def _tautomerize(self, reaction: ReactionContainer) -> ReactionContainer:
"""
Perform ChemAxon tautomerization.
:param reaction: reaction that needs to be tautomerized
:return: ReactionContainer
"""
new_molecules = []
for part in [reaction.reactants, reaction.reagents, reaction.products]:
tmp = []
for mol in part:
with io.StringIO() as f, SDFWrite(f) as i:
i.write(mol)
sdf = f.getvalue()
mol_handler = self._MolHandler(sdf)
mol_handler.clean(True, '2')
molecule = mol_handler.getMolecule()
self._standardizer.standardize(molecule)
new_mol_handler = self._MolHandler(molecule)
new_sdf = new_mol_handler.toFormat('SDF')
with io.StringIO('\n ' + new_sdf.strip()) as f, SDFRead(f, remap=False) as i:
new_mol = next(i)
tmp.append(new_mol)
new_molecules.append(tmp)
return ReactionContainer(reactants=tuple(new_molecules[0]), reagents=tuple(new_molecules[1]),
products=tuple(new_molecules[2]), meta=reaction.meta)
from RNNSynthesis.helper import get_feature, get_feature_bits
logger = logging.getLogger("exampleApp")
logger.setLevel(logging.INFO)
# create the logging file handler
fh = logging.FileHandler("GA.log")
formatter = logging.Formatter()
fh.setFormatter(formatter)
# add handler to logger object
logger.addHandler(fh)
logger.info("Program started")
target = next(SDFRead(open('./data/tylenol.sdf', encoding='UTF-8')))
env = SimpleSynthesis(target, steps=10)
target_bits = get_feature_bits(target)
step_per_score = dict()
def fit_func(hromosoma):
for action in hromosoma:
state, reward, done, info = env.step(action)
if done:
if state == target_bits:
logger.info(
f'синтетический путь для молекулы {target} = {[step for step in env.render()]}'
)
print(
f'синтетический путь для молекулы {target} = {[step for step in env.render()]}'
import os
os.environ['DB'] = '/home/ilnur/PycharmProjects/RLFS/data/db.shelve'
os.environ['DATA'] = '/home/ilnur/PycharmProjects/RLFS/data/rules/'
from RNNSynthesis.environment import SimpleSynthesis
from CGRtools.files import SDFRead
target = next(SDFRead(open('/home/ilnur/PycharmProjects/RLFS/data/tylenol.sdf', encoding='UTF-8')))
env = SimpleSynthesis(target, steps=1000, reward_at_end=True)
# self.af = activation
# self.
#
# def forward(self, mc, state, action_space): #шаг вперед
# fp = get_feature_bits(mc)
#
#
# def loss(self): #на основании награды считать лосс функцию
# ...
# mine | gym:
# state = observation_space
# action_space = action_space
# reward = reward
with SDFRead('/home/ilnur/Загрузки/molSet_largestCluster.sdf', 'rb') as f:
mc = next(f)
device = device("cuda" if cuda.is_available() else "cpu")
lr = 0.0001
env = SimpleSynthesis(mc)
class Actor(Module):
def __init__(self, action_size, inp_size=8192, learning_rate=0.0001): # state == molecule_container
super(Actor, self).__init__()
self.inps = inp_size
self.ac = action_size
self.lr = learning_rate
self.linear1 = Linear(self.inps, 128)
self.linear2 = Linear(128, 256)