Index

_

__init__() (boltzkit.evaluation.eval.EnergyHistEval method) (boltzkit.evaluation.eval.EvalData method) (boltzkit.evaluation.eval.Evaluation method) (boltzkit.evaluation.eval.ReverseLogWeightsEval method) (boltzkit.evaluation.molecular_eval.BondAngleEval method) (boltzkit.evaluation.molecular_eval.BondLengthEval method) (boltzkit.evaluation.molecular_eval.DihedralAngleEval method) (boltzkit.evaluation.molecular_eval.TicaEval method) (boltzkit.evaluation.molecular_eval.TorsionMarginalEval method) (boltzkit.evaluation.sample_based.histogram_comparison.HistogramMetric method) (boltzkit.utils.cached_repo.CachedRepo method) (boltzkit.utils.cached_repo.HuggingfaceRepo method) (boltzkit.utils.cached_repo.LocalRepo method) (boltzkit.utils.cached_repo.VirtualRepo method) (boltzkit.utils.dataloader.CachedRepoDatasetLoader method) (boltzkit.utils.dataloader.CacheLoadingArgs method) (boltzkit.utils.dataloader.DomainScaledDatasetLoader method) (boltzkit.utils.dataset.Dataset method) (boltzkit.utils.framework.FrameworkAgnosticFunction method) (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) (boltzkit.utils.histogram.VisualizationMode method) (boltzkit.utils.key_value_store.FileKV method) (boltzkit.utils.molecular.energy_eval.EnergyEval method) (boltzkit.utils.molecular.energy_eval.ParallelEnergyEval method) (boltzkit.utils.molecular.energy_eval.SequentialEnergyEval method) (boltzkit.utils.molecular.tica.TicaModelWithLengthScale method) (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory method) (boltzkit.utils.pdf.PdfBuffer method)

_get_cache_path() (in module boltzkit.utils.dataloader) _test_ABI_set_positions_compatibility() (in module boltzkit.utils.molecular.energy_eval)

A

allow_autogen (boltzkit.utils.dataloader.CacheLoadingArgs attribute)

B

bin_edges (boltzkit.utils.histogram.Histogram1D property) bin_edges_x (boltzkit.utils.histogram.Histogram2D property) bin_edges_y (boltzkit.utils.histogram.Histogram2D property) boltzkit module boltzkit.evaluation module boltzkit.evaluation.density_based module boltzkit.evaluation.density_based.divergence module boltzkit.evaluation.density_based.entropy module boltzkit.evaluation.density_based.ess module boltzkit.evaluation.density_based.evidence module boltzkit.evaluation.eval module boltzkit.evaluation.molecular_eval module boltzkit.evaluation.sample_based module boltzkit.evaluation.sample_based.energy_histogram module boltzkit.evaluation.sample_based.histogram_comparison module boltzkit.evaluation.sample_based.internal_coordinate_eval module boltzkit.evaluation.sample_based.tica module boltzkit.evaluation.sample_based.torsion_marginals module boltzkit.evaluation.sample_based.wasserstein module boltzkit.targets module boltzkit.targets.many_well module boltzkit.utils module boltzkit.utils.cached_repo module

boltzkit.utils.dataloader module boltzkit.utils.dataset module boltzkit.utils.framework module boltzkit.utils.histogram module boltzkit.utils.key_value_store module boltzkit.utils.langevin module boltzkit.utils.molecular module boltzkit.utils.molecular.augmentation module boltzkit.utils.molecular.conversion module boltzkit.utils.molecular.energy_eval module boltzkit.utils.molecular.marginals module boltzkit.utils.molecular.pdbpatch module boltzkit.utils.molecular.plot_molecule module boltzkit.utils.molecular.tica module boltzkit.utils.molecular.z_matrix_factory module boltzkit.utils.molecular.z_matrix_templates module boltzkit.utils.pdf module boltzkit.utils.shape_utils module BondAngleEval (class in boltzkit.evaluation.molecular_eval) BondLengthEval (class in boltzkit.evaluation.molecular_eval) buffer (boltzkit.utils.pdf.PdfBuffer attribute) build_fake_topology() (in module boltzkit.utils.molecular.z_matrix_factory) build_naive() (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory method) build_with_system() (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory method) build_with_templates() (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory method)

C

cache_load_sample_derived_data() (in module boltzkit.utils.dataloader) cache_log_probs (boltzkit.utils.dataloader.CacheLoadingArgs attribute) cache_scores (boltzkit.utils.dataloader.CacheLoadingArgs attribute) CachedRepo (class in boltzkit.utils.cached_repo) CachedRepoDatasetLoader (class in boltzkit.utils.dataloader) CacheLoadingArgs (class in boltzkit.utils.dataloader) config (boltzkit.utils.cached_repo.CachedRepo property)

Content (in module boltzkit.utils.cached_repo) copy_required() (boltzkit.evaluation.eval.EvalData method) create_cached_repo() (in module boltzkit.utils.cached_repo) create_deeptime_tica_model() (in module boltzkit.utils.molecular.tica) create_dispatch() (in module boltzkit.utils.framework) create_pytorch_value_and_grad_fn() (in module boltzkit.utils.framework) create_simulation() (in module boltzkit.utils.molecular.energy_eval) create_symmetry_augmentation() (in module boltzkit.utils.molecular.augmentation)

D

Dataset (class in boltzkit.utils.dataset) DatasetLoader (class in boltzkit.utils.dataloader)

detect_framework() (in module boltzkit.utils.framework) DihedralAngleEval (class in boltzkit.evaluation.molecular_eval) DomainScaledDatasetLoader (class in boltzkit.utils.dataloader)

E

EnergyEval (class in boltzkit.utils.molecular.energy_eval) EnergyHistEval (class in boltzkit.evaluation.eval) eval() (boltzkit.evaluation.eval.Evaluation method) EvalData (class in boltzkit.evaluation.eval)

evaluate_batch() (boltzkit.utils.molecular.energy_eval.EnergyEval method) (boltzkit.utils.molecular.energy_eval.ParallelEnergyEval method) (boltzkit.utils.molecular.energy_eval.SequentialEnergyEval method) evaluate_energy_single() (in module boltzkit.utils.molecular.energy_eval) Evaluation (class in boltzkit.evaluation.eval)

F

FileKV (class in boltzkit.utils.key_value_store) filter_z_matrix_columns() (in module boltzkit.utils.molecular.marginals) find_file() (boltzkit.utils.cached_repo.CachedRepo method) find_rings() (in module boltzkit.utils.molecular.z_matrix_factory) fits_requirements() (boltzkit.evaluation.eval.EvalData method) fixed (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory attribute) (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory property)

fixed_atom_names() (in module boltzkit.utils.molecular.pdbpatch) FrameworkAgnosticFunction (class in boltzkit.utils.framework) from_numpy() (in module boltzkit.utils.framework) from_numpy_recursive() (in module boltzkit.utils.framework) from_path() (boltzkit.utils.molecular.tica.TicaModelWithLengthScale class method)

G

get() (boltzkit.utils.key_value_store.FileKV method) get_alpha_divergence_p() (in module boltzkit.evaluation.density_based.divergence) get_alpha_divergence_q() (in module boltzkit.evaluation.density_based.divergence) get_approximate_absolute_counts() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) get_as_density() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) get_balanced_grid() (in module boltzkit.utils.shape_utils) get_bin_area() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) get_bin_centers() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) get_bond_angle_hist() (in module boltzkit.evaluation.sample_based.internal_coordinate_eval) get_bond_angles() (in module boltzkit.utils.molecular.marginals) get_bond_length_hist() (in module boltzkit.evaluation.sample_based.internal_coordinate_eval) get_bond_lengths() (in module boltzkit.utils.molecular.marginals) get_cached_key_value_store() (boltzkit.utils.cached_repo.CachedRepo method) get_dihedral_angle_hist() (in module boltzkit.evaluation.sample_based.internal_coordinate_eval) get_dihedral_angles() (in module boltzkit.utils.molecular.marginals) get_elbo() (in module boltzkit.evaluation.density_based.evidence) get_energies() (boltzkit.utils.dataset.Dataset method) get_eubo() (in module boltzkit.evaluation.density_based.evidence) get_euclidean_wasserstein_1_2() (in module boltzkit.evaluation.sample_based.wasserstein) get_extend() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) get_forces() (boltzkit.utils.dataset.Dataset method) get_forward_ess() (in module boltzkit.evaluation.density_based.ess) get_forward_logZ() (in module boltzkit.evaluation.density_based.divergence) get_free_energy_difference() (in module boltzkit.evaluation.sample_based.torsion_marginals) get_grad() (boltzkit.utils.framework.FrameworkAgnosticFunction method) get_histogram_1d() (in module boltzkit.utils.histogram) get_histogram_2d() (in module boltzkit.utils.histogram) get_histogram_fwd_kullback_leibler() (in module boltzkit.evaluation.sample_based.histogram_comparison) get_histogram_jensen_shannon_divergence() (in module boltzkit.evaluation.sample_based.histogram_comparison) get_histogram_metrics() (in module boltzkit.evaluation.sample_based.histogram_comparison) get_histogram_total_variation_distance() (in module boltzkit.evaluation.sample_based.histogram_comparison)

get_histograms() (in module boltzkit.evaluation.eval) get_kl_divergence_p() (in module boltzkit.evaluation.density_based.divergence) get_kl_divergence_q() (in module boltzkit.evaluation.density_based.divergence) get_log_probs() (boltzkit.utils.dataset.Dataset method) get_missing_requirements() (boltzkit.evaluation.eval.EvalData method) get_name_from_uri() (boltzkit.utils.cached_repo.CachedRepo class method) (boltzkit.utils.cached_repo.HuggingfaceRepo class method) (boltzkit.utils.cached_repo.LocalRepo class method) (boltzkit.utils.cached_repo.VirtualRepo class method) get_nll() (in module boltzkit.evaluation.density_based.evidence) get_normalized_counts() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) get_num_bins() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) get_openmm_platform() (in module boltzkit.utils.molecular.energy_eval) get_pdfs() (in module boltzkit.evaluation.eval) get_phi_psi_vectors() (in module boltzkit.utils.molecular.marginals) get_reduced_energy_hist() (in module boltzkit.evaluation.sample_based.energy_histogram) get_required_fields() (boltzkit.evaluation.eval.EvalData method) get_reverse_ess() (in module boltzkit.evaluation.density_based.ess) get_reverse_logZ() (in module boltzkit.evaluation.density_based.divergence) get_samples() (boltzkit.utils.dataset.Dataset method) get_scalar_metrics() (in module boltzkit.evaluation.eval) get_scores() (boltzkit.utils.dataset.Dataset method) get_shannon_entropy() (in module boltzkit.evaluation.density_based.entropy) get_tica_features() (in module boltzkit.utils.molecular.tica) get_tica_hist() (in module boltzkit.evaluation.sample_based.tica) get_tica_wasserstein_1_2() (in module boltzkit.evaluation.sample_based.tica) get_torsion_angles() (in module boltzkit.evaluation.sample_based.torsion_marginals) get_torsion_marginal_hists() (in module boltzkit.evaluation.sample_based.torsion_marginals) get_torus_wasserstein() (in module boltzkit.evaluation.sample_based.wasserstein) get_torus_wasserstein_2() (in module boltzkit.evaluation.sample_based.torsion_marginals) get_trajectory() (in module boltzkit.utils.molecular.marginals) get_tsallis_entropy() (in module boltzkit.evaluation.density_based.entropy) get_value() (boltzkit.utils.framework.FrameworkAgnosticFunction method) get_value_and_grad() (boltzkit.utils.framework.FrameworkAgnosticFunction method)

H

Histogram1D (class in boltzkit.utils.histogram) Histogram2D (class in boltzkit.utils.histogram)

HistogramMetric (class in boltzkit.evaluation.sample_based.histogram_comparison) HuggingfaceRepo (class in boltzkit.utils.cached_repo)

I

id (boltzkit.evaluation.sample_based.histogram_comparison.HistogramMetric property) (boltzkit.utils.histogram.VisualizationMode property) integrate_langevin() (in module boltzkit.utils.langevin) integrate_langevin_middle() (in module boltzkit.utils.langevin) is_chiral_torsion() (in module boltzkit.utils.molecular.z_matrix_factory) is_independent() (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory static method)

is_jax_array() (in module boltzkit.utils.framework) is_methyl_torsion() (in module boltzkit.utils.molecular.z_matrix_factory) is_proper_torsion() (in module boltzkit.utils.molecular.z_matrix_factory) is_ramachandran_torsion() (in module boltzkit.utils.molecular.z_matrix_factory) is_ring_torsion() (in module boltzkit.utils.molecular.z_matrix_factory) is_torch_tensor() (in module boltzkit.utils.framework) is_type_torsion() (in module boltzkit.utils.molecular.z_matrix_factory)

L

list_remote_files() (boltzkit.utils.cached_repo.CachedRepo method) (boltzkit.utils.cached_repo.HuggingfaceRepo method) (boltzkit.utils.cached_repo.LocalRepo method) (boltzkit.utils.cached_repo.VirtualRepo method) load_all_files() (boltzkit.utils.cached_repo.CachedRepo method) (boltzkit.utils.cached_repo.HuggingfaceRepo method) (boltzkit.utils.cached_repo.LocalRepo method) (boltzkit.utils.cached_repo.VirtualRepo method) load_dataset() (boltzkit.utils.dataloader.CachedRepoDatasetLoader method) (boltzkit.utils.dataloader.DatasetLoader method) (boltzkit.utils.dataloader.DomainScaledDatasetLoader method)

load_file() (boltzkit.utils.cached_repo.CachedRepo method) (boltzkit.utils.cached_repo.HuggingfaceRepo method) (boltzkit.utils.cached_repo.LocalRepo method) (boltzkit.utils.cached_repo.VirtualRepo method) load_from_file() (in module boltzkit.utils.dataloader) load_histogram() (in module boltzkit.utils.histogram) load_tica_model() (in module boltzkit.utils.dataloader) load_topology() (in module boltzkit.utils.dataloader) local_path (boltzkit.utils.cached_repo.CachedRepo attribute) (boltzkit.utils.cached_repo.CachedRepo property) LocalRepo (class in boltzkit.utils.cached_repo)

M

make_agnostic() (in module boltzkit.utils.framework) make_agnostic_simple() (in module boltzkit.utils.framework) make_wandb_compatible() (in module boltzkit.evaluation.eval) match_uri() (boltzkit.utils.cached_repo.CachedRepo class method) (boltzkit.utils.cached_repo.HuggingfaceRepo class method) (boltzkit.utils.cached_repo.LocalRepo class method) (boltzkit.utils.cached_repo.VirtualRepo class method) matplotlib_to_pdf_buffer() (in module boltzkit.utils.pdf) ModelShannonEntropyEval (class in boltzkit.evaluation.eval) module boltzkit boltzkit.evaluation boltzkit.evaluation.density_based boltzkit.evaluation.density_based.divergence boltzkit.evaluation.density_based.entropy boltzkit.evaluation.density_based.ess boltzkit.evaluation.density_based.evidence boltzkit.evaluation.eval boltzkit.evaluation.molecular_eval boltzkit.evaluation.sample_based boltzkit.evaluation.sample_based.energy_histogram boltzkit.evaluation.sample_based.histogram_comparison boltzkit.evaluation.sample_based.internal_coordinate_eval boltzkit.evaluation.sample_based.tica boltzkit.evaluation.sample_based.torsion_marginals boltzkit.evaluation.sample_based.wasserstein boltzkit.targets boltzkit.targets.many_well boltzkit.utils boltzkit.utils.cached_repo boltzkit.utils.dataloader boltzkit.utils.dataset boltzkit.utils.framework boltzkit.utils.histogram boltzkit.utils.key_value_store boltzkit.utils.langevin boltzkit.utils.molecular boltzkit.utils.molecular.augmentation boltzkit.utils.molecular.conversion boltzkit.utils.molecular.energy_eval boltzkit.utils.molecular.marginals boltzkit.utils.molecular.pdbpatch boltzkit.utils.molecular.plot_molecule boltzkit.utils.molecular.tica boltzkit.utils.molecular.z_matrix_factory boltzkit.utils.molecular.z_matrix_templates boltzkit.utils.pdf boltzkit.utils.shape_utils

N

n_producing_samples (boltzkit.utils.histogram.Histogram1D property) (boltzkit.utils.histogram.Histogram2D property)

NllEval (class in boltzkit.evaluation.eval) normalize_path() (in module boltzkit.utils.cached_repo) numpy_to_vec3_list() (in module boltzkit.utils.molecular.conversion)

P

ParallelEnergyEval (class in boltzkit.utils.molecular.energy_eval) pdf_to_pillow_image() (in module boltzkit.utils.pdf) pdf_to_wandb_image() (in module boltzkit.utils.pdf) PdfBuffer (class in boltzkit.utils.pdf) plot_as_density() (in module boltzkit.utils.histogram) plot_as_free_energy() (in module boltzkit.utils.histogram)

plot_as_log_density() (in module boltzkit.utils.histogram) plot_matplotlib_molecule() (in module boltzkit.utils.molecular.plot_molecule) plot_pdf() (in module boltzkit.utils.pdf) post_init() (boltzkit.utils.cached_repo.CachedRepo method) pred_samples_model_log_prob (boltzkit.evaluation.eval.EvalData attribute) pred_samples_target_log_prob (boltzkit.evaluation.eval.EvalData attribute) project_from_cartesian() (boltzkit.utils.molecular.tica.TicaModelWithLengthScale method)

R

remote_uri (boltzkit.utils.cached_repo.CachedRepo attribute) (boltzkit.utils.cached_repo.CachedRepo property) render_independent() (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory method) requirements (boltzkit.evaluation.eval.EnergyHistEval attribute) (boltzkit.evaluation.eval.Evaluation attribute) (boltzkit.evaluation.eval.ModelShannonEntropyEval attribute) (boltzkit.evaluation.eval.NllEval attribute) (boltzkit.evaluation.eval.ReverseLogWeightsEval attribute) (boltzkit.evaluation.molecular_eval.BondAngleEval attribute) (boltzkit.evaluation.molecular_eval.BondLengthEval attribute) (boltzkit.evaluation.molecular_eval.DihedralAngleEval attribute) (boltzkit.evaluation.molecular_eval.TicaEval attribute) (boltzkit.evaluation.molecular_eval.TorsionMarginalEval attribute)

ReverseLogWeightsEval (class in boltzkit.evaluation.eval) rewire_chiral_torsions() (in module boltzkit.utils.molecular.z_matrix_factory) run_eval() (in module boltzkit.evaluation.eval)

S

samples_pred (boltzkit.evaluation.eval.EvalData attribute) samples_true (boltzkit.evaluation.eval.EvalData attribute) save() (boltzkit.utils.histogram.Histogram1D method) (boltzkit.utils.histogram.Histogram2D method) save_histograms() (in module boltzkit.utils.histogram) save_pdf() (in module boltzkit.utils.pdf)

save_pdfs() (in module boltzkit.utils.pdf) scale_domain() (boltzkit.utils.dataset.Dataset method) SequentialEnergyEval (class in boltzkit.utils.molecular.energy_eval) set() (boltzkit.utils.key_value_store.FileKV method) size (boltzkit.utils.dataset.Dataset property) squeeze_last_dim() (in module boltzkit.utils.shape_utils) strip_repo_prefix() (in module boltzkit.utils.cached_repo)

T

TicaEval (class in boltzkit.evaluation.molecular_eval) TicaModelWithLengthScale (class in boltzkit.utils.molecular.tica) to_free_energy() (in module boltzkit.utils.molecular.conversion) to_numpy() (in module boltzkit.utils.framework) to_numpy_recursive() (in module boltzkit.utils.framework)

TorsionMarginalEval (class in boltzkit.evaluation.molecular_eval) true_samples_model_log_prob (boltzkit.evaluation.eval.EvalData attribute) true_samples_target_log_prob (boltzkit.evaluation.eval.EvalData attribute) try_jit_jax() (in module boltzkit.utils.framework) try_load_dataset() (boltzkit.utils.dataloader.DatasetLoader method) try_load_file() (boltzkit.utils.cached_repo.CachedRepo method)

U

update_dict_with_id() (in module boltzkit.evaluation.eval)

V

vec3_list_to_numpy() (in module boltzkit.utils.molecular.conversion) VirtualRepo (class in boltzkit.utils.cached_repo) VisualizationMode (class in boltzkit.utils.histogram) visualize_energy_hist_dual() (in module boltzkit.evaluation.sample_based.energy_histogram) visualize_histogram_1d() (in module boltzkit.utils.histogram)

visualize_histogram_2d() (in module boltzkit.utils.histogram) visualize_histograms() (in module boltzkit.utils.histogram) visualize_tica() (in module boltzkit.evaluation.sample_based.tica) visualize_tica_true_and_pred() (in module boltzkit.evaluation.sample_based.tica) visualize_torsion_marginals_all() (in module boltzkit.evaluation.sample_based.torsion_marginals) visualize_torsion_marginals_dual() (in module boltzkit.evaluation.sample_based.torsion_marginals)

Z

z_matrix (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory attribute) (boltzkit.utils.molecular.z_matrix_factory.ZMatrixFactory property)

ZMatrixFactory (class in boltzkit.utils.molecular.z_matrix_factory)