emb_graph = tf.tile(emb_graph, [1, tf.shape(emb_node)[1], 1])
emb_node = tf.concat([emb_node, emb_graph], axis=2)
return emb_node
#### debug
if __name__ == "__main__":
adj_np = np.ones((5, 3, 4, 4))
adj = tf.placeholder(shape=(5, 3, 4, 4), dtype=tf.float32)
node_feature_np = np.ones((5, 1, 4, 3))
node_feature = tf.placeholder(shape=(5, 1, 4, 3), dtype=tf.float32)
ob_space = {}
atom_type = 5
ob_space['adj'] = gym.Space(shape=[3, 5, 5])
ob_space['node'] = gym.Space(shape=[1, 5, atom_type])
ac_space = gym.spaces.MultiDiscrete([10, 10, 3])
policy = GCNPolicy(name='policy', ob_space=ob_space, ac_space=ac_space)
stochastic = True
env = gym.make('molecule-v0') # in gym format
env.init()
ob = env.reset()
# ob['adj'] = np.repeat(ob['adj'][None],2,axis=0)
# ob['node'] = np.repeat(ob['node'][None],2,axis=0)
print('adj', ob['adj'].shape)
print('node', ob['node'].shape)
with tf.Session() as sess:
def __init__(self,
dt=0.01,
nt=1000,
seed=0,
task='no_collision',
map_file=None,
simulator_conf=None,
healthy_reward=1.0,
**kwargs):
# TODO: other possible tasks: precision_landing
assert task in [
'velocity_control', 'no_collision', 'hovering_control'
], 'Invalid task setting'
if simulator_conf is None:
simulator_conf = os.path.join(os.path.dirname(__file__),
'config.json')
assert os.path.exists(simulator_conf), \
'Simulator config file does not exist'
self.dt = dt
self.nt = nt
self.ct = 0
self.task = task
self.healthy_reward = healthy_reward
self.simulator = QuadrotorSim()
cfg_dict = self.simulator.get_config(simulator_conf)
self.valid_range = cfg_dict['range']
self.action_space = gym.spaces.Box(
low=np.array([cfg_dict['action_space_low']] * 4, dtype='float32'),
high=np.array([cfg_dict['action_space_high']] * 4,
dtype='float32'),
shape=[4])
self.body_velocity_keys = ['b_v_x', 'b_v_y', 'b_v_z']
self.body_position_keys = ['b_x', 'b_y', 'b_z']
self.accelerator_keys = ['acc_x', 'acc_y', 'acc_z']
self.gyroscope_keys = ['gyro_x', 'gyro_y', 'gyro_z']
self.flight_pose_keys = ['pitch', 'roll', 'yaw']
self.barometer_keys = ['z']
self.task_velocity_control_keys = \
['next_target_g_v_x', 'next_target_g_v_y', 'next_target_g_v_z']
obs_dim = len(self.body_velocity_keys) + \
len(self.body_position_keys) + \
len(self.accelerator_keys) + len(self.gyroscope_keys) + \
len(self.flight_pose_keys) + len(self.barometer_keys)
if self.task == 'velocity_control':
obs_dim += len(self.task_velocity_control_keys)
self.observation_space = gym.Space(shape=[obs_dim], dtype='float32')
self.state = {}
self.viewer = None
self.x_offset = self.y_offset = self.z_offset = 0
self.pos_0 = np.array([0.0] * 3).astype(np.float32)
if self.task == 'velocity_control':
self.velocity_targets = \
self.simulator.define_velocity_control_task(
dt, nt, seed)
elif self.task in ['no_collision', 'hovering_control']:
self.map_matrix = Quadrotor.load_map(map_file)
# Only for single quadrotor, also mark its start position
y_offsets, x_offsets = np.where(self.map_matrix == -1)
assert len(y_offsets) == 1
self.y_offset = y_offsets[0]
self.x_offset = x_offsets[0]
self.z_offset = 5. # TODO: setup a better init height
self.map_matrix[self.y_offset, self.x_offset] = 0
def __init__(self,
dataset_name,
logp_ratio=1,
qed_ratio=1,
sa_ratio=1,
reward_step_total=1,
is_normalize=0,
reward_type='gan',
reward_target=0.5,
has_scaffold=False,
has_feature=False,
is_conditional=False,
conditional='low',
max_action=128,
min_action=20,
force_final=False):
self.dataset = all_datasets.get(dataset_name)
if self.dataset is None:
raise ValueError("dataset \"{}\" not found in [{}]".format(
dataset_name, ", ".join(all_datasets.keys())))
self.is_normalize = bool(is_normalize)
self.is_conditional = is_conditional
self.has_feature = has_feature
self.reward_type = reward_type
self.reward_target = reward_target
self.force_final = force_final
self.conditional_list = load_conditional(conditional)
if self.is_conditional:
self.conditional = random.sample(self.conditional_list, 1)[0]
self.mol = Chem.RWMol(Chem.MolFromSmiles(self.conditional[0]))
Chem.SanitizeMol(self.mol,
sanitizeOps=Chem.SanitizeFlags.SANITIZE_KEKULIZE)
else:
self.mol = Chem.RWMol()
self.smile_list = []
if dataset_name == 'gdb':
possible_atoms = ['C', 'N', 'O', 'S', 'Cl'] # gdb 13
elif dataset_name == 'zinc':
possible_atoms = ['C', 'N', 'O', 'S', 'P', 'F', 'I', 'Cl',
'Br'] # ZINC
if self.has_feature:
self.possible_formal_charge = np.array([-1, 0, 1])
self.possible_implicit_valence = np.array([-1, 0, 1, 2, 3, 4])
self.possible_ring_atom = np.array([True, False])
self.possible_degree = np.array([0, 1, 2, 3, 4, 5, 6, 7])
self.possible_hybridization = np.array([
Chem.rdchem.HybridizationType.SP,
Chem.rdchem.HybridizationType.SP2,
Chem.rdchem.HybridizationType.SP3,
Chem.rdchem.HybridizationType.SP3D,
Chem.rdchem.HybridizationType.SP3D2
],
dtype=object)
possible_bonds = [
Chem.rdchem.BondType.SINGLE, Chem.rdchem.BondType.DOUBLE,
Chem.rdchem.BondType.TRIPLE
] # , Chem.rdchem.BondType.AROMATIC
self.atom_type_num = len(possible_atoms)
self.possible_atom_types = np.array(possible_atoms)
self.possible_bond_types = np.array(possible_bonds, dtype=object)
if self.has_feature:
# self.d_n = len(self.possible_atom_types) + len(
# self.possible_formal_charge) + len(
# self.possible_implicit_valence) + len(self.possible_ring_atom) + \
# len(self.possible_degree) + len(self.possible_hybridization)
self.d_n = len(
self.possible_atom_types) + 6 # 6 is the ring feature
else:
self.d_n = len(self.possible_atom_types)
self.max_action = max_action
self.min_action = min_action
if dataset_name == 'gdb':
self.max_atom = 13 + len(possible_atoms) # gdb 13
elif dataset_name == 'zinc':
if self.is_conditional:
self.max_atom = 38 + len(
possible_atoms) + self.min_action # ZINC
else:
self.max_atom = 38 + len(
possible_atoms) # ZINC + self.min_action
self.logp_ratio = logp_ratio
self.qed_ratio = qed_ratio
self.sa_ratio = sa_ratio
self.reward_step_total = reward_step_total
self.action_space = gym.spaces.MultiDiscrete(
[self.max_atom, self.max_atom, 3, 2])
self.observation_space = {}
self.observation_space['adj'] = gym.Space(
shape=[len(possible_bonds), self.max_atom, self.max_atom])
self.observation_space['node'] = gym.Space(
shape=[1, self.max_atom, self.d_n])
self.counter = 0
# load scaffold data if necessary
self.has_scaffold = has_scaffold
if has_scaffold:
self.scaffold = load_scaffold()
self.max_scaffold = 6
self.level = 0 # for curriculum learning, level starts with 0, and increase afterwards
def init(self,
reward_function,
n_iterations,
max_iterations,
max_molecule_size=38,
possible_atoms=None,
terminate_on_done=False,
expected_reward=0.5,
target_reward=0.5,
molecule_rollback=False,
reward_func_sees_all=True):
"""
Constructor that exists outside of the __init__ method because gym doesn't allow addition of
additional parameters when calling gym.make() function
Parameters
----------
reward_function : function
A function that returns a reward value, which is a float
n_iterations: int
The number of iterations before an interim reward is returned
max_iterations: int
User specified, the environment stop after this many iterations
max_molecule_size: int
The maximum permitted number of atoms in this molecule
possible_atoms: list[str]
List of elements of the periodic table to be used in the environment, which are strings
terminate_on_done: boolean
Boolean signifying whether to terminate on the done flag of step method becoming True
expected_reward: float
Argument that will be passed into the RL method the user specifies
target_reward: float
Target reward for the RL method the user specifies
molecule_rollback: boolean
If this is set to true, then changes made to the molecule will be rolled back upon getting negative rewards
reward_func_sees_all: boolean
For reducing the visibility of the class to the reward function, useful for optimization purposes
since it drastically reduces the amount of information passed to the reward function. Being false,
it only provides the RWMol object to the reward function object
"""
if possible_atoms is None:
possible_atoms = ['C', 'N', 'O', 'S', 'Cl']
self.possible_atoms = possible_atoms
self.possible_bonds = [
Chem.rdchem.BondType.SINGLE, Chem.rdchem.BondType.DOUBLE,
Chem.rdchem.BondType.TRIPLE
]
self.max_molecule_size = max_molecule_size
self.n_iterations = n_iterations
self.max_iterations = max_iterations
self.interim_reward = 0
self.cumulative_reward = 0
self.mol = Chem.RWMol()
# dim d_n. Array that contains the possible atom symbols strs
self.possible_atom_types = np.array(self.possible_atoms)
# dim d_e. Array that contains the possible rdkit.Chem.rdchem.BondType objects
self.possible_bond_types = np.array(self.possible_bonds, dtype=object)
self.current_atom_index = None
self.reward_function = reward_function
# step_counter for number of iterations that occured
self.step_counter = 0
self.action_space = gym.spaces.MultiDiscrete([
len(self.possible_atom_types), self.max_molecule_size,
self.max_molecule_size,
len(self.possible_bonds)
])
# param adj: adjacency matrix, numpy array, dim k x k.
# param edge: edge attribute matrix, numpy array, dim k x k x d_e.
# param node: node attribute matrix, numpy array, dim k x d_n.
# k: maximum atoms in molecule
# de: possible bond types
# dn: possible atom types
self.observation_space = {
'adj':
gym.Space(
shape=[1, self.max_molecule_size, self.max_molecule_size]),
'edge':
gym.Space(shape=[
len(self.possible_bonds), self.max_molecule_size,
self.max_molecule_size
]),
'node':
gym.Space(shape=[
1, self.max_molecule_size,
len(self.possible_atom_types)
])
}
self.pymol_window_flag = False
self.terminate_on_done = terminate_on_done
self.molecule_rollback = molecule_rollback
self.reward_func_sees_all = reward_func_sees_all
self.expected_reward = expected_reward
self.target_reward = target_reward
try:
os.makedirs("./pymol_renderings")
except OSError as e:
if e.errno != errno.EEXIST:
raise
def init(self,
data_type='zinc',
logp_ratio=1,
qed_ratio=1,
sa_ratio=1,
reward_step_total=1,
is_normalize=0,
reward_type='gan',
reward_target=0.5,
has_scaffold=False,
has_feature=False,
is_conditional=False,
conditional='low',
max_action=128,
min_action=20,
force_final=False):
'''
own init function, since gym does not support passing argument
'''
self.is_normalize = bool(is_normalize)
self.is_conditional = is_conditional
self.has_feature = has_feature
self.reward_type = reward_type
self.reward_target = reward_target
self.force_final = force_final
self.conditional_list = load_conditional(conditional)
if self.is_conditional:
self.conditional = random.sample(self.conditional_list, 1)[0]
self.mol = Chem.RWMol(Chem.MolFromSmiles(self.conditional[0]))
Chem.SanitizeMol(self.mol,
sanitizeOps=Chem.SanitizeFlags.SANITIZE_KEKULIZE)
else:
self.mol = Chem.RWMol()
self.smile_list = []
if data_type == 'zinc':
possible_atoms = ['C', 'N', 'O', 'S', 'P', 'F', 'I', 'Cl',
'Br'] # ZINC
if self.has_feature:
self.possible_formal_charge = np.array([-1, 0, 1])
self.possible_implicit_valence = np.array([-1, 0, 1, 2, 3, 4])
self.possible_ring_atom = np.array([True, False])
self.possible_degree = np.array([0, 1, 2, 3, 4, 5, 6, 7])
self.possible_hybridization = np.array([
Chem.rdchem.HybridizationType.SP,
Chem.rdchem.HybridizationType.SP2,
Chem.rdchem.HybridizationType.SP3,
Chem.rdchem.HybridizationType.SP3D,
Chem.rdchem.HybridizationType.SP3D2
],
dtype=object)
possible_bonds = [
Chem.rdchem.BondType.SINGLE, Chem.rdchem.BondType.DOUBLE,
Chem.rdchem.BondType.TRIPLE
] #, Chem.rdchem.BondType.AROMATIC
self.atom_type_num = len(possible_atoms)
self.possible_atom_types = np.array(possible_atoms)
self.possible_bond_types = np.array(possible_bonds, dtype=object)
if self.has_feature:
# self.d_n = len(self.possible_atom_types) + len(
# self.possible_formal_charge) + len(
# self.possible_implicit_valence) + len(self.possible_ring_atom) + \
# len(self.possible_degree) + len(self.possible_hybridization)
self.d_n = len(
self.possible_atom_types) + 6 # 6 is the ring feature
else:
self.d_n = len(self.possible_atom_types)
self.max_action = max_action
self.min_action = min_action
if data_type == 'zinc':
if self.is_conditional:
self.max_atom = 38 + len(
possible_atoms) + self.min_action # ZINC
else:
self.max_atom = 38 + len(
possible_atoms) # ZINC + self.min_action
self.logp_ratio = logp_ratio
self.qed_ratio = qed_ratio
self.sa_ratio = sa_ratio
self.reward_step_total = reward_step_total
self.action_space = gym.spaces.MultiDiscrete(
[self.max_atom, self.max_atom, 3, 2])
self.observation_space = {}
self.observation_space['adj'] = gym.Space(
shape=[len(possible_bonds), self.max_atom, self.max_atom])
self.observation_space['node'] = gym.Space(
shape=[1, self.max_atom, self.d_n])
self.counter = 0
## load expert data
cwd = os.path.dirname(__file__)
if data_type == 'zinc':
path = os.path.join(
os.path.dirname(cwd), 'dataset',
'250k_rndm_zinc_drugs_clean_sorted.smi') # ZINC
self.dataset = gdb_dataset(path)
## load scaffold data if necessary
self.has_scaffold = has_scaffold
if has_scaffold:
self.scaffold = load_scaffold()
self.max_scaffold = 6
self.level = 0 # for curriculum learning, level starts with 0, and increase afterwards
