Index

A

atomselect() (PDBData method)

Autoencoder (class in molearn.models.CNN_autoencoder) AutoEncoder (class in molearn.models.foldingnet)

B

backward() (openmm_clamped_energy_function static method) (openmm_energy_function static method)

C

checkpoint() (Trainer method) common_physics_step() (OpenMM_Physics_Trainer method) (Torch_Physics_Trainer method)

common_step() (Trainer method)

D

DOPE_Score (class in molearn.scoring)

E

execute() (OpenmmPluginScore method)

F

fix_terminal() (PDBData method) forward() (openmm_clamped_energy_function static method) (openmm_energy_function static method)

frame() (PDBData method)

G

generate() (MolearnAnalysis method) get_all_dope() (DOPE_Score method) get_all_dope_score() (MolearnAnalysis method) get_all_ramachandran_score() (MolearnAnalysis method) get_atominfo() (PDBData method) get_dataloader() (PDBData method) get_dataset() (MolearnAnalysis method) get_datasets() (PDBData method) get_decoded() (MolearnAnalysis method) get_dope() (DOPE_Score method) (MolearnAnalysis method)

get_encoded() (MolearnAnalysis method) get_energy() (OpenmmPluginScore method) get_error() (MolearnAnalysis method) get_network_summary() (Trainer method) get_path() (in module molearn.analysis.path) get_path_aggregate() (in module molearn.analysis.path) get_ramachandran() (MolearnAnalysis method) get_score() (Parallel_DOPE_Score method) (Parallel_Ramachandran_Score method) (Ramachandran_Score method)

I

import_pdb() (PDBData method)

L

learning_rate_sweep() (Trainer method)

load_checkpoint() (Trainer method) log() (Trainer method)

M

ModifiedForceField (class in molearn.loss_functions.openmm_thread) module molearn.analysis.path molearn.loss_functions.openmm_thread molearn.loss_functions.torch_protein_energy molearn.analysis.path module

molearn.loss_functions.openmm_thread module molearn.loss_functions.torch_protein_energy module MolearnAnalysis (class in molearn.analysis) MolearnGUI (class in molearn.analysis)

N

num_trainable_params() (MolearnAnalysis method)

O

openmm_clamped_energy_function (class in molearn.loss_functions.openmm_thread) openmm_energy (class in molearn.loss_functions.openmm_thread) openmm_energy_function (class in molearn.loss_functions.openmm_thread) OpenMM_Physics_Trainer (class in molearn.trainers)

OpenmmPluginScore (class in molearn.loss_functions.openmm_thread) OpenMMPluginScoreSoftForceField (class in molearn.loss_functions.openmm_thread) OpenmmTorchEnergyMinimizer (class in molearn.loss_functions.openmm_thread) oversample() (in module molearn.analysis.path)

P

Parallel_DOPE_Score (class in molearn.scoring) Parallel_Ramachandran_Score (class in molearn.scoring) PDBData (class in molearn.data)

prepare_dataset() (PDBData method) prepare_optimiser() (Trainer method) prepare_physics() (OpenMM_Physics_Trainer method) (Torch_Physics_Trainer method)

R

Ramachandran_Score (class in molearn.scoring)

reference_dope_score() (MolearnAnalysis method) run() (Trainer method)

S

scan_custom() (MolearnAnalysis method) scan_dope() (MolearnAnalysis method) scan_error() (MolearnAnalysis method) scan_error_from_target() (MolearnAnalysis method) scan_ramachandran() (MolearnAnalysis method) scheduler_step() (Trainer method) set_autoencoder() (Trainer method)

set_data() (Trainer method) set_dataloader() (Trainer method) set_dataset() (MolearnAnalysis method) set_decoded() (MolearnAnalysis method) set_encoded() (MolearnAnalysis method) set_network() (MolearnAnalysis method) setup_grid() (MolearnAnalysis method) split() (PDBData method)

T

Torch_Physics_Trainer (class in molearn.trainers) train_epoch() (Trainer method) train_step() (OpenMM_Physics_Trainer method) (Torch_Physics_Trainer method) (Trainer method)

Trainer (class in molearn.trainers)

U

update_optimiser_hyperparameters() (Trainer method)

V

valid_epoch() (Trainer method) valid_step() (OpenMM_Physics_Trainer method) (Torch_Physics_Trainer method) (Trainer method)