def write_pb2(cmpd, filename, binary=True):
"""Convert mb.Compound to Protobuf Message file.
Parameters
----------
cmpd : mb.Compound
filename : str
binary: bool, default True
If True, will print a binary file
If False, will print to a text file
"""
cmpd_to_proto = {}
root_proto = compound_pb2.Compound()
root_proto = _mb_to_proto(cmpd, root_proto)
cmpd_to_proto[cmpd] = root_proto
for sub_cmpd in cmpd.successors():
parent_cmpd = sub_cmpd.parent
sub_proto = cmpd_to_proto[parent_cmpd].children.add()
sub_proto = _mb_to_proto(sub_cmpd, sub_proto)
cmpd_to_proto[sub_cmpd] = sub_proto
_add_proto_bonds(cmpd, root_proto)
if binary:
with open(filename, "wb") as f:
f.write(root_proto.SerializeToString())
else:
with open(filename, "w") as f:
PrintMessage(root_proto, f)
def write_proto(message: Message, filename: str):
if not os.path.exists(os.path.dirname(filename)):
try:
os.makedirs(os.path.dirname(filename))
except OSError as exc: # Guard against race condition
if exc.errno != errno.EEXIST:
raise
binary_filename = filename + '.binarypb'
with open(binary_filename, "wb") as f:
f.write(message.SerializeToString())
text_filename = filename + '.textproto'
with open(text_filename, "w") as f:
# These comments point to the proto to use as a schema for IDEs.
f.write("# proto-file: proto/npc_infos.proto\n")
f.write("# proto-message: NpcInfos\n\n")
PrintMessage(message, f)
def write_pb2(cmpd, filename, binary=True):
""" Convert mb.Compound to Protobuf Message file
Parameters
---------
cmpd : mb.Compound
filename : str
binary: bool, default True
If True, will print a binary file
If False, will print to a text file
Todo: This could be more elegantly detected
Notes
----
Todo: Handle Ports in the protocol buffer (.proto) and in this writer/reader
"""
cmpd_to_proto = {}
root_proto = compound_pb2.Compound()
root_proto = _mb_to_proto(cmpd, root_proto)
cmpd_to_proto[cmpd] = root_proto
for sub_cmpd in cmpd.successors():
parent_cmpd = sub_cmpd.parent
sub_proto = cmpd_to_proto[parent_cmpd].children.add()
sub_proto = _mb_to_proto(sub_cmpd, sub_proto)
cmpd_to_proto[sub_cmpd] = sub_proto
_add_proto_bonds(cmpd, root_proto)
if binary:
with open(filename, 'wb') as f:
f.write(root_proto.SerializeToString())
else:
with open(filename, 'w') as f:
PrintMessage(root_proto, f)
def identity_list(dim):
"""Returns the list of entries of a dim-dimensional identity matrix."""
ide = dim * dim * [0.0]
for i in range(0, dim * dim, dim + 1):
ide[i] = 1.0
return ide
if __name__ == "__main__":
# DP gamma hyperprior
dp_prior = mixing_prior_pb2.DPPrior()
dp_prior.gamma_prior.totalmass_prior.shape = 4.0
dp_prior.gamma_prior.totalmass_prior.rate = 2.0
with open("resources/asciipb/dp_gamma_prior.asciipb", "w") as f:
PrintMessage(dp_prior, f)
# PY fixed values
py_prior = mixing_prior_pb2.PYPrior()
py_prior.fixed_values.strength = 1.0
py_prior.fixed_values.discount = 0.1
with open("resources/asciipb/py_fixed.asciipb", "w") as f:
PrintMessage(py_prior, f)
# NNIG NGG hyperprior
nnig_prior = hierarchy_prior_pb2.NNIGPrior()
nnig_prior.ngg_prior.mean_prior.mean = 5.5
nnig_prior.ngg_prior.mean_prior.var = 2.25
nnig_prior.ngg_prior.var_scaling_prior.shape = 0.2
nnig_prior.ngg_prior.var_scaling_prior.rate = 0.6
nnig_prior.ngg_prior.shape = 1.5
def identity_list(dim):
"""Returns the list of entries of a dim-dimensional identity matrix."""
ide = dim * dim * [0.0]
for i in range(0, dim * dim, dim + 1):
ide[i] = 1.0
return ide
if __name__ == "__main__":
# DP gamma hyperprior
dp_prior = mixing_prior_pb2.DPPrior()
dp_prior.gamma_prior.totalmass_prior.shape = 4.0
dp_prior.gamma_prior.totalmass_prior.rate = 2.0
with open("resources/asciipb/dp_gamma_prior.asciipb", "w") as f:
PrintMessage(dp_prior, f)
# PY fixed values
py_prior = mixing_prior_pb2.PYPrior()
py_prior.fixed_values.strength = 1.0
py_prior.fixed_values.discount = 0.1
with open("resources/asciipb/py_fixed.asciipb", "w") as f:
PrintMessage(py_prior, f)
# LSB normal hyperprior
dim = 2
mu00 = dim * [0.0]
sig00 = [5.0 * _ for _ in identity_list(dim)]
step = 0.025
n_comp = 3
lsb_prior = mixing_prior_pb2.LogSBPrior()