Index

A

aa_count_filter() (in module openfold.data.data_modules) aatype (Protein attribute) aatype_to_str_sequence() (in module openfold.np.residue_constants) add() (in module openfold.utils.tensor_utils) add_arguments() (ArgparseAlphabetizer method) add_assembly_features() (in module openfold.data.data_pipeline) add_constant_field() (in module openfold.data.data_transforms) add_distillation_flag() (in module openfold.data.data_transforms) add_pdb_headers() (in module openfold.np.protein) add_usage() (ArgparseAlphabetizer method) align() (Kalign method) aligned_cols (TemplateHit attribute) AlignmentRunner (class in openfold.data.data_pipeline) AlignRatioError all_seq_len_filter() (in module openfold.data.data_modules) AlphaFold (class in openfold.model.model) AlphaFoldLoss (class in openfold.utils.loss) AlphaFoldLRScheduler (class in openfold.utils.lr_schedulers) AmberRelaxation (class in openfold.np.relax.relax) angle_rad (BondAngle attribute) AngleResnet (class in openfold.model.structure_module) AngleResnetBlock (class in openfold.model.structure_module) apply() (Rigid method) (Rigid3Array method) (Rotation method) apply_inverse_to_point() (Rigid3Array method) (Rot3Array method) apply_rot_fn() (Rigid method) apply_to_point() (Rigid3Array method) (Rot3Array method) apply_trans_fn() (Rigid method) ArgparseAlphabetizer (class in openfold.utils.argparse_utils)

assert_array_close_to_rotation_matrix() (in module openfold.utils.geometry.test_utils) assert_array_close_to_vector() (in module openfold.utils.geometry.test_utils) assert_array_equal_to_rotation_matrix() (in module openfold.utils.geometry.test_utils) assert_array_equal_to_vector() (in module openfold.utils.geometry.test_utils) assert_equal_nonterminal_atom_types() (in module openfold.np.relax.utils) assert_rigid_close_to_rigid() (in module openfold.utils.geometry.test_utils) assert_rigid_equal_to_rigid() (in module openfold.utils.geometry.test_utils) assert_rot_trans_close_to_rigid() (in module openfold.utils.geometry.test_utils) assert_rot_trans_equal_to_rigid() (in module openfold.utils.geometry.test_utils) assert_rotation_matrix_close() (in module openfold.utils.geometry.test_utils) assert_rotation_matrix_equal() (in module openfold.utils.geometry.test_utils) assert_vectors_close() (in module openfold.utils.geometry.test_utils) assert_vectors_equal() (in module openfold.utils.geometry.test_utils) assign() (in module openfold.utils.import_weights) atom14_to_atom37() (in module openfold.utils.all_atom_multimer) (in module openfold.utils.feats) atom1_name (Bond attribute) (BondAngle attribute) atom2_name (Bond attribute) (BondAngle attribute) atom37_to_atom14() (in module openfold.utils.all_atom_multimer) atom37_to_frames() (in module openfold.data.data_transforms) (in module openfold.utils.all_atom_multimer) atom37_to_torsion_angles() (in module openfold.data.data_transforms) atom3name (BondAngle attribute) atom_mask (Protein attribute) atom_positions (Protein attribute) AtomSite (class in openfold.data.mmcif_parsing) Attention (class in openfold.model.primitives) AttentionCoreFunction (class in openfold.utils.kernel.attention_core) author_chain_id (AtomSite attribute) author_seq_num (AtomSite attribute) AuxiliaryHeads (class in openfold.model.heads)

B

b_factors (Protein attribute) backbone_loss() (in module openfold.utils.loss) BackboneUpdate (class in openfold.model.structure_module) backward() (AttentionCoreFunction static method) BaseTriangleMultiplicativeUpdate (class in openfold.model.triangular_multiplicative_update) batched_gather() (in module openfold.utils.tensor_utils) between_residue_bond_loss() (in module openfold.utils.loss) between_residue_clash_loss() (in module openfold.utils.loss) block_delete_msa() (in module openfold.data.data_transforms)

block_diag() (in module openfold.data.msa_pairing) Bond (class in openfold.np.residue_constants) BondAngle (class in openfold.np.residue_constants) build_extra_msa_feat() (in module openfold.data.data_transforms_multimer) (in module openfold.utils.feats) build_profile_from_a3m() (Hmmbuild method) build_profile_from_sto() (Hmmbuild method) build_template_angle_feat() (in module openfold.utils.feats) build_template_pair_feat() (in module openfold.utils.feats)

C

CaDistanceError calculate_input_mask() (in module openfold.utils.multi_chain_permutation) calculate_optimal_transform() (in module openfold.utils.multi_chain_permutation) cast_all() (in module openfold.utils.precision_utils) cast_tensor() (in module openfold.utils.precision_utils) cast_to_64bit_ints() (in module openfold.data.data_transforms) cat() (Rigid static method) (Rigid3Array class method) (Rot3Array class method) (Rotation static method) (Vec3Array class method) chain (HitMetadata attribute) chain_center_of_mass_loss() (in module openfold.utils.loss) chain_id (ResiduePosition attribute) chain_id_to_idx() (OpenFoldSingleDataset method) chain_index (Protein attribute) chain_to_seqres (MmcifObject attribute) checkpoint_blocks() (in module openfold.utils.checkpointing) chi_angle_atom() (in module openfold.np.residue_constants) chunk_layer() (in module openfold.utils.chunk_utils) ChunkSizeTuner (class in openfold.utils.chunk_utils) clean_protein() (in module openfold.np.relax.amber_minimize) clean_structure() (in module openfold.np.relax.cleanup) clone() (Vec3Array method) compose() (in module openfold.data.input_pipeline) (in module openfold.data.input_pipeline_multimer) (Rigid method) (Rigid3Array method) compose_q() (Rotation method) compose_q_update_vec() (Rigid method) (Rotation method)

compose_r() (Rotation method) compose_rotation() (Rigid3Array method) compute_chi_angles() (in module openfold.utils.all_atom_multimer) compute_fape() (in module openfold.utils.loss) compute_permutation_alignment() (in module openfold.utils.multi_chain_permutation) compute_plddt() (in module openfold.utils.loss) compute_predicted_aligned_error() (in module openfold.utils.loss) compute_renamed_ground_truth() (in module openfold.utils.loss) compute_rmsd() (in module openfold.utils.multi_chain_permutation) compute_tm() (in module openfold.utils.loss) compute_violation_metrics() (in module openfold.utils.loss) compute_violation_metrics_np() (in module openfold.utils.loss) convert_deprecated_v1_keys() (in module openfold.utils.import_weights) convert_monomer_features() (in module openfold.data.data_pipeline) convert_stockholm_to_a3m() (in module openfold.data.parsers) correct_msa_restypes() (in module openfold.data.data_transforms) create_msa_feat() (in module openfold.data.data_transforms_multimer) create_paired_features() (in module openfold.data.msa_pairing) create_target_feat() (in module openfold.data.data_transforms_multimer) crop_chains() (in module openfold.data.feature_processing_multimer) crop_extra_msa() (in module openfold.data.data_transforms) crop_templates() (in module openfold.data.data_transforms) cross() (in module openfold.utils.geometry.vector) (Vec3Array method) cuda() (Rigid method) (Rigid3Array method) (Rotation method) curry1() (in module openfold.data.data_transforms) CustomHitFeaturizer (class in openfold.data.templates)

D

DataPipeline (class in openfold.data.data_pipeline) DataPipelineMultimer (class in openfold.data.data_pipeline) DateError deduplicate_stockholm_msa() (in module openfold.data.parsers) deduplicate_unpaired_sequences() (in module openfold.data.msa_pairing) delete_extra_msa() (in module openfold.data.data_transforms) deletion_matrix (Msa attribute) descriptions (Msa attribute) detach() (Rotation method) deterministic_train_filter() (OpenFoldDataset static method) (OpenFoldMultimerDataset static method) device (Rigid property) (Rigid3Array property) (Rotation property) dgram_from_positions() (in module openfold.utils.feats) dict_map() (in module openfold.utils.tensor_utils) dict_multimap() (in module openfold.utils.tensor_utils)

dihedral_angle() (in module openfold.utils.geometry.vector) distogram_loss() (in module openfold.utils.loss) DistogramHead (class in openfold.model.heads) do_step() (PerformanceLoggingCallback method) dot() (in module openfold.utils.geometry.vector) (Vec3Array method) drmsd() (in module openfold.utils.validation_metrics) drmsd_np() (in module openfold.utils.validation_metrics) Dropout (class in openfold.model.dropout) DropoutColumnwise (class in openfold.model.dropout) DropoutRowwise (class in openfold.model.dropout) dtype (Rigid property) (Rigid3Array property) (Rotation property) DummyDataLoader (class in openfold.data.data_modules) DummyDataset (class in openfold.data.data_modules) DuplicateError

E

EarlyStoppingVerbose (class in openfold.utils.callbacks) embed_templates() (AlphaFold method) embed_templates_average() (in module openfold.model.template) embed_templates_offload() (in module openfold.model.template) empty_template_feats() (in module openfold.data.templates) end (HitMetadata attribute) enforce_config_constraints() (in module openfold.config) ensembled_transform_fns() (in module openfold.data.input_pipeline) (in module openfold.data.input_pipeline_multimer) Error error (PrefilterResult attribute) (SingleHitResult attribute)

errors (ParsingResult attribute) (TemplateSearchResult attribute) euclidean_distance() (in module openfold.utils.geometry.vector) EvoformerBlock (class in openfold.model.evoformer) EvoformerStack (class in openfold.model.evoformer) experimentally_resolved_loss() (in module openfold.utils.loss) ExperimentallyResolvedHead (class in openfold.model.heads) ExponentialMovingAverage (class in openfold.utils.exponential_moving_average) ExtraMSABlock (class in openfold.model.evoformer) ExtraMSAEmbedder (class in openfold.model.embedders) ExtraMSAStack (class in openfold.model.evoformer) extreme_ca_ca_distance_violations() (in module openfold.utils.all_atom_multimer) (in module openfold.utils.loss)

F

fape_loss() (in module openfold.utils.loss) FeaturePipeline (class in openfold.data.feature_pipeline) features (SingleHitResult attribute) (TemplateSearchResult attribute) file_id (MmcifObject attribute) final_init_() (in module openfold.model.primitives) find_structural_violations() (in module openfold.utils.loss) find_structural_violations_np() (in module openfold.utils.loss) find_violations() (in module openfold.np.relax.amber_minimize) fix_pdb() (in module openfold.np.relax.cleanup) fix_templates_aatype() (in module openfold.data.data_transforms) flatten_final_dims() (in module openfold.utils.tensor_utils) forward() (AlphaFold method) (AlphaFoldLoss method) (AngleResnet method) (AngleResnetBlock method) (Attention method) (AttentionCoreFunction static method) (AuxiliaryHeads method) (BackboneUpdate method) (BaseTriangleMultiplicativeUpdate method) (DistogramHead method) (Dropout method) (EvoformerBlock method) (EvoformerStack method) (ExperimentallyResolvedHead method) (ExtraMSABlock method) (ExtraMSAEmbedder method) (ExtraMSAStack method) (FusedTriangleMultiplicativeUpdate method) (GlobalAttention method) (InputEmbedder method) (InputEmbedderMultimer method) (InvariantPointAttention method) (InvariantPointAttentionMultimer method) (LayerNorm method) (Linear method) (MaskedMSAHead method) (MSAAttention method) (MSABlock method) (MSAColumnAttention method) (MSAColumnGlobalAttention method) (MSATransition method) (OuterProductMean method) (PairStack method) (PairTransition method) (PerResidueLDDTCaPredictor method) (PointProjection method) (PrecisionWrapper method) (PreembeddingEmbedder method) (QuatRigid method) (RecyclingEmbedder method) (StructureModule method) (StructureModuleTransition method) (StructureModuleTransitionLayer method) (TemplateEmbedder method) (TemplateEmbedderMultimer method) (TemplatePairEmbedder method) (TemplatePairEmbedderMultimer method) (TemplatePairStack method) (TemplatePairStackBlock method) (TemplatePointwiseAttention method) (TemplateSingleEmbedder method) (TemplateSingleEmbedderMultimer method) (TMScoreHead method) (TriangleAttention method) (TriangleMultiplicativeUpdate method)

frames_and_literature_positions_to_atom14_pos() (in module openfold.utils.all_atom_multimer) (in module openfold.utils.feats) (StructureModule method) from_3_points() (Rigid static method) from_array() (Rigid3Array class method) (Rot3Array class method) (Vec3Array class method) from_array4x4() (Rigid3Array class method) from_pdb_string() (in module openfold.np.protein) from_prediction() (in module openfold.np.protein) from_proteinnet_string() (in module openfold.np.protein) from_quaternion() (Rot3Array class method) from_tensor_4x4() (Rigid static method) (Rigid3Array class method) from_tensor_7() (Rigid static method) from_two_vectors() (Rot3Array class method) FusedTriangleMultiplicationIncoming (class in openfold.model.triangular_multiplicative_update) FusedTriangleMultiplicationOutgoing (class in openfold.model.triangular_multiplicative_update) FusedTriangleMultiplicativeUpdate (class in openfold.model.triangular_multiplicative_update)

G

gating_init_() (in module openfold.model.primitives) gdt() (in module openfold.utils.validation_metrics) gdt_ha() (in module openfold.utils.validation_metrics) gdt_ts() (in module openfold.utils.validation_metrics) generate_release_dates_cache() (in module openfold.data.templates) generate_translation_dict() (in module openfold.utils.import_weights) get_alt_atom14() (in module openfold.utils.all_atom_multimer) get_atom_coords() (in module openfold.data.mmcif_parsing) get_backbone_frames() (in module openfold.data.data_transforms) get_checkpoint_fn() (in module openfold.utils.checkpointing) get_chi_angles() (in module openfold.data.data_transforms) get_chi_atom_indices() (in module openfold.data.data_transforms) (in module openfold.utils.all_atom_multimer) get_contiguous_crop_idx() (in module openfold.data.data_transforms_multimer) get_cur_rot() (Rotation method) get_custom_template_features() (in module openfold.data.templates) get_entity_2_asym_list() (in module openfold.utils.multi_chain_permutation) get_field_names() (in module openfold.utils.geometry.utils) get_identifiers() (in module openfold.data.msa_identifiers) get_interface_residues() (in module openfold.data.data_transforms_multimer) get_least_asym_entity_or_longest_length() (in module openfold.utils.multi_chain_permutation) get_lr() (AlphaFoldLRScheduler method) get_mmcif_features() (DataPipelineMultimer method) get_optimal_transform() (in module openfold.utils.multi_chain_permutation)

get_pdb_headers() (in module openfold.np.protein) get_per_asym_residue_index() (in module openfold.utils.multi_chain_permutation) get_quats() (Rotation method) get_rc_tensor() (in module openfold.utils.all_atom_multimer) get_release_date() (in module openfold.data.mmcif_parsing) get_rot_mats() (Rotation method) get_rots() (Rigid method) get_spatial_crop_idx() (in module openfold.data.data_transforms_multimer) get_stochastic_train_filter_prob() (OpenFoldDataset static method) (OpenFoldMultimerDataset static method) get_template_hits() (HHSearch static method) (Hmmsearch static method) get_templates() (CustomHitFeaturizer method) (HhsearchHitFeaturizer method) (HmmsearchHitFeaturizer method) (TemplateHitFeaturizer method) get_trans() (Rigid method) get_violation_metrics() (in module openfold.np.relax.amber_minimize) GlobalAttention (class in openfold.model.primitives) glorot_uniform_init_() (in module openfold.model.primitives) greedy_align() (in module openfold.utils.multi_chain_permutation) groundtruth_transforms_fns() (in module openfold.data.input_pipeline_multimer) gumbel_argsort_sample_idx() (in module openfold.data.data_transforms_multimer) gumbel_max_sample() (in module openfold.data.data_transforms_multimer) gumbel_noise() (in module openfold.data.data_transforms_multimer)

H

he_normal_init_() (in module openfold.model.primitives) header (MmcifObject attribute) hetatm_atom (AtomSite attribute) hetflag (ResidueAtPosition attribute) HHBlits (class in openfold.data.tools.hhblits) HHSearch (class in openfold.data.tools.hhsearch)

HhsearchHitFeaturizer (class in openfold.data.templates) hit_sequence (TemplateHit attribute) HitMetadata (class in openfold.data.parsers) Hmmbuild (class in openfold.data.tools.hmmbuild) Hmmsearch (class in openfold.data.tools.hmmsearch) HmmsearchHitFeaturizer (class in openfold.data.templates)

I

id (Monomer attribute) ideal_atom_mask() (in module openfold.np.protein) Identifiers (class in openfold.data.msa_identifiers) identity() (Rigid static method) (Rigid3Array class method) (Rot3Array class method) (Rotation static method) identity_quats() (in module openfold.utils.rigid_utils) identity_rot_mats() (in module openfold.utils.rigid_utils) identity_trans() (in module openfold.utils.rigid_utils) idx_to_chain_id() (OpenFoldSingleDataset method) idx_to_mmcif_id() (OpenFoldSingleMultimerDataset method) import_jax_weights_() (in module openfold.utils.import_weights) import_openfold_weights_() (in module openfold.utils.import_weights) index (TemplateHit attribute) indices_hit (TemplateHit attribute) indices_query (TemplateHit attribute) input_format (HHSearch property) (Hmmsearch property) InputEmbedder (class in openfold.model.embedders)

InputEmbedderMultimer (class in openfold.model.embedders) insertion_code (AtomSite attribute) (ResiduePosition attribute) int_id_to_str_id() (in module openfold.data.data_pipeline) InvariantPointAttention (class in openfold.model.structure_module) InvariantPointAttentionMultimer (class in openfold.model.structure_module) inverse() (Rigid3Array method) (Rot3Array method) invert() (Rigid method) (Rotation method) invert_apply() (Rigid method) (Rigid3Array method) (Rotation method) invert_quat() (in module openfold.utils.rigid_utils) invert_rot_mat() (in module openfold.utils.rigid_utils) ipa_point_weights_init_() (in module openfold.model.primitives) is_fp16_enabled() (in module openfold.utils.precision_utils) is_main_process() (in module openfold.utils.logger) is_missing (ResidueAtPosition attribute) iteration() (AlphaFold method)

J

Jackhmmer (class in openfold.data.tools.jackhmmer)

K

kabsch_rotation() (in module openfold.utils.multi_chain_permutation)

Kalign (class in openfold.data.tools.kalign)

L

LayerNorm (class in openfold.model.primitives) lddt() (in module openfold.utils.loss) lddt_ca() (in module openfold.utils.loss) lddt_loss() (in module openfold.utils.loss) lecun_normal_init_() (in module openfold.model.primitives) length (Bond attribute) (HitMetadata attribute) LengthError Linear (class in openfold.model.primitives) LinearBiasMHA (ParamType attribute) LinearBiasMultimer (ParamType attribute)

LinearMHAOutputWeight (ParamType attribute) LinearWeight (ParamType attribute) LinearWeightMHA (ParamType attribute) LinearWeightMultimer (ParamType attribute) LinearWeightOPM (ParamType attribute) load_state_dict() (AlphaFoldLRScheduler method) (ExponentialMovingAverage method) load_stereo_chemical_props() (in module openfold.np.residue_constants) looped_samples() (OpenFoldDataset method) (OpenFoldMultimerDataset method) looped_shuffled_dataset_idx() (OpenFoldDataset method) loss() (AlphaFoldLoss method)

M

main() (in module openfold.data.tools.parse_msa_files) make_all_atom_aatype() (in module openfold.data.data_transforms) make_atom14_dists_bounds() (in module openfold.np.residue_constants) make_atom14_masks() (in module openfold.data.data_transforms) make_atom14_masks_np() (in module openfold.data.data_transforms) make_atom14_positions() (in module openfold.data.data_transforms) (in module openfold.np.relax.amber_minimize) make_backbone_affine() (in module openfold.utils.all_atom_multimer) make_data_config() (in module openfold.data.feature_pipeline) make_dummy_msa_feats() (in module openfold.data.data_pipeline) make_dummy_msa_obj() (in module openfold.data.data_pipeline) make_fixed_size() (in module openfold.data.data_transforms) make_hhblits_profile() (in module openfold.data.data_transforms) make_masked_msa() (in module openfold.data.data_transforms) (in module openfold.data.data_transforms_multimer) make_mmcif_features() (in module openfold.data.data_pipeline) make_msa_feat() (in module openfold.data.data_transforms) make_msa_features() (in module openfold.data.data_pipeline) make_msa_mask() (in module openfold.data.data_transforms) make_msa_profile() (in module openfold.data.data_transforms_multimer) make_one_hot() (in module openfold.data.data_transforms) make_pdb_features() (in module openfold.data.data_pipeline) make_protein_features() (in module openfold.data.data_pipeline) make_pseudo_beta() (in module openfold.data.data_transforms) make_seq_mask() (in module openfold.data.data_transforms) make_sequence_features() (in module openfold.data.data_pipeline) make_sequence_features_with_custom_template() (in module openfold.data.data_pipeline) make_template_features() (in module openfold.data.data_pipeline) make_template_mask() (in module openfold.data.data_transforms) make_transform_from_reference() (in module openfold.utils.all_atom_multimer) (Rigid static method) map_fn() (in module openfold.data.input_pipeline) (in module openfold.data.input_pipeline_multimer) map_tensor_fn() (Rigid method) (Rigid3Array method) (Rot3Array method) (Rotation method) (Vec3Array method) masked_mean() (in module openfold.utils.tensor_utils) masked_msa_loss() (in module openfold.utils.loss) MaskedMSAHead (class in openfold.model.heads) maybe_to() (in module openfold.utils.tensor_utils) merge_chain_features() (in module openfold.data.msa_pairing) merge_labels() (in module openfold.utils.multi_chain_permutation) mmcif_chain_id (AtomSite attribute) mmcif_id_to_idx() (OpenFoldSingleMultimerDataset method) mmcif_loop_to_dict() (in module openfold.data.mmcif_parsing) mmcif_loop_to_list() (in module openfold.data.mmcif_parsing) mmcif_object (ParsingResult attribute) mmcif_seq_num (AtomSite attribute) MmcifObject (class in openfold.data.mmcif_parsing) model_config() (in module openfold.config) model_num (AtomSite attribute) module openfold openfold.config openfold.data openfold.data.data_modules openfold.data.data_pipeline openfold.data.data_transforms openfold.data.data_transforms_multimer openfold.data.errors openfold.data.feature_pipeline openfold.data.feature_processing_multimer openfold.data.input_pipeline openfold.data.input_pipeline_multimer openfold.data.mmcif_parsing openfold.data.msa_identifiers openfold.data.msa_pairing openfold.data.parsers openfold.data.templates openfold.data.tools openfold.data.tools.hhblits openfold.data.tools.hhsearch openfold.data.tools.hmmbuild openfold.data.tools.hmmsearch openfold.data.tools.jackhmmer openfold.data.tools.kalign openfold.data.tools.parse_msa_files openfold.data.tools.utils openfold.model openfold.model.dropout openfold.model.embedders openfold.model.evoformer openfold.model.heads openfold.model.model openfold.model.msa openfold.model.outer_product_mean openfold.model.pair_transition openfold.model.primitives openfold.model.structure_module openfold.model.template openfold.model.torchscript openfold.model.triangular_attention openfold.model.triangular_multiplicative_update openfold.np openfold.np.protein openfold.np.relax openfold.np.relax.amber_minimize openfold.np.relax.cleanup openfold.np.relax.relax openfold.np.relax.utils openfold.np.residue_constants openfold.resources openfold.utils openfold.utils.all_atom_multimer openfold.utils.argparse_utils openfold.utils.callbacks openfold.utils.checkpointing openfold.utils.chunk_utils openfold.utils.exponential_moving_average openfold.utils.feats openfold.utils.geometry openfold.utils.geometry.quat_rigid openfold.utils.geometry.rigid_matrix_vector openfold.utils.geometry.rotation_matrix openfold.utils.geometry.test_utils openfold.utils.geometry.utils openfold.utils.geometry.vector openfold.utils.import_weights openfold.utils.kernel openfold.utils.kernel.attention_core openfold.utils.logger openfold.utils.loss openfold.utils.lr_schedulers openfold.utils.multi_chain_permutation openfold.utils.precision_utils openfold.utils.rigid_utils openfold.utils.superimposition openfold.utils.tensor_utils openfold.utils.trace_utils openfold.utils.validation_metrics

Monomer (class in openfold.data.mmcif_parsing) Msa (class in openfold.data.parsers) MSAAttention (class in openfold.model.msa) MSABlock (class in openfold.model.evoformer) MSAColumnAttention (class in openfold.model.msa) MSAColumnGlobalAttention (class in openfold.model.msa) MSARowAttentionWithPairBias (class in openfold.model.msa) MSATransition (class in openfold.model.evoformer) multi_chain_permutation_align() (in module openfold.utils.multi_chain_permutation) MultipleChainsError

N

name (ResidueAtPosition attribute) (TemplateHit attribute) nearest_neighbor_clusters() (in module openfold.data.data_transforms) (in module openfold.data.data_transforms_multimer) NoAtomDataInTemplateError NoChainsError nonensembled_transform_fns() (in module openfold.data.input_pipeline) (in module openfold.data.input_pipeline_multimer)

norm() (in module openfold.utils.geometry.vector) (Vec3Array method) norm2() (Vec3Array method) normal_init_() (in module openfold.model.primitives) normalized() (in module openfold.utils.geometry.vector) (Vec3Array method) np_example_to_features() (in module openfold.data.feature_pipeline) np_to_tensor_dict() (in module openfold.data.feature_pipeline) num (Monomer attribute)

O

on_epoch_end() (PerformanceLoggingCallback method) on_test_batch_start() (PerformanceLoggingCallback method) on_train_batch_start() (PerformanceLoggingCallback method) on_train_end() (PerformanceLoggingCallback method) one_hot() (in module openfold.utils.tensor_utils) openfold module openfold.config module openfold.data module openfold.data.data_modules module openfold.data.data_pipeline module openfold.data.data_transforms module openfold.data.data_transforms_multimer module openfold.data.errors module openfold.data.feature_pipeline module openfold.data.feature_processing_multimer module openfold.data.input_pipeline module openfold.data.input_pipeline_multimer module openfold.data.mmcif_parsing module openfold.data.msa_identifiers module openfold.data.msa_pairing module openfold.data.parsers module openfold.data.templates module openfold.data.tools module openfold.data.tools.hhblits module openfold.data.tools.hhsearch module openfold.data.tools.hmmbuild module openfold.data.tools.hmmsearch module openfold.data.tools.jackhmmer module openfold.data.tools.kalign module openfold.data.tools.parse_msa_files module openfold.data.tools.utils module openfold.model module openfold.model.dropout module openfold.model.embedders module openfold.model.evoformer module openfold.model.heads module openfold.model.model module openfold.model.msa module openfold.model.outer_product_mean module openfold.model.pair_transition module openfold.model.primitives module openfold.model.structure_module module openfold.model.template module openfold.model.torchscript module openfold.model.triangular_attention module openfold.model.triangular_multiplicative_update module

openfold.np module openfold.np.protein module openfold.np.relax module openfold.np.relax.amber_minimize module openfold.np.relax.cleanup module openfold.np.relax.relax module openfold.np.relax.utils module openfold.np.residue_constants module openfold.resources module openfold.utils module openfold.utils.all_atom_multimer module openfold.utils.argparse_utils module openfold.utils.callbacks module openfold.utils.checkpointing module openfold.utils.chunk_utils module openfold.utils.exponential_moving_average module openfold.utils.feats module openfold.utils.geometry module openfold.utils.geometry.quat_rigid module openfold.utils.geometry.rigid_matrix_vector module openfold.utils.geometry.rotation_matrix module openfold.utils.geometry.test_utils module openfold.utils.geometry.utils module openfold.utils.geometry.vector module openfold.utils.import_weights module openfold.utils.kernel module openfold.utils.kernel.attention_core module openfold.utils.logger module openfold.utils.loss module openfold.utils.lr_schedulers module openfold.utils.multi_chain_permutation module openfold.utils.precision_utils module openfold.utils.rigid_utils module openfold.utils.superimposition module openfold.utils.tensor_utils module openfold.utils.trace_utils module openfold.utils.validation_metrics module OpenFoldBatchCollator (class in openfold.data.data_modules) OpenFoldDataLoader (class in openfold.data.data_modules) OpenFoldDataModule (class in openfold.data.data_modules) OpenFoldDataset (class in openfold.data.data_modules) OpenFoldMultimerDataModule (class in openfold.data.data_modules) OpenFoldMultimerDataset (class in openfold.data.data_modules) OpenFoldSingleDataset (class in openfold.data.data_modules) OpenFoldSingleMultimerDataset (class in openfold.data.data_modules) Other (ParamType attribute) OuterProductMean (class in openfold.model.outer_product_mean) output_format (HHSearch property) (Hmmsearch property) overwrite_b_factors() (in module openfold.np.relax.utils) overwrite_pdb_coordinates() (in module openfold.np.relax.utils)

P

pad_feature_dict_seq() (in module openfold.utils.trace_utils) pad_features() (in module openfold.data.msa_pairing) (in module openfold.utils.multi_chain_permutation) pad_msa() (in module openfold.data.data_pipeline) pair_and_merge() (in module openfold.data.feature_processing_multimer) pair_sequences() (in module openfold.data.msa_pairing) PairStack (class in openfold.model.evoformer) PairTransition (class in openfold.model.pair_transition) Param (class in openfold.utils.import_weights) param (Param attribute) param_type (Param attribute) ParamType (class in openfold.utils.import_weights) parents (Protein attribute) parents_chain_index (Protein attribute) parse() (in module openfold.data.mmcif_parsing) parse_a3m() (in module openfold.data.parsers) parse_a3m_file() (in module openfold.data.tools.parse_msa_files) parse_e_values_from_tblout() (in module openfold.data.parsers) parse_fasta() (in module openfold.data.parsers) parse_hhr() (in module openfold.data.parsers) parse_hmmsearch_a3m() (in module openfold.data.parsers) parse_hmmsearch_sto() (in module openfold.data.parsers) parse_stockholm() (in module openfold.data.parsers) parse_stockholm_file() (in module openfold.data.tools.parse_msa_files) ParseError ParsingResult (class in openfold.data.mmcif_parsing) pdb_id (HitMetadata attribute) PerformanceLoggingCallback (class in openfold.utils.logger)

permute_final_dims() (in module openfold.utils.tensor_utils) PerResidueLDDTCaPredictor (class in openfold.model.heads) PointProjection (class in openfold.model.structure_module) position (ResidueAtPosition attribute) PrecisionWrapper (class in openfold.utils.precision_utils) predict_dataloader() (OpenFoldDataModule method) PreembeddingEmbedder (class in openfold.model.embedders) PrefilterError PrefilterResult (class in openfold.data.templates) prepare_ground_truth_features() (in module openfold.data.input_pipeline_multimer) process() (AmberRelaxation method) process_core() (DataPipeline method) process_fasta() (DataPipeline method) (DataPipelineMultimer method) process_features() (FeaturePipeline method) process_final() (in module openfold.data.feature_processing_multimer) process_mmcif() (DataPipeline method) (DataPipelineMultimer method) process_multiseq_fasta() (DataPipeline method) process_pdb() (DataPipeline method) process_performance_stats() (PerformanceLoggingCallback method) process_tensors_from_config() (in module openfold.data.input_pipeline) (in module openfold.data.input_pipeline_multimer) process_translation_dict() (in module openfold.utils.import_weights) process_unmerged_features() (in module openfold.data.feature_processing_multimer) Protein (class in openfold.np.protein) pseudo_beta_fn() (in module openfold.data.data_transforms) (in module openfold.utils.feats) pts_to_distogram() (in module openfold.utils.tensor_utils)

Q

quat_multiply() (in module openfold.utils.rigid_utils) quat_multiply_by_vec() (in module openfold.utils.rigid_utils) quat_to_rot() (in module openfold.utils.rigid_utils) QuatRigid (class in openfold.utils.geometry.quat_rigid) query (TemplateHit attribute) query() (HHBlits method) (HHSearch method) (Hmmsearch method) (Jackhmmer method)

query_multiple() (Jackhmmer method) query_with_hmm() (Hmmsearch method) QueryToTemplateAlignError

R

randint() (in module openfold.data.data_transforms_multimer) random_crop_to_size() (in module openfold.data.data_transforms) (in module openfold.data.data_transforms_multimer) randomly_replace_msa_with_unknown() (in module openfold.data.data_transforms) raw_string (MmcifObject attribute) RecyclingEmbedder (class in openfold.model.embedders) relpos() (InputEmbedder method) (InputEmbedderMultimer method) (PreembeddingEmbedder method) remark (Protein attribute) remove_arguments() (in module openfold.utils.argparse_utils) remove_empty_columns_from_stockholm_msa() (in module openfold.data.parsers) reorder_paired_rows() (in module openfold.data.msa_pairing) requires_grad (Rotation property) reroll() (OpenFoldDataset method) reshape() (Rigid3Array method) (Rot3Array method) (Vec3Array method)

residue_index (Protein attribute) residue_name (AtomSite attribute) residue_number (ResiduePosition attribute) ResidueAtPosition (class in openfold.data.mmcif_parsing) ResiduePosition (class in openfold.data.mmcif_parsing) resolution_filter() (in module openfold.data.data_modules) Rigid (class in openfold.utils.rigid_utils) Rigid3Array (class in openfold.utils.geometry.rigid_matrix_vector) Rot3Array (class in openfold.utils.geometry.rotation_matrix) rot_matmul() (in module openfold.utils.rigid_utils) rot_to_quat() (in module openfold.utils.rigid_utils) rot_vec_mul() (in module openfold.utils.rigid_utils) Rotation (class in openfold.utils.rigid_utils) rotation (Rigid3Array attribute) run() (AlignmentRunner method) run_msa_tool() (in module openfold.data.data_pipeline) run_parse_all_msa_files_multiprocessing() (in module openfold.data.tools.parse_msa_files) run_pipeline() (in module openfold.np.relax.amber_minimize)

S

sample_msa() (in module openfold.data.data_transforms) (in module openfold.data.data_transforms_multimer) sample_msa_distillation() (in module openfold.data.data_transforms) scale_translation() (Rigid method) (Rigid3Array method) script_preset_() (in module openfold.model.torchscript) script_submodules_() (in module openfold.model.torchscript) select_feat() (in module openfold.data.data_transforms) seqres_to_structure (MmcifObject attribute) sequence_to_onehot() (in module openfold.np.residue_constants) SequenceNotInTemplateError sequences (Msa attribute) set_inf() (in module openfold.config) setup() (OpenFoldDataModule method) (OpenFoldMultimerDataModule method) shape (Rigid property) (Rigid3Array property) (Rotation property) (Vec3Array property) shaped_categorical() (in module openfold.data.data_transforms) sidechain_loss() (in module openfold.utils.loss) sigmoid_cross_entropy() (in module openfold.utils.loss) SingleHitResult (class in openfold.data.templates) softmax_cross_entropy() (in module openfold.utils.loss) softmax_no_cast() (in module openfold.model.primitives)

sort_actions() (ArgparseAlphabetizer static method) species_id (Identifiers attribute) split_ground_truth_labels() (in module openfold.utils.multi_chain_permutation) square_euclidean_distance() (in module openfold.utils.geometry.vector) squared_difference() (in module openfold.utils.all_atom_multimer) squeeze_features() (in module openfold.data.data_transforms) stacked (Param attribute) stacked() (in module openfold.utils.import_weights) start (HitMetadata attribute) state_dict() (AlphaFoldLRScheduler method) (ExponentialMovingAverage method) stddev (Bond attribute) (BondAngle attribute) stop_gradient() (Rot3Array method) stop_rot_gradient() (Rigid method) (Rigid3Array method) structure (MmcifObject attribute) StructureModule (class in openfold.model.structure_module) StructureModuleTransition (class in openfold.model.structure_module) StructureModuleTransitionLayer (class in openfold.model.structure_module) sum() (Vec3Array method) sum_probs (TemplateHit attribute) summarize_clusters() (in module openfold.data.data_transforms) superimpose() (in module openfold.utils.superimposition) supervised_chi_loss() (in module openfold.utils.loss) swap (Param attribute)

T

temp_fasta_file() (in module openfold.data.data_pipeline) TemplateAtomMaskAllZerosError TemplateEmbedder (class in openfold.model.embedders) TemplateEmbedderMultimer (class in openfold.model.embedders) TemplateHit (class in openfold.data.parsers) TemplateHitFeaturizer (class in openfold.data.templates) TemplatePairEmbedder (class in openfold.model.embedders) TemplatePairEmbedderMultimer (class in openfold.model.embedders) TemplatePairStack (class in openfold.model.template) TemplatePairStackBlock (class in openfold.model.template) TemplatePointwiseAttention (class in openfold.model.template) TemplateSearchResult (class in openfold.data.templates) TemplateSingleEmbedder (class in openfold.model.embedders) TemplateSingleEmbedderMultimer (class in openfold.model.embedders) tensor_tree_map() (in module openfold.utils.tensor_utils) text (HitMetadata attribute) timing() (in module openfold.data.tools.utils) tm_loss() (in module openfold.utils.loss) tmpdir_manager() (in module openfold.data.tools.utils) TMScoreHead (class in openfold.model.heads) to() (ExponentialMovingAverage method) (Rotation method) to_date() (in module openfold.data.tools.utils) to_modelcif() (in module openfold.np.protein) to_pdb() (in module openfold.np.protein) to_tensor() (Rigid3Array method) (Rot3Array method) (Vec3Array method)

to_tensor_4x4() (Rigid method) (Rigid3Array method) to_tensor_7() (Rigid method) tolerance_reached() (AlphaFold method) torsion_angle_loss() (in module openfold.utils.loss) torsion_angles_to_frames() (in module openfold.utils.all_atom_multimer) (in module openfold.utils.feats) (StructureModule method) trace_model_() (in module openfold.utils.trace_utils) train_dataloader() (DummyDataLoader method) (OpenFoldDataModule method) translation (Rigid3Array attribute) tree_map() (in module openfold.utils.tensor_utils) tri_att_start_end() (TemplatePairStackBlock method) tri_mul_out_in() (TemplatePairStackBlock method) TriangleAttention (class in openfold.model.triangular_attention) TriangleAttentionEndingNode (class in openfold.model.triangular_attention) TriangleAttentionStartingNode (in module openfold.model.triangular_attention) TriangleMultiplicationIncoming (class in openfold.model.triangular_multiplicative_update) TriangleMultiplicationOutgoing (class in openfold.model.triangular_multiplicative_update) TriangleMultiplicativeUpdate (class in openfold.model.triangular_multiplicative_update) trunc_normal_init_() (in module openfold.model.primitives) truncate() (Msa method) truncate_stockholm_msa() (in module openfold.data.parsers) tune_chunk_size() (ChunkSizeTuner method)

U

unify_template_features() (in module openfold.data.data_pipeline) unsorted_segment_sum() (in module openfold.data.data_transforms) unsqueeze() (Rigid method) (Rigid3Array method) (Rot3Array method) (Rotation method) (Vec3Array method)

update() (ExponentialMovingAverage method)

V

val_dataloader() (OpenFoldDataModule method) valid (PrefilterResult attribute)

Vec3Array (class in openfold.utils.geometry.vector) violation_loss() (in module openfold.utils.loss)

W

warning (PrefilterResult attribute) (SingleHitResult attribute) warnings (TemplateSearchResult attribute)

will_restrain() (in module openfold.np.relax.amber_minimize) within_residue_violations() (in module openfold.utils.loss) wrap_for_precision() (in module openfold.utils.precision_utils)

X

x (Vec3Array attribute) xx (Rot3Array attribute)

xy (Rot3Array attribute) xz (Rot3Array attribute)

Y

y (Vec3Array attribute) yx (Rot3Array attribute)

yy (Rot3Array attribute) yz (Rot3Array attribute)

Z

z (Vec3Array attribute) zeros() (Vec3Array class method)

zx (Rot3Array attribute) zy (Rot3Array attribute) zz (Rot3Array attribute)