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# Get the inputs for each batch
inputs = self._generate_inputs(batch_index)
# Make the graph data
inputs = self._combine_graph_data(*inputs)
# Return the batch
if self.targets is None:
return inputs
else:
# get targets
it = itemgetter(*batch_index)
target_temp = itemgetter_list(self.targets, batch_index)
target_temp = np.atleast_2d(target_temp)
return inputs, expand_1st(target_temp)
# assemble bond indices
index1 = []
index2 = []
offset_ind = 0
for ind1, ind2 in zip(index1_temp, index2_temp):
index1 += [i + offset_ind for i in ind1]
index2 += [i + offset_ind for i in ind2]
offset_ind += (max(ind1) + 1)
# Compile the inputs in needed order
inputs = [expand_1st(feature_list_temp),
expand_1st(connection_list_temp),
expand_1st(global_list_temp),
expand_1st(index1),
expand_1st(index2),
expand_1st(gnode),
expand_1st(gbond)]
return inputs
def graph_to_input(self, graph: Dict) -> List[np.ndarray]:
"""
Turns a graph into model input
Args:
(dict): Dictionary description of the graph
Return:
([np.ndarray]): Inputs in the form needed by MEGNet
"""
gnode = [0] * len(graph['atom'])
gbond = [0] * len(graph['index1'])
return [expand_1st(self.atom_converter.convert(graph['atom'])),
expand_1st(self.bond_converter.convert(graph['bond'])),
expand_1st(np.array(graph['state'])),
expand_1st(np.array(graph['index1'])),
expand_1st(np.array(graph['index2'])),
expand_1st(np.array(gnode)),
expand_1st(np.array(gbond))]
index1 = []
index2 = []
offset_ind = 0
for ind1, ind2 in zip(index1_temp, index2_temp):
index1 += [i + offset_ind for i in ind1]
index2 += [i + offset_ind for i in ind2]
offset_ind += (max(ind1) + 1)
# Compile the inputs in needed order
inputs = [expand_1st(feature_list_temp),
expand_1st(connection_list_temp),
expand_1st(global_list_temp),
expand_1st(index1),
expand_1st(index2),
expand_1st(gnode),
expand_1st(gbond)]
return inputs
# assemble bond indices
index1 = []
index2 = []
offset_ind = 0
for ind1, ind2 in zip(index1_temp, index2_temp):
index1 += [i + offset_ind for i in ind1]
index2 += [i + offset_ind for i in ind2]
offset_ind += (max(ind1) + 1)
# Compile the inputs in needed order
inputs = [expand_1st(feature_list_temp),
expand_1st(connection_list_temp),
expand_1st(global_list_temp),
expand_1st(index1),
expand_1st(index2),
expand_1st(gnode),
expand_1st(gbond)]
return inputs
global_list_temp = self.process_state_feature(global_list_temp)
# assemble bond indices
index1 = []
index2 = []
offset_ind = 0
for ind1, ind2 in zip(index1_temp, index2_temp):
index1 += [i + offset_ind for i in ind1]
index2 += [i + offset_ind for i in ind2]
offset_ind += (max(ind1) + 1)
# Compile the inputs in needed order
inputs = [expand_1st(feature_list_temp),
expand_1st(connection_list_temp),
expand_1st(global_list_temp),
expand_1st(index1),
expand_1st(index2),
expand_1st(gnode),
expand_1st(gbond)]
return inputs
def graph_to_input(self, graph: Dict) -> List[np.ndarray]:
"""
Turns a graph into model input
Args:
(dict): Dictionary description of the graph
Return:
([np.ndarray]): Inputs in the form needed by MEGNet
"""
gnode = [0] * len(graph['atom'])
gbond = [0] * len(graph['index1'])
return [expand_1st(self.atom_converter.convert(graph['atom'])),
expand_1st(self.bond_converter.convert(graph['bond'])),
expand_1st(np.array(graph['state'])),
expand_1st(np.array(graph['index1'])),
expand_1st(np.array(graph['index2'])),
expand_1st(np.array(gnode)),
expand_1st(np.array(gbond))]
# assemble state feature together
global_list_temp = np.concatenate(global_list_temp, axis=0)
global_list_temp = self.process_state_feature(global_list_temp)
# assemble bond indices
index1 = []
index2 = []
offset_ind = 0
for ind1, ind2 in zip(index1_temp, index2_temp):
index1 += [i + offset_ind for i in ind1]
index2 += [i + offset_ind for i in ind2]
offset_ind += (max(ind1) + 1)
# Compile the inputs in needed order
inputs = [expand_1st(feature_list_temp),
expand_1st(connection_list_temp),
expand_1st(global_list_temp),
expand_1st(index1),
expand_1st(index2),
expand_1st(gnode),
expand_1st(gbond)]
return inputs
# assemble state feature together
global_list_temp = np.concatenate(global_list_temp, axis=0)
global_list_temp = self.process_state_feature(global_list_temp)
# assemble bond indices
index1 = []
index2 = []
offset_ind = 0
for ind1, ind2 in zip(index1_temp, index2_temp):
index1 += [i + offset_ind for i in ind1]
index2 += [i + offset_ind for i in ind2]
offset_ind += (max(ind1) + 1)
# Compile the inputs in needed order
inputs = [expand_1st(feature_list_temp),
expand_1st(connection_list_temp),
expand_1st(global_list_temp),
expand_1st(index1),
expand_1st(index2),
expand_1st(gnode),
expand_1st(gbond)]
return inputs