Index

_

__init__() (AdaLayerNorm method) (AttentionPooling method) (BME method) (BMEResult method) (BondConstraint method) (Candidate method) (Constraint method) (ConstraintLogger method) (ContinuousDiffusion method) (CosineSimFilter method) (CrossAttention method) (CrossAttentionResnetLayer method) (DDIMSampler method) (DDPMSampler method) (DiagonalGaussianDistribution method) (DiffusionModel method) (DistanceConstraint method) (DiTBlock method) (Downsample method) (DownsampleBlock method) (EMA method) (Ensemble method) (ExactMatchFilter method) (ExperimentalObservable method) (FeedForward method) (GeGLU method) (HelicityConstraint method) (IndexBuilder method) (KLDWeightScheduler method) (L2DistanceFilter method) (LayerNorm method) (LearnablePositionalEncoding1D method) (LearnablePositionalEncoding2D method) (LengthFilter method) (MinPool2d method) (MLP method) (ModelManager method) (MultiConstraint method) (MultiHeadAttention method) (PatchEmbed method) (PLMSSampler method) (PositionalEncoding1D method) (PositionalEncoding2D method) (ReConstraint method) (ResBlockDecBasic method) (ResBlockDecBottleneck method) (ResBlockEncBasic method) (ResBlockEncBottleneck method) (ResizeConv2d method) (ResNet_Decoder method) (ResNet_Decoder_Original method) (ResNet_Encoder method) (ResNet_Encoder_Original method) (ResnetLayer method) (RgConstraint method) (RMSNorm method) (ScoreConverter method) (SearchEngine method) (SelfAttention method) (SelfAttentionConv method) (SequenceEncoder method) (SequenceIdentityFilter method) (SinusoidalPosEmb method), [1] (SpatialTransformer method) (StarlingTokenizer method) (StericClashConstraint method) (ThetaScanResult method) (TransformerEncoder method) (UNetConditional method) (UpsampleBlock method) (VAE method) (vanilla_Decoder method) (vanilla_Encoder method) (VectorQuantizer2 method) (ViT method)

A

aa_to_int (StarlingTokenizer attribute) AdaLayerNorm (class in starling.models.transformer) alpha_cosine_log_snr() (in module starling.models.continuous_diffusion) apply() (CandidateFilter method) (Constraint method) (CosineSimFilter method) (ExactMatchFilter method) (L2DistanceFilter method) (LengthFilter method) (SequenceIdentityFilter method) (ValidGidFilter method)

as_tuple() (Candidate method) AttentionPooling (class in starling.models.attention)

B

bell_shaped_schedule() (Constraint method) benchmark_methods() (in module starling.inference.benchmark_mds) beta_linear_log_snr() (in module starling.models.continuous_diffusion) BME (class in starling.structure.bme) bme_result (Ensemble property)

BMEResult (class in starling.structure.bme_utils) BondConstraint (class in starling.inference.constraints) build_ensemble_trajectory() (Ensemble method) build_index() (in module starling.search) (IndexBuilder method) build_sequence_store() (IndexBuilder method)

C

calculated_values (BMEResult attribute) Candidate (class in starling.search.search_utils) CandidateFilter (class in starling.search.search_utils) check_device() (in module starling.utilities) check_distance_map_for_error() (in module starling.utilities) check_file_exists() (in module starling.utilities) check_for_errors() (Ensemble method) check_for_errors_trajectory() (Ensemble method) check_positive_int() (in module starling.frontend.ensemble_generation) chi_squared_final (BMEResult attribute) chi_squared_initial (BMEResult attribute) chi_squared_values (ThetaScanResult attribute) close() (ConstraintLogger method) (SequenceStore method) close_publish() (SequenceStore method) compare_distance_matrices() (in module starling.structure.coordinates) compile() (ModelManager method) compute_loss() (BondConstraint method) (Constraint method) (DistanceConstraint method) (HelicityConstraint method) (MultiConstraint method) (ReConstraint method) (RgConstraint method) (StericClashConstraint method)

compute_pairwise_distances() (in module starling.structure.coordinates) compute_snr() (DiffusionModel method) ConditionalSequential (class in starling.models.unet) (class in starling.models.vae_components) configure() (KLDWeightScheduler method) configure_optimizers() (ContinuousDiffusion method) (DiffusionModel method) (VAE method) Constraint (class in starling.inference.constraints) constraint (ExperimentalObservable attribute) ConstraintLogger (class in starling.inference.constraints) contact_map() (Ensemble method) ContinuousDiffusion (class in starling.models.continuous_diffusion) contraction (ResBlockDecBasic attribute) (ResBlockDecBottleneck attribute) convert() (ScoreConverter method) cosine_beta_schedule() (in module starling.data.schedulers) cosine_weight() (Constraint method) CosineSimFilter (class in starling.search.search_utils) create_ca_topology_from_coords() (in module starling.structure.coordinates) create_incremental_coordinates() (in module starling.structure.coordinates) CrossAttention (class in starling.models.attention) CrossAttentionResnetLayer (class in starling.models.unet) current_weight (KLDWeightScheduler property)

D

DDIMSampler (class in starling.samplers.ddim_sampler) DDPMSampler (class in starling.samplers.ddpm_sampler) decode() (StarlingTokenizer method) (VAE method) decode_header() (SequenceStore static method) decode_seq() (SequenceStore static method) default() (in module starling.models.continuous_diffusion) device (ContinuousDiffusion property) diagnostics() (BMEResult method) DiagonalGaussianDistribution (class in starling.data.distributions)

DiffusionModel (class in starling.models.diffusion) distance_maps() (Ensemble method) distance_matrix_to_3d_structure_gd() (in module starling.structure.coordinates) distance_matrix_to_3d_structure_mds() (in module starling.structure.coordinates) distance_matrix_to_3d_structure_torch_mds() (in module starling.structure.coordinates) DistanceConstraint (class in starling.inference.constraints) DiTBlock (class in starling.models.transformer) Downsample (class in starling.models.unet) DownsampleBlock (class in starling.models.blocks) dynamic_thresholding_fn() (in module starling.samplers.plms_sampler)

E

EMA (class in starling.models.ema) encode() (StarlingTokenizer method) (VAE method) encode_header() (SequenceStore static method) encode_seq() (SequenceStore static method) end_to_end_distance() (Ensemble method) Ensemble (class in starling.structure.ensemble) ensemble_encoder() (in module starling.frontend.ensemble_generation)

ensemble_encoder_backend() (in module starling.inference.generation) ensure_search_artifacts() (in module starling.configs) ExactMatchFilter (class in starling.search.search_utils) exists() (in module starling.models.continuous_diffusion) expansion (ResBlockEncBasic attribute) (ResBlockEncBottleneck attribute) ExperimentalObservable (class in starling.structure.bme_utils) extract() (in module starling.models.diffusion) (in module starling.samplers.ddpm_sampler)

F

FeedForward (class in starling.models.transformer) finches_potential_energy() (in module starling.inference.evaluate_vae) find_optimal_theta() (in module starling.structure.bme_utils) fit() (BME method) fix_ref_to_home() (in module starling.utilities) forward() (AdaLayerNorm method) (AttentionPooling method) (ConditionalSequential method), [1] (ContinuousDiffusion method) (CrossAttention method) (CrossAttentionResnetLayer method) (DiffusionModel method) (DiTBlock method) (Downsample method) (DownsampleBlock method) (FeedForward method) (GeGLU method) (LayerNorm method) (LearnablePositionalEncoding1D method) (LearnablePositionalEncoding2D method) (MinPool2d method) (MLP method) (MultiHeadAttention method) (PatchEmbed method) (PositionalEncoding1D method) (PositionalEncoding2D method) (ResBlockDecBasic method) (ResBlockDecBottleneck method) (ResBlockEncBasic method) (ResBlockEncBottleneck method) (ResizeConv2d method) (ResNet_Decoder method) (ResNet_Decoder_Original method) (ResNet_Encoder method) (ResNet_Encoder_Original method) (ResnetLayer method) (RMSNorm method) (SelfAttention method) (SelfAttentionConv method) (SequenceEncoder method) (SinusoidalPosEmb method), [1] (SpatialTransformer method) (TransformerEncoder method) (UNetConditional method) (UpsampleBlock method) (VAE method) (vanilla_Decoder method) (vanilla_Encoder method) (VectorQuantizer2 method) (ViT method)

G

gaussian_likelihood() (VAE method) GeGLU (class in starling.models.transformer) generate() (in module starling) (in module starling.frontend.ensemble_generation) generate_3d_coordinates_from_distances() (in module starling.structure.coordinates) generate_backend() (in module starling.inference.generation) generate_labels() (DDIMSampler method) (DDPMSampler method) (PLMSSampler method) generate_pe() (PositionalEncoding2D method) get_adaptive_clip_threshold() (Constraint method) get_bounds() (ExperimentalObservable method) get_checkpoint_path() (in module starling.training.vae_train) get_codebook_entry() (VectorQuantizer2 method) get_data() (in module starling.utilities) get_errors() (in module starling.inference.evaluate_vae) get_gids_by_length_range() (SequenceStore method) get_header_len() (SequenceStore method) get_macOS_version() (in module starling.utilities)

get_many_header_len() (SequenceStore method) get_many_meta() (SequenceStore method) get_models() (ModelManager method) get_name() (CandidateFilter method) (CosineSimFilter method) (ExactMatchFilter method) (L2DistanceFilter method) (LengthFilter method) (SequenceIdentityFilter method) (ValidGidFilter method) get_off_diagonals() (in module starling.utilities) get_params() (in module starling.data.argument_parser) get_seq() (SequenceStore method) get_tensor_dtype() (in module starling.structure.coordinates) get_time_scale() (Constraint method) get_vae_params() (in module starling.data.argument_parser) get_weight() (KLDWeightScheduler method) get_x_prev_and_pred_x0() (DDIMSampler method) gid (Candidate attribute)

H

handle_input() (in module starling.frontend.ensemble_generation) has_bme_weights (Ensemble property) has_structures (Ensemble property) hash8() (SequenceStore static method)

header (Candidate attribute) HelicityConstraint (class in starling.inference.constraints) helix_dm() (in module starling.utilities) hydrodynamic_radius() (Ensemble method)

I

IndexBuilder (class in starling.search.builder) initial_weights (BMEResult attribute) initialize() (Constraint method) (MultiConstraint method)

insert_rows() (SequenceStore method) instance_norm() (in module starling.models.blocks) int_to_aa (StarlingTokenizer attribute) int_to_seq() (in module starling.inference.evaluate_vae)

K

karras_log_snr() (in module starling.models.continuous_diffusion) kl() (DiagonalGaussianDistribution method)

kl_divergence (BMEResult property) kl_divergence_values (ThetaScanResult attribute) KLDWeightScheduler (class in starling.models.vae)

L

L2DistanceFilter (class in starling.search.search_utils) lambdas (BMEResult attribute) layer_norm() (in module starling.models.blocks) LayerNorm (class in starling.models.blocks) LearnablePositionalEncoding1D (class in starling.data.positional_encodings) LearnablePositionalEncoding2D (class in starling.data.positional_encodings) length (Candidate attribute) LengthFilter (class in starling.search.search_utils) linear_beta_schedule() (in module starling.data.schedulers) load() (SearchEngine class method)

load_engine() (in module starling.search) load_ensemble() (in module starling) (in module starling.structure.ensemble) load_hdf5_compressed() (in module starling.data.data_wrangler) (in module starling.inference.evaluate_vae) load_models() (ModelManager method) load_user_config() (in module starling.configs) local_radius_of_gyration() (Ensemble method) log() (in module starling.models.continuous_diffusion) loss_function() (in module starling.structure.coordinates)

M

main() (in module starling.inference.evaluate_vae) make_ddim_sampling_parameters() (in module starling.samplers.plms_sampler) max_weight (KLDWeightScheduler property) MaxPad() (in module starling.data.data_wrangler) message (BMEResult attribute) metadata (BMEResult attribute) method (ThetaScanResult attribute) MinPool2d (class in starling.models.blocks) MLP (class in starling.models.transformer) mode() (DiagonalGaussianDistribution method) ModelManager (class in starling.inference.model_loading) module starling.configs starling.data.argument_parser starling.data.data_wrangler starling.data.distributions starling.data.positional_encodings starling.data.schedulers starling.data.tokenizer starling.frontend.ensemble_generation starling.frontend.starling_viz starling.inference starling.inference.benchmark_mds starling.inference.constraints starling.inference.evaluate_vae starling.inference.generation starling.inference.model_loading starling.models.attention starling.models.blocks starling.models.continuous_diffusion starling.models.diffusion starling.models.ema starling.models.normalization starling.models.quantize starling.models.resnets_original starling.models.transformer starling.models.unet starling.models.vae starling.models.vae_components starling.models.vit starling.samplers.ddim_sampler starling.samplers.ddpm_sampler starling.samplers.plms_sampler starling.search starling.search.builder starling.search.search_engine starling.search.search_utils starling.search.similarity_search starling.search.store starling.structure.bme starling.structure.bme_utils starling.structure.coordinates starling.structure.ensemble starling.training starling.training.vae_train starling.utilities

MultiConstraint (class in starling.inference.constraints) MultiHeadAttention (class in starling.models.attention)

N

n_iterations (BMEResult attribute)

name (ExperimentalObservable attribute) nll() (DiagonalGaussianDistribution method)

O

observables (BMEResult attribute) on_train_epoch_end() (VAE method) on_train_start() (VAE method) one_hot_encode() (in module starling.data.data_wrangler)

open_reader() (SequenceStore class method) open_writer() (SequenceStore class method) optimal_idx (ThetaScanResult attribute) optimal_theta (ThetaScanResult attribute)

P

p_loss() (DiffusionModel method) p_losses() (ContinuousDiffusion method) p_sample() (DDIMSampler method) (DDPMSampler method) p_sample_loop() (DDPMSampler method) p_sample_plms() (PLMSSampler method) parse_output_path() (in module starling.utilities) PatchEmbed (class in starling.models.vit) phi (BMEResult attribute) phi_values (ThetaScanResult attribute) PLMSSampler (class in starling.samplers.plms_sampler)

plot() (ThetaScanResult method) plot_error_distributions() (in module starling.inference.benchmark_mds) plot_matrices() (in module starling.frontend.starling_viz) plot_protein_arcs() (in module starling.frontend.starling_viz) plot_timing_comparison() (in module starling.inference.benchmark_mds) PositionalEncoding1D (class in starling.data.positional_encodings) PositionalEncoding2D (class in starling.data.positional_encodings) predict() (BME method) prepare_data() (in module starling.inference.evaluate_vae) print_diagnostics() (BMEResult method) print_summary() (ThetaScanResult method)

Q

q_sample() (ContinuousDiffusion method) (DiffusionModel method)

R

radius_of_gyration() (Ensemble method) random_times() (ContinuousDiffusion method) read_input_file() (in module starling.inference.evaluate_vae) read_starling_ensemble() (in module starling.utilities) read_tsv_file() (in module starling.data.data_wrangler) ReConstraint (class in starling.inference.constraints) reconstruct() (in module starling.inference.evaluate_vae) remap_to_used() (VectorQuantizer2 method) remove_extension() (in module starling.utilities) reparameterize() (VAE method) ResBlockDecBasic (class in starling.models.blocks) ResBlockDecBottleneck (class in starling.models.blocks) ResBlockEncBasic (class in starling.models.blocks) ResBlockEncBottleneck (class in starling.models.blocks) reset_parameters() (EMA method) ResizeConv2d (class in starling.models.blocks) Resnet101_Decoder() (in module starling.models.resnets_original) Resnet101_Encoder() (in module starling.models.resnets_original) Resnet152_Decoder() (in module starling.models.resnets_original) Resnet152_Encoder() (in module starling.models.resnets_original) Resnet18_Decoder() (in module starling.models.resnets_original) (in module starling.models.vae_components)

Resnet18_Encoder() (in module starling.models.resnets_original) (in module starling.models.vae_components) Resnet34_Decoder() (in module starling.models.resnets_original) (in module starling.models.vae_components) Resnet34_Encoder() (in module starling.models.resnets_original) (in module starling.models.vae_components) Resnet50_Decoder() (in module starling.models.resnets_original) Resnet50_Encoder() (in module starling.models.resnets_original) ResNet_Decoder (class in starling.models.vae_components) ResNet_Decoder_Original (class in starling.models.resnets_original) ResNet_Encoder (class in starling.models.vae_components) ResNet_Encoder_Original (class in starling.models.resnets_original) ResnetLayer (class in starling.models.unet) result (BME property) results (ThetaScanResult attribute) reweight_bme() (Ensemble method) RgConstraint (class in starling.inference.constraints) right_pad_dims_to() (in module starling.models.continuous_diffusion) rij() (Ensemble method) RMSNorm (class in starling.models.normalization) run_benchmark_comparison() (in module starling.inference.benchmark_mds)

S

sample() (DDIMSampler method) (DDPMSampler method) (DiagonalGaussianDistribution method) (PLMSSampler method) sample_vectors() (IndexBuilder method) save() (Ensemble method) save_config() (in module starling.training.vae_train) save_index() (IndexBuilder method) save_manifest() (IndexBuilder method) save_trajectory() (Ensemble method) (in module starling.structure.coordinates) scan_theta() (BME method) SCHEDULER_MAPPING (DiffusionModel attribute) score (Candidate attribute) ScoreConverter (class in starling.search.search_utils) search() (SearchEngine method) SearchEngine (class in starling.search.search_engine) SelfAttention (class in starling.models.attention) SelfAttentionConv (class in starling.models.attention) sequence2labels() (ContinuousDiffusion method) (DiffusionModel method) sequence_encoder() (in module starling) (in module starling.frontend.ensemble_generation) sequence_encoder_backend() (in module starling.inference.generation) SequenceEncoder (class in starling.models.transformer) SequenceIdentityFilter (class in starling.search.search_utils) SequenceStore (class in starling.search.store) set_compilation_options() (in module starling) setup() (ConstraintLogger method) (VAE method) setup_checkpoints() (in module starling.training.vae_train) setup_data_module() (in module starling.training.vae_train) setup_directories() (in module starling.training.vae_train) setup_vae_model() (in module starling.training.vae_train) should_apply_guidance() (Constraint method) sigmoid_beta_schedule() (in module starling.data.schedulers) SinusoidalPosEmb (class in starling.models.transformer) (class in starling.models.unet) SpatialTransformer (class in starling.models.transformer) starling.configs module starling.data.argument_parser module starling.data.data_wrangler module starling.data.distributions module starling.data.positional_encodings module starling.data.schedulers module starling.data.tokenizer module starling.frontend.ensemble_generation module starling.frontend.starling_viz module starling.inference module starling.inference.benchmark_mds module starling.inference.constraints module starling.inference.evaluate_vae module starling.inference.generation module starling.inference.model_loading module

starling.models.attention module starling.models.blocks module starling.models.continuous_diffusion module starling.models.diffusion module starling.models.ema module starling.models.normalization module starling.models.quantize module starling.models.resnets_original module starling.models.transformer module starling.models.unet module starling.models.vae module starling.models.vae_components module starling.models.vit module starling.samplers.ddim_sampler module starling.samplers.ddpm_sampler module starling.samplers.plms_sampler module starling.search module starling.search.builder module starling.search.search_engine module starling.search.search_utils module starling.search.similarity_search module starling.search.store module starling.structure.bme module starling.structure.bme_utils module starling.structure.coordinates module starling.structure.ensemble module starling.training module starling.training.vae_train module starling.utilities module StarlingTokenizer (class in starling.data.tokenizer) step_ema() (EMA method) StericClashConstraint (class in starling.inference.constraints) stored_hash (Candidate attribute) success (BMEResult attribute) symmetrize() (in module starling.data.data_wrangler) (in module starling.inference.evaluate_vae) (VAE method) symmetrize_distance_map() (in module starling.inference.generation) symmetrize_distance_maps() (in module starling.inference.constraints) (in module starling.utilities)

T

theta (BME property) (BMEResult attribute) theta_scan() (in module starling.structure.bme_utils) theta_scan_result (BME property) (Ensemble property) theta_values (ThetaScanResult attribute) ThetaScanResult (class in starling.structure.bme_utils)

to_score() (ScoreConverter method) to_similarity() (ScoreConverter method) training_step() (ContinuousDiffusion method) (DiffusionModel method) (VAE method) trajectory (Ensemble property) TransformerEncoder (class in starling.models.transformer)

U

uncertainty (ExperimentalObservable attribute) UNetConditional (class in starling.models.unet) unmap_to_all() (VectorQuantizer2 method)

update() (ConstraintLogger method) update_average() (EMA method) update_model_average() (EMA method) UpsampleBlock (class in starling.models.blocks)

V

VAE (class in starling.models.vae) vae_loss() (VAE method) validation_step() (ContinuousDiffusion method) (DiffusionModel method) (VAE method) ValidGidFilter (class in starling.search.search_utils)

value (ExperimentalObservable attribute) vanilla_Decoder (class in starling.models.blocks) vanilla_Encoder (class in starling.models.blocks) VectorQuantizer2 (class in starling.models.quantize) view_theta_scan() (Ensemble method) visualize_comparison() (in module starling.inference.benchmark_mds) ViT (class in starling.models.vit)

W

wandb_init() (in module starling.training.vae_train)

weights (BMEResult attribute) write_starling_ensemble() (in module starling.utilities)