Index

A

aa_chem_comps() (in module atomworks.io.utils.ccd) AA_LIKE_CHEM_TYPES (in module atomworks.io.constants) AA_OR_NA_CHEM_COMP_TYPES (in module atomworks.io.constants) add_af3_chiral_features() (in module atomworks.ml.transforms.chirals) add_atomic_number_annotation() (in module atomworks.io.transforms.atom_array) add_chain_iid_annotation() (in module atomworks.io.transforms.atom_array) add_chain_type_annotation() (in module atomworks.io.transforms.atom_array) add_charge_from_ccd_codes() (in module atomworks.io.transforms.atom_array) add_global_atom_id_annotation() (in module atomworks.ml.transforms.atom_array) add_global_res_id_annotation() (in module atomworks.ml.transforms.atom_array) add_global_token_id_annotation() (in module atomworks.ml.transforms.atom_array) add_hydrogen_atom_positions() (in module atomworks.io.transforms.atom_array) add_hydrogens() (in module atomworks.io.tools.rdkit) add_id_and_entity_annotations() (in module atomworks.io.transforms.atom_array) add_iid_annotations_to_assemblies() (in module atomworks.io.transforms.atom_array) add_input_file_template() (in module atomworks.ml.transforms.template) add_missing_atoms (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) add_molecule_id_annotation() (in module atomworks.io.transforms.atom_array) add_molecule_iid_annotation() (in module atomworks.io.transforms.atom_array) add_pn_unit_id_annotation() (in module atomworks.io.transforms.atom_array) add_pn_unit_iid_annotation() (in module atomworks.io.transforms.atom_array) add_polymer_annotation() (in module atomworks.io.transforms.atom_array) add_protein_termini_annotation() (in module atomworks.ml.transforms.atom_array) AddAF3ChiralFeatures (class in atomworks.ml.transforms.chirals) AddAF3TokenBondFeatures (class in atomworks.ml.transforms.bonds) AddAtomFrames (class in atomworks.ml.transforms.atom_frames) AddAtomLevelBondAdjacencyMatrix (class in atomworks.ml.transforms.bonds) AddData (class in atomworks.ml.transforms.base) AddGlobalAtomIdAnnotation (class in atomworks.ml.transforms.atom_array) AddGlobalResIdAnnotation (class in atomworks.ml.transforms.atom_array) AddGlobalTokenIdAnnotation (class in atomworks.ml.transforms.atom_array) AddInputFileTemplate (class in atomworks.ml.transforms.template) AddIsRealAtom (class in atomworks.ml.transforms.atom_frames) AddMoleculeSymmetricIdAnnotation (class in atomworks.ml.transforms.atom_array) AddPolymerFrameIndices (class in atomworks.ml.transforms.atom_frames) AddPostCropMoleculeEntityToFreeFloatingLigands (class in atomworks.ml.transforms.symmetry) AddProteinTerminiAnnotation (class in atomworks.ml.transforms.atom_array) AddRDKitMoleculesForAtomizedMolecules (class in atomworks.ml.transforms.rdkit_utils) AddRF2AABondFeaturesMatrix (class in atomworks.ml.transforms.bonds) AddRF2AAChiralFeatures (class in atomworks.ml.transforms.chirals) AddRF2AATraversalDistanceMatrix (class in atomworks.ml.transforms.bonds) AddRFTemplates (class in atomworks.ml.transforms.template) AddSpatialKNNMask (class in atomworks.ml.transforms.masks) AddTokenAnnotation (class in atomworks.ml.transforms.encoding) AddTokenBondAdjacency (class in atomworks.ml.transforms.bonds) AddWithinChainInstanceResIdx (class in atomworks.ml.transforms.atom_array) AddWithinPolyResIdxAnnotation (class in atomworks.ml.transforms.atom_array) AF2_ATOM14_ENCODING (in module atomworks.ml.encoding_definitions) AF2_ATOM37_ENCODING (in module atomworks.ml.encoding_definitions) AF2FB_DistillationParser (class in atomworks.ml.datasets.parsers.custom_metadata_row_parsers) AF3_EXCLUDED_LIGANDS (in module atomworks.io.constants) AF3_EXCLUDED_LIGANDS_REGEX (in module atomworks.io.constants) AF3_TOKENS (in module atomworks.ml.encoding_definitions) AF3SequenceEncoding (class in atomworks.ml.encoding_definitions) align_atom_arrays() (in module atomworks.ml.utils.geometry) alignment_confidence (atomworks.ml.transforms.template.RF2AATemplate property) annot_start_stop_idxs() (in module atomworks.io.utils.selection) annotate_entities() (in module atomworks.io.transforms.atom_array) apply_and_spread_chain_wise() (in module atomworks.ml.transforms.atom_array) apply_and_spread_residue_wise() (in module atomworks.ml.transforms.atom_array) apply_and_spread_token_wise() (in module atomworks.ml.utils.token) apply_automorphs() (in module atomworks.ml.transforms.symmetry) apply_batched_rigid() (in module atomworks.ml.utils.geometry) apply_inverse_rigid() (in module atomworks.ml.utils.geometry) apply_rigid() (in module atomworks.ml.utils.geometry) apply_segment_wise_2d() (in module atomworks.ml.utils.token) apply_token_wise() (in module atomworks.ml.utils.token) ApplyFunction (class in atomworks.ml.transforms.base) ApplyFunctionToAtomArray (class in atomworks.ml.transforms.atom_array) argunsort() (in module atomworks.ml.utils.misc) as_dict() (atomworks.io.tools.inference.ChemicalComponent method) as_list() (in module atomworks.ml.common) assert_nonpoly_come_after_polys() (atomworks.ml.transforms.symmetry.CreateSymmetryCopyAxisLikeRF2AA method) assert_same_atom_array() (in module atomworks.io.utils.testing) assert_satisfies_rf2aa_assumptions() (in module atomworks.ml.transforms.rf2aa_assumptions) assert_valid_chain_type() (atomworks.io.tools.inference.SequenceComponent static method) AssertRF2AAAssumptions (class in atomworks.ml.transforms.rf2aa_assumptions) assign_res_name_from_atom_array_hash() (in module atomworks.io.tools.inference) atom_array_from_ccd_code() (in module atomworks.io.utils.ccd) atom_array_from_encoding() (in module atomworks.ml.transforms.encoding) atom_array_from_rdkit() (in module atomworks.io.tools.rdkit) atom_array_to_encoding() (in module atomworks.ml.transforms.encoding) atom_array_to_rdkit() (in module atomworks.io.tools.rdkit) atom_id_to_atom_idx() (in module atomworks.ml.transforms.atom_array) atom_id_to_token_idx() (in module atomworks.ml.transforms.atom_array) atom_to_idx (atomworks.ml.encoding_definitions.TokenEncoding property) ATOMIC_NUMBER_TO_ELEMENT (in module atomworks.io.constants) atomize_by_ccd_name() (in module atomworks.ml.transforms.atomize) AtomizeByCCDName (class in atomworks.ml.transforms.atomize) atomworks.io.common module atomworks.io.constants module atomworks.io.parser module atomworks.io.tools.fasta module atomworks.io.tools.inference module atomworks.io.tools.rdkit module atomworks.io.transforms.atom_array module atomworks.io.transforms.categories module atomworks.io.utils.assembly module atomworks.io.utils.bonds module atomworks.io.utils.ccd module atomworks.io.utils.chain module

atomworks.io.utils.io_utils module atomworks.io.utils.non_rcsb module atomworks.io.utils.selection module atomworks.io.utils.sequence module atomworks.io.utils.testing module atomworks.io.utils.visualize module atomworks.ml.common module atomworks.ml.datasets.parsers.base module atomworks.ml.datasets.parsers.custom_metadata_row_parsers module atomworks.ml.encoding_definitions module atomworks.ml.pipelines.af3 module atomworks.ml.preprocessing.constants module atomworks.ml.preprocessing.get_pn_unit_data_from_structure module atomworks.ml.preprocessing.utils module atomworks.ml.preprocessing.utils.clustering module atomworks.ml.preprocessing.utils.fasta module atomworks.ml.preprocessing.utils.structure_utils module atomworks.ml.samplers module atomworks.ml.transforms._checks module atomworks.ml.transforms.af3_reference_molecule module atomworks.ml.transforms.atom_array module atomworks.ml.transforms.atom_frames module atomworks.ml.transforms.atomize module atomworks.ml.transforms.base module atomworks.ml.transforms.bonds module atomworks.ml.transforms.center_random_augmentation module atomworks.ml.transforms.chirals module atomworks.ml.transforms.covalent_modifications module atomworks.ml.transforms.crop module atomworks.ml.transforms.diffusion module atomworks.ml.transforms.diffusion.batch_structures module atomworks.ml.transforms.diffusion.edm module atomworks.ml.transforms.dna module atomworks.ml.transforms.dna.pad_dna module atomworks.ml.transforms.encoding module atomworks.ml.transforms.feature_aggregation module, [1] atomworks.ml.transforms.featurize_unresolved_residues module atomworks.ml.transforms.filters module atomworks.ml.transforms.masks module atomworks.ml.transforms.msa module, [1] atomworks.ml.transforms.rdkit_utils module atomworks.ml.transforms.rf2aa_assumptions module atomworks.ml.transforms.sasa module atomworks.ml.transforms.symmetry module atomworks.ml.transforms.template module atomworks.ml.utils.debug module atomworks.ml.utils.error module atomworks.ml.utils.geometry module atomworks.ml.utils.io module atomworks.ml.utils.misc module atomworks.ml.utils.nested_dict module atomworks.ml.utils.numpy module atomworks.ml.utils.rng module atomworks.ml.utils.testing module atomworks.ml.utils.timer module atomworks.ml.utils.token module

B

base_pairs() (in module atomworks.ml.transforms.dna.pad_dna) BatchStructuresForDiffusionNoising (class in atomworks.ml.transforms.diffusion.batch_structures) BIDIRECTIONAL (atomworks.ml.preprocessing.utils.clustering.CoverageMode attribute) BIOTITE_BOND_TYPE_TO_BOND_ORDER (in module atomworks.io.constants) BIOTITE_BOND_TYPE_TO_RDKIT (in module atomworks.io.tools.rdkit) BIOTITE_DEFAULT_ANNOTATIONS (in module atomworks.io.constants)

blank_af3_template_features() (in module atomworks.ml.transforms.template) blank_rf2aa_template_features() (in module atomworks.ml.transforms.template) build_af3_transform_pipeline() (in module atomworks.ml.pipelines.af3) build_assemblies_from_asym_unit() (in module atomworks.io.utils.assembly) build_assembly (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) build_msa_paths_by_chain_id_from_component_list() (in module atomworks.io.tools.inference)

C

cache_based_on_subset_of_args() (in module atomworks.ml.utils.io) cache_to_disk_as_pickle() (in module atomworks.ml.utils.io) cached_parse() (in module atomworks.ml.utils.testing) calculate_af3_example_weights() (in module atomworks.ml.samplers) calculate_atomwise_rasa() (in module atomworks.ml.transforms.sasa) calculate_atomwise_sasa() (in module atomworks.ml.transforms.sasa) calculate_molecule_diameter() (in module atomworks.ml.preprocessing.utils.structure_utils) calculate_weights_by_inverse_cluster_size() (in module atomworks.ml.samplers) calculate_weights_for_pdb_dataset_df() (in module atomworks.ml.samplers) CalculateSASA (class in atomworks.ml.transforms.sasa) capture_rng_states() (in module atomworks.ml.utils.rng) CARBOHYDRATE_D_CHEM_TYPES (in module atomworks.io.constants) CARBOHYDRATE_L_CHEM_TYPES (in module atomworks.io.constants) CARBOHYDRATE_LIKE_CHEM_TYPES (in module atomworks.io.constants) category_to_df() (in module atomworks.io.transforms.categories) category_to_dict() (in module atomworks.io.transforms.categories) ccd_code (atomworks.io.tools.inference.CCDComponent attribute) ccd_code_to_annotated_atom_array() (in module atomworks.io.tools.inference) ccd_code_to_rdkit() (in module atomworks.io.tools.rdkit) ccd_code_to_rdkit_with_conformers() (in module atomworks.ml.transforms.rdkit_utils) CCD_MIRROR_PATH (in module atomworks.io.constants) CCDComponent (class in atomworks.io.tools.inference) CenterRandomAugmentation (class in atomworks.ml.transforms.center_random_augmentation) chain_id (atomworks.io.tools.inference.CCDComponent attribute) (atomworks.io.tools.inference.SDFComponent attribute) (atomworks.io.tools.inference.SequenceComponent attribute) (atomworks.io.tools.inference.SmilesComponent attribute) chain_ids (atomworks.ml.transforms.template.RF2AATemplate property) chain_instance_iter() (in module atomworks.ml.transforms.atom_array) chain_type (atomworks.io.tools.inference.CCDComponent attribute) (atomworks.io.tools.inference.CIFOrPDBFileComponent attribute) (atomworks.io.tools.inference.DNA attribute) (atomworks.io.tools.inference.Peptide attribute) (atomworks.io.tools.inference.Protein attribute) (atomworks.io.tools.inference.RNA attribute) (atomworks.io.tools.inference.SDFComponent attribute) (atomworks.io.tools.inference.SequenceComponent attribute) (atomworks.io.tools.inference.SmilesComponent attribute) change_metal_bonds_to_dative() (in module atomworks.io.tools.rdkit) check_atom_array_annotation() (in module atomworks.ml.transforms._checks) check_atom_array_has_bonds() (in module atomworks.ml.transforms._checks) check_ccd_codes_are_available() (in module atomworks.io.utils.ccd) check_contains_keys() (in module atomworks.ml.transforms._checks) check_does_not_contain_keys() (in module atomworks.ml.transforms._checks) check_input() (atomworks.ml.transforms.af3_reference_molecule.GetAF3ReferenceMoleculeFeatures method) (atomworks.ml.transforms.atom_array.AddGlobalAtomIdAnnotation method) (atomworks.ml.transforms.atom_array.AddGlobalResIdAnnotation method) (atomworks.ml.transforms.atom_array.AddGlobalTokenIdAnnotation method) (atomworks.ml.transforms.atom_array.AddMoleculeSymmetricIdAnnotation method) (atomworks.ml.transforms.atom_array.AddProteinTerminiAnnotation method) (atomworks.ml.transforms.atom_array.AddWithinChainInstanceResIdx method) (atomworks.ml.transforms.atom_array.AddWithinPolyResIdxAnnotation method) (atomworks.ml.transforms.atom_array.ApplyFunctionToAtomArray method) (atomworks.ml.transforms.atom_array.ComputeAtomToTokenMap method) (atomworks.ml.transforms.atom_array.CopyAnnotation method) (atomworks.ml.transforms.atom_array.RaiseIfTooManyAtoms method) (atomworks.ml.transforms.atom_array.RenumberNonPolymerResidueIdx method) (atomworks.ml.transforms.atom_array.SortLikeRF2AA method) (atomworks.ml.transforms.atom_array.SortPolyThenNonPoly method) (atomworks.ml.transforms.atom_frames.AddAtomFrames method) (atomworks.ml.transforms.atom_frames.AddIsRealAtom method) (atomworks.ml.transforms.atom_frames.AddPolymerFrameIndices method) (atomworks.ml.transforms.atomize.AtomizeByCCDName method) (atomworks.ml.transforms.atomize.FlagNonPolymersForAtomization method) (atomworks.ml.transforms.base.AddData method) (atomworks.ml.transforms.base.ApplyFunction method) (atomworks.ml.transforms.base.Compose method) (atomworks.ml.transforms.base.ConditionalRoute method) (atomworks.ml.transforms.base.ConvertToTorch method) (atomworks.ml.transforms.base.LogData method) (atomworks.ml.transforms.base.PickleToDisk method) (atomworks.ml.transforms.base.RaiseError method) (atomworks.ml.transforms.base.RaiseOnCondition method) (atomworks.ml.transforms.base.RandomRoute method) (atomworks.ml.transforms.base.RemoveKeys method) (atomworks.ml.transforms.base.SubsetToKeys method) (atomworks.ml.transforms.base.Transform method) (atomworks.ml.transforms.bonds.AddAF3TokenBondFeatures method) (atomworks.ml.transforms.bonds.AddAtomLevelBondAdjacencyMatrix method) (atomworks.ml.transforms.bonds.AddRF2AABondFeaturesMatrix method) (atomworks.ml.transforms.bonds.AddRF2AATraversalDistanceMatrix method) (atomworks.ml.transforms.bonds.AddTokenBondAdjacency method) (atomworks.ml.transforms.center_random_augmentation.CenterRandomAugmentation method) (atomworks.ml.transforms.chirals.AddAF3ChiralFeatures method) (atomworks.ml.transforms.chirals.AddRF2AAChiralFeatures method) (atomworks.ml.transforms.covalent_modifications.FlagAndReassignCovalentModifications method) (atomworks.ml.transforms.crop.CropContiguousLikeAF3 method) (atomworks.ml.transforms.crop.CropSpatialLikeAF3 method) (atomworks.ml.transforms.diffusion.batch_structures.BatchStructuresForDiffusionNoising method) (atomworks.ml.transforms.diffusion.edm.SampleEDMNoise method) (atomworks.ml.transforms.dna.pad_dna.PadDNA method) (atomworks.ml.transforms.encoding.AddTokenAnnotation method) (atomworks.ml.transforms.encoding.EncodeAF3TokenLevelFeatures method) (atomworks.ml.transforms.encoding.EncodeAtomArray method) (atomworks.ml.transforms.featurize_unresolved_residues.MaskPolymerResiduesWithUnresolvedFrameAtoms method) (atomworks.ml.transforms.featurize_unresolved_residues.MaskResiduesWithSpecificUnresolvedAtoms method) (atomworks.ml.transforms.featurize_unresolved_residues.PlaceUnresolvedTokenAtomsOnRepresentativeAtom method) (atomworks.ml.transforms.featurize_unresolved_residues.PlaceUnresolvedTokenOnClosestResolvedTokenInSequence method) (atomworks.ml.transforms.filters.FilterToSpecifiedPNUnits method) (atomworks.ml.transforms.filters.HandleUndesiredResTokens method) (atomworks.ml.transforms.filters.RandomlyRemoveLigands method) (atomworks.ml.transforms.filters.RandomlyRemovePNUnitsByAnnotationQuery method) (atomworks.ml.transforms.filters.RemoveHydrogens method) (atomworks.ml.transforms.filters.RemoveNucleicAcidTerminalOxygen method) (atomworks.ml.transforms.filters.RemovePolymersWithTooFewResolvedResidues method) (atomworks.ml.transforms.filters.RemoveTerminalOxygen method) (atomworks.ml.transforms.filters.RemoveUnresolvedLigandAtomsIfTooMany method) (atomworks.ml.transforms.filters.RemoveUnresolvedPNUnits method) (atomworks.ml.transforms.filters.RemoveUnresolvedTokens method) (atomworks.ml.transforms.filters.RemoveUnsupportedChainTypes method) (atomworks.ml.transforms.masks.AddSpatialKNNMask method) (atomworks.ml.transforms.rdkit_utils.AddRDKitMoleculesForAtomizedMolecules method) (atomworks.ml.transforms.rdkit_utils.GenerateRDKitConformers method) (atomworks.ml.transforms.rdkit_utils.GetRDKitChiralCenters method) (atomworks.ml.transforms.rf2aa_assumptions.AssertRF2AAAssumptions method) (atomworks.ml.transforms.sasa.CalculateSASA method) (atomworks.ml.transforms.symmetry.AddPostCropMoleculeEntityToFreeFloatingLigands method) (atomworks.ml.transforms.symmetry.CreateSymmetryCopyAxisLikeRF2AA method) (atomworks.ml.transforms.symmetry.FindAutomorphismsWithNetworkX method) (atomworks.ml.transforms.template.AddInputFileTemplate method) (atomworks.ml.transforms.template.AddRFTemplates method) (atomworks.ml.transforms.template.FeaturizeTemplatesLikeAF3 method) (atomworks.ml.transforms.template.FeaturizeTemplatesLikeRF2AA method) (atomworks.ml.transforms.template.OneHotTemplateRestype method) (atomworks.ml.transforms.template.RandomSubsampleTemplates method)

check_is_instance() (in module atomworks.ml.transforms._checks) check_is_shape() (in module atomworks.ml.transforms._checks) check_nonzero_length() (in module atomworks.ml.transforms._checks) chem_comp_to_one_letter() (in module atomworks.io.utils.ccd) CHEM_COMP_TYPES (in module atomworks.io.constants) CHEM_TYPE_POLYMERIZATION_ATOMS (in module atomworks.io.constants) ChEMBLNormalizer (class in atomworks.io.tools.rdkit) chemcomp_type_to_unknown (atomworks.ml.encoding_definitions.TokenEncoding attribute) ChemicalComponent (class in atomworks.io.tools.inference) ChildProcessError CIFOrPDBFileComponent (class in atomworks.io.tools.inference) clash_distance (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) ClashSeverity (class in atomworks.ml.preprocessing.constants) close_distance (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) cluster_all_sequences() (in module atomworks.ml.preprocessing.utils.clustering) cluster_identity (atomworks.ml.preprocessing.utils.clustering.MMSeqs2Config attribute) cluster_mode (atomworks.ml.preprocessing.utils.clustering.MMSeqs2Config attribute) ClusterMode (class in atomworks.ml.preprocessing.utils.clustering) components_to_atom_array() (in module atomworks.io.tools.inference) Compose (class in atomworks.ml.transforms.base) compose_rigids() (in module atomworks.ml.utils.geometry) compute_atom_to_token_map() (in module atomworks.ml.transforms.atom_array) compute_local_hash() (in module atomworks.ml.transforms.crop) compute_spatial_knn_mask() (in module atomworks.ml.transforms.masks) ComputeAtomToTokenMap (class in atomworks.ml.transforms.atom_array) ConditionalRoute (class in atomworks.ml.transforms.base) CONNECTED_COMPONENT (atomworks.ml.preprocessing.utils.clustering.ClusterMode attribute) contact_distance (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) context() (in module atomworks.ml.utils.error) convert_af3_model_output_to_atom_array_stack() (in module atomworks.ml.utils.io) convert_mse_to_met (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) convert_pn_unit_iids_to_pn_unit_ids() (in module atomworks.ml.utils.misc) convert_to_torch() (in module atomworks.ml.transforms.base) CONVERTIBLE_RDKIT_BOND_TYPES (in module atomworks.io.tools.rdkit) ConvertToTorch (class in atomworks.ml.transforms.base) copy_annotation() (in module atomworks.ml.transforms.atom_array) CopyAnnotation (class in atomworks.ml.transforms.atom_array) coverage (atomworks.ml.preprocessing.utils.clustering.MMSeqs2Config attribute) coverage_mode (atomworks.ml.preprocessing.utils.clustering.MMSeqs2Config attribute) CoverageMode (class in atomworks.ml.preprocessing.utils.clustering) create_chain_id_generator() (in module atomworks.io.utils.chain) create_fasta_file_from_df() (in module atomworks.ml.preprocessing.utils.fasta) create_rng_state_from_seeds() (in module atomworks.ml.utils.rng) CreateSymmetryCopyAxisLikeRF2AA (class in atomworks.ml.transforms.symmetry) crop_center_cutoff_distance (atomworks.ml.transforms.crop.CropSpatialLikeAF3 attribute) crop_contiguous_af2_multimer() (in module atomworks.ml.transforms.crop) crop_size (atomworks.ml.transforms.crop.CropContiguousLikeAF3 attribute) (atomworks.ml.transforms.crop.CropSpatialLikeAF3 attribute) crop_spatial_like_af3() (in module atomworks.ml.transforms.crop) CropContiguousLikeAF3 (class in atomworks.ml.transforms.crop) CropSpatialLikeAF3 (class in atomworks.ml.transforms.crop) CropTransformBase (class in atomworks.ml.transforms.crop) CRYSTALLIZATION_AIDS (in module atomworks.io.constants) cumcount() (in module atomworks.ml.utils.misc) custom_parse_kwargs (atomworks.io.tools.inference.CIFOrPDBFileComponent attribute)

D

DataPreprocessor (class in atomworks.ml.preprocessing.get_pn_unit_data_from_structure) decode() (atomworks.ml.encoding_definitions.AF3SequenceEncoding method), [1] deduplicate_iterator() (in module atomworks.io.common) default() (in module atomworks.io.common) DEFAULT_CIF_PARSER_ARGS (in module atomworks.ml.datasets.parsers.base) DEFAULT_VALENCE (in module atomworks.io.constants) dfill() (in module atomworks.ml.utils.misc)

DICT_THREE_TO_ONE (in module atomworks.io.constants) DistributedMixedSampler (class in atomworks.ml.samplers) DNA (class in atomworks.io.tools.inference) dna_chem_comps() (in module atomworks.io.utils.ccd) DNA_LIKE_CHEM_TYPES (in module atomworks.io.constants) DO_NOT_MATCH_CCD (in module atomworks.io.constants) do_nothing() (in module atomworks.ml.utils.timer)

E

ELEMENT_NAME_TO_ATOMIC_NUMBER (in module atomworks.io.constants) element_to_atomic_number() (in module atomworks.io.tools.rdkit) encode() (atomworks.ml.encoding_definitions.AF3SequenceEncoding method), [1] EncodeAF3TokenLevelFeatures (class in atomworks.ml.transforms.encoding)

EncodeAtomArray (class in atomworks.ml.transforms.encoding) ensure_atom_array_stack() (in module atomworks.io.transforms.atom_array) exists() (in module atomworks.io.common) extract_crystallization_details() (in module atomworks.io.transforms.categories) extract_transformation_id_from_pn_unit_iid() (in module atomworks.ml.utils.misc)

F

f0d (atomworks.ml.transforms.template.RF2AATemplate attribute) f1d (atomworks.ml.transforms.template.RF2AATemplate attribute) FallbackSamplerWrapper (class in atomworks.ml.samplers) featurize_templates_like_af3() (in module atomworks.ml.transforms.template) FeaturizeTemplatesLikeAF3 (class in atomworks.ml.transforms.template) FeaturizeTemplatesLikeRF2AA (class in atomworks.ml.transforms.template) filter_residue_atoms() (in module atomworks.ml.utils.io) filter_to_specified_pn_units() (in module atomworks.ml.transforms.filters) FilterToProteins (class in atomworks.ml.transforms.filters) FilterToSpecifiedPNUnits (class in atomworks.ml.transforms.filters) find_all_paths_of_length_n() (in module atomworks.ml.transforms.atom_frames) find_automorphisms() (in module atomworks.ml.transforms.symmetry) find_automorphisms_with_networkx() (in module atomworks.ml.transforms.symmetry) find_automorphisms_with_rdkit() (in module atomworks.ml.transforms.rdkit_utils) FindAutomorphismsWithNetworkX (class in atomworks.ml.transforms.symmetry) fix_arginines (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) fix_charge_based_on_valence() (in module atomworks.io.tools.rdkit) fix_ligands_at_symmetry_centers (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) fix_mol() (in module atomworks.io.tools.rdkit) flag_and_reassign_covalent_modifications() (in module atomworks.ml.transforms.covalent_modifications) FlagAndReassignCovalentModifications (class in atomworks.ml.transforms.covalent_modifications) FlagNonPolymersForAtomization (class in atomworks.ml.transforms.atomize) flatten() (in module atomworks.ml.utils.nested_dict) format_traceback() (in module atomworks.ml.utils.error) forward() (atomworks.ml.transforms.af3_reference_molecule.GetAF3ReferenceMoleculeFeatures method) (atomworks.ml.transforms.af3_reference_molecule.RandomApplyGroundTruthConformerByChainType method) (atomworks.ml.transforms.atom_array.AddGlobalAtomIdAnnotation method) (atomworks.ml.transforms.atom_array.AddGlobalResIdAnnotation method) (atomworks.ml.transforms.atom_array.AddGlobalTokenIdAnnotation method) (atomworks.ml.transforms.atom_array.AddMoleculeSymmetricIdAnnotation method) (atomworks.ml.transforms.atom_array.AddProteinTerminiAnnotation method) (atomworks.ml.transforms.atom_array.AddWithinChainInstanceResIdx method) (atomworks.ml.transforms.atom_array.AddWithinPolyResIdxAnnotation method) (atomworks.ml.transforms.atom_array.ApplyFunctionToAtomArray method) (atomworks.ml.transforms.atom_array.ComputeAtomToTokenMap method) (atomworks.ml.transforms.atom_array.CopyAnnotation method) (atomworks.ml.transforms.atom_array.RaiseIfTooManyAtoms method) (atomworks.ml.transforms.atom_array.RenumberNonPolymerResidueIdx method) (atomworks.ml.transforms.atom_array.SortLikeRF2AA method) (atomworks.ml.transforms.atom_array.SortPolyThenNonPoly method) (atomworks.ml.transforms.atom_frames.AddAtomFrames method) (atomworks.ml.transforms.atom_frames.AddIsRealAtom method) (atomworks.ml.transforms.atom_frames.AddPolymerFrameIndices method) (atomworks.ml.transforms.atomize.AtomizeByCCDName method) (atomworks.ml.transforms.atomize.FlagNonPolymersForAtomization method) (atomworks.ml.transforms.base.AddData method) (atomworks.ml.transforms.base.ApplyFunction method) (atomworks.ml.transforms.base.Compose method) (atomworks.ml.transforms.base.ConditionalRoute method) (atomworks.ml.transforms.base.ConvertToTorch method) (atomworks.ml.transforms.base.Identity method) (atomworks.ml.transforms.base.LogData method) (atomworks.ml.transforms.base.PickleToDisk method) (atomworks.ml.transforms.base.RaiseError method) (atomworks.ml.transforms.base.RaiseOnCondition method) (atomworks.ml.transforms.base.RandomRoute method) (atomworks.ml.transforms.base.RemoveKeys method) (atomworks.ml.transforms.base.SubsetToKeys method) (atomworks.ml.transforms.base.Transform method) (atomworks.ml.transforms.bonds.AddAF3TokenBondFeatures method) (atomworks.ml.transforms.bonds.AddAtomLevelBondAdjacencyMatrix method) (atomworks.ml.transforms.bonds.AddRF2AABondFeaturesMatrix method) (atomworks.ml.transforms.bonds.AddRF2AATraversalDistanceMatrix method) (atomworks.ml.transforms.bonds.AddTokenBondAdjacency method) (atomworks.ml.transforms.center_random_augmentation.CenterRandomAugmentation method) (atomworks.ml.transforms.chirals.AddAF3ChiralFeatures method) (atomworks.ml.transforms.chirals.AddRF2AAChiralFeatures method) (atomworks.ml.transforms.covalent_modifications.FlagAndReassignCovalentModifications method) (atomworks.ml.transforms.crop.CropContiguousLikeAF3 method) (atomworks.ml.transforms.crop.CropSpatialLikeAF3 method) (atomworks.ml.transforms.diffusion.batch_structures.BatchStructuresForDiffusionNoising method) (atomworks.ml.transforms.diffusion.edm.SampleEDMNoise method) (atomworks.ml.transforms.dna.pad_dna.PadDNA method) (atomworks.ml.transforms.encoding.AddTokenAnnotation method) (atomworks.ml.transforms.encoding.EncodeAF3TokenLevelFeatures method) (atomworks.ml.transforms.encoding.EncodeAtomArray method) (atomworks.ml.transforms.featurize_unresolved_residues.MaskPolymerResiduesWithUnresolvedFrameAtoms method) (atomworks.ml.transforms.featurize_unresolved_residues.MaskResiduesWithSpecificUnresolvedAtoms method) (atomworks.ml.transforms.featurize_unresolved_residues.PlaceUnresolvedTokenAtomsOnRepresentativeAtom method) (atomworks.ml.transforms.featurize_unresolved_residues.PlaceUnresolvedTokenOnClosestResolvedTokenInSequence method) (atomworks.ml.transforms.filters.FilterToSpecifiedPNUnits method) (atomworks.ml.transforms.filters.HandleUndesiredResTokens method) (atomworks.ml.transforms.filters.RandomlyRemovePNUnitsByAnnotationQuery method) (atomworks.ml.transforms.filters.RemoveHydrogens method) (atomworks.ml.transforms.filters.RemoveNucleicAcidTerminalOxygen method) (atomworks.ml.transforms.filters.RemovePolymersWithTooFewResolvedResidues method) (atomworks.ml.transforms.filters.RemoveTerminalOxygen method) (atomworks.ml.transforms.filters.RemoveUnresolvedLigandAtomsIfTooMany method) (atomworks.ml.transforms.filters.RemoveUnresolvedPNUnits method) (atomworks.ml.transforms.filters.RemoveUnresolvedTokens method) (atomworks.ml.transforms.filters.RemoveUnsupportedChainTypes method) (atomworks.ml.transforms.masks.AddSpatialKNNMask method) (atomworks.ml.transforms.rdkit_utils.AddRDKitMoleculesForAtomizedMolecules method) (atomworks.ml.transforms.rdkit_utils.GenerateRDKitConformers method) (atomworks.ml.transforms.rdkit_utils.GetRDKitChiralCenters method) (atomworks.ml.transforms.rf2aa_assumptions.AssertRF2AAAssumptions method) (atomworks.ml.transforms.sasa.CalculateSASA method) (atomworks.ml.transforms.symmetry.AddPostCropMoleculeEntityToFreeFloatingLigands method) (atomworks.ml.transforms.symmetry.CreateSymmetryCopyAxisLikeRF2AA method) (atomworks.ml.transforms.symmetry.FindAutomorphismsWithNetworkX method) (atomworks.ml.transforms.template.AddInputFileTemplate method) (atomworks.ml.transforms.template.AddRFTemplates method) (atomworks.ml.transforms.template.FeaturizeTemplatesLikeAF3 method) (atomworks.ml.transforms.template.FeaturizeTemplatesLikeRF2AA method) (atomworks.ml.transforms.template.OneHotTemplateRestype method) (atomworks.ml.transforms.template.RandomSubsampleTemplates method)

from_dict() (atomworks.io.tools.inference.ChemicalComponent static method) (atomworks.ml.transforms.base.RandomRoute class method) from_list() (atomworks.ml.transforms.base.RandomRoute class method) from_rcsb (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) from_seq() (atomworks.io.tools.inference.SequenceComponent static method)

G

GAP (in module atomworks.io.constants) GAP_ONE_LETTER (in module atomworks.io.constants) generate_automorphisms_from_atom_array_with_networkx() (in module atomworks.ml.transforms.symmetry) generate_bform_dna() (in module atomworks.ml.transforms.dna.pad_dna) generate_conformers() (in module atomworks.ml.transforms.rdkit_utils) generate_example_id() (in module atomworks.ml.common) generate_inter_level_bond_hash() (in module atomworks.io.utils.bonds) GenerateRDKitConformers (class in atomworks.ml.transforms.rdkit_utils) get() (in module atomworks.ml.utils.nested_dict) get_1_from_3_letter_code() (in module atomworks.io.utils.sequence) get_3_from_1_letter_code() (in module atomworks.io.utils.sequence) get_af3_reference_molecule_features() (in module atomworks.ml.transforms.af3_reference_molecule) get_af3_token_bond_features() (in module atomworks.ml.transforms.bonds) get_af3_token_center_coords() (in module atomworks.ml.utils.token) get_af3_token_center_idxs() (in module atomworks.ml.utils.token) get_af3_token_center_masks() (in module atomworks.ml.utils.token) get_af3_token_representative_coords() (in module atomworks.ml.utils.token) get_af3_token_representative_idxs() (in module atomworks.ml.utils.token) get_af3_token_representative_masks() (in module atomworks.ml.utils.token) get_annotation() (in module atomworks.io.utils.selection) get_atom_mask_from_cell_list() (in module atomworks.ml.preprocessing.utils.structure_utils) get_available_ccd_codes() (in module atomworks.io.utils.ccd) get_available_ccd_codes_in_biotite() (in module atomworks.io.utils.ccd) get_available_ccd_codes_in_mirror() (in module atomworks.io.utils.ccd) get_bond_distance_matrix() (in module atomworks.ml.transforms.bonds) get_bond_distances() (in module atomworks.ml.transforms.bonds) get_bonded_polymer_pn_units() (in module atomworks.ml.preprocessing.utils.structure_utils) get_ccd_component_from_biotite() (in module atomworks.io.utils.ccd) get_ccd_component_from_mirror() (in module atomworks.io.utils.ccd) get_chain_instance_starts() (in module atomworks.ml.transforms.atom_array) get_chain_type_from_ccd_code() (in module atomworks.io.utils.ccd) get_chain_type_from_chem_comp_type() (in module atomworks.io.utils.ccd) get_chem_comp_leaving_atom_names() (in module atomworks.io.utils.ccd) get_chem_comp_type() (in module atomworks.io.utils.ccd) get_chembl_normalizer() (in module atomworks.io.tools.rdkit) get_chiral_centers() (in module atomworks.ml.transforms.rdkit_utils) get_clashing_pn_units() (in module atomworks.ml.preprocessing.utils.structure_utils) get_cluster_sizes() (in module atomworks.ml.samplers) get_coarse_graph_as_nodes_and_edges() (in module atomworks.io.utils.bonds) get_connected_components_from_adjacency() (in module atomworks.ml.utils.numpy) get_connected_nodes() (in module atomworks.io.utils.bonds) get_contacting_pn_units() (in module atomworks.ml.preprocessing.utils.structure_utils) get_dih() (in module atomworks.ml.transforms.chirals) get_identity_assembly_gen_category() (in module atomworks.io.utils.non_rcsb) get_identity_op_expr_category() (in module atomworks.io.utils.non_rcsb) get_indices_of_non_constant_columns() (in module atomworks.ml.utils.numpy) get_inferred_polymer_bonds() (in module atomworks.io.utils.bonds)

get_inter_pn_unit_bond_mask() (in module atomworks.ml.preprocessing.utils.structure_utils) get_intra_pn_unit_bonds() (in module atomworks.ml.preprocessing.utils.structure_utils) get_isomorphisms_from_symmetry_groups() (in module atomworks.ml.transforms.symmetry) get_ligand_of_interest_info() (in module atomworks.io.transforms.categories) get_ligand_validity_scores_from_pdb_id() (in module atomworks.ml.preprocessing.utils.structure_utils) get_metadata_from_category() (in module atomworks.io.transforms.categories) get_morgan_fingerprint_from_rdkit_mol() (in module atomworks.io.tools.rdkit) get_msa_tax_id() (in module atomworks.ml.utils.misc) get_nearest_true_index_for_each_false() (in module atomworks.ml.utils.numpy) get_numpy_rng_state_hash() (in module atomworks.ml.utils.rng) get_pdb_mirror_path() (in module atomworks.ml.utils.testing) get_pn_units_clashing_with_pn_unit() (in module atomworks.ml.preprocessing.utils.structure_utils) get_pn_units_with_non_biological_bonds() (in module atomworks.ml.preprocessing.utils.structure_utils) get_random_rigid() (in module atomworks.ml.utils.geometry) get_random_rots() (in module atomworks.ml.utils.geometry) get_rdkit_chiral_centers() (in module atomworks.ml.transforms.rdkit_utils) get_residue_starts() (in module atomworks.io.utils.selection) get_rf2aa_atom_frames() (in module atomworks.ml.transforms.atom_frames) get_rf2aa_chiral_features() (in module atomworks.ml.transforms.chirals) get_rng_state_hash() (in module atomworks.ml.utils.rng) get_rows() (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor method) get_sharded_file_path() (in module atomworks.ml.utils.io) get_soi_ligands_from_pdb_id() (in module atomworks.ml.preprocessing.utils.structure_utils) get_spatial_crop_center() (in module atomworks.ml.transforms.crop) get_spatial_crop_mask() (in module atomworks.ml.transforms.crop) get_std_to_alt_atom_name_map() (in module atomworks.io.utils.ccd) get_struct_conn_bonds() (in module atomworks.io.utils.bonds) get_structure() (in module atomworks.io.utils.io_utils) get_token_bond_adjacency() (in module atomworks.ml.transforms.bonds) get_token_count() (in module atomworks.ml.utils.token) get_token_masks() (in module atomworks.ml.utils.token) get_token_starts() (in module atomworks.ml.utils.token) get_token_starts_for() (in module atomworks.ml.utils.token) get_torch_eps() (in module atomworks.ml.utils.geometry) get_unknown_ccd_code_for_chem_comp_type() (in module atomworks.io.utils.ccd) get_valence_checker() (in module atomworks.io.tools.rdkit) get_within_entity_idx() (in module atomworks.ml.transforms.atom_array) get_within_group_atom_idx() (in module atomworks.ml.transforms.atom_array) get_within_group_res_idx() (in module atomworks.ml.transforms.atom_array) get_within_poly_res_idx() (in module atomworks.ml.transforms.atom_array) GetAF3ReferenceMoleculeFeatures (class in atomworks.ml.transforms.af3_reference_molecule) getitem() (in module atomworks.ml.utils.nested_dict) GetRDKitChiralCenters (class in atomworks.ml.transforms.rdkit_utils) GREEDY_INCREMENTAL (atomworks.ml.preprocessing.utils.clustering.ClusterMode attribute) GREEDY_SET_COVER (atomworks.ml.preprocessing.utils.clustering.ClusterMode attribute) grouped_count() (in module atomworks.ml.utils.misc) grouped_sum() (in module atomworks.ml.utils.misc)

H

handle_clashing_pn_units() (in module atomworks.ml.preprocessing.utils.structure_utils) handle_nonpoly_automorphisms() (atomworks.ml.transforms.symmetry.CreateSymmetryCopyAxisLikeRF2AA method) handle_polymer_isomorphisms() (atomworks.ml.transforms.symmetry.CreateSymmetryCopyAxisLikeRF2AA method) HandleUndesiredResTokens (class in atomworks.ml.transforms.filters)

hash_atom_array() (in module atomworks.io.utils.bonds) hash_graph() (in module atomworks.io.utils.bonds) hash_sequence() (in module atomworks.ml.utils.misc) HYDROGEN_LIKE_SYMBOLS (in module atomworks.io.constants) hydrogen_policy (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute)

I

identify_isomorphic_chains_based_on_chain_entity() (in module atomworks.ml.transforms.symmetry) identify_isomorphic_chains_based_on_molecule_entity() (in module atomworks.ml.transforms.symmetry) Identity (class in atomworks.ml.transforms.base) ids (atomworks.ml.transforms.template.RF2AATemplate attribute) idx_to_atom (atomworks.ml.encoding_definitions.TokenEncoding property) idx_to_element (atomworks.ml.encoding_definitions.TokenEncoding property) idx_to_token (atomworks.ml.encoding_definitions.AF3SequenceEncoding property) (atomworks.ml.encoding_definitions.TokenEncoding property) ignore_residues (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) immutable_lru_cache() (in module atomworks.io.common) incompatible_previous_transforms (atomworks.ml.transforms.af3_reference_molecule.RandomApplyGroundTruthConformerByChainType attribute) (atomworks.ml.transforms.atom_array.AddGlobalAtomIdAnnotation attribute) (atomworks.ml.transforms.atom_array.AddGlobalResIdAnnotation attribute) (atomworks.ml.transforms.atom_array.AddGlobalTokenIdAnnotation attribute) (atomworks.ml.transforms.atom_array.AddProteinTerminiAnnotation attribute) (atomworks.ml.transforms.atom_array.AddWithinPolyResIdxAnnotation attribute) (atomworks.ml.transforms.atom_array.SortLikeRF2AA attribute) (atomworks.ml.transforms.atom_array.SortPolyThenNonPoly attribute) (atomworks.ml.transforms.atomize.AtomizeByCCDName attribute) (atomworks.ml.transforms.atomize.FlagNonPolymersForAtomization attribute) (atomworks.ml.transforms.base.Transform attribute) (atomworks.ml.transforms.covalent_modifications.FlagAndReassignCovalentModifications attribute) (atomworks.ml.transforms.crop.CropContiguousLikeAF3 attribute) (atomworks.ml.transforms.crop.CropSpatialLikeAF3 attribute) (atomworks.ml.transforms.diffusion.batch_structures.BatchStructuresForDiffusionNoising attribute) (atomworks.ml.transforms.featurize_unresolved_residues.MaskPolymerResiduesWithUnresolvedFrameAtoms attribute) (atomworks.ml.transforms.featurize_unresolved_residues.MaskResiduesWithSpecificUnresolvedAtoms attribute) (atomworks.ml.transforms.rdkit_utils.AddRDKitMoleculesForAtomizedMolecules attribute) (atomworks.ml.transforms.template.RandomSubsampleTemplates attribute)

infer_chain_type() (atomworks.io.tools.inference.SequenceComponent static method) initialize_chain_info_from_atom_array() (in module atomworks.io.utils.non_rcsb) initialize_chain_info_from_category() (in module atomworks.io.transforms.categories) insert_data_by_id_() (in module atomworks.ml.utils.numpy) instance_to_token_lvl_isomorphisms() (in module atomworks.ml.transforms.symmetry) invert_rigid() (in module atomworks.ml.utils.geometry) is_any_coord_nan() (in module atomworks.io.transforms.atom_array) is_clash() (in module atomworks.ml.utils.testing) is_mask_contiguous() (in module atomworks.ml.utils.numpy) is_polymer (atomworks.io.tools.inference.CCDComponent attribute) (atomworks.io.tools.inference.Peptide attribute) (atomworks.io.tools.inference.Polymer attribute) (atomworks.io.tools.inference.SDFComponent attribute) (atomworks.io.tools.inference.SequenceComponent attribute) (atomworks.io.tools.inference.SmilesComponent attribute)

J

jitter_scale (atomworks.ml.transforms.crop.CropSpatialLikeAF3 attribute)

K

keep_last_residue() (in module atomworks.io.transforms.atom_array) keep_uncropped_atom_array (atomworks.ml.transforms.crop.CropContiguousLikeAF3 attribute) (atomworks.ml.transforms.crop.CropSpatialLikeAF3 attribute)

KeyToIntMapper (class in atomworks.io.common)

L

label (atomworks.ml.transforms.template.RF2AATemplate attribute) LazyWeightedRandomSampler (class in atomworks.ml.samplers) LIGAND_LIKE_CHEM_TYPES (in module atomworks.io.constants) LigandComponent (class in atomworks.io.tools.inference) listmap() (in module atomworks.io.common)

load_any() (in module atomworks.io.utils.io_utils) load_example_from_metadata_row() (in module atomworks.ml.datasets.parsers.base) load_monomer_sequence_information_from_category() (in module atomworks.io.transforms.categories) LoadBalancedDistributedSampler (class in atomworks.ml.samplers) LogData (class in atomworks.ml.transforms.base) lookup_id (atomworks.ml.transforms.template.RF2AATemplate property)

M

mask (atomworks.ml.transforms.template.RF2AATemplate attribute) MASK_LIKE_CHEM_TYPES (in module atomworks.io.constants) mask_polymer_residues_with_unresolved_frame_atoms() (in module atomworks.ml.transforms.featurize_unresolved_residues) mask_residues_with_specific_unresolved_atoms() (in module atomworks.ml.transforms.featurize_unresolved_residues) masked_center() (in module atomworks.ml.utils.geometry) masked_mean() (in module atomworks.ml.utils.misc) MaskPolymerResiduesWithUnresolvedFrameAtoms (class in atomworks.ml.transforms.featurize_unresolved_residues) MaskResiduesWithSpecificUnresolvedAtoms (class in atomworks.ml.transforms.featurize_unresolved_residues) max_aligned_query_res_idx (atomworks.ml.transforms.template.RF2AATemplate property) max_atoms_in_crop (atomworks.ml.transforms.crop.CropContiguousLikeAF3 attribute) maybe_fix_non_polymer_at_symmetry_center() (in module atomworks.io.transforms.atom_array) md5_hash_string() (in module atomworks.io.common) MetadataRowParser (class in atomworks.ml.datasets.parsers.base) METAL_ELEMENTS (in module atomworks.io.constants) MILD (atomworks.ml.preprocessing.constants.ClashSeverity attribute) MixedSampler (class in atomworks.ml.samplers) MMSeqs2Config (class in atomworks.ml.preprocessing.utils.clustering) MODERATE (atomworks.ml.preprocessing.constants.ClashSeverity attribute) module atomworks.io.common atomworks.io.constants atomworks.io.parser atomworks.io.tools.fasta atomworks.io.tools.inference atomworks.io.tools.rdkit atomworks.io.transforms.atom_array atomworks.io.transforms.categories atomworks.io.utils.assembly atomworks.io.utils.bonds atomworks.io.utils.ccd atomworks.io.utils.chain atomworks.io.utils.io_utils atomworks.io.utils.non_rcsb atomworks.io.utils.selection atomworks.io.utils.sequence atomworks.io.utils.testing atomworks.io.utils.visualize atomworks.ml.common atomworks.ml.datasets.parsers.base atomworks.ml.datasets.parsers.custom_metadata_row_parsers atomworks.ml.encoding_definitions atomworks.ml.pipelines.af3 atomworks.ml.preprocessing.constants atomworks.ml.preprocessing.get_pn_unit_data_from_structure atomworks.ml.preprocessing.utils atomworks.ml.preprocessing.utils.clustering atomworks.ml.preprocessing.utils.fasta atomworks.ml.preprocessing.utils.structure_utils atomworks.ml.samplers atomworks.ml.transforms._checks atomworks.ml.transforms.af3_reference_molecule atomworks.ml.transforms.atom_array atomworks.ml.transforms.atom_frames atomworks.ml.transforms.atomize atomworks.ml.transforms.base atomworks.ml.transforms.bonds atomworks.ml.transforms.center_random_augmentation atomworks.ml.transforms.chirals atomworks.ml.transforms.covalent_modifications atomworks.ml.transforms.crop atomworks.ml.transforms.diffusion atomworks.ml.transforms.diffusion.batch_structures atomworks.ml.transforms.diffusion.edm atomworks.ml.transforms.dna atomworks.ml.transforms.dna.pad_dna atomworks.ml.transforms.encoding atomworks.ml.transforms.feature_aggregation, [1] atomworks.ml.transforms.featurize_unresolved_residues atomworks.ml.transforms.filters atomworks.ml.transforms.masks atomworks.ml.transforms.msa, [1] atomworks.ml.transforms.rdkit_utils atomworks.ml.transforms.rf2aa_assumptions atomworks.ml.transforms.sasa atomworks.ml.transforms.symmetry atomworks.ml.transforms.template atomworks.ml.utils.debug atomworks.ml.utils.error atomworks.ml.utils.geometry atomworks.ml.utils.io atomworks.ml.utils.misc atomworks.ml.utils.nested_dict atomworks.ml.utils.numpy atomworks.ml.utils.rng atomworks.ml.utils.testing atomworks.ml.utils.timer atomworks.ml.utils.token

msa_path (atomworks.io.tools.inference.SequenceComponent attribute) msa_paths (atomworks.io.tools.inference.CIFOrPDBFileComponent attribute) mse_to_met() (in module atomworks.io.transforms.atom_array)

N

n_atoms_per_token (atomworks.ml.encoding_definitions.TokenEncoding property) n_res_per_template (atomworks.ml.transforms.template.RF2AATemplate property) n_templates (atomworks.ml.transforms.template.RF2AATemplate property) n_tokens (atomworks.ml.encoding_definitions.AF3SequenceEncoding property) (atomworks.ml.encoding_definitions.TokenEncoding property) n_tokens() (atomworks.ml.encoding_definitions.AF3SequenceEncoding method)

na_chem_comps() (in module atomworks.io.utils.ccd) NA_LIKE_CHEM_TYPES (in module atomworks.io.constants) NO_CLASH (atomworks.ml.preprocessing.constants.ClashSeverity attribute) normalize_in_place() (atomworks.io.tools.rdkit.ChEMBLNormalizer method) not_isin() (in module atomworks.io.common) (in module atomworks.ml.utils.numpy) NUCLEIC_ACID_FRAME_ATOM_NAMES (in module atomworks.io.constants)

O

one_letter_to_ccd_code() (in module atomworks.io.tools.fasta) OneHotTemplateRestype (class in atomworks.ml.transforms.template)

open_file() (in module atomworks.ml.utils.io) optimize_conformers() (in module atomworks.ml.transforms.rdkit_utils)

P

PadDNA (class in atomworks.ml.transforms.dna.pad_dna) parse() (atomworks.ml.datasets.parsers.base.MetadataRowParser method) (in module atomworks.io.parser) parse_ccd_cif() (in module atomworks.io.utils.ccd) parse_example_id() (in module atomworks.ml.common) path (atomworks.io.tools.inference.CIFOrPDBFileComponent attribute) (atomworks.io.tools.inference.SDFComponent attribute) pdb_dna_lengths (atomworks.ml.transforms.dna.pad_dna.PadDNA attribute) pdb_ids (atomworks.ml.transforms.template.RF2AATemplate property) PDB_ISOTOPE_SYMBOL_TO_ELEMENT_SYMBOL (in module atomworks.io.constants) PDB_MIRROR_PATH (in module atomworks.io.constants) Peptide (class in atomworks.io.tools.inference) PEPTIDE_MAX_RESIDUES (in module atomworks.io.constants)

PickleToDisk (class in atomworks.ml.transforms.base) place_unresolved_token_atoms_on_token_representative_atom() (in module atomworks.ml.transforms.featurize_unresolved_residues) place_unresolved_token_on_closest_resolved_token_in_sequence() (in module atomworks.ml.transforms.featurize_unresolved_residues) PlaceUnresolvedTokenAtomsOnRepresentativeAtom (class in atomworks.ml.transforms.featurize_unresolved_residues) PlaceUnresolvedTokenOnClosestResolvedTokenInSequence (class in atomworks.ml.transforms.featurize_unresolved_residues) Polymer (class in atomworks.io.tools.inference) polymer_pn_unit_limit (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) POLYPEPTIDE_D_CHEM_TYPES (in module atomworks.io.constants) POLYPEPTIDE_L_CHEM_TYPES (in module atomworks.io.constants) preserve_annotations() (in module atomworks.io.tools.rdkit) previous_transforms_order_matters (atomworks.ml.transforms.base.Transform attribute) (atomworks.ml.transforms.symmetry.CreateSymmetryCopyAxisLikeRF2AA attribute) Protein (class in atomworks.io.tools.inference) PROTEIN_FRAME_ATOM_NAMES (in module atomworks.io.constants)

Q

qmap (atomworks.ml.transforms.template.RF2AATemplate attribute)

QUERY (atomworks.ml.preprocessing.utils.clustering.CoverageMode attribute) QUERY_IN_TARGET (atomworks.ml.preprocessing.utils.clustering.CoverageMode attribute)

R

raise_if_invalid_input (atomworks.ml.transforms.base.Identity attribute) (atomworks.ml.transforms.base.RandomRoute attribute) (atomworks.ml.transforms.base.Transform attribute) RaiseError (class in atomworks.ml.transforms.base) RaiseIfTooManyAtoms (class in atomworks.ml.transforms.atom_array) RaiseOnCondition (class in atomworks.ml.transforms.base) random_apply_ground_truth_conformer_by_chain_type() (in module atomworks.ml.transforms.af3_reference_molecule) random_remove_pn_units_by_annotation_query() (in module atomworks.ml.transforms.filters) random_rigid_augmentation() (in module atomworks.ml.utils.geometry) random_subsample_templates() (in module atomworks.ml.transforms.template) RandomApplyGroundTruthConformerByChainType (class in atomworks.ml.transforms.af3_reference_molecule) RandomlyRemoveLigands (class in atomworks.ml.transforms.filters) RandomlyRemovePNUnitsByAnnotationQuery (class in atomworks.ml.transforms.filters) RandomRoute (class in atomworks.ml.transforms.base) RandomSubsampleTemplates (class in atomworks.ml.transforms.template) RDKIT_BOND_TYPE_TO_BIOTITE (in module atomworks.io.tools.rdkit) RDKIT_HYBRIDIZATION_TO_INT (in module atomworks.io.tools.rdkit) read_any() (in module atomworks.io.utils.io_utils) read_chai_fasta() (in module atomworks.io.tools.inference) read_parquet_with_metadata() (in module atomworks.ml.utils.io) remove_ccd_components() (in module atomworks.io.transforms.atom_array) remove_ccds (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) remove_hydrogens() (in module atomworks.io.tools.rdkit) (in module atomworks.io.transforms.atom_array) (in module atomworks.ml.transforms.filters) remove_nan_coords() (in module atomworks.io.transforms.atom_array) remove_nucleic_acid_terminal_oxygen() (in module atomworks.ml.transforms.filters) remove_polymers_with_too_few_resolved_residues() (in module atomworks.ml.transforms.filters) remove_protein_terminal_oxygen() (in module atomworks.ml.transforms.filters) remove_unresolved_atoms() (in module atomworks.ml.transforms.filters) remove_unresolved_pn_units() (in module atomworks.ml.transforms.filters) remove_unresolved_tokens() (in module atomworks.ml.transforms.filters) remove_unsupported_chain_types() (in module atomworks.ml.transforms.filters) remove_waters (atomworks.ml.preprocessing.get_pn_unit_data_from_structure.DataPreprocessor attribute) remove_waters() (in module atomworks.io.transforms.atom_array) RemoveHydrogens (class in atomworks.ml.transforms.filters) RemoveKeys (class in atomworks.ml.transforms.base) RemoveNucleicAcidTerminalOxygen (class in atomworks.ml.transforms.filters) RemovePolymersWithTooFewResolvedResidues (class in atomworks.ml.transforms.filters) RemoveTerminalOxygen (class in atomworks.ml.transforms.filters) RemoveUnresolvedAtoms (class in atomworks.ml.transforms.filters) RemoveUnresolvedLigandAtomsIfTooMany (class in atomworks.ml.transforms.filters) RemoveUnresolvedPNUnits (class in atomworks.ml.transforms.filters) RemoveUnresolvedTokens (class in atomworks.ml.transforms.filters) RemoveUnsupportedChainTypes (class in atomworks.ml.transforms.filters)

RenumberNonPolymerResidueIdx (class in atomworks.ml.transforms.atom_array) replace_negative_res_ids_with_auth_seq_id() (in module atomworks.io.transforms.atom_array) required_schema (atomworks.ml.datasets.parsers.base.MetadataRowParser attribute) requires_previous_transforms (atomworks.ml.transforms.atom_array.ComputeAtomToTokenMap attribute) (atomworks.ml.transforms.atom_array.SortLikeRF2AA attribute) (atomworks.ml.transforms.atom_frames.AddAtomFrames attribute) (atomworks.ml.transforms.atom_frames.AddIsRealAtom attribute) (atomworks.ml.transforms.base.Transform attribute) (atomworks.ml.transforms.bonds.AddAF3TokenBondFeatures attribute) (atomworks.ml.transforms.bonds.AddRF2AABondFeaturesMatrix attribute) (atomworks.ml.transforms.bonds.AddTokenBondAdjacency attribute) (atomworks.ml.transforms.center_random_augmentation.CenterRandomAugmentation attribute) (atomworks.ml.transforms.chirals.AddAF3ChiralFeatures attribute) (atomworks.ml.transforms.chirals.AddRF2AAChiralFeatures attribute) (atomworks.ml.transforms.crop.CropContiguousLikeAF3 attribute) (atomworks.ml.transforms.crop.CropSpatialLikeAF3 attribute) (atomworks.ml.transforms.diffusion.edm.SampleEDMNoise attribute) (atomworks.ml.transforms.featurize_unresolved_residues.PlaceUnresolvedTokenAtomsOnRepresentativeAtom attribute) (atomworks.ml.transforms.featurize_unresolved_residues.PlaceUnresolvedTokenOnClosestResolvedTokenInSequence attribute) (atomworks.ml.transforms.filters.RemoveUnsupportedChainTypes attribute) (atomworks.ml.transforms.rdkit_utils.AddRDKitMoleculesForAtomizedMolecules attribute) (atomworks.ml.transforms.rdkit_utils.GenerateRDKitConformers attribute) (atomworks.ml.transforms.rdkit_utils.GetRDKitChiralCenters attribute) (atomworks.ml.transforms.symmetry.CreateSymmetryCopyAxisLikeRF2AA attribute) (atomworks.ml.transforms.symmetry.FindAutomorphismsWithNetworkX attribute) (atomworks.ml.transforms.template.FeaturizeTemplatesLikeAF3 attribute) (atomworks.ml.transforms.template.FeaturizeTemplatesLikeRF2AA attribute) res_name (atomworks.io.tools.inference.SDFComponent attribute) (atomworks.io.tools.inference.SmilesComponent attribute) res_name_to_af3_token() (atomworks.ml.encoding_definitions.AF3SequenceEncoding method) resize_crop_info_if_too_many_atoms() (in module atomworks.ml.transforms.crop) resolve_arginine_naming_ambiguity() (in module atomworks.io.transforms.atom_array) resolve_unknown_token_name() (atomworks.ml.encoding_definitions.TokenEncoding method) RF2_ATOM14_ENCODING (in module atomworks.ml.encoding_definitions) RF2_ATOM23_ENCODING (in module atomworks.ml.encoding_definitions) RF2AA_ATOM36_ENCODING (in module atomworks.ml.encoding_definitions) RF2AA_INIT_TEMPLATE_COORDINATES (atomworks.ml.transforms.template.RF2AATemplate attribute) RF2AA_STANDARDIZED_TOKENS (in module atomworks.ml.encoding_definitions) RF2AA_TOKEN_TO_STANDARD_TOKEN (in module atomworks.ml.encoding_definitions) RF2AATemplate (class in atomworks.ml.transforms.template) rigid_from_3_points() (in module atomworks.ml.utils.geometry) RNA (class in atomworks.io.tools.inference) rna_chem_comps() (in module atomworks.io.utils.ccd) RNA_LIKE_CHEM_TYPES (in module atomworks.io.constants) rng_state() (in module atomworks.ml.utils.rng) run_mmseqs2_clustering() (in module atomworks.ml.preprocessing.utils.clustering)

S

sample_noise_edm() (in module atomworks.ml.transforms.diffusion.edm) sample_rdkit_conformer_for_atom_array() (in module atomworks.ml.transforms.rdkit_utils) sample_t_edm() (in module atomworks.ml.transforms.diffusion.edm) SampleEDMNoise (class in atomworks.ml.transforms.diffusion.edm) save_failed_example_to_disk() (in module atomworks.ml.utils.debug) sdf_to_annotated_atom_array() (in module atomworks.io.tools.inference) sdf_to_rdkit() (in module atomworks.io.tools.rdkit) SDFComponent (class in atomworks.io.tools.inference) select_data_by_id() (in module atomworks.ml.utils.numpy) sensitivity (atomworks.ml.preprocessing.utils.clustering.MMSeqs2Config attribute) seq (atomworks.io.tools.inference.SequenceComponent attribute) (atomworks.ml.transforms.template.RF2AATemplate attribute) seq_similarity_to_query (atomworks.ml.transforms.template.RF2AATemplate property) sequence_to_annotated_atom_array() (in module atomworks.io.tools.inference) SequenceComponent (class in atomworks.io.tools.inference) serialize_rng_state_dict() (in module atomworks.ml.utils.rng) set() (in module atomworks.ml.utils.nested_dict) set_epoch() (atomworks.ml.samplers.DistributedMixedSampler method) (atomworks.ml.samplers.FallbackSamplerWrapper method) set_sampler_epoch() (in module atomworks.ml.samplers) SEVERE (atomworks.ml.preprocessing.constants.ClashSeverity attribute) SHORTER_IN_OTHER (atomworks.ml.preprocessing.utils.clustering.CoverageMode attribute) smiles (atomworks.io.tools.inference.SmilesComponent attribute) smiles_to_annotated_atom_array() (in module atomworks.io.tools.inference)

smiles_to_rdkit() (in module atomworks.io.tools.rdkit) SmilesComponent (class in atomworks.io.tools.inference) sort_like_rf2aa() (in module atomworks.ml.transforms.atom_array) sort_poly_then_non_poly() (in module atomworks.ml.transforms.atom_array) SortLikeRF2AA (class in atomworks.ml.transforms.atom_array) SortPolyThenNonPoly (class in atomworks.ml.transforms.atom_array) split_generalized_fasta_sequence() (in module atomworks.io.tools.fasta) spread_token_wise() (in module atomworks.ml.utils.token) STANDARD_AA (in module atomworks.io.constants) STANDARD_AA_ONE_LETTER (in module atomworks.io.constants) STANDARD_AA_TIP_ATOM_NAMES (in module atomworks.io.constants) STANDARD_DNA (in module atomworks.io.constants) STANDARD_DNA_ONE_LETTER (in module atomworks.io.constants) STANDARD_NA (in module atomworks.io.constants) STANDARD_PURINE_RESIDUES (in module atomworks.io.constants) STANDARD_PYRIMIDINE_RESIDUES (in module atomworks.io.constants) STANDARD_RNA (in module atomworks.io.constants) standardize_component_keys() (in module atomworks.io.tools.inference) STRUCT_CONN_BOND_ORDER_TO_INT (in module atomworks.io.constants) STRUCT_CONN_BOND_TYPES (in module atomworks.io.constants) subset() (atomworks.ml.transforms.template.RF2AATemplate method) subset_atom_array() (in module atomworks.io.transforms.atom_array) SubsetToKeys (class in atomworks.ml.transforms.base) sum_string_arrays() (in module atomworks.io.common)

T

TARGET (atomworks.ml.preprocessing.utils.clustering.CoverageMode attribute) TARGET_IN_QUERY (atomworks.ml.preprocessing.utils.clustering.CoverageMode attribute) template_ids (atomworks.ml.transforms.template.RF2AATemplate property) timeout() (in module atomworks.ml.utils.timer) timeout_using_signal() (in module atomworks.ml.utils.timer) timeout_using_subprocess() (in module atomworks.ml.utils.timer) to_atom_array() (atomworks.ml.transforms.template.RF2AATemplate method) to_cif_buffer() (in module atomworks.io.utils.io_utils) to_cif_file() (in module atomworks.io.utils.io_utils) to_cif_string() (in module atomworks.io.utils.io_utils) to_hashable() (in module atomworks.io.common) to_parquet_with_metadata() (in module atomworks.ml.utils.io)

to_reverse_complement() (in module atomworks.ml.transforms.dna.pad_dna) to_str() (atomworks.ml.encoding_definitions.TokenEncoding method) token_atoms (atomworks.ml.encoding_definitions.TokenEncoding attribute) token_iter() (in module atomworks.ml.utils.token) token_to_idx (atomworks.ml.encoding_definitions.AF3SequenceEncoding property) (atomworks.ml.encoding_definitions.TokenEncoding property) TokenEncoding (class in atomworks.ml.encoding_definitions) tokens (atomworks.ml.encoding_definitions.AF3SequenceEncoding property) (atomworks.ml.encoding_definitions.TokenEncoding property) tokens() (atomworks.ml.encoding_definitions.AF3SequenceEncoding method) Transform (class in atomworks.ml.transforms.base) TransformedDict (class in atomworks.ml.transforms.base) TransformPipelineError

U

unflatten() (in module atomworks.ml.utils.nested_dict) unique_by_first_occurrence() (in module atomworks.ml.utils.numpy) UNKNOWN_AA (in module atomworks.io.constants) UNKNOWN_ATOM (in module atomworks.io.constants) UNKNOWN_ATOMIC_NUMBER (in module atomworks.io.constants) UNKNOWN_DNA (in module atomworks.io.constants)

UNKNOWN_ELEMENT (in module atomworks.io.constants) UNKNOWN_ELEMENT_TOKEN (in module atomworks.ml.encoding_definitions) UNKNOWN_LIGAND (in module atomworks.io.constants) UNKNOWN_RNA (in module atomworks.io.constants) unknown_tokens (atomworks.ml.encoding_definitions.TokenEncoding property) update_nonpoly_seq_ids() (in module atomworks.io.transforms.atom_array)

V

validate_input (atomworks.ml.transforms.base.Identity attribute) (atomworks.ml.transforms.base.RandomRoute attribute) (atomworks.ml.transforms.base.Transform attribute)

validate_output() (atomworks.ml.datasets.parsers.base.MetadataRowParser method) ValidationDFParserLikeAF3 (class in atomworks.ml.datasets.parsers.custom_metadata_row_parsers) view() (in module atomworks.io.utils.visualize)

W

WATER_LIKE_CCDS (in module atomworks.io.constants)

wrap_sequence() (in module atomworks.ml.preprocessing.utils.fasta)

X

xyz (atomworks.ml.transforms.template.RF2AATemplate attribute)