Index

A

ACCEPTED_FORMATS (in module moleculib.molecule.utils) ACCEPTED_TYPES (in module moleculib.molecule.utils) align_to() (moleculib.nucleic.datum.NucleicDatum method) (moleculib.protein.datum.ProteinDatum method) AlignedRootMeanSquareDeviation (class in moleculib.protein.metrics) all_atoms (in module moleculib.nucleic.alphabet), [1] (in module moleculib.protein.alphabet), [1] all_atoms_elements (in module moleculib.nucleic.alphabet) (in module moleculib.protein.alphabet) all_atoms_radii (in module moleculib.protein.alphabet) all_atoms_tokens (in module moleculib.nucleic.alphabet) (in module moleculib.protein.alphabet) all_nucs (in module moleculib.nucleic.alphabet), [1] all_nucs_atom_mask (in module moleculib.nucleic.alphabet) all_nucs_atom_tokens (in module moleculib.nucleic.alphabet) all_nucs_tokens (in module moleculib.nucleic.alphabet) all_residues (in module moleculib.protein.alphabet), [1] all_residues_atom_mask (in module moleculib.protein.alphabet) all_residues_atom_tokens (in module moleculib.protein.alphabet) all_residues_tokens (in module moleculib.protein.alphabet) allowed_aa (in module moleculib.sequence.datum) alphabet (in module moleculib.sequence.utils) angle_deviation (moleculib.protein.metrics.StandardChemicalDeviation attribute) angle_transform (moleculib.protein.transform.DescribeChemistry attribute) AngleLoss (class in moleculib.loss.chemistry) angles_list (moleculib.protein.datum.ProteinDatum attribute) angles_mask (moleculib.protein.datum.ProteinDatum attribute) AnnotateSecondaryStructure (class in moleculib.protein.transform) API_URL (in module moleculib.sequence.datum) apply() (moleculib.protein.datum.ProteinDatum method) apply_angles() (moleculib.protein.datum.ProteinDatum method)

apply_bonds() (moleculib.protein.datum.ProteinDatum method) apply_dihedrals() (moleculib.protein.datum.ProteinDatum method) ApplyMetricsToProtein (class in moleculib.assembly.metrics) ApplyToProteins (class in moleculib.assembly.transform) AssemblyDatum (class in moleculib.assembly.datum) AssemblyMetric (class in moleculib.assembly.metrics) AssemblyTransform (class in moleculib.assembly.transform) atom_arrays (moleculib.protein.dataset.FastFoldingDataset attribute) (moleculib.protein.dataset.ShardedFastFoldingDataset attribute) atom_coord (moleculib.molecule.datum.MoleculeDatum attribute) (moleculib.nucleic.datum.NucleicDatum attribute) (moleculib.protein.datum.ProteinDatum attribute) atom_element (moleculib.protein.datum.ProteinDatum attribute) atom_features (moleculib.molecule.dataset.QM9Dataset attribute) (moleculib.molecule.dataset.RSDataset attribute) atom_index() (in module moleculib.nucleic.alphabet) (in module moleculib.protein.alphabet) atom_mask (moleculib.molecule.datum.MoleculeDatum attribute) (moleculib.nucleic.datum.NucleicDatum attribute) (moleculib.protein.datum.ProteinDatum attribute) atom_radius (moleculib.protein.datum.ProteinDatum attribute) atom_to_nucs_index (in module moleculib.nucleic.alphabet) atom_to_nucs_mask (in module moleculib.nucleic.alphabet) atom_to_residues_index (in module moleculib.protein.alphabet) atom_to_residues_mask (in module moleculib.protein.alphabet) atom_token (moleculib.nucleic.datum.NucleicDatum attribute) (moleculib.protein.datum.ProteinDatum attribute) atom_type (moleculib.molecule.datum.MoleculeDatum attribute) atomic_numbers_Map (in module moleculib.molecule.h5_to_pdb) atoms_per_nuc (in module moleculib.nucleic.alphabet) atoms_per_residue (in module moleculib.protein.alphabet) attention (moleculib.nucleic.datum.NucleicDatum attribute)

B

backbone_atoms (in module moleculib.protein.alphabet) backbone_atoms_DNA (in module moleculib.nucleic.alphabet) backbone_atoms_RNA (in module moleculib.nucleic.alphabet) backbone_chemistry (in module moleculib.protein.alphabet) BackboneOnly (class in moleculib.protein.transform) base_atoms_per_nuc (in module moleculib.nucleic.alphabet) base_path (in module moleculib.assembly.datasets.d3pm.D3PM) (moleculib.molecule.dataset.PDBMoleculeDataset attribute) (moleculib.protein.dataset.FastFoldingDataset attribute) (moleculib.protein.dataset.PDBDataset attribute) (moleculib.protein.dataset.ShardedFastFoldingDataset attribute) (moleculib.sequence.dataset.ElutedLigandDataset attribute) (moleculib.sequence.dataset.GFPFitnessDataset attribute) (moleculib.sequence.dataset.MHCBindingAffinityDataset attribute)

batch_index (moleculib.molecule.batch.MoleculeGeometricBatch attribute) batch_size (moleculib.protein.dataset.ShardedFastFoldingDataset attribute) BETA_BACKBONE (in module moleculib.protein.alphabet) bond_deviation (moleculib.protein.metrics.StandardChemicalDeviation attribute) bond_lens_arr (in module moleculib.protein.alphabet), [1] bond_transform (moleculib.protein.transform.DescribeChemistry attribute) BondLoss (class in moleculib.loss.chemistry) bonds_list (moleculib.protein.datum.ProteinDatum attribute) bonds_mask (moleculib.protein.datum.ProteinDatum attribute) build() (moleculib.assembly.datasets.d3pm.D3PM.D3PM class method) (moleculib.molecule.dataset.PDBMoleculeDataset class method) (moleculib.protein.dataset.PDBDataset class method)

C

CaOnly (class in moleculib.protein.transform) centralize (moleculib.molecule.dataset.QM9Dataset attribute) centralize() (moleculib.protein.datum.ProteinDatum method) CHAIN_COUNTER_FIELDS (in module moleculib.protein.dataset) chain_token (moleculib.nucleic.datum.NucleicDatum attribute) (moleculib.protein.datum.ProteinDatum attribute) (moleculib.protein.datum.ProteinSequence attribute) check_dataloader_batch_size() (in module moleculib.molecule.tests.loader_test) ChemicalDeviationMetric (class in moleculib.protein.metrics) ChemicalViolationLoss (class in moleculib.loss.chemistry) ChromaDataset (class in moleculib.assembly.dataset) ClashLoss (class in moleculib.loss.chemistry) collate() (moleculib.molecule.batch.MoleculeCollator class method) (moleculib.molecule.batch.MoleculeGeometricBatch class method) (moleculib.molecule.batch.MoleculePadBatch class method)

ComplexPad (class in moleculib.assembly.transform) config (in module moleculib.molecule.utils) (in module moleculib.nucleic.datum) (in module moleculib.nucleic.utils) (in module moleculib.protein.utils) contact_map (moleculib.nucleic.datum.NucleicDatum attribute) contiguous (moleculib.protein.transform.MaskResidues attribute) count_clashes (moleculib.protein.metrics.StandardChemicalDeviation attribute) CountClashes (class in moleculib.protein.metrics) create_pdb() (in module moleculib.molecule.h5_to_pdb) create_pdb_lines_MD() (in module moleculib.molecule.h5_to_pdb) create_pdb_lines_QM() (in module moleculib.molecule.h5_to_pdb) crop_size (moleculib.molecule.transform.NucCrop attribute) (moleculib.nucleic.transform.NucCrop attribute) (moleculib.protein.transform.ProteinCrop attribute) CrossEntropyLoss (class in moleculib.loss.label)

D

D3PM (class in moleculib.assembly.datasets.d3pm.D3PM) data (moleculib.molecule.dataset.QM9Dataset attribute) (moleculib.molecule.dataset.RSDataset attribute) data_frame (moleculib.sequence.dataset.ElutedLigandDataset attribute) (moleculib.sequence.dataset.GFPFitnessDataset attribute) (moleculib.sequence.dataset.MHCBindingAffinityDataset attribute) Dataset (class in moleculib.abstract.dataset) decode_one_hot() (in module moleculib.sequence.utils) DensityDataDir (class in moleculib.molecule.dataset)

describe() (moleculib.protein.dataset.FastFoldingDataset method) describe_chemistry (moleculib.protein.metrics.StandardChemicalDeviation attribute) DescribeChemistry (class in moleculib.protein.transform) dihedral_deviation (moleculib.protein.metrics.StandardChemicalDeviation attribute) dihedral_transform (moleculib.protein.transform.DescribeChemistry attribute) DihedralLoss (class in moleculib.loss.chemistry) dihedrals_list (moleculib.protein.datum.ProteinDatum attribute) dihedrals_mask (moleculib.protein.datum.ProteinDatum attribute) directory (moleculib.molecule.dataset.DensityDataDir attribute)

E

elements (in module moleculib.nucleic.alphabet) (in module moleculib.protein.alphabet) ElutedLigandDataset (class in moleculib.sequence.dataset) empty() (moleculib.protein.datum.ProteinDatum class method) empty_nuc() (moleculib.nucleic.datum.NucleicDatum class method)

empty_seqrecord() (moleculib.sequence.datum.SeqDatum class method) encode_one_hot (moleculib.sequence.dataset.ElutedLigandDataset attribute) (moleculib.sequence.dataset.GFPFitnessDataset attribute) EnzymeCommissionDataset (class in moleculib.protein.dataset) epoch_size (moleculib.protein.dataset.FastFoldingDataset attribute) extract_rdkit_mol_properties() (in module moleculib.molecule.utils)

F

factor (moleculib.protein.transform.ProteinRescale attribute) FAST_FOLDING_PROTEINS (in module moleculib.protein.dataset) FastFoldingDataset (class in moleculib.protein.dataset) fetch_pdb_id() (moleculib.assembly.datum.AssemblyDatum class method) (moleculib.nucleic.datum.NucleicDatum class method) (moleculib.protein.datum.ProteinDatum class method) filter (moleculib.protein.transform.BackboneOnly attribute) (moleculib.protein.transform.CaOnly attribute) filter_ids (moleculib.protein.dataset.PDBDataset attribute) filter_proteins() (moleculib.assembly.datum.AssemblyDatum method) FilterProteinChains (class in moleculib.assembly.transform) fmtoks (moleculib.nucleic.datum.NucleicDatum attribute) FoldDataset (class in moleculib.protein.dataset) FoldingDiffDataset (class in moleculib.protein.dataset) FrameDiffDataset (class in moleculib.protein.dataset)

from_atom_array() (moleculib.molecule.datum.MoleculeDatum class method) (moleculib.nucleic.datum.NucleicDatum class method) (moleculib.protein.datum.ProteinDatum class method) from_datalist() (moleculib.assembly.datum.AssemblyDatum method) from_filepath() (moleculib.assembly.datum.AssemblyDatum class method) (moleculib.nucleic.datum.NucleicDatum class method) (moleculib.protein.datum.ProteinDatum class method) (moleculib.sequence.datum.SeqDatum class method) from_pdb_id() (moleculib.sequence.datum.SeqDatum class method) from_pytree() (moleculib.nucleic.datum.NucleicDatum method) from_sequence() (moleculib.sequence.datum.SeqDatum class method) from_tensor_cloud() (moleculib.protein.datum.ProteinDatum class method) from_tokens() (moleculib.sequence.datum.SeqDatum class method) from_uniprot_id() (moleculib.sequence.datum.SeqDatum class method) FuncDataset (class in moleculib.protein.dataset)

G

GeneOntologyDataset (class in moleculib.protein.dataset) geometry_to_per_residue_indexing_array() (in module moleculib.protein.alphabet) get_atom_name() (in module moleculib.molecule.h5_to_pdb) get_entries() (in module moleculib.molecule.h5_to_pdb) get_entries_QM() (in module moleculib.molecule.h5_to_pdb) get_maps() (in module moleculib.molecule.h5_to_pdb)

get_nucleotide_index() (in module moleculib.nucleic.alphabet) get_residue_index() (in module moleculib.protein.alphabet) get_sequence() (moleculib.protein.datum.ProteinDatum method) GFPFitnessDataset (class in moleculib.sequence.dataset) graph (moleculib.molecule.dataset.QM9Dataset attribute) grid_size (moleculib.molecule.dataset.DensityDataDir attribute)

H

hand (moleculib.protein.transform.MaybeMirror attribute) HELIX_BACKBONE (in module moleculib.protein.alphabet) HELIX_ROTAMERS (in module moleculib.protein.alphabet)

home_dir (in module moleculib.molecule.utils) (in module moleculib.nucleic.datum) (in module moleculib.nucleic.utils) (in module moleculib.protein.utils)

I

idcode (moleculib.assembly.datum.AssemblyDatum attribute) (moleculib.molecule.datum.MoleculeDatum attribute) (moleculib.nucleic.datum.NucleicDatum attribute) (moleculib.protein.datum.ProteinDatum attribute) (moleculib.protein.datum.ProteinSequence attribute) (moleculib.sequence.datum.SeqDatum attribute)

inner_split() (in module moleculib.molecule.utils) inner_stack() (in module moleculib.molecule.utils) insert_TERS() (in module moleculib.molecule.h5_to_pdb)

K

keep_seq (moleculib.protein.transform.BackboneOnly attribute) (moleculib.protein.transform.CaOnly attribute)

key (moleculib.loss.chemistry.ChemicalViolationLoss attribute) (moleculib.protein.metrics.ChemicalDeviationMetric attribute)

L

ligands (moleculib.assembly.datum.AssemblyDatum attribute) ListAngles (class in moleculib.protein.transform) ListBonds (class in moleculib.protein.transform)

ListDihedrals (class in moleculib.protein.transform) load_fasta_file() (in module moleculib.sequence.utils) load_index() (moleculib.molecule.dataset.PDBMoleculeDataset method) (moleculib.protein.dataset.PDBDataset method)

M

main() (in module moleculib.molecule.h5_to_pdb) mask_ratio (moleculib.protein.transform.MaskResidues attribute) MaskResidues (class in moleculib.protein.transform) max_arr_size (in module moleculib.protein.alphabet) max_atoms (moleculib.molecule.dataset.DensityDataDir attribute) MAX_COMPLEX_SIZE (in module moleculib.protein.dataset) MAX_DNA_ATOMS (in module moleculib.nucleic.alphabet) max_error (moleculib.loss.structure.VectorMapLoss attribute) max_num_atoms (moleculib.molecule.dataset.RSDataset attribute) max_radius (moleculib.loss.structure.VectorMapLoss attribute) MAX_RES_ATOMS (in module moleculib.nucleic.alphabet) MaybeMirror (class in moleculib.protein.transform) measure (moleculib.loss.chemistry.ChemicalViolationLoss attribute) (moleculib.protein.metrics.ChemicalDeviationMetric attribute) measure_angles() (in module moleculib.protein.metrics) (moleculib.loss.chemistry.AngleLoss static method) measure_bonds() (in module moleculib.protein.metrics) (moleculib.loss.chemistry.BondLoss static method) measure_chirality() (in module moleculib.protein.transform) measure_dihedrals() (in module moleculib.protein.metrics) (moleculib.loss.chemistry.DihedralLoss static method) measure_fn (moleculib.loss.structure.VectorMapLoss attribute) measure_rmsd() (in module moleculib.protein.utils) member_list (moleculib.molecule.dataset.DensityDataDir attribute) metadata (moleculib.molecule.dataset.PDBMoleculeDataset attribute) (moleculib.protein.dataset.PDBDataset attribute) metrics_list (moleculib.abstract.metrics.MetricsPipe attribute) MetricsPipe (class in moleculib.abstract.metrics) MHCBindingAffinityDataset (class in moleculib.sequence.dataset) module moleculib moleculib.abstract moleculib.abstract.dataset moleculib.abstract.metrics moleculib.abstract.transform moleculib.assembly moleculib.assembly.dataset moleculib.assembly.datasets.d3pm.D3PM moleculib.assembly.datum moleculib.assembly.metrics moleculib.assembly.transform moleculib.loss.chemistry moleculib.loss.label moleculib.loss.structure moleculib.molecule moleculib.molecule.alphabet moleculib.molecule.batch moleculib.molecule.dataset moleculib.molecule.datum moleculib.molecule.h5_to_pdb moleculib.molecule.tests moleculib.molecule.tests.loader_test moleculib.molecule.transform moleculib.molecule.utils moleculib.nucleic moleculib.nucleic.alphabet moleculib.nucleic.batch moleculib.nucleic.dataset moleculib.nucleic.datum moleculib.nucleic.transform moleculib.nucleic.utils moleculib.protein moleculib.protein.alphabet moleculib.protein.dataset moleculib.protein.datum moleculib.protein.measures moleculib.protein.metrics moleculib.protein.transform moleculib.protein.utils moleculib.sequence moleculib.sequence.dataset moleculib.sequence.datum moleculib.sequence.metrics moleculib.sequence.transform moleculib.sequence.utils MoleculeCollator (class in moleculib.molecule.batch) MoleculeDatum (class in moleculib.molecule.datum) MoleculeGeometricBatch (class in moleculib.molecule.batch) MoleculePadBatch (class in moleculib.molecule.batch) moleculib module moleculib.abstract module moleculib.abstract.dataset module moleculib.abstract.metrics module

moleculib.abstract.transform module moleculib.assembly module moleculib.assembly.dataset module moleculib.assembly.datasets.d3pm.D3PM module moleculib.assembly.datum module moleculib.assembly.metrics module moleculib.assembly.transform module moleculib.loss.chemistry module moleculib.loss.label module moleculib.loss.structure module moleculib.molecule module moleculib.molecule.alphabet module moleculib.molecule.batch module moleculib.molecule.dataset module moleculib.molecule.datum module moleculib.molecule.h5_to_pdb module moleculib.molecule.tests module moleculib.molecule.tests.loader_test module moleculib.molecule.transform module moleculib.molecule.utils module moleculib.nucleic module moleculib.nucleic.alphabet module moleculib.nucleic.batch module moleculib.nucleic.dataset module moleculib.nucleic.datum module moleculib.nucleic.transform module moleculib.nucleic.utils module moleculib.protein module moleculib.protein.alphabet module moleculib.protein.dataset module moleculib.protein.datum module moleculib.protein.measures module moleculib.protein.metrics module moleculib.protein.transform module moleculib.protein.utils module moleculib.sequence module moleculib.sequence.dataset module moleculib.sequence.datum module moleculib.sequence.metrics module moleculib.sequence.transform module moleculib.sequence.utils module MonomerDataset (class in moleculib.protein.dataset) msa (moleculib.nucleic.datum.NucleicDatum attribute) msa_depth (moleculib.molecule.transform.PrepareForPipeline attribute) (moleculib.nucleic.transform.PrepareForPipeline attribute)

N

norm() (in module moleculib.protein.metrics) norm_only (moleculib.loss.structure.VectorMapLoss attribute) normalize() (in module moleculib.protein.metrics) (in module moleculib.protein.transform) nuc_index (moleculib.nucleic.datum.NucleicDatum attribute) nuc_mask (moleculib.nucleic.datum.NucleicDatum attribute) nuc_token (moleculib.nucleic.datum.NucleicDatum attribute) NucCrop (class in moleculib.molecule.transform) (class in moleculib.nucleic.transform) NucleicDatum (class in moleculib.nucleic.datum)

NucPad (class in moleculib.molecule.transform) (class in moleculib.nucleic.transform) NucTransform (class in moleculib.molecule.transform) (class in moleculib.nucleic.transform) num_chains (moleculib.assembly.transform.ComplexPad attribute) (moleculib.assembly.transform.FilterProteinChains attribute) num_folders (moleculib.protein.dataset.FastFoldingDataset attribute) num_interactive_atoms (moleculib.protein.metrics.ChemicalDeviationMetric attribute) num_nodes (moleculib.molecule.batch.MoleculeGeometricBatch attribute) num_shards (moleculib.protein.dataset.ShardedFastFoldingDataset attribute)

O

one_hot_encode_seq() (in module moleculib.sequence.utils) onehot_encode_datum() (in module moleculib.sequence.dataset) (in module moleculib.sequence.utils) (moleculib.sequence.datum.SeqDatum method)

P

pad_array() (in module moleculib.molecule.utils) (in module moleculib.nucleic.utils) (in module moleculib.protein.utils) pad_mask (moleculib.nucleic.datum.NucleicDatum attribute) pad_size (moleculib.molecule.transform.NucPad attribute) (moleculib.nucleic.transform.NucPad attribute) (moleculib.protein.transform.ProteinPad attribute) padding (moleculib.molecule.dataset.DensityDataDir attribute) (moleculib.molecule.dataset.QM9Dataset attribute) (moleculib.molecule.dataset.RSDataset attribute) parse() (moleculib.protein.dataset.MonomerDataset method) (moleculib.protein.dataset.PDBDataset method) parser (in module moleculib.molecule.h5_to_pdb) PDB_HEADER_FIELDS (in module moleculib.protein.dataset) PDB_METADATA_FIELDS (in module moleculib.protein.dataset) pdb_to_atom_array() (in module moleculib.molecule.utils) (in module moleculib.nucleic.datum) (in module moleculib.nucleic.utils) (in module moleculib.protein.utils) PDBDataset (class in moleculib.protein.dataset) PDBMoleculeDataset (class in moleculib.molecule.dataset) peptide_bonds (moleculib.protein.transform.ListBonds attribute) PERIODIC_TABLE (in module moleculib.molecule.alphabet) permute (moleculib.molecule.dataset.QM9Dataset attribute) (moleculib.molecule.dataset.RSDataset attribute)

pids_file_to_list() (in module moleculib.molecule.utils) (in module moleculib.nucleic.utils) (in module moleculib.protein.utils) plot() (moleculib.assembly.datum.AssemblyDatum method) (moleculib.molecule.datum.MoleculeDatum method) (moleculib.nucleic.datum.NucleicDatum method) (moleculib.protein.datum.ProteinDatum method) plot_dock() (in module moleculib.molecule.utils) plot_py3dmol_grid() (in module moleculib.molecule.utils) preload (moleculib.molecule.dataset.PDBMoleculeDataset attribute) PrepareForPipeline (class in moleculib.molecule.transform) (class in moleculib.nucleic.transform) PreProcessedDataset (class in moleculib.abstract.dataset) (class in moleculib.molecule.dataset) protein_metrics (moleculib.assembly.metrics.ApplyMetricsToProtein attribute) protein_transform (moleculib.assembly.transform.ApplyToProteins attribute) ProteinCrop (class in moleculib.protein.transform) ProteinDatum (class in moleculib.protein.datum) ProteinMetric (class in moleculib.protein.metrics) ProteinPad (class in moleculib.protein.transform) ProteinRescale (class in moleculib.protein.transform) proteins (moleculib.assembly.datum.AssemblyDatum attribute) (moleculib.protein.dataset.FastFoldingDataset attribute) (moleculib.protein.dataset.ShardedFastFoldingDataset attribute) ProteinSequence (class in moleculib.protein.datum) ProteinTransform (class in moleculib.protein.transform)

Q

QM9Dataset (class in moleculib.molecule.dataset)

R

radius_multiplier (moleculib.protein.metrics.CountClashes attribute) random_position (moleculib.protein.transform.ProteinPad attribute) register_pytree() (in module moleculib.molecule.utils) replace() (moleculib.protein.datum.ProteinDatum method) residue_index (moleculib.protein.datum.ProteinDatum attribute) (moleculib.protein.datum.ProteinSequence attribute) residue_mask (moleculib.protein.datum.ProteinDatum attribute) (moleculib.protein.datum.ProteinSequence attribute) residue_token (moleculib.protein.datum.ProteinDatum attribute) (moleculib.protein.datum.ProteinSequence attribute) (moleculib.sequence.datum.SeqDatum attribute)

residue_tokens_to_sequence() (in module moleculib.sequence.utils) resolution (moleculib.nucleic.datum.NucleicDatum attribute) (moleculib.protein.datum.ProteinDatum attribute) revert() (moleculib.molecule.batch.MoleculeCollator method) (moleculib.molecule.batch.MoleculeGeometricBatch method) (moleculib.molecule.batch.MoleculePadBatch method) rigid_Kabsch_3D() (in module moleculib.protein.utils) RNADataset (class in moleculib.nucleic.dataset) rotate_voxel (moleculib.molecule.dataset.DensityDataDir attribute) rotate_voxel() (in module moleculib.molecule.dataset) RSDataset (class in moleculib.molecule.dataset)

S

safe_norm() (in module moleculib.loss.chemistry) (in module moleculib.loss.structure) (in module moleculib.protein.metrics) safe_normalize() (in module moleculib.loss.chemistry) SAMPLE_PDBS (in module moleculib.protein.dataset) samples (moleculib.molecule.dataset.DensityDataDir attribute) save_fasta_file() (in module moleculib.sequence.utils) ScaffoldsDataset (class in moleculib.protein.dataset) secondary_dot_bracket_to_contact_map() (in module moleculib.nucleic.dataset) separate_chains() (moleculib.protein.datum.ProteinDatum static method) SeqDatum (class in moleculib.sequence.datum) sequence (moleculib.nucleic.datum.NucleicDatum attribute) (moleculib.protein.datum.ProteinDatum attribute) (moleculib.protein.datum.ProteinSequence attribute) (moleculib.sequence.datum.SeqDatum attribute) set() (moleculib.nucleic.datum.NucleicDatum method) (moleculib.protein.datum.ProteinDatum method) ShardedFastFoldingDataset (class in moleculib.protein.dataset) sidechain_atoms_per_residue (in module moleculib.protein.alphabet) sidechain_chemistry_per_residue (in module moleculib.protein.alphabet) smooth (moleculib.protein.metrics.CountClashes attribute)

sorter (moleculib.molecule.dataset.QM9Dataset attribute) special_tokens (in module moleculib.nucleic.alphabet) (in module moleculib.protein.alphabet) split_datum_by_chain() (in module moleculib.nucleic.dataset) splits (moleculib.abstract.dataset.PreProcessedDataset attribute) (moleculib.molecule.dataset.PDBMoleculeDataset attribute) (moleculib.molecule.dataset.PreProcessedDataset attribute) (moleculib.protein.dataset.FastFoldingDataset attribute) (moleculib.protein.dataset.MonomerDataset attribute) (moleculib.protein.dataset.ShardedFastFoldingDataset attribute) (moleculib.sequence.dataset.ElutedLigandDataset attribute) (moleculib.sequence.dataset.GFPFitnessDataset attribute) (moleculib.sequence.dataset.MHCBindingAffinityDataset attribute) SSE_TOKENS (in module moleculib.protein.transform) StackProteins (class in moleculib.assembly.transform) STANDARD_CHEMICAL_MEASURES (in module moleculib.protein.measures) StandardAngleDeviation (class in moleculib.protein.metrics) StandardBondDeviation (class in moleculib.protein.metrics) StandardChemicalDeviation (class in moleculib.protein.metrics) StandardDihedralDeviation (class in moleculib.protein.metrics) standardize (moleculib.molecule.dataset.QM9Dataset attribute) stride (moleculib.protein.dataset.FastFoldingDataset attribute)

T

tau (moleculib.protein.dataset.FastFoldingDataset attribute) (moleculib.protein.dataset.ShardedFastFoldingDataset attribute) TAUS (in module moleculib.protein.dataset) test_dataload_from_filesystem() (in module moleculib.molecule.tests.loader_test) test_dataloader() (in module moleculib.molecule.tests.loader_test) time_sort (moleculib.protein.dataset.FastFoldingDataset attribute) (moleculib.protein.dataset.ShardedFastFoldingDataset attribute) TinyPDBDataset (class in moleculib.protein.dataset), [1] to() (moleculib.molecule.batch.MoleculeCollator method) to_atom_array() (moleculib.protein.datum.ProteinDatum method) to_dict() (moleculib.molecule.batch.MoleculeCollator method) (moleculib.nucleic.datum.NucleicDatum method) to_pdb_str() (moleculib.molecule.datum.MoleculeDatum method) (moleculib.nucleic.datum.NucleicDatum method) (moleculib.protein.datum.ProteinDatum method) to_pytree() (moleculib.nucleic.datum.NucleicDatum method) to_tensor_cloud() (moleculib.nucleic.datum.NucleicDatum method) (moleculib.protein.datum.ProteinDatum method) TokenizeSequenceBoundaries (class in moleculib.protein.transform) torch() (moleculib.molecule.batch.MoleculeCollator method) transform (moleculib.abstract.dataset.Dataset attribute) (moleculib.abstract.dataset.PreProcessedDataset attribute) (moleculib.molecule.dataset.PDBMoleculeDataset attribute) (moleculib.molecule.dataset.PreProcessedDataset attribute) (moleculib.protein.dataset.PDBDataset attribute) (moleculib.sequence.dataset.ElutedLigandDataset attribute) (moleculib.sequence.dataset.GFPFitnessDataset attribute) (moleculib.sequence.dataset.MHCBindingAffinityDataset attribute)

transform() (moleculib.assembly.metrics.AssemblyMetric method) (moleculib.assembly.transform.ApplyToProteins method) (moleculib.assembly.transform.AssemblyTransform method) (moleculib.assembly.transform.ComplexPad method) (moleculib.assembly.transform.FilterProteinChains method) (moleculib.assembly.transform.StackProteins method) (moleculib.assembly.transform.UnstackProteins method) (moleculib.molecule.transform.NucCrop method) (moleculib.molecule.transform.NucPad method) (moleculib.molecule.transform.NucTransform method) (moleculib.molecule.transform.PrepareForPipeline method) (moleculib.nucleic.transform.NucCrop method) (moleculib.nucleic.transform.NucPad method) (moleculib.nucleic.transform.NucTransform method) (moleculib.nucleic.transform.PrepareForPipeline method)

U

UNK_TOKEN (in module moleculib.protein.alphabet) UnstackProteins (class in moleculib.assembly.transform)

update_residue_indices() (in module moleculib.molecule.h5_to_pdb) use_atom_features (moleculib.molecule.dataset.QM9Dataset attribute) (moleculib.molecule.dataset.RSDataset attribute)

V

van_der_walls_radii (in module moleculib.protein.alphabet)

var_clip (moleculib.protein.metrics.ChemicalDeviationMetric attribute) VectorMapLoss (class in moleculib.loss.structure)

W

web_ds (moleculib.protein.dataset.ShardedFastFoldingDataset attribute)

write_pdb() (in module moleculib.molecule.h5_to_pdb)