API Reference

This section contains the complete API reference for PrxteinMPNN.

API Reference:

• io: Input/Output for Structure and Trajectories
  • _check_if_file_empty()
  • string_key_to_index()
  • string_to_protein_sequence()
  • protein_sequence_to_string()
  • residue_names_to_aatype()
  • atom_names_to_index()
  • _check_atom_array_length()
  • _get_chain_index()
  • _process_chain_id()
  • _fill_in_cb_coordinates()
  • process_atom_array()
  • from_structure_file()
  • from_trajectory()
  • from_string()
  • protein_structure_to_model_inputs()
• mpnn: Fetch model parameters
  • ProteinMPNNModelVersion
  • ModelWeights
  • get_mpnn_model()
• model: MPNN model architecture
  • MaskedAttentionEnum
  • dense_layer()
  • extract_features()
  • final_projection()
  • make_decoder()
  • make_encoder()
  • encoder
  • decoder
  • projection
  • masked_attention
  • features
• sampling: Sampling methods for MPNN
  • SamplingConfig
  • SamplingEnum
  • make_sample_sequences()
  • initialize
  • sample
  • sampling_step
  • ste
• scoring: Scoring functions for MPNN
  • score
• utils: Utility functions for MPNN
  • aa_convert
  • autoregression
  • concatenate
  • coordinates
  • data_structures
  • decoding_order
  • foldcomp_utils
  • gelu
  • graph
  • normalize
  • radial_basis
  • residue_constants
  • types