utils module

Utilities for PrxteinMPNN.

• aa_convert
  • af_to_mpnn()
  • mpnn_to_af()
• autoregression
  • generate_ar_mask()
• concatenate
  • concatenate_neighbor_nodes()
• coordinates
  • apply_noise_to_coordinates()
  • compute_backbone_coordinates()
  • compute_c_beta()
  • compute_backbone_distance()
  • extend_coordinate()
  • compute_cb_precise()
• data_structures
  • ProteinStructure
    • ProteinStructure.coordinates
    • ProteinStructure.aatype
    • ProteinStructure.atom_mask
    • ProteinStructure.residue_index
    • ProteinStructure.coordinates
    • ProteinStructure.aatype
    • ProteinStructure.atom_mask
    • ProteinStructure.residue_index
    • ProteinStructure.chain_index
    • ProteinStructure.dihedrals
    • ProteinStructure.replace()
  • ModelInputs
    • ModelInputs.structure_coordinates
    • ModelInputs.sequence
    • ModelInputs.mask
    • ModelInputs.residue_index
    • ModelInputs.chain_index
    • ModelInputs.lengths
    • ModelInputs.bias
    • ModelInputs.structure_coordinates
    • ModelInputs.sequence
    • ModelInputs.mask
    • ModelInputs.residue_index
    • ModelInputs.chain_index
    • ModelInputs.lengths
    • ModelInputs.bias
    • ModelInputs.k_neighbors
    • ModelInputs.augment_eps
    • ModelInputs.replace()
  • SamplingInputs
    • SamplingInputs.prng_key
    • SamplingInputs.initial_sequence
    • SamplingInputs.structure_coordinates
    • SamplingInputs.mask
    • SamplingInputs.residue_index
    • SamplingInputs.chain_index
    • SamplingInputs.bias
    • SamplingInputs.k_neighbors
    • SamplingInputs.augment_eps
    • SamplingInputs.hyperparameters
    • SamplingInputs.iterations
    • SamplingInputs.replace()
    • SamplingInputs.prng_key
    • SamplingInputs.hyperparameters
    • SamplingInputs.iterations
  • OligomerType
    • OligomerType.MONOMER
    • OligomerType.HETEROMER
    • OligomerType.HOMOOLIGOMER
    • OligomerType.TIED_HOMOOLIGOMER
• decoding_order
  • random_decoding_order()
  • single_decoding_order()
• foldcomp_utils
  • FoldCompDatabaseEnum
    • FoldCompDatabaseEnum.ESMATLAS_FULL
    • FoldCompDatabaseEnum.ESMATLAS_v2023_02
    • FoldCompDatabaseEnum.ESMATLAS_HIGH_QUALITY
    • FoldCompDatabaseEnum.AFDB_UNIPROT_V4
    • FoldCompDatabaseEnum.AFDB_SWISSPROT_V4
    • FoldCompDatabaseEnum.AFDB_REP_V4
    • FoldCompDatabaseEnum.AFDB_REP_DARK_V4
    • FoldCompDatabaseEnum.AFDB_H_SAPIENS
    • FoldCompDatabaseEnum.AFDB_A_THALIANA
    • FoldCompDatabaseEnum.AFDB_C_ALBICANS
    • FoldCompDatabaseEnum.AFDB_C_ELEGANS
    • FoldCompDatabaseEnum.AFDB_D_DISCOIDEUM
    • FoldCompDatabaseEnum.AFDB_D_MELANOGASTER
    • FoldCompDatabaseEnum.AFDB_D_RERIO
    • FoldCompDatabaseEnum.AFDB_E_COLI
    • FoldCompDatabaseEnum.AFDB_G_MAX
    • FoldCompDatabaseEnum.AFDB_M_JANNASCHII
    • FoldCompDatabaseEnum.AFDB_M_MUSCULUS
    • FoldCompDatabaseEnum.AFDB_O_SATIVA
    • FoldCompDatabaseEnum.AFDB_R_NORVEGICUS
    • FoldCompDatabaseEnum.AFDB_S_CEREVISIAE
    • FoldCompDatabaseEnum.AFDB_S_POMBE
    • FoldCompDatabaseEnum.AFDB_Z_MAYS
  • _setup_foldcomp_database()
  • _from_fcz()
  • get_protein_structures()
  • model_from_id()
• gelu
• graph
  • compute_neighbor_offsets()
• normalize
  • layer_normalization()
  • normalize()
• radial_basis
  • compute_radial_basis()
• residue_constants
  • Bond
    • Bond.atom1_name
    • Bond.atom2_name
    • Bond.length
    • Bond.stddev
  • BondAngle
    • BondAngle.atom1_name
    • BondAngle.atom2_name
    • BondAngle.atom3name
    • BondAngle.angle_rad
    • BondAngle.stddev
  • process_lines_iter_chemical_props()
  • load_stereo_chemical_props()
  • _make_standard_atom_mask()
  • chi_angle_atom()
  • _make_rigid_transformation_4x4()
  • _make_rigid_group_constants()
  • make_atom14_dists_bounds()
• types