def evaluate_pathway_AT_with_SP(src_dir,
data_dir,
top_n=5,
flag="",
n_traj=10000,
atom_followed="C",
traj_max_t=100.0,
tau=10.0,
begin_t=0.0,
end_t=1.0,
top_n_s=10,
spe_oriented=True,
end_s_idx=None,
species_path=False):
"""
evaluate pathway probability
top_n_s is top N species number
num_t is number of time points
"""
os.chdir(src_dir)
if spe_oriented is True:
if end_s_idx is None or end_s_idx is []:
end_s_idx, _, _ = trajectory.get_species_with_top_n_concentration(
data_dir,
exclude=None,
top_n=top_n_s,
traj_max_t=traj_max_t,
tau=tau,
end_t=end_t,
tag="M",
atoms=[atom_followed])
n_path = ppnt.prepare_pathway_name(data_dir,
top_n=top_n,
flag=flag,
end_s_idx=end_s_idx,
species_path=species_path)
us.update_eval_path_AT_with_SP(data_dir,
top_n=n_path,
n_traj=n_traj,
tau=tau,
begin_t=begin_t,
end_t=end_t)
else:
n_path = ppnt.prepare_pathway_name(data_dir,
top_n=top_n,
flag=flag,
end_s_idx=None,
species_path=species_path)
us.update_eval_path_AT_with_SP(data_dir,
top_n=n_path,
n_traj=n_traj,
tau=tau,
begin_t=begin_t,
end_t=end_t)
make_run(src_dir, data_dir)
def evaluate_pathway_probability(src_dir,
data_dir,
top_n=5,
num_t=1,
flag="",
n_traj=10000,
atom_followed="C",
init_spe=114,
traj_max_t=100.0,
tau=10.0,
begin_t=0.0,
end_t=1.0,
top_n_s=10,
spe_oriented=True,
end_s_idx=None,
species_path=False,
path_reg=None,
no_path_reg=None,
spe_idx=None,
spe_production_oriented=False,
fixed_t0_or_tf=None,
same_path_list=False):
"""
evaluate pathway probability
top_n_s is top N species number
num_t is number of time points
"""
os.chdir(src_dir)
if spe_oriented is True:
if end_s_idx is None or end_s_idx is []:
end_s_idx, _, _ = trajectory.get_species_with_top_n_concentration(
data_dir,
exclude=None,
top_n=top_n_s,
traj_max_t=traj_max_t,
tau=tau,
end_t=end_t,
tag="M",
atoms=[atom_followed])
n_path = ppnt.prepare_pathway_name(
data_dir,
top_n=top_n,
flag=flag,
end_s_idx=end_s_idx,
species_path=species_path,
path_reg=path_reg,
no_path_reg=no_path_reg,
spe_idx=spe_idx,
spe_production_oriented=spe_production_oriented,
same_path_list=same_path_list)
ppnt.prepare_pathway_time(data_dir,
top_n=n_path,
num=num_t,
flag=flag,
begin_t=begin_t,
end_t=end_t,
species_path=species_path,
fixed_t0_or_tf=fixed_t0_or_tf)
us.update_eval_path_integral(data_dir,
top_n=n_path,
n_traj=n_traj,
atom_followed=atom_followed,
init_spe=init_spe,
tau=tau,
begin_t=begin_t,
end_t=end_t,
species_path=species_path)
else:
n_path = ppnt.prepare_pathway_name(
data_dir,
top_n=top_n,
flag=flag,
end_s_idx=end_s_idx,
species_path=species_path,
path_reg=path_reg,
no_path_reg=no_path_reg,
spe_idx=spe_idx,
spe_production_oriented=spe_production_oriented,
same_path_list=same_path_list)
ppnt.prepare_pathway_time(data_dir,
top_n=n_path,
num=num_t,
flag=flag,
begin_t=begin_t,
end_t=end_t,
species_path=species_path,
fixed_t0_or_tf=fixed_t0_or_tf)
us.update_eval_path_integral(data_dir,
top_n=n_path,
n_traj=n_traj,
atom_followed=atom_followed,
init_spe=init_spe,
tau=tau,
begin_t=begin_t,
end_t=end_t,
species_path=species_path)
make_run(src_dir, data_dir)