bapred package

Subpackages

• bapred.data package
  • Submodules
  • bapred.data.atom_feature module
    • atom_feature()
    • bond_feature()
    • get_atom_feature()
    • get_bond_feature()
    • get_distance_feature()
    • get_indices()
    • get_indices_sparse()
    • get_interact_feature()
    • get_mol_coordinate()
    • get_smarts_feature()
  • bapred.data.data module
    • BAPredDataset
      • BAPredDataset.comp_dummy_graph()
      • BAPredDataset.complex_to_graph()
      • BAPredDataset.get_pocket_with_ligand_in_protein()
      • BAPredDataset.get_protein_info()
      • BAPredDataset.lig_dummy_graph()
      • BAPredDataset.mol_to_graph()
      • BAPredDataset.prot_dummy_graph()
    • load_ligands()
    • process_ligand_file()
  • bapred.data.utils module
    • calculate_pair_distance()
    • is_one()
    • load_obj()
    • one_hot()
    • save_obj()
  • Module contents
• bapred.model package
  • Submodules
  • bapred.model.GatedGCNLSPE module
    • GatedGCNLSPELayer
      • GatedGCNLSPELayer.compute_normalized_eta()
      • GatedGCNLSPELayer.forward()
      • GatedGCNLSPELayer.message_func_for_pj()
      • GatedGCNLSPELayer.message_func_for_vij()
  • bapred.model.GraphGPS module
    • GraphGPS
      • GraphGPS.forward()
  • bapred.model.MHA module
    • MultiHeadAttention
      • MultiHeadAttention.forward()
  • bapred.model.model module
    • PredictionPKD
      • PredictionPKD.forward()
  • Module contents

Submodules

bapred.inference module

bapred.inference.inference(protein_pdb, ligand_file, output, batch_size, model_path, device='cpu')

Module contents