
mdp_options["nstxout"] = mdp_options["nstenergy"]
mdp_options_dirty = True
elif (b and a):
assert (mdp_options["nstxout"] == mdp_options["nstenergy"]
), "nstxout should equal nstenergy"
if (int(mdp_options["nsteps"]) > 1e6):
msg = "Number of MD-steps?"
mdp_options["nsteps"] = str(
userinput(msg, "int", default=int(mdp_options["nsteps"])))
# create a fixed mdp-file
if (mdp_options_dirty):
print("Creating copy of mdp-file and adding missing options.")
out_fn = options.grompp.rsplit(".", 1)[0] + "_fixed.mdp"
f = open(out_fn, "w") # append
f.write("; Generated by zgf_create_pool\n")
for i in sorted(mdp_options.items()):
f.write("%s = %s\n" % i)
f.write("; EOF\n")
f.close()
options.grompp = out_fn
# check if subsampling is reasonable
if (os.path.getsize(options.presampling) > 100e6): # 100MB
print("Presampling trajectory is large")
trr = TrrFile(options.presampling)
dt = trr.first_frame.next().t - trr.first_frame.t
trr.close()
print("Presampling timestep is %.2f ps" % dt)
if (dt < 10): # picoseconds
#TODO: maybe calculate subsampling factor individually, or ask?
msg = "Subsample presampling trajectory by a tenth?"
if (userinput(msg, "bool")):
out_fn = options.presampling.rsplit(".", 1)[0] + "_tenth.trr"
cmd = [
"trjconv", "-f", options.presampling, "-o", out_fn,
"-skip", "10"
]
check_call(cmd)
options.presampling = out_fn
# balance linears
if (options.balance_linears):
print("Balance Linears")
old_converter = Converter(options.internals)
print("Loading presampling....")
frames = old_converter.read_trajectory(options.presampling)
new_coord_list = []
for c in old_converter:
if (not isinstance(c, LinearCoordinate)):
new_coord_list.append(c)
continue # we do not work on other Coordinate-Types
#TODO: is this a good way to determine new_weight and new_offset???
new_weight = c.weight / sqrt(2 * frames.var().getcoord(c))
new_offset = c.offset + frames.mean().getcoord(c)
new_coord = LinearCoordinate(*c.atoms,
label=c.label,
weight=new_weight,
offset=new_offset)
new_coord_list.append(new_coord)
new_converter = Converter(coord_list=new_coord_list)
assert (old_converter.filename.endswith(".int"))
options.internals = old_converter.filename[:-4] + "_balanced.int"
print("Writing balanced Converter to: " + options.internals)
f = open(options.internals, "w")
f.write(new_converter.serialize())
f.close()
assert (len(Converter(options.internals)) == len(new_coord_list)
) #try parsing
# Finally: Create root-node and pool
pool = Pool()
if (len(pool) != 0):
print("ERROR: A pool already exists here.")
sys.exit(1)
pool.int_fn = options.internals
pool.mdp_fn = options.grompp
pool.top_fn = options.topology
pool.ndx_fn = options.index
pool.temperature = int(temperature)
pool.gr_threshold = options.gr_threshold
pool.gr_chains = options.gr_chains
pool.alpha = None
pool.save() # save pool for the first time...
# ... then we can save the first node...
node0 = Node()
node0.state = "refined"
node0.save() # also creates the node directory ... needed for symlink
os.symlink(os.path.relpath(options.presampling, node0.dir), node0.trr_fn)
os.symlink(os.path.relpath(options.molecule, node0.dir), node0.pdb_fn)
pool.root_name = node0.name
pool.save() #... now we have to save the pool again.
if (not path.exists("analysis")):
os.mkdir("analysis")
