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 converter(self): #TODO maybe cache instance
if (hasattr(self, "int_fn")):
return (Converter(self.int_fn))
return (None)
def main():
usage_txt = "\nTakes trr-trajectory and internals-definition and outputs timeseries as npz- or mat-file.\nOutput-filetype is decided based on given filename-extension.\n\n %prog [options] <trr-input-file> <int-file> <output-file>"
parser = OptionParser(usage=usage_txt, version="%prog 0.1")
parser.add_option("-d",
"--degrees",
action="store_true",
default=False,
help="save dihedrals in [deg]")
(options, args) = parser.parse_args()
if (len(args) != 3):
parser.error("incorrect number of arguments")
if (options.degrees):
print("\nDihedral angles will be saved in [deg].\n")
else:
print("\nDihedral angles will be saved in [rad].\n")
trr_fn = args[0]
internals_fn = args[1]
out_fn = args[2]
converter = Converter(internals_fn)
all_frames_int = converter.read_trajectory(trr_fn)
print("loaded trr-file with %d frames" % len(all_frames_int))
if (options.degrees):
all_frames_int.dihedral_array = np.degrees(
all_frames_int.dihedral_array)
dih_labels = [c.label for c in converter.dihedrals]
lin_labels = [c.label for c in converter.linears]
if (out_fn.endswith(".npz")):
print("Writing NumPy file: " + out_fn)
if (all_frames_int.has_dihedrals and all_frames_int.has_linears):
np.savez(out_fn,
linears=all_frames_int.linear_array,
linear_labels=lin_labels,
dihedrals=all_frames_int.dihedral_array,
dihedral_labels=dih_labels)
elif (all_frames_int.has_dihedrals):
np.savez(out_fn,
dihedrals=all_frames_int.dihedral_array,
dihedral_labels=dih_labels)
else:
np.savez(out_fn,
linears=all_frames_int.linear_array,
linear_labels=lin_labels)
elif (out_fn.endswith(".mat")):
print("Writing Matlab file: " + out_fn)
if (all_frames_int.has_dihedrals and all_frames_int.has_linears):
savemat(
out_fn, {
'linears': all_frames_int.linear_array,
'dihedrals': all_frames_int.dihedral_array
})
elif (all_frames_int.has_dihedrals):
savemat(out_fn, {'dihedrals': all_frames_int.dihedral_array})
else:
savemat(out_fn, {'linears': all_frames_int.linear_array})
else:
raise (Exception("Unkown output filetype: " + out_fn))
