Index

_

__init__() (molprop.powertoys.logging.indent_logger.IndentLogger method) (molprop.utils.early_stopping.EarlyStopping method)

_dataset (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD attribute) _model_name (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD attribute)

A

add_module() (molprop.models.graph_neural_network.GNN method) addFilter() (molprop.powertoys.logging.indent_logger.IndentLogger method) addHandler() (molprop.powertoys.logging.indent_logger.IndentLogger method) apply() (molprop.models.graph_neural_network.GNN method) (molprop.pyg_molgraph.MultiGraphData method)

apply_() (molprop.pyg_molgraph.MultiGraphData method) as_integer_ratio() (molprop.training_type.TrainingType method) atom_GetNeighbors() (in module molprop.utils.mol_features) atom_GetTotalNumHs() (in module molprop.utils.mol_features) AtomFeatures (class in molprop.utils.mol_features)

B

bfloat16() (molprop.models.graph_neural_network.GNN method) bit_count() (molprop.training_type.TrainingType method)

bit_length() (molprop.training_type.TrainingType method) BondFeatures (class in molprop.utils.mol_features) buffers() (molprop.models.graph_neural_network.GNN method)

C

calculate_classification_metrics() (in module molprop.utils.analyze_results) calculate_regression_metrics() (in module molprop.utils.analyze_results) callHandlers() (molprop.powertoys.logging.indent_logger.IndentLogger method) check_model_path() (in module molprop.utils.utils) children() (molprop.models.graph_neural_network.GNN method) clone() (molprop.pyg_molgraph.MultiGraphData method) cmp() (in module tests.environments.test_conda_installed_packages) coalesce() (molprop.pyg_molgraph.MultiGraphData method) collate() (molprop.pyg_molgraph.PyGMolgraphDataset static method) compile() (molprop.models.graph_neural_network.GNN method) compose_hydra_config() (in module molprop.powertoys.hydra_utils) concat() (molprop.pyg_molgraph.MultiGraphData method) conjugate() (molprop.training_type.TrainingType method) contiguous() (molprop.pyg_molgraph.MultiGraphData method) convert_to_float() (in module molprop.utils.utils)

coo() (molprop.pyg_molgraph.MultiGraphData method) copy() (molprop.pyg_molgraph.PyGMolgraphDataset method) cpu() (molprop.models.graph_neural_network.GNN method) (molprop.pyg_molgraph.MultiGraphData method) (molprop.pyg_molgraph.PyGMolgraphDataset method) create_console_logger() (in module molprop.info) create_plots() (in module molprop.utils.analyze_results) critical() (molprop.powertoys.logging.indent_logger.IndentLogger method) cross_check_data() (in module molprop.utils.analyze_mol_data) csc() (molprop.pyg_molgraph.MultiGraphData method) csr() (molprop.pyg_molgraph.MultiGraphData method) cuda() (molprop.models.graph_neural_network.GNN method) (molprop.pyg_molgraph.MultiGraphData method) (molprop.pyg_molgraph.PyGMolgraphDataset method) custom_color_list() (in module molprop.utils.utils)

D

data_get_input_cols() (in module molprop.utils.utils) data_get_output_cols() (in module molprop.utils.utils) dataset (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD property) debug() (molprop.powertoys.logging.indent_logger.IndentLogger method) decrease() (molprop.powertoys.logging.indent_logger.IndentLogger method) denominator (molprop.training_type.TrainingType attribute)

DescriptorCalculator (class in molprop.utils.mol_features) detach() (molprop.pyg_molgraph.MultiGraphData method) detach_() (molprop.pyg_molgraph.MultiGraphData method) DMPNNTransform (class in molprop.utils.graph_transform) double() (molprop.models.graph_neural_network.GNN method) download() (molprop.pyg_molgraph.PyGMolgraphDataset method)

E

EarlyStopping (class in molprop.utils.early_stopping) edge_attrs() (molprop.pyg_molgraph.MultiGraphData method) edge_subgraph() (molprop.pyg_molgraph.MultiGraphData method) ENSEMBLE_MODEL (molprop.training_type.TrainingType attribute) ensemble_model_run_sequential() (in module molprop.train_ensemble_model) error() (molprop.powertoys.logging.indent_logger.IndentLogger method)

eval() (in module molprop.inference) (molprop.models.graph_neural_network.GNN method) eval_datamodule() (in module molprop.inference) exception() (molprop.powertoys.logging.indent_logger.IndentLogger method) extra_repr() (molprop.models.graph_neural_network.GNN method) extract_mol_features() (in module molprop.utils.analyze_mol_data)

F

fatal() (molprop.powertoys.logging.indent_logger.IndentLogger method) filter() (molprop.powertoys.logging.indent_logger.IndentLogger method) findCaller() (molprop.powertoys.logging.indent_logger.IndentLogger method) float() (molprop.models.graph_neural_network.GNN method)

forward() (molprop.models.graph_neural_network.GNN method) freeze() (in module molprop.utils.transfer_learning) from_bytes() (molprop.training_type.TrainingType class method) from_dict() (molprop.pyg_molgraph.MultiGraphData class method)

G

gamma (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD attribute) generate_ids() (molprop.pyg_molgraph.MultiGraphData method) get() (molprop.pyg_molgraph.PyGMolgraphDataset method) get_active_conda_env() (in module molprop.info) get_all_edge_attrs() (molprop.pyg_molgraph.MultiGraphData method) get_all_smiles_from_df() (in module molprop.utils.utils) get_all_tensor_attrs() (molprop.pyg_molgraph.MultiGraphData method) get_average_metric() (in module molprop.utils.analyze_results) get_buffer() (molprop.models.graph_neural_network.GNN method) get_dict_hash() (in module molprop.utils.utils) get_edge_index() (molprop.pyg_molgraph.MultiGraphData method) get_extra_state() (molprop.models.graph_neural_network.GNN method) get_info() (in module molprop.info) get_joint_dataloader() (molprop.data_processing.PyGDataModule method) get_latest_folder() (in module molprop.powertoys.pathlib_utils) get_latest_model_path() (in module molprop.powertoys.hydra_utils)

get_latest_model_path_by_cfg() (in module molprop.powertoys.hydra_utils) get_latest_single_model_folder() (in module molprop.utils.utils) get_mol_features() (in module molprop.utils.analyze_mol_data) get_mol_features_from_cfg() (in module molprop.utils.analyze_mol_data) get_mol_w() (in module molprop.utils.utils) get_parameter() (molprop.models.graph_neural_network.GNN method) get_pkg_str() (in module tests.environments.test_conda_installed_packages) get_pre_transform() (in module molprop.utils.omegaconf_resolvers) get_submodule() (molprop.models.graph_neural_network.GNN method) get_summary() (molprop.pyg_molgraph.PyGMolgraphDataset method) get_tensor() (molprop.pyg_molgraph.MultiGraphData method) get_tensor_size() (molprop.pyg_molgraph.MultiGraphData method) get_yml_file() (in module tests.environments.test_conda_installed_packages) getChild() (molprop.powertoys.logging.indent_logger.IndentLogger method) getEffectiveLevel() (molprop.powertoys.logging.indent_logger.IndentLogger method) GNN (class in molprop.models.graph_neural_network)

H

half() (molprop.models.graph_neural_network.GNN method) handle() (molprop.powertoys.logging.indent_logger.IndentLogger method) has_download (molprop.pyg_molgraph.PyGMolgraphDataset property) has_isolated_nodes() (molprop.pyg_molgraph.MultiGraphData method)

has_process (molprop.pyg_molgraph.PyGMolgraphDataset property) has_self_loops() (molprop.pyg_molgraph.MultiGraphData method) hasHandlers() (molprop.powertoys.logging.indent_logger.IndentLogger method) hyperparameters (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD property)

I

imag (molprop.training_type.TrainingType attribute) increase() (molprop.powertoys.logging.indent_logger.IndentLogger method) IndentLogger (class in molprop.powertoys.logging.indent_logger) index_select() (molprop.pyg_molgraph.PyGMolgraphDataset method) infer() (in module molprop.inference) infer_ensemble() (in module molprop.inference) info() (molprop.powertoys.logging.indent_logger.IndentLogger method) ipu() (molprop.models.graph_neural_network.GNN method) is_coalesced() (molprop.pyg_molgraph.MultiGraphData method) is_cuda (molprop.pyg_molgraph.MultiGraphData property)

is_directed() (molprop.pyg_molgraph.MultiGraphData method) is_edge_attr() (molprop.pyg_molgraph.MultiGraphData method) is_integer() (molprop.training_type.TrainingType method) is_node_attr() (molprop.pyg_molgraph.MultiGraphData method) is_pixi() (in module molprop.info) is_single_model_folder() (in module molprop.utils.utils) is_sorted() (molprop.pyg_molgraph.MultiGraphData method) is_sorted_by_time() (molprop.pyg_molgraph.MultiGraphData method) is_undirected() (molprop.pyg_molgraph.MultiGraphData method) isEnabledFor() (molprop.powertoys.logging.indent_logger.IndentLogger method)

J

json_convert_tensor_tolist() (in module molprop.utils.utils)

K

kernel (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD attribute)

keys() (molprop.pyg_molgraph.MultiGraphData method)

L

len() (molprop.pyg_molgraph.PyGMolgraphDataset method) load() (molprop.pyg_molgraph.PyGMolgraphDataset method) load_config() (in module molprop.utils.utils) load_pretrained_params() (in module molprop.utils.transfer_learning)

load_state_dict() (molprop.models.graph_neural_network.GNN method) log() (in module molprop.powertoys.logging.log_decorator) (molprop.powertoys.logging.indent_logger.IndentLogger method) log_info_values() (in module molprop.info) log_transform() (in module molprop.utils.data_transform)

M

makeRecord() (molprop.powertoys.logging.indent_logger.IndentLogger method) MixDescriptorCalculator (class in molprop.utils.mol_features) model_name (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD property) module molprop molprop.applicability_domain_methods molprop.applicability_domain_methods.support_vector_machine molprop.applicability_domain_methods.support_vector_machine.ocsvm molprop.applicability_domain_methods.support_vector_machine.utils molprop.data_processing molprop.inference molprop.info molprop.models molprop.models.graph_neural_network molprop.powertoys molprop.powertoys.hydra_utils molprop.powertoys.logging molprop.powertoys.logging.indent_logger molprop.powertoys.logging.log_decorator molprop.powertoys.pathlib_utils molprop.predict molprop.pyg_molgraph molprop.train_ensemble_model molprop.train_single_model molprop.training molprop.training_type molprop.utils molprop.utils.analyze_mol_data molprop.utils.analyze_results molprop.utils.data_transform molprop.utils.early_stopping molprop.utils.graph_transform molprop.utils.mol_features molprop.utils.omegaconf_resolvers molprop.utils.transfer_learning molprop.utils.utils tests tests.conftest tests.environments tests.environments.test_conda_installed_packages tests.environments.test_log_info tests.samples tests.samples.test_run_samples tests.test_sklearn_torch_tensor_device tests.test_torch_cuda tests.test_torch_sparse_coalesce modules() (molprop.models.graph_neural_network.GNN method) MolDescriptorCalculator (class in molprop.utils.mol_features) MolFeatures (class in molprop.utils.mol_features) MolFeaturizationError molprop module molprop.applicability_domain_methods module molprop.applicability_domain_methods.support_vector_machine module molprop.applicability_domain_methods.support_vector_machine.ocsvm module molprop.applicability_domain_methods.support_vector_machine.utils module

molprop.data_processing module molprop.inference module molprop.info module molprop.models module molprop.models.graph_neural_network module molprop.powertoys module molprop.powertoys.hydra_utils module molprop.powertoys.logging module molprop.powertoys.logging.indent_logger module molprop.powertoys.logging.log_decorator module molprop.powertoys.pathlib_utils module molprop.predict module molprop.pyg_molgraph module molprop.train_ensemble_model module molprop.train_single_model module molprop.training module molprop.training_type module molprop.utils module molprop.utils.analyze_mol_data module molprop.utils.analyze_results module molprop.utils.data_transform module molprop.utils.early_stopping module molprop.utils.graph_transform module molprop.utils.mol_features module molprop.utils.omegaconf_resolvers module molprop.utils.transfer_learning module molprop.utils.utils module mtia() (molprop.models.graph_neural_network.GNN method) multi_get_tensor() (molprop.pyg_molgraph.MultiGraphData method) MultiGraphData (class in molprop.pyg_molgraph) MultiGraphTransform (class in molprop.utils.graph_transform)

N

named_buffers() (molprop.models.graph_neural_network.GNN method) named_children() (molprop.models.graph_neural_network.GNN method) named_modules() (molprop.models.graph_neural_network.GNN method) named_parameters() (molprop.models.graph_neural_network.GNN method) node_attrs() (molprop.pyg_molgraph.MultiGraphData method) nu (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD attribute) num_classes (molprop.pyg_molgraph.PyGMolgraphDataset property) num_edge_features (molprop.pyg_molgraph.MultiGraphData property) (molprop.pyg_molgraph.PyGMolgraphDataset property)

num_edge_types (molprop.pyg_molgraph.MultiGraphData property) num_edges (molprop.pyg_molgraph.MultiGraphData property) num_faces (molprop.pyg_molgraph.MultiGraphData property) num_features (molprop.pyg_molgraph.MultiGraphData property) (molprop.pyg_molgraph.PyGMolgraphDataset property) num_node_features (molprop.pyg_molgraph.MultiGraphData property) (molprop.pyg_molgraph.PyGMolgraphDataset property) num_node_types (molprop.pyg_molgraph.MultiGraphData property) num_nodes (molprop.pyg_molgraph.MultiGraphData property) numerator (molprop.training_type.TrainingType attribute)

P

parameters() (molprop.models.graph_neural_network.GNN method) parity_plot() (in module molprop.utils.analyze_results) parse_args() (in module molprop.predict) perform_train_test_split() (in module molprop.utils.utils) pin_memory() (molprop.pyg_molgraph.MultiGraphData method) plot_results_2D() (in module molprop.applicability_domain_methods.support_vector_machine.utils) predict() (in module molprop.predict) prepare_prediction_data() (in module molprop.predict)

print_summary() (molprop.pyg_molgraph.PyGMolgraphDataset method) process() (molprop.pyg_molgraph.PyGMolgraphDataset method) processed_file_names (molprop.pyg_molgraph.PyGMolgraphDataset property) processed_paths (molprop.pyg_molgraph.PyGMolgraphDataset property) put_edge_index() (molprop.pyg_molgraph.MultiGraphData method) put_tensor() (molprop.pyg_molgraph.MultiGraphData method) PyGDataModule (class in molprop.data_processing) PyGMolgraphDataset (class in molprop.pyg_molgraph)

R

raw_file_names (molprop.pyg_molgraph.PyGMolgraphDataset property) raw_paths (molprop.pyg_molgraph.PyGMolgraphDataset property) read_csv_data() (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD method) read_data_to_df() (in module molprop.utils.utils) real (molprop.training_type.TrainingType attribute) record_stream() (molprop.pyg_molgraph.MultiGraphData method) register_backward_hook() (molprop.models.graph_neural_network.GNN method) register_buffer() (molprop.models.graph_neural_network.GNN method) register_forward_hook() (molprop.models.graph_neural_network.GNN method) register_forward_pre_hook() (molprop.models.graph_neural_network.GNN method) register_full_backward_hook() (molprop.models.graph_neural_network.GNN method) register_full_backward_pre_hook() (molprop.models.graph_neural_network.GNN method) register_load_state_dict_post_hook() (molprop.models.graph_neural_network.GNN method) register_load_state_dict_pre_hook() (molprop.models.graph_neural_network.GNN method)

register_module() (molprop.models.graph_neural_network.GNN method) register_parameter() (molprop.models.graph_neural_network.GNN method) register_state_dict_post_hook() (molprop.models.graph_neural_network.GNN method) register_state_dict_pre_hook() (molprop.models.graph_neural_network.GNN method) remove_edge_index() (molprop.pyg_molgraph.MultiGraphData method) remove_outliers() (in module molprop.utils.data_transform) remove_tensor() (molprop.pyg_molgraph.MultiGraphData method) removeFilter() (molprop.powertoys.logging.indent_logger.IndentLogger method) removeHandler() (molprop.powertoys.logging.indent_logger.IndentLogger method) requires_grad_() (molprop.models.graph_neural_network.GNN method) (molprop.pyg_molgraph.MultiGraphData method) reverse_log_transform() (in module molprop.utils.data_transform) reverse_standardize() (in module molprop.utils.data_transform) roc_curve_plot() (in module molprop.utils.analyze_results)

S

sanity_check_compounds() (in module molprop.utils.analyze_mol_data) sanity_check_data() (in module molprop.utils.analyze_mol_data) sanity_check_features() (in module molprop.utils.analyze_mol_data) sanity_check_pipeline() (in module molprop.utils.analyze_mol_data) save() (molprop.pyg_molgraph.PyGMolgraphDataset class method) save_checkpoint() (molprop.utils.early_stopping.EarlyStopping method) save_model_to_json() (in module molprop.applicability_domain_methods.support_vector_machine.utils) save_results() (in module molprop.utils.utils) save_results_metrics() (in module molprop.utils.utils) save_results_to_csv() (in module molprop.utils.utils) seed_everything() (in module molprop.utils.utils) set_extra_state() (molprop.models.graph_neural_network.GNN method) set_submodule() (molprop.models.graph_neural_network.GNN method) setLevel() (molprop.powertoys.logging.indent_logger.IndentLogger method) share_memory() (molprop.models.graph_neural_network.GNN method)

share_memory_() (molprop.pyg_molgraph.MultiGraphData method) shuffle() (molprop.pyg_molgraph.PyGMolgraphDataset method) SINGLE_MODEL (molprop.training_type.TrainingType attribute) single_model_run() (in module molprop.train_single_model) SingleMolFeature (class in molprop.utils.mol_features) size() (molprop.pyg_molgraph.MultiGraphData method) Skip (class in tests.samples.test_run_samples) snapshot() (molprop.pyg_molgraph.MultiGraphData method) sort() (molprop.pyg_molgraph.MultiGraphData method) sort_by_time() (molprop.pyg_molgraph.MultiGraphData method) split_data() (in module molprop.utils.data_transform) standardize() (in module molprop.utils.data_transform) state_dict() (molprop.models.graph_neural_network.GNN method) subgraph() (molprop.pyg_molgraph.MultiGraphData method) svm (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD property) SVM_AD (class in molprop.applicability_domain_methods.support_vector_machine.ocsvm)

T

test_coalesce_crash_on_cpu() (in module tests.test_torch_sparse_coalesce) test_create_tensor() (in module tests.test_torch_cuda) test_log_info() (in module tests.environments.test_log_info) test_package_versions() (in module tests.environments.test_conda_installed_packages) test_torch_devices() (in module tests.test_torch_cuda) test_unsupported_device() (tests.test_sklearn_torch_tensor_device.TestClass method) TestClass (class in tests.test_sklearn_torch_tensor_device) tests module tests.conftest module tests.environments module tests.environments.test_conda_installed_packages module tests.environments.test_log_info module tests.samples module tests.samples.test_run_samples module tests.test_sklearn_torch_tensor_device module

tests.test_torch_cuda module tests.test_torch_sparse_coalesce module TestSamples (class in tests.samples.test_run_samples) TestSamplesConfig (class in tests.samples.test_run_samples) to() (molprop.models.graph_neural_network.GNN method) (molprop.pyg_molgraph.MultiGraphData method) (molprop.pyg_molgraph.PyGMolgraphDataset method) to_bytes() (molprop.training_type.TrainingType method) to_datapipe() (molprop.pyg_molgraph.PyGMolgraphDataset method) to_dict() (molprop.pyg_molgraph.MultiGraphData method) to_empty() (molprop.models.graph_neural_network.GNN method) to_heterogeneous() (molprop.pyg_molgraph.MultiGraphData method) to_namedtuple() (molprop.pyg_molgraph.MultiGraphData method) to_on_disk_dataset() (molprop.pyg_molgraph.PyGMolgraphDataset method) tol (molprop.applicability_domain_methods.support_vector_machine.ocsvm.SVM_AD attribute) train() (molprop.models.graph_neural_network.GNN method) train_model() (in module molprop.training) TrainingType (class in molprop.training_type) type() (molprop.models.graph_neural_network.GNN method)

U

up_to() (molprop.pyg_molgraph.MultiGraphData method) update() (molprop.pyg_molgraph.MultiGraphData method)

update_config_w_data_features() (molprop.data_processing.PyGDataModule method) update_data_transformation_cfg() (in module molprop.utils.transfer_learning) update_tensor() (molprop.pyg_molgraph.MultiGraphData method)

V

validate() (molprop.pyg_molgraph.MultiGraphData method)

view() (molprop.pyg_molgraph.MultiGraphData method)

W

warning() (molprop.powertoys.logging.indent_logger.IndentLogger method)

write_metrics_to_txt() (in module molprop.utils.utils)

X

xpu() (molprop.models.graph_neural_network.GNN method)

Z

zero_grad() (molprop.models.graph_neural_network.GNN method)