def set_water_control_file(env):
if env.waters or env.n_waters:
env.water_arg = hp.retrieve_all_waters(
env.system
) if env.waters == "all_waters" else env.waters # IDs of waters to perturb
env.parameters = env.parameters.rstrip("]\n") + pp.WATER_PARAMS
all_waters = ""
water_string = []
env.water_radius = env.water_radius if env.water_radius else 6
water_inputs = [
input.strip().strip('"') for input in env.adap_ex_input.split(",")
]
water_inputs = [
os.path.join(env.pele_dir, elem) for elem in water_inputs
]
for inp in water_inputs:
com = ligand_com(inp, env.residue)
com_format = ['{:.10f}'.format(elem) for elem in com[0]]
env.water_center = ", ".join(com_format)
template = '{{"watersToPerturb": {{"links": {{"ids": [{index}] }}}}, "Box": {{"radius": {radius}, "fixedCenter": [{com}], "type": "sphericalBox"}}}}'
waters = hp.retrieve_all_waters(inp)
waters = ", ".join(['"{}"'.format(water) for water in waters])
all_waters = all_waters + waters + ", "
water_string.append(
template.format(index=waters,
radius=env.water_radius,
com=env.water_center))
env.waters = [w.strip("'") for w in water_string]
all_waters = all_waters.rstrip(", ")
env.water = cs.WATER.format(all_waters, env.allow_empty_selectors,
env.water_temp, env.water_trials,
env.water_overlap, env.water_constr,
env.waters).replace("'", "")
env.water_energy = None # TEMPORARY FIX
# self.water_energy = "\n".join([ cs.WATER_ENERGY.format(water.split(":")[0]) for water in water_arg ])
else:
env.water_energy = None
env.water = None
env.water_radius = None
env.water_center = None
env.water = ""
def water_params(self, args):
self.water_temp = (
args.water_temp
if args.water_temp
else self.simulation_params.get("water_temp", 5000)
)
self.water_overlap = (
args.water_overlap
if args.water_overlap
else self.simulation_params.get("water_overlap", 0.78)
)
self.water_constr = (
args.water_constr
if args.water_constr
else self.simulation_params.get("water_constr", 0)
)
self.water_trials = (
args.water_trials
if args.water_trials
else self.simulation_params.get("water_trials", 10000)
)
self.allow_empty_selectors = (
'"allowEmptyWaterSelectors": true,' if args.water_empty_selector else ""
)
self.water_arg = (
hp.retrieve_all_waters(self.system)
if args.waters == "all_waters"
else args.waters
) # IDs of waters
self.n_waters = (
args.n_waters
if args.n_waters
else self.simulation_params.get("n_waters", 0)
)
self.waters = (
args.waters if args.waters else self.simulation_params.get("waters", [])
)
self.water_radius = args.water_radius if args.water_radius else 6
self.water_center = None
self.water = ""
self.water_energy = None
def set_water_input(self, inp):
"""
Sets water sites JSON (box, radius, water IDs) by formatting the TEMPLATE.
"""
try:
self.set_box_center(inp)
except TypeError:
raise ce.NotCenterOfWaterBox(
'Center of water box not found. Set it with "water_center" flag or ensure '
"you specified the residue name, so it can be retrieved automatically."
)
self.set_box_radius()
waters = sorted(
hp.retrieve_all_waters(inp, exclude=self.water_to_exclude))
self.water_ids_to_track = self.retrieve_indices_to_track(waters)
waters = ", ".join(['"{}"'.format(water) for water in waters])
self.all_waters += waters + ", "
return TEMPLATE.format(index=waters,
radius=self.water_radius,
com=self.water_center)
def set_user_waters(self):
"""
If the user set waters: "all_waters", it extracts them from the pdb.
"""
if self.user_waters == "all_waters":
self.user_waters = hp.retrieve_all_waters(self.input_pdbs[0])