Index

A

add_esp_charges() (in module ml.process)

B

build_dataloaders() (in module ml.mlp) (in module ml.mlp_kfold)

C

calculate_esp() (in module ml.process) check_file_exists() (in module ml.process) cli() (in module ml.cli) collect_esp_components() (in module ml.process)

combine_qm_charges() (in module ml.process) combine_qm_replicates() (in module ml.process) combine_replicates() (in module ml.process) combine_sp_xyz() (in module ml.process) create_layers() (in module ml.mlp)

E

evaluate() (in module ml.rf)

evaluate_model() (in module ml.mlp) (in module ml.mlp_kfold)

F

final_charge_dataset() (in module ml.process) format_plots() (in module ml.mlp) (in module ml.rf)

forward() (ml.mlp.MimoMLP method) (ml.mlp_kfold.MimoMLP method)

G

get_residue_identifiers() (in module ml.process)

gradient_step() (in module ml.mlp)

H

hyperparam_opt() (in module ml.rf)

L

load_data() (in module ml.mlp) (in module ml.mlp_kfold) (in module ml.rf)

M

MDDataset (class in ml.mlp) MimoMLP (class in ml.mlp) (class in ml.mlp_kfold) ml module ml.cli module ml.mlp module, [1] ml.mlp_kfold module

ml.process module, [1] ml.rf module, [1] module ml ml.cli ml.mlp, [1] ml.mlp_kfold ml.process, [1] ml.rf, [1]

O

optuna_mlp() (in module ml.mlp)

P

pairwise_charge_features() (in module ml.process) pairwise_distances_csv() (in module ml.process) parser (in module ml.mlp) (in module ml.rf) plot_confusion_matrices() (in module ml.mlp) (in module ml.rf) plot_data() (in module ml.mlp) (in module ml.rf)

plot_gini_importance() (in module ml.rf) plot_roc_curve() (in module ml.mlp) (in module ml.rf) plot_train_val_losses() (in module ml.mlp) preprocess_data() (in module ml.mlp) (in module ml.rf)

R

rf_analysis() (in module ml.rf)

run_mlp() (in module ml.mlp) (in module ml.mlp_kfold)

S

shap_analysis() (in module ml.mlp)

summed_residue_charge() (in module ml.process)

T

train() (in module ml.mlp) (in module ml.mlp_kfold)

train_random_forest() (in module ml.rf) train_random_forest_with_optimization() (in module ml.rf) train_with_hyperparameters() (in module ml.mlp)

V

validate() (in module ml.mlp) (in module ml.mlp_kfold)

W

welcome() (in module ml.cli)

X

xyz2pdb_traj() (in module ml.process)