Index

A

accuracy() (in module megnet.utils.metrics) AllAtomPairs (class in megnet.data.local_env)

as_dict() (StructureGraph method) AtomNumberToTypeConverter (class in megnet.data.qm9)

B

BaseGraphBatchGenerator (class in megnet.data.graph) build() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GaussianExpansion method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (LinearWithIndex method), [1], [2] (MEGNetLayer method), [1], [2], [3], [4], [5] (Set2Set method), [1], [2]

C

call() (CrystalGraphLayer method), [1], [2] (GaussianExpansion method), [1] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2] (LinearWithIndex method), [1], [2] (Set2Set method), [1], [2] check_dimension() (GraphModel method), [1] check_shape() (in module megnet.utils.general) compute_output_shape() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GaussianExpansion method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (LinearWithIndex method), [1], [2] (MEGNetLayer method), [1], [2], [3], [4], [5] (Set2Set method), [1], [2] convert() (AtomNumberToTypeConverter method) (Converter method) (CrystalGraphWithBondTypes method) (DummyConverter method) (EmbeddingMap method) (GaussianDistance method) (MolecularGraph method) (StructureGraph method) (StructureGraphFixedRadius method)

Converter (class in megnet.data.graph) create_bond_feature() (MolecularGraph static method) create_cached_generator() (MolecularGraphBatchGenerator method) CrystalGraph (class in megnet.data.crystal) CrystalGraphDisordered (class in megnet.data.crystal) CrystalGraphLayer (class in megnet.layers) (class in megnet.layers.graph) (class in megnet.layers.graph.cgcnn) CrystalGraphWithBondTypes (class in megnet.data.crystal)

D

DataType (class in megnet.config) deserialize() (in module megnet.data.local_env)

dijkstra_distance() (in module megnet.data.molecule) DummyConverter (class in megnet.data.graph) DummyScaler (class in megnet.utils.preprocessing)

E

EmbeddingMap (class in megnet.data.graph)

expand_1st() (in module megnet.utils.general)

F

fast_label_binarize() (in module megnet.utils.general) from_dict() (StructureGraph class method) from_file() (GraphModel class method), [1] from_mvl_models() (MEGNetModel class method), [1]

from_structure_graph() (StructureGraphFixedRadius class method) from_training_data() (DummyScaler class method) (StandardScaler class method) from_url() (MEGNetModel class method), [1]

G

gather() (in module megnet.utils.layer) GaussianDistance (class in megnet.data.graph) GaussianExpansion (class in megnet.layers) (class in megnet.layers.featurizer) get() (in module megnet.activations) (in module megnet.data.local_env) get_all_graphs_targets() (GraphModel method), [1] get_atom_feature() (MolecularGraph method) get_atom_features() (CrystalGraphDisordered static method) (MEGNetDescriptor method) (StructureGraph static method) get_bond_features() (MEGNetDescriptor method) get_config() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GaussianExpansion method), [1] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (LinearWithIndex method), [1], [2] (MEGNetLayer method), [1], [2], [3], [4], [5] (Set2Set method), [1], [2]

get_elemental_embeddings() (in module megnet.data.crystal) get_flat_data() (StructureGraph static method) get_global_features() (MEGNetDescriptor method) get_graphs_within_cutoff() (in module megnet.utils.data) get_input() (StructureGraph method) get_nn_info() (AllAtomPairs method) (MinimumDistanceNNAll method) get_pair_feature() (MolecularGraph method) get_pmg_mol_from_smiles() (in module megnet.utils.molecule) get_set2set() (MEGNetDescriptor method) get_structure_features() (MEGNetDescriptor method) graph_to_input() (StructureGraph method) GraphBatchDistanceConvert (class in megnet.data.graph) GraphBatchGenerator (class in megnet.data.graph) GraphModel (class in megnet.models) (class in megnet.models.base) GraphNetworkLayer (class in megnet.layers.graph) (class in megnet.layers.graph.base)

I

InteractionLayer (class in megnet.layers) (class in megnet.layers.graph) (class in megnet.layers.graph.schnet)

inverse_transform() (DummyScaler static method) (Scaler method) (StandardScaler method) itemgetter_list() (in module megnet.data.graph)

K

keras_layer_deserialize() (in module megnet.layers)

L

LinearWithIndex (class in megnet.layers) (class in megnet.layers.readout) (class in megnet.layers.readout.linear)

load_model() (in module megnet.utils.models)

M

mae() (in module megnet.utils.metrics) main() (in module megnet.cli.meg) make_megnet_model() (in module megnet.models.megnet) ManualStop (class in megnet.callbacks) mean_squared_error_with_scale() (in module megnet.layers) (in module megnet.losses) megnet module megnet.activations module megnet.callbacks module megnet.cli module megnet.cli.meg module megnet.config module megnet.data module megnet.data.crystal module megnet.data.graph module megnet.data.local_env module megnet.data.molecule module megnet.data.qm9 module megnet.layers module megnet.layers.featurizer module megnet.layers.graph module megnet.layers.graph.base module megnet.layers.graph.cgcnn module megnet.layers.graph.megnet module megnet.layers.graph.schnet module megnet.layers.readout module megnet.layers.readout.linear module megnet.layers.readout.set2set module megnet.losses module megnet.models module megnet.models.base module megnet.models.megnet module megnet.utils module megnet.utils.data module megnet.utils.descriptor module

megnet.utils.general module megnet.utils.layer module megnet.utils.metrics module megnet.utils.models module megnet.utils.molecule module megnet.utils.preprocessing module megnet.utils.typing module MEGNetDescriptor (class in megnet.utils.descriptor) MEGNetLayer (class in megnet.layers) (class in megnet.layers.graph) (class in megnet.layers.graph.megnet) MEGNetModel (class in megnet.models) (class in megnet.models.megnet) MinimumDistanceNNAll (class in megnet.data.local_env) ModelCheckpointMAE (class in megnet.callbacks) module megnet megnet.activations megnet.callbacks megnet.cli megnet.cli.meg megnet.config megnet.data megnet.data.crystal megnet.data.graph megnet.data.local_env megnet.data.molecule megnet.data.qm9 megnet.layers megnet.layers.featurizer megnet.layers.graph megnet.layers.graph.base megnet.layers.graph.cgcnn megnet.layers.graph.megnet megnet.layers.graph.schnet megnet.layers.readout megnet.layers.readout.linear megnet.layers.readout.set2set megnet.losses megnet.models megnet.models.base megnet.models.megnet megnet.utils megnet.utils.data megnet.utils.descriptor megnet.utils.general megnet.utils.layer megnet.utils.metrics megnet.utils.models megnet.utils.molecule megnet.utils.preprocessing megnet.utils.typing mol_from_file() (in module megnet.data.molecule) mol_from_pymatgen() (in module megnet.data.molecule) mol_from_smiles() (in module megnet.data.molecule) MolecularGraph (class in megnet.data.molecule) MolecularGraphBatchGenerator (class in megnet.data.molecule) mse_scale() (in module megnet.losses)

N

np_float (DataType attribute)

np_int (DataType attribute)

O

on_batch_end() (ManualStop method) on_epoch_end() (BaseGraphBatchGenerator method) (ModelCheckpointMAE method) (ReduceLRUponNan method)

P

phi_e() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (MEGNetLayer method), [1], [2], [3], [4], [5] phi_u() (CrystalGraphLayer method), [1], [2] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2] (MEGNetLayer method), [1], [2] phi_v() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (MEGNetLayer method), [1], [2], [3], [4], [5]

predict() (in module megnet.cli.meg) predict_graph() (GraphModel method), [1] predict_graphs() (GraphModel method), [1] predict_structure() (GraphModel method), [1] predict_structures() (GraphModel method), [1] process_atom_feature() (BaseGraphBatchGenerator method) process_bond_feature() (BaseGraphBatchGenerator method) (GraphBatchDistanceConvert method) process_state_feature() (BaseGraphBatchGenerator method)

R

ReduceLRUponNan (class in megnet.callbacks) repeat_with_index() (in module megnet.utils.layer) reshape() (in module megnet.utils.general) rho_e_u() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (MEGNetLayer method), [1], [2], [3], [4], [5] rho_e_v() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (MEGNetLayer method), [1], [2], [3], [4], [5]

rho_v_u() (CrystalGraphLayer method), [1], [2], [3], [4], [5] (GraphNetworkLayer method), [1] (InteractionLayer method), [1], [2], [3], [4], [5] (MEGNetLayer method), [1], [2], [3], [4], [5] ring_to_vector() (in module megnet.data.qm9)

S

save_model() (GraphModel method), [1] Scaler (class in megnet.utils.preprocessing) serialize() (in module megnet.data.local_env) Set2Set (class in megnet.layers) (class in megnet.layers.readout) (class in megnet.layers.readout.set2set) set_dtype() (DataType class method) set_global_dtypes() (in module megnet.config)

SimpleMolGraph (class in megnet.data.molecule) softplus2() (in module megnet.activations) (in module megnet.layers) StandardScaler (class in megnet.utils.preprocessing) StructureGraph (class in megnet.data.graph) StructureGraphFixedRadius (class in megnet.data.graph) swish() (in module megnet.activations) (in module megnet.layers)

T

tf_float (DataType attribute) tf_int (DataType attribute) to_list() (in module megnet.utils.general) train() (GraphModel method), [1]

train_from_graphs() (GraphModel method), [1] transform() (DummyScaler static method) (Scaler method) (StandardScaler method), [1]