Index _ | A | B | C | D | E | F | G | H | I | J | K | L | M | N | O | P | Q | R | S | T | U | V | W _ __class_vars__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __del__() (pallatom.helpers.data.ProteinDataset method) __getitem__() (pallatom.helpers.data.ProteinDataset method) __getstate__() (pallatom.helpers.data.ProteinDataset method) __len__() (pallatom.helpers.data.ProteinDataset method) __private_attributes__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_complete__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_computed_fields__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_core_schema__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_custom_init__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_decorators__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_extra__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_fields__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_fields_set__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_generic_metadata__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_parent_namespace__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_post_init__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_private__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_root_model__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_serializer__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __pydantic_validator__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) __signature__ (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.AtomDistogramParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) A aa_embedding (pallatom.architecture.main_trunk.MainTrunk attribute) aa_indices (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.AllAtomContext attribute) aatype (pallatom.helpers.atom_utils.Protein attribute) AllAtomContext (class in sampling) alpha_0 (train_config.LossParams attribute) alpha_1 (train_config.LossParams attribute) alpha_2 (train_config.LossParams attribute) alpha_3 (train_config.LossParams attribute) alpha_4 (train_config.LossParams attribute) apply_conditioning_dropout() (in module pallatom.helpers.featurize) apply_transform() (in module pallatom.helpers.alignment) ATOM37_C (in module pallatom.helpers.atom_utils) ATOM37_CA (in module pallatom.helpers.atom_utils) ATOM37_CB (in module pallatom.helpers.atom_utils) ATOM37_N (in module pallatom.helpers.atom_utils) ATOM37_O (in module pallatom.helpers.atom_utils) atom37_to_atom5() (in module pallatom.helpers.atom_utils) atom37_to_cb() (in module pallatom.helpers.atom_utils) ATOM5_C (in module pallatom.helpers.atom_utils) ATOM5_CA (in module pallatom.helpers.atom_utils) ATOM5_CB (in module pallatom.helpers.atom_utils) ATOM5_ELEMENTS (in module pallatom.helpers.atom_utils) atom5_mask (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.AllAtomContext attribute) ATOM5_N (in module pallatom.helpers.atom_utils) ATOM5_NAMES (in module pallatom.helpers.atom_utils) ATOM5_O (in module pallatom.helpers.atom_utils) ATOM5_TO_ATOM37 (in module sampling) atom5_to_atom37() (in module sampling) atom_decoders (pallatom.architecture.main_trunk.MainTrunk attribute) atom_distogram_head (pallatom.architecture.main_trunk.MainTrunk attribute) atom_encoder (pallatom.architecture.main_trunk.MainTrunk attribute) atom_loss() (in module pallatom.architecture.losses) atom_mask (pallatom.helpers.atom_utils.Protein attribute) (pallatom.helpers.featurize.ProteinBatch attribute) atom_positions (pallatom.helpers.atom_utils.Protein attribute) (pallatom.helpers.featurize.ProteinBatch attribute) atom_types (in module pallatom.helpers.atom_utils) AtomAttentionDecoder (class in pallatom.architecture.atom_transformers) AtomDistogramParams (class in train_config) AtomFeatureEncoder (class in pallatom.architecture.atom_transformers) AtomTransformer (class in pallatom.architecture.atom_transformers) AtomTransformerBlock (class in pallatom.architecture.atom_transformers) AttentionPairBias (class in pallatom.architecture.node_update) attn_pair_bias (pallatom.architecture.node_update.NodeUpdate attribute) B b_factors (pallatom.helpers.atom_utils.Protein attribute) batch_size (train_config.LoaderConfig attribute) blocks (pallatom.architecture.atom_transformers.AtomTransformer attribute) (pallatom.architecture.pairformer_stack.PairformerStack attribute) build_AA_context() (in module sampling) build_sampling_context() (in module sampling) build_sparse_pairs() (in module pallatom.architecture.atom_transformers) build_template_context() (in module sampling) C c_atom (train_config.ModelParams attribute) c_atompair (train_config.ModelParams attribute) c_pair (train_config.ModelParams attribute) c_res (train_config.ModelParams attribute) center_positions() (in module pallatom.helpers.atom_utils) center_uid (pallatom.helpers.featurize.FeaturizedBatch attribute) centers (pallatom.architecture.pair_update.TransformRBF attribute) chain_index (pallatom.helpers.atom_utils.Protein attribute) checkpoint (sample_config.SampleConfig attribute) (train_config.TrainConfig attribute) checkpoint_path (sample_config.SampleCheckpointParams attribute) (train_config.CheckpointParams attribute) CheckpointParams (class in train_config) compute_edm_noise_params() (in module pallatom.helpers.compute_EDM_data_params) compute_sigma_data() (in module pallatom.helpers.compute_EDM_data_params) conditioning_dropout (train_config.TrainConfig attribute) ConditioningDropoutConfig (class in train_config) context (sampling.EDMPrecond attribute) D ddim_steps (sample_config.SamplerParams attribute) denoiser (sampling.EDMSampler attribute) Distogram (class in pallatom.helpers.featurize) distogram_atom (train_config.TrainConfig attribute) distogram_loss_atom() (in module pallatom.architecture.losses) distogram_loss_residue() (in module pallatom.architecture.losses) distogram_res (train_config.TrainConfig attribute) drop_col (pallatom.architecture.pair_update.PairUpdate attribute) drop_row (pallatom.architecture.pair_update.PairUpdate attribute) dropout_row (pallatom.architecture.node_update.NodeUpdate attribute) DropoutColumnwise (class in pallatom.architecture.pair_update) DropoutRowwise (class in pallatom.architecture.pair_update) E EDMPrecond (class in sampling) EDMSampler (class in sampling) evaluate() (in module train_loop) evaluate_ddp() (in module train_loop) extra_repr() (pallatom.helpers.featurize.Distogram method) F f_pseudo_beta_mask (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.TemplateContext attribute) f_ref_dim (train_config.ModelParams attribute) f_residue_idx (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.AllAtomContext attribute) f_template_distogram (sampling.TemplateContext attribute) featurize_batch() (in module pallatom.helpers.featurize) FeaturizedBatch (class in pallatom.helpers.featurize) ff1 (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.pair_update.Transition attribute) (pallatom.architecture.pairformer_stack.PairformerBlock attribute) ff2 (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.pair_update.Transition attribute) (pallatom.architecture.pairformer_stack.PairformerBlock attribute) forward() (pallatom.architecture.atom_transformers.AtomAttentionDecoder method) (pallatom.architecture.atom_transformers.AtomFeatureEncoder method) (pallatom.architecture.atom_transformers.AtomTransformer method) (pallatom.architecture.atom_transformers.AtomTransformerBlock method) (pallatom.architecture.main_trunk.MainTrunk method) (pallatom.architecture.node_update.AttentionPairBias method) (pallatom.architecture.node_update.NodeUpdate method) (pallatom.architecture.pair_update.DropoutColumnwise method) (pallatom.architecture.pair_update.DropoutRowwise method) (pallatom.architecture.pair_update.PairUpdate method) (pallatom.architecture.pair_update.TransformRBF method) (pallatom.architecture.pair_update.Transition method) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias method) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias method) (pallatom.architecture.pairformer_stack.PairformerBlock method) (pallatom.architecture.pairformer_stack.PairformerStack method) (pallatom.architecture.template_embedder.TemplateEmbedder method) (pallatom.helpers.featurize.Distogram method) (sampling.EDMPrecond method) G g_col (pallatom.architecture.pairformer_stack.PairformerBlock attribute) g_row (pallatom.architecture.pairformer_stack.PairformerBlock attribute) gamma (train_config.LossParams attribute) generation (sample_config.SampleConfig attribute) GenerationParams (class in sample_config) get_cb_coords() (in module pallatom.helpers.atom_utils) grad_clip (train_config.TrainingParams attribute) gt_atom_distogram_mask_sparse (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.AllAtomContext attribute) gt_atom_distogram_sparse (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.AllAtomContext attribute) gt_res_distogram (pallatom.helpers.featurize.FeaturizedBatch attribute) H head_dim (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) (pallatom.architecture.pairformer_stack.PairformerBlock attribute) I inter_proj_seq (pallatom.architecture.main_trunk.MainTrunk attribute) inter_seq_logits (pallatom.architecture.main_trunk.MainTrunk attribute) J jsonl_path (pallatom.helpers.data.ProteinDataset attribute) K k_col (pallatom.architecture.pairformer_stack.PairformerBlock attribute) k_row (pallatom.architecture.pairformer_stack.PairformerBlock attribute) K_unit (pallatom.architecture.main_trunk.MainTrunk attribute) (train_config.ModelParams attribute) kabsch_align() (in module pallatom.helpers.alignment) kabsch_rmsd() (in module pallatom.helpers.alignment) kabsch_rotation() (in module pallatom.helpers.alignment) L lam (train_config.LossParams attribute) LinearNoBias (class in pallatom.architecture.atom_transformers) loader (train_config.TrainConfig attribute) LoaderConfig (class in train_config) log (in module sampling) (in module train_loop) log_interval (train_config.LoggingParams attribute) logging (train_config.TrainConfig attribute) LoggingParams (class in train_config) loss (train_config.TrainConfig attribute) LossParams (class in train_config) lr (train_config.TrainingParams attribute) M m (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) MainTrunk (class in pallatom.architecture.main_trunk) make_data_loaders() (in module pallatom.helpers.data) make_ddp_data_loaders() (in module pallatom.helpers.data) make_fixed_size() (in module pallatom.helpers.atom_utils) make_np_example() (in module pallatom.helpers.atom_utils) max_dist (pallatom.helpers.featurize.Distogram attribute) (train_config.AtomDistogramParams attribute) (train_config.ResidueDistogramParams attribute) max_residues (train_config.ModelParams attribute) max_seq_length (pallatom.helpers.data.ProteinDataset attribute) (train_config.LoaderConfig attribute) med_loss() (in module pallatom.architecture.losses) med_loss_per_block() (in module pallatom.architecture.losses) min_dist (pallatom.helpers.featurize.Distogram attribute) (train_config.AtomDistogramParams attribute) (train_config.ResidueDistogramParams attribute) min_lt_max() (train_config.ResidueDistogramParams method) mlp_p (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) model (sample_config.SampleConfig attribute) (sampling.EDMPrecond attribute) (train_config.TrainConfig attribute) model_config (sample_config.GenerationParams attribute) (sample_config.SampleCheckpointParams attribute) (sample_config.SampleConfig attribute) (sample_config.SampleOutputParams attribute) (sample_config.SamplerParams attribute) (train_config.CheckpointParams attribute) (train_config.ConditioningDropoutConfig attribute) (train_config.LoaderConfig attribute) (train_config.LoggingParams attribute) (train_config.LossParams attribute) (train_config.ModelParams attribute) (train_config.NoiseScheduleParams attribute) (train_config.ResidueDistogramParams attribute) (train_config.TrainConfig attribute) (train_config.TrainingParams attribute) ModelParams (class in train_config) module pallatom pallatom.architecture pallatom.architecture.atom_transformers pallatom.architecture.losses pallatom.architecture.main_trunk pallatom.architecture.node_update pallatom.architecture.pair_update pallatom.architecture.pairformer_stack pallatom.architecture.template_embedder pallatom.helpers pallatom.helpers.alignment pallatom.helpers.atom_utils pallatom.helpers.compute_EDM_data_params pallatom.helpers.data pallatom.helpers.featurize sample_config sampling train_config train_loop N n_bins (pallatom.helpers.featurize.Distogram attribute) (train_config.AtomDistogramParams attribute) (train_config.ModelParams attribute) (train_config.ResidueDistogramParams attribute) n_heads (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) (pallatom.architecture.pairformer_stack.PairformerBlock attribute) n_res (sample_config.GenerationParams attribute) n_samples (sample_config.GenerationParams attribute) NATOM (in module sampling) node_updates (pallatom.architecture.main_trunk.MainTrunk attribute) NodeUpdate (class in pallatom.architecture.node_update) noise (sample_config.SampleConfig attribute) (train_config.TrainConfig attribute) NoiseScheduleParams (class in train_config) norm (pallatom.architecture.pair_update.Transition attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) norm_b (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) norm_c (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) norm_col (pallatom.architecture.pairformer_stack.PairformerBlock attribute) norm_ff (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.pairformer_stack.PairformerBlock attribute) norm_pair (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) norm_q (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) norm_q_out (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) norm_row (pallatom.architecture.pairformer_stack.PairformerBlock attribute) norm_s (pallatom.architecture.node_update.AttentionPairBias attribute) norm_s_c (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) norm_s_init (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) (pallatom.architecture.main_trunk.MainTrunk attribute) norm_s_q (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) norm_t (pallatom.architecture.node_update.AttentionPairBias attribute) norm_v (pallatom.architecture.template_embedder.TemplateEmbedder attribute) norm_z (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.template_embedder.TemplateEmbedder attribute) norm_z_init (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) num_epochs (train_config.TrainingParams attribute) O out_col (pallatom.architecture.pairformer_stack.PairformerBlock attribute) out_row (pallatom.architecture.pairformer_stack.PairformerBlock attribute) output (sample_config.SampleConfig attribute) output_path (sample_config.SampleOutputParams attribute) overflow_bin (pallatom.helpers.featurize.Distogram attribute) P p (pallatom.architecture.pair_update.DropoutColumnwise attribute) (pallatom.architecture.pair_update.DropoutRowwise attribute) p_atom (train_config.ConditioningDropoutConfig attribute) p_distogram (train_config.ConditioningDropoutConfig attribute) P_mean (train_config.NoiseScheduleParams attribute) p_seq (train_config.ConditioningDropoutConfig attribute) P_std (train_config.NoiseScheduleParams attribute) pair_bias (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) pair_updates (pallatom.architecture.main_trunk.MainTrunk attribute) pairformer (pallatom.architecture.template_embedder.TemplateEmbedder attribute) PairformerBlock (class in pallatom.architecture.pairformer_stack) PairformerStack (class in pallatom.architecture.pairformer_stack) PairUpdate (class in pallatom.architecture.pair_update) pallatom module pallatom.architecture module pallatom.architecture.atom_transformers module pallatom.architecture.losses module pallatom.architecture.main_trunk module pallatom.architecture.node_update module pallatom.architecture.pair_update module pallatom.architecture.pairformer_stack module pallatom.architecture.template_embedder module pallatom.helpers module pallatom.helpers.alignment module pallatom.helpers.atom_utils module pallatom.helpers.compute_EDM_data_params module pallatom.helpers.data module pallatom.helpers.featurize module parser (in module pallatom.helpers.compute_EDM_data_params) (in module sampling) (in module train_loop) PDB_CHAIN_IDS (in module pallatom.helpers.atom_utils) PDB_MAX_CHAINS (in module pallatom.helpers.atom_utils) pretrained_weights (train_config.TrainingParams attribute) proj (pallatom.architecture.pair_update.TransformRBF attribute) proj_a (pallatom.architecture.template_embedder.TemplateEmbedder attribute) proj_agg (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_cl_pair (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_cm_pair (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_d_vec (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_fref_c (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_inv_sq (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_out (pallatom.architecture.template_embedder.TemplateEmbedder attribute) proj_r (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) proj_r_scaled (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_residue_idx (pallatom.architecture.main_trunk.MainTrunk attribute) proj_s_c (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) proj_s_init (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) (pallatom.architecture.main_trunk.MainTrunk attribute) proj_s_q (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) proj_seq (pallatom.architecture.main_trunk.MainTrunk attribute) proj_t (pallatom.architecture.node_update.AttentionPairBias attribute) proj_v (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) proj_z (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) (pallatom.architecture.template_embedder.TemplateEmbedder attribute) proj_z_init (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) Protein (class in pallatom.helpers.atom_utils) protein_from_pdb() (in module pallatom.helpers.atom_utils) ProteinBatch (class in pallatom.helpers.featurize) ProteinDataset (class in pallatom.helpers.data) pseudo_cb() (in module pallatom.helpers.atom_utils) Q q_col (pallatom.architecture.pairformer_stack.PairformerBlock attribute) q_row (pallatom.architecture.pairformer_stack.PairformerBlock attribute) R r_gt (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.AllAtomContext attribute) r_input (pallatom.helpers.featurize.FeaturizedBatch attribute) rbf (pallatom.architecture.pair_update.PairUpdate attribute) ref_element (pallatom.helpers.featurize.FeaturizedBatch attribute) ref_pos (pallatom.helpers.featurize.FeaturizedBatch attribute) ref_space_uid (pallatom.helpers.featurize.FeaturizedBatch attribute) rel_pos_enc (pallatom.architecture.main_trunk.MainTrunk attribute) residue_distogram_head (pallatom.architecture.main_trunk.MainTrunk attribute) residue_index (pallatom.helpers.atom_utils.Protein attribute) (pallatom.helpers.featurize.ProteinBatch attribute) residue_mask (pallatom.helpers.featurize.FeaturizedBatch attribute) (sampling.AllAtomContext attribute) ResidueDistogramParams (class in train_config) restype_1to3 (in module pallatom.helpers.atom_utils) restype_3to1 (in module pallatom.helpers.atom_utils) restype_num (in module pallatom.helpers.atom_utils) restype_order (in module pallatom.helpers.atom_utils) restypes (in module pallatom.helpers.atom_utils) rho (sample_config.SamplerParams attribute) (sampling.EDMSampler attribute) rigid_group_atom_positions (in module pallatom.helpers.atom_utils) rmsd() (in module pallatom.helpers.alignment) S S_churn (sample_config.SamplerParams attribute) (sampling.EDMSampler attribute) S_noise (sample_config.SamplerParams attribute) (sampling.EDMSampler attribute) S_tmax (sample_config.SamplerParams attribute) (sampling.EDMSampler attribute) S_tmin (sample_config.SamplerParams attribute) (sampling.EDMSampler attribute) sample() (sampling.EDMSampler method) sample_config module SampleCheckpointParams (class in sample_config) SampleConfig (class in sample_config) SampleOutputParams (class in sample_config) sampler (sample_config.SampleConfig attribute) SamplerParams (class in sample_config) sampling module save_every (train_config.CheckpointParams attribute) seq (pallatom.helpers.featurize.ProteinBatch attribute) seq_logits (pallatom.architecture.main_trunk.MainTrunk attribute) sigma (pallatom.architecture.pair_update.TransformRBF attribute) sigma_data (pallatom.architecture.main_trunk.MainTrunk attribute) (train_config.NoiseScheduleParams attribute) sigma_max (sampling.EDMPrecond attribute) (sampling.EDMSampler attribute) (train_config.NoiseScheduleParams attribute) sigma_min (sampling.EDMPrecond attribute) (sampling.EDMSampler attribute) (train_config.NoiseScheduleParams attribute) sigma_min_lt_max() (train_config.NoiseScheduleParams method) sinusoidal_encoding() (in module pallatom.helpers.featurize) smooth_lddt_cutoff (train_config.LossParams attribute) smooth_lddt_loss() (in module pallatom.architecture.losses) T t_hat (pallatom.helpers.featurize.FeaturizedBatch attribute) t_normalized (pallatom.helpers.featurize.FeaturizedBatch attribute) template_embedder (pallatom.architecture.main_trunk.MainTrunk attribute) TemplateContext (class in sampling) TemplateEmbedder (class in pallatom.architecture.template_embedder) test_loader (train_config.TrainConfig attribute) TestLoaderConfig (in module train_config) time_fourier (pallatom.architecture.main_trunk.MainTrunk attribute) to_b (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) to_bias (pallatom.architecture.node_update.AttentionPairBias attribute) to_g (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) to_k (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) to_out (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) to_pdb() (in module pallatom.helpers.atom_utils) to_q (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) to_v (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute) (pallatom.architecture.node_update.AttentionPairBias attribute) (pallatom.architecture.pair_update.TriangleAttentionEndingNodeWithBias attribute) (pallatom.architecture.pair_update.TriangleAttentionStartingNodeWithBias attribute) tok_emb_dim (train_config.ResidueDistogramParams attribute) tok_idx (pallatom.helpers.featurize.FeaturizedBatch attribute) train() (in module train_loop) train_config module train_ddp() (in module train_loop) train_loader (train_config.TrainConfig attribute) train_loop module TrainConfig (class in train_config) training (train_config.TrainConfig attribute) TrainingParams (class in train_config) TrainLoaderConfig (in module train_config) transformer (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) TransformRBF (class in pallatom.architecture.pair_update) Transition (class in pallatom.architecture.pair_update) transition (pallatom.architecture.node_update.NodeUpdate attribute) (pallatom.architecture.pair_update.PairUpdate attribute) tri_end (pallatom.architecture.pair_update.PairUpdate attribute) tri_start (pallatom.architecture.pair_update.PairUpdate attribute) TriangleAttentionEndingNodeWithBias (class in pallatom.architecture.pair_update) TriangleAttentionStartingNodeWithBias (class in pallatom.architecture.pair_update) U use_wandb (train_config.LoggingParams attribute) V v_col (pallatom.architecture.pairformer_stack.PairformerBlock attribute) v_row (pallatom.architecture.pairformer_stack.PairformerBlock attribute) W wandb_project (train_config.LoggingParams attribute) weight_decay (train_config.TrainingParams attribute) WINDOW_SIZE (in module pallatom.architecture.atom_transformers) window_size (pallatom.architecture.atom_transformers.AtomAttentionDecoder attribute) (pallatom.architecture.atom_transformers.AtomFeatureEncoder attribute) (pallatom.architecture.atom_transformers.AtomTransformer attribute) (pallatom.architecture.atom_transformers.AtomTransformerBlock attribute)