Index

_

__getitem__() (Dock2D.Utility.TorchDataLoader.InteractionFactDataset method) (Dock2D.Utility.TorchDataLoader.InteractionPoseDataset method) __init__() (Dock2D.DatasetGeneration.DatasetGenerator.DatasetGenerator method) (Dock2D.DatasetGeneration.Protein.Protein method) (Dock2D.DatasetGeneration.ProteinPool.ParamDistribution method) (Dock2D.DatasetGeneration.ProteinPool.ProteinPool method) (Dock2D.Models.model_docking.Docking method) (Dock2D.Models.model_interaction.Interaction method) (Dock2D.Models.model_sampling.SamplingDocker method) (Dock2D.Models.model_sampling.SamplingModel method) (Dock2D.Models.TrainerFI.TrainerFI method) (Dock2D.Models.TrainerIP.TrainerIP method) (Dock2D.Tests.check_param_state_dict_cuda.DummyModel method) (Dock2D.Tests.check_shape_distributions.ShapeDistributions method) (Dock2D.Utility.PlotterFI.PlotterFI method) (Dock2D.Utility.PlotterIP.PlotterIP method) (Dock2D.Utility.SampleBuffer.SampleBuffer method) (Dock2D.Utility.TorchDataLoader.InteractionFactDataset method) (Dock2D.Utility.TorchDataLoader.InteractionPoseDataset method) (Dock2D.Utility.TorchDockingFFT.TorchDockingFFT method) (Dock2D.Utility.ValidationMetrics.APR method) (Dock2D.Utility.ValidationMetrics.RMSD method)

__len__() (Dock2D.Utility.SampleBuffer.SampleBuffer method) (Dock2D.Utility.TorchDataLoader.InteractionFactDataset method) (Dock2D.Utility.TorchDataLoader.InteractionPoseDataset method)

A

APR (class in Dock2D.Utility.ValidationMetrics)

C

calc_APR() (Dock2D.Utility.ValidationMetrics.APR method) calc_rmsd() (Dock2D.Utility.ValidationMetrics.RMSD method) check_APR() (Dock2D.Models.TrainerFI.TrainerFI method)

check_fft_predictions() (Dock2D.Utility.TorchDockingFFT.TorchDockingFFT method) check_missing_examples() (Dock2D.Tests.check_shape_distributions.ShapeDistributions method) check_model_gradients() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method) classify() (Dock2D.Models.TrainerFI.TrainerFI static method)

D

DatasetGenerator (class in Dock2D.DatasetGeneration.DatasetGenerator) Dock2D.Models.BruteForce.train_bruteforce_FI module Dock2D.Models.BruteForce.train_bruteforce_IP module Dock2D.Models.Sampling.train_brutesimplified_IP module Dock2D.Models.Sampling.train_montecarlo_FI module Dock2D.Models.TrainerFI module Dock2D.Utility.PlotterFI module Dock2D.Utility.PlotterIP module

Dock2D.Utility.SampleBuffer module Dock2D.Utility.TorchDataLoader module Dock2D.Utility.TorchDockingFFT module Dock2D.Utility.UtilityFunctions module Dock2D.Utility.ValidationMetrics module dock_rotations() (Dock2D.Utility.TorchDockingFFT.TorchDockingFFT method) dock_translations() (Dock2D.Utility.TorchDockingFFT.TorchDockingFFT method) Docking (class in Dock2D.Models.model_docking) DummyModel (class in Dock2D.Tests.check_param_state_dict_cuda)

E

encode_transform() (Dock2D.Utility.TorchDockingFFT.TorchDockingFFT method)

extract_params() (Dock2D.DatasetGeneration.ProteinPool.ParamDistribution method) extract_transform() (Dock2D.Utility.TorchDockingFFT.TorchDockingFFT method)

F

Fact-of-Interaction (FI): forward() (Dock2D.Models.model_docking.Docking method) (Dock2D.Models.model_interaction.Interaction method) (Dock2D.Models.model_sampling.SamplingDocker method) (Dock2D.Models.model_sampling.SamplingModel method) (Dock2D.Tests.check_param_state_dict_cuda.DummyModel method)

freeze_weights() (Dock2D.Models.TrainerFI.TrainerFI method)

G

gaussian_1d() (in module Dock2D.Tests.check_torchFFT) gaussian_2d() (in module Dock2D.Tests.check_torchFFT) generate() (Dock2D.DatasetGeneration.ProteinPool.ProteinPool class method) generate_datasets() (Dock2D.DatasetGeneration.DatasetGenerator.DatasetGenerator method) generate_interactions() (Dock2D.DatasetGeneration.DatasetGenerator.DatasetGenerator method) generate_pool() (Dock2D.DatasetGeneration.DatasetGenerator.DatasetGenerator method) generateConcave() (Dock2D.DatasetGeneration.Protein.Protein class method) get_alpha() (Dock2D.Utility.SampleBuffer.SampleBuffer method)

get_counts() (Dock2D.Tests.check_shape_distributions.ShapeDistributions method) get_dict_counts() (Dock2D.Tests.check_shape_distributions.ShapeDistributions method) get_docking_stream() (in module Dock2D.Utility.TorchDataLoader) get_free_energies_indices() (Dock2D.Utility.SampleBuffer.SampleBuffer method) get_interaction_stream() (in module Dock2D.Utility.TorchDataLoader) get_random_points() (in module Dock2D.DatasetGeneration.Protein) get_shape_distributions() (Dock2D.Tests.check_shape_distributions.ShapeDistributions method) get_unique_fracs() (Dock2D.Tests.check_shape_distributions.ShapeDistributions method) get_XC() (Dock2D.Utility.ValidationMetrics.RMSD method)

H

hull2array() (in module Dock2D.DatasetGeneration.Protein)

I

Interaction (class in Dock2D.Models.model_interaction) Interaction Pose (IP):

InteractionFactDataset (class in Dock2D.Utility.TorchDataLoader) InteractionPoseDataset (class in Dock2D.Utility.TorchDataLoader)

L

load() (Dock2D.DatasetGeneration.ProteinPool.ProteinPool class method) load_checkpoint() (Dock2D.Models.TrainerFI.TrainerFI static method) (Dock2D.Models.TrainerIP.TrainerIP method) (Dock2D.Tests.check_param_state_dict_cuda.DummyModel static method)

M

make_boundary() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method) module Dock2D.Models.BruteForce.train_bruteforce_FI Dock2D.Models.BruteForce.train_bruteforce_IP Dock2D.Models.Sampling.train_brutesimplified_IP Dock2D.Models.Sampling.train_montecarlo_FI Dock2D.Models.TrainerFI Dock2D.Utility.PlotterFI Dock2D.Utility.PlotterIP Dock2D.Utility.SampleBuffer Dock2D.Utility.TorchDataLoader Dock2D.Utility.TorchDockingFFT Dock2D.Utility.UtilityFunctions Dock2D.Utility.ValidationMetrics

N

normalize() (Dock2D.DatasetGeneration.ProteinPool.ParamDistribution method)

O

orthogonalize_feats() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method)

P

ParamDistribution (class in Dock2D.DatasetGeneration.ProteinPool) plot_accepted_rejected_shapes() (Dock2D.DatasetGeneration.DatasetGenerator.DatasetGenerator method) plot_assembly() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method) plot_deltaF_distribution() (Dock2D.Utility.PlotterFI.PlotterFI method) plot_energy_distributions() (Dock2D.DatasetGeneration.DatasetGenerator.DatasetGenerator method) plot_features() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method) plot_loss() (Dock2D.Utility.PlotterFI.PlotterFI method) (Dock2D.Utility.PlotterIP.PlotterIP method) plot_predicted_pose() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method)

plot_rmsd_distribution() (Dock2D.Utility.PlotterIP.PlotterIP method) plot_rotation_energysurface() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method) plot_shapes_and_params() (Dock2D.Tests.check_shape_distributions.ShapeDistributions method) PlotterFI (class in Dock2D.Utility.PlotterFI) PlotterIP (class in Dock2D.Utility.PlotterIP) Protein (class in Dock2D.DatasetGeneration.Protein) ProteinPool (class in Dock2D.DatasetGeneration.ProteinPool) push_alpha() (Dock2D.Utility.SampleBuffer.SampleBuffer method) push_free_energies_indices() (Dock2D.Utility.SampleBuffer.SampleBuffer method)

R

read_pkl() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method) resume_training_or_not() (Dock2D.Models.TrainerFI.TrainerFI method) (Dock2D.Models.TrainerIP.TrainerIP method) RMSD (class in Dock2D.Utility.ValidationMetrics) rotate() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method) rotate_gridligand() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method)

run_epoch() (Dock2D.Models.TrainerFI.TrainerFI method) (Dock2D.Models.TrainerIP.TrainerIP method) run_generator() (Dock2D.DatasetGeneration.DatasetGenerator.DatasetGenerator method) run_model() (Dock2D.Models.TrainerFI.TrainerFI method) (Dock2D.Models.TrainerIP.TrainerIP method) run_trainer() (Dock2D.Models.TrainerFI.TrainerFI method) (Dock2D.Models.TrainerIP.TrainerIP method)

S

SampleBuffer (class in Dock2D.Utility.SampleBuffer) SamplingDocker (class in Dock2D.Models.model_sampling) SamplingModel (class in Dock2D.Models.model_sampling) save() (Dock2D.DatasetGeneration.ProteinPool.ProteinPool method) save_checkpoint() (Dock2D.Models.TrainerFI.TrainerFI static method) (Dock2D.Models.TrainerIP.TrainerIP method) (Dock2D.Tests.check_param_state_dict_cuda.DummyModel static method)

set_docking_model_state() (Dock2D.Models.TrainerFI.TrainerFI method) ShapeDistributions (class in Dock2D.Tests.check_shape_distributions) swap_quadrants() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method)

T

TorchDockingFFT (class in Dock2D.Utility.TorchDockingFFT) train_model() (Dock2D.Models.TrainerFI.TrainerFI method) (Dock2D.Models.TrainerIP.TrainerIP method)

TrainerFI (class in Dock2D.Models.TrainerFI) TrainerIP (class in Dock2D.Models.TrainerIP) translate_gridligand() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method)

U

UtilityFunctions (class in Dock2D.Utility.UtilityFunctions)

W

weights_init() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method)

write_pkl() (Dock2D.Utility.UtilityFunctions.UtilityFunctions method)