Index

A

Attribute (class in openchem.utils.graph)

augment_smiles() (in module data.utils)

B

build_training() (in module models.openchem_model)

by_iteration() (optimizer.openchem_lr_scheduler.OpenChemLRScheduler property)

C

calculate_metrics() (in module openchem.utils.utils) canonize_smiles() (in module data.utils) cast_inputs() (models.Graph2Label.Graph2Label static method) (models.MoleculeProtein2Label.MoleculeProtein2Label method) (models.openchem_model.OpenChemModel static method) (models.Smiles2Label.Smiles2Label static method)

charset() (data.smiles_enumerator.SmilesEnumerator property) check_params() (in module openchem.utils.utils) ConvBNReLU (class in layers.conv_bn_relu) create_loader() (in module data.utils) cross_validation_split() (in module openchem.utils.utils) cut_padding() (in module data.utils)

D

data module data.smiles_data_layer module data.smiles_enumerator module data.smiles_protein_data_layer module

data.utils module data.vanilla_data_layer module deco_print() (in module openchem.utils.utils) DummyDataLoader (class in data.utils) DummyDataset (class in data.utils)

E

Edge (class in openchem.utils.graph)

Embedding (class in modules.embeddings.basic_embedding) evaluate() (in module models.openchem_model)

F

fit() (data.smiles_enumerator.SmilesEnumerator method) (in module models.openchem_model) flatten_dict() (in module openchem.utils.utils) forward() (layers.conv_bn_relu.ConvBNReLU method) (layers.gcn.GraphConvolution method) (models.Graph2Label.Graph2Label method) (models.MoleculeProtein2Label.MoleculeProtein2Label method) (models.openchem_model.OpenChemModel method) (models.Smiles2Label.Smiles2Label method) (modules.embeddings.basic_embedding.Embedding method) (modules.embeddings.openchem_embedding.OpenChemEmbedding method) (modules.encoders.openchem_encoder.OpenChemEncoder method) (modules.encoders.rnn_encoder.RNNEncoder method) (modules.mlp.openchem_mlp.OpenChemMLP method) (modules.mlp.openchem_mlp.OpenChemMLPSimple method) (openchem.criterion.multitask_loss.MultitaskLoss method)

G

get_edge_attr_adj_matrix() (openchem.utils.graph.Graph method) get_fp() (in module data.utils) get_latest_checkpoint() (in module openchem.utils.utils) get_lr() (optimizer.openchem_optimizer.OpenChemOptimizer method) get_node_attr_adj_matrix() (openchem.utils.graph.Graph method) get_node_feature_matrix() (openchem.utils.graph.Graph method) get_optional_params() (models.openchem_model.OpenChemModel static method) (modules.embeddings.openchem_embedding.OpenChemEmbedding static method) (modules.encoders.openchem_encoder.OpenChemEncoder static method) (modules.encoders.rnn_encoder.RNNEncoder static method) (modules.mlp.openchem_mlp.OpenChemMLP static method) (modules.mlp.openchem_mlp.OpenChemMLPSimple static method)

get_required_params() (models.openchem_model.OpenChemModel static method) (modules.embeddings.basic_embedding.Embedding static method) (modules.embeddings.openchem_embedding.OpenChemEmbedding static method) (modules.encoders.openchem_encoder.OpenChemEncoder static method) (modules.encoders.rnn_encoder.RNNEncoder static method) (modules.mlp.openchem_mlp.OpenChemMLP static method) (modules.mlp.openchem_mlp.OpenChemMLPSimple static method) get_tokens() (in module data.utils) Graph (class in openchem.utils.graph) Graph2Label (class in models.Graph2Label) GraphConvolution (class in layers.gcn)

I

identity() (in module openchem.utils.utils) init_cell() (modules.encoders.rnn_encoder.RNNEncoder method)

init_hidden() (modules.encoders.rnn_encoder.RNNEncoder method) Iterator (class in data.smiles_enumerator)

L

layers module layers.conv_bn_relu module

layers.gcn module load_model() (models.openchem_model.OpenChemModel method) load_state_dict() (optimizer.openchem_optimizer.OpenChemOptimizer method)

M

make_positions() (in module openchem.utils.utils) models module models.Graph2Label module models.MoleculeProtein2Label module models.openchem_model module models.Smiles2Label module module data data.smiles_data_layer data.smiles_enumerator data.smiles_protein_data_layer data.utils data.vanilla_data_layer layers layers.conv_bn_relu layers.gcn models models.Graph2Label models.MoleculeProtein2Label models.openchem_model models.Smiles2Label modules modules.embeddings modules.embeddings.basic_embedding modules.embeddings.openchem_embedding modules.encoders modules.encoders.openchem_encoder modules.encoders.rnn_encoder modules.mlp.openchem_mlp openchem.criterion openchem.criterion.multitask_loss openchem.utils openchem.utils.graph openchem.utils.utils optimizer optimizer.openchem_lr_scheduler optimizer.openchem_optimizer

modules module modules.embeddings module modules.embeddings.basic_embedding module modules.embeddings.openchem_embedding module modules.encoders module modules.encoders.openchem_encoder module modules.encoders.rnn_encoder module modules.mlp.openchem_mlp module mol2image() (in module data.utils) MoleculeProtein2Label (class in models.MoleculeProtein2Label) move_to_cuda() (in module openchem.utils.utils) MultitaskLoss (class in openchem.criterion.multitask_loss)

N

nest_dict() (in module openchem.utils.utils) nested_update() (in module openchem.utils.utils)

next() (data.smiles_enumerator.SmilesIterator method) Node (class in openchem.utils.graph)

O

openchem.criterion module openchem.criterion.multitask_loss module openchem.utils module openchem.utils.graph module openchem.utils.utils module OpenChemEmbedding (class in modules.embeddings.openchem_embedding) OpenChemEncoder (class in modules.encoders.openchem_encoder)

OpenChemLRScheduler (class in optimizer.openchem_lr_scheduler) OpenChemMLP (class in modules.mlp.openchem_mlp) OpenChemMLPSimple (class in modules.mlp.openchem_mlp) OpenChemModel (class in models.openchem_model) OpenChemOptimizer (class in optimizer.openchem_optimizer) optimizer module optimizer() (optimizer.openchem_optimizer.OpenChemOptimizer property) optimizer.openchem_lr_scheduler module optimizer.openchem_optimizer module

P

pad_sequences() (in module data.utils) param_groups() (optimizer.openchem_optimizer.OpenChemOptimizer property)

predict() (in module models.openchem_model) process_graphs() (in module data.utils) process_smiles() (in module data.utils)

R

randomize_smiles() (data.smiles_enumerator.SmilesEnumerator method) read_smi_file() (in module data.utils) read_smiles_property_file() (in module data.utils) reduce_tensor() (in module models.openchem_model)

reduction (openchem.criterion.multitask_loss.MultitaskLoss attribute) reset() (data.smiles_enumerator.Iterator method) reset_parameters() (layers.gcn.GraphConvolution method) reverse_transform() (data.smiles_enumerator.SmilesEnumerator method) RNNEncoder (class in modules.encoders.rnn_encoder)

S

sanitize_smiles() (in module data.utils) save_model() (models.openchem_model.OpenChemModel method) save_smi_to_file() (in module data.utils) save_smiles_property_file() (in module data.utils) scheduler() (optimizer.openchem_lr_scheduler.OpenChemLRScheduler property) seq2tensor() (in module data.utils) set_lr() (optimizer.openchem_optimizer.OpenChemOptimizer method)

Smiles2Label (class in models.Smiles2Label) SmilesDataset (class in data.smiles_data_layer) SmilesEnumerator (class in data.smiles_enumerator) SmilesIterator (class in data.smiles_enumerator) SmilesProteinDataset (class in data.smiles_protein_data_layer) state_dict() (optimizer.openchem_optimizer.OpenChemOptimizer method) step() (optimizer.openchem_lr_scheduler.OpenChemLRScheduler method) (optimizer.openchem_optimizer.OpenChemOptimizer method)

T

time_since() (in module data.utils) (in module openchem.utils.utils) train_step() (in module models.openchem_model) training (layers.conv_bn_relu.ConvBNReLU attribute) (layers.gcn.GraphConvolution attribute) (models.Graph2Label.Graph2Label attribute) (models.MoleculeProtein2Label.MoleculeProtein2Label attribute) (models.openchem_model.OpenChemModel attribute) (models.Smiles2Label.Smiles2Label attribute) (modules.embeddings.basic_embedding.Embedding attribute) (modules.embeddings.openchem_embedding.OpenChemEmbedding attribute) (modules.encoders.openchem_encoder.OpenChemEncoder attribute) (modules.encoders.rnn_encoder.RNNEncoder attribute) (modules.mlp.openchem_mlp.OpenChemMLP attribute) (modules.mlp.openchem_mlp.OpenChemMLPSimple attribute)

transform() (data.smiles_enumerator.SmilesEnumerator method)

V

VanillaDataset (class in data.vanilla_data_layer)

X

xyz_to_zmat() (openchem.utils.graph.Graph method)

Z

zero_grad() (optimizer.openchem_optimizer.OpenChemOptimizer method)

zmat_to_xyz() (openchem.utils.graph.Graph method)