utils module

Utilities for PrxteinMPNN.

• aa_convert
  • af_to_mpnn()
  • mpnn_to_af()
  • string_key_to_index()
  • string_to_protein_sequence()
  • protein_sequence_to_string()
• autoregression
  • get_decoding_step_map()
  • make_autoregressive_mask()
  • resolve_tie_groups()
  • 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
  • ProteinTuple
    • ProteinTuple.coordinates
    • ProteinTuple.aatype
    • ProteinTuple.atom_mask
    • ProteinTuple.residue_index
    • ProteinTuple.chain_index
    • ProteinTuple.dihedrals
    • ProteinTuple.coordinates
    • ProteinTuple.aatype
    • ProteinTuple.atom_mask
    • ProteinTuple.residue_index
    • ProteinTuple.chain_index
    • ProteinTuple.full_coordinates
    • ProteinTuple.dihedrals
    • ProteinTuple.source
    • ProteinTuple.mapping
    • ProteinTuple.charges
    • ProteinTuple.radii
    • ProteinTuple.estat_backbone_mask
    • ProteinTuple.estat_resid
    • ProteinTuple.estat_chain_index
  • TrajectoryStaticFeatures
    • TrajectoryStaticFeatures.aatype
    • TrajectoryStaticFeatures.static_atom_mask_37
    • TrajectoryStaticFeatures.residue_indices
    • TrajectoryStaticFeatures.chain_index
    • TrajectoryStaticFeatures.valid_atom_mask
    • TrajectoryStaticFeatures.nitrogen_mask
    • TrajectoryStaticFeatures.num_residues
  • include_feature()
  • EstatInfo
    • EstatInfo.charges
    • EstatInfo.radii
    • EstatInfo.estat_backbone_mask
    • EstatInfo.estat_resid
    • EstatInfo.estat_chain_index
    • EstatInfo.charges
    • EstatInfo.radii
    • EstatInfo.estat_backbone_mask
    • EstatInfo.estat_resid
    • EstatInfo.estat_chain_index
    • EstatInfo.replace()
  • Protein
    • Protein.coordinates
    • Protein.aatype
    • Protein.mask
    • Protein.residue_index
    • Protein.chain_index
    • Protein.dihedrals
    • Protein.mapping
    • Protein.full_coordinates
    • Protein.full_atom_mask
    • Protein.coordinates
    • Protein.aatype
    • Protein.one_hot_sequence
    • Protein.mask
    • Protein.residue_index
    • Protein.chain_index
    • Protein.dihedrals
    • Protein.mapping
    • Protein.full_coordinates
    • Protein.full_atom_mask
    • Protein.charges
    • Protein.radii
    • Protein.estat_backbone_mask
    • Protein.estat_resid
    • Protein.estat_chain_index
    • Protein.from_tuple()
    • Protein.replace()
  • _EStepState
    • _EStepState.component_counts
    • _EStepState.weighted_data
    • _EStepState.weighted_squared_data
    • _EStepState.log_likelihood_total
    • _EStepState.replace()
  • GMM
    • GMM.means
    • GMM.covariances
    • GMM.weights
    • GMM.responsibilities
    • GMM.n_components
    • GMM.n_features
    • GMM.replace()
  • EMLoopState
    • EMLoopState.gmm
    • EMLoopState.n_iter
    • EMLoopState.log_likelihood
    • EMLoopState.log_likelihood_diff
  • EMFitterResult
    • EMFitterResult.gmm
    • EMFitterResult.n_iter
    • EMFitterResult.log_likelihood
    • EMFitterResult.log_likelihood_diff
    • EMFitterResult.converged
    • EMFitterResult.features
    • EMFitterResult.bic
    • EMFitterResult.replace()
• decoding_order
  • random_decoding_order()
  • single_decoding_order()
• foldcomp_utils
  • _setup_foldcomp_database()
  • get_protein_structures()
• 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