Index

A

analysis_bundle() (PDBData method) atomselect() (PDBData method)

atomwise_rmsd() (MolearnAnalysis method) AutoEncoder (class in molearn.models.foldingnet)

B

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

C

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

common_step() (Trainer method) create_dendrogram() (DataAssembler method) create_trajectories() (DataAssembler method) create_trajectories_by_dendrogram() (DataAssembler method)

D

DataAssembler (class in molearn.data) distance_cluster() (DataAssembler method)

DOPE_Score (class in molearn.scoring) dry_run() (Trainer method)

E

execute() (OpenmmPluginScore method)

F

fit() (Trainer method) fix_terminal() (PDBData method) forward() (AutoEncoder method) (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_atomwise_error() (MolearnAnalysis method) get_bondlengths() (MolearnAnalysis 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_inversions() (MolearnAnalysis method) get_network_summary() (Trainer method) get_path() (in module molearn.analysis.path) get_path_aggregate() (in module molearn.analysis.path) get_point_index() (in module molearn.analysis.path) get_ramachandran() (MolearnAnalysis method) get_scale() (Trainer method) get_score() (Parallel_DOPE_Score method) (Parallel_Ramachandran_Score method) (Ramachandran_Score method)

I

import_pdb() (PDBData method)

L

load_checkpoint() (Trainer method)

log() (Trainer method)

M

metadata() (PDBData method) ModifiedForceField (class in molearn.loss_functions.openmm_thread) module molearn.analysis.path molearn.analysis.plot molearn.loss_functions.openmm_thread molearn.loss_functions.torch_protein_energy molearn.analysis.path module

molearn.analysis.plot 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) own_idx() (DataAssembler method)

P

Parallel_DOPE_Score (class in molearn.scoring) Parallel_Ramachandran_Score (class in molearn.scoring) pca_cluster() (DataAssembler method) PDBData (class in molearn.data) plot_analysis_surface() (in module molearn.analysis.plot) plot_angle_hist() (in module molearn.analysis.plot) plot_bondlength_hist() (in module molearn.analysis.plot) plot_dihedral_hist() (in module molearn.analysis.plot) plot_dope_hist() (in module molearn.analysis.plot)

plot_dope_surface() (in module molearn.analysis.plot) plot_inversion_hist() (in module molearn.analysis.plot) plot_inversion_surface() (in module molearn.analysis.plot) plot_network_rmsd_surface() (in module molearn.analysis.plot) plot_rmsd_hist() (in module molearn.analysis.plot) prepare_dataset() (PDBData method) prepare_logs() (Trainer method) prepare_optimiser() (Trainer method) prepare_physics() (OpenMM_Physics_Trainer method) (Torch_Physics_Trainer method)

R

Ramachandran_Score (class in molearn.scoring) read_traj() (DataAssembler method)

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

S

scan_bondlength() (MolearnAnalysis method) scan_ca_chirality() (MolearnAnalysis method) scan_custom() (MolearnAnalysis method) scan_dope() (MolearnAnalysis method) scan_error() (MolearnAnalysis method) scan_error_from_target() (MolearnAnalysis method) scan_ramachandran() (MolearnAnalysis 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) stride() (DataAssembler 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)

W

write_statistics() (PDBData method)