bindingrmsd package

Subpackages

• bindingrmsd.data package
  • Submodules
  • bindingrmsd.data.data module
    • PoseSelectionDataset
      • PoseSelectionDataset.lig_dummy_graph()
    • load_ligands()
    • process_ligand_file()
  • bindingrmsd.data.data_bck module
    • PoseSelectionDataset
      • PoseSelectionDataset.lig_dummy_graph()
    • load_ligands()
    • process_dlg()
    • process_ligand_file()
  • bindingrmsd.data.ligand_atom_feature module
    • atom_feature()
    • bond_feature()
    • calculate_pair_distance()
    • get_atom_feature()
    • get_bond_feature()
    • get_distance_feature()
    • get_indices()
    • get_indices_sparse()
    • get_interact_feature()
    • get_mol_coordinate()
    • get_smarts_feature()
    • is_one()
    • load_obj()
    • mol_to_graph()
    • one_hot()
    • save_obj()
  • bindingrmsd.data.protein_atom_feature module
    • get_all_graph()
    • pl_to_c_graph()
    • prot_to_graph()
    • scaler()
  • bindingrmsd.data.utils module
    • is_one()
    • load_obj()
    • one_hot()
    • save_obj()
  • Module contents
• bindingrmsd.model package
  • Submodules
  • bindingrmsd.model.GatedGCNLSPE module
    • GatedGCNLSPELayer
      • GatedGCNLSPELayer.compute_normalized_eta()
      • GatedGCNLSPELayer.forward()
      • GatedGCNLSPELayer.message_func_for_pj()
      • GatedGCNLSPELayer.message_func_for_vij()
  • bindingrmsd.model.model module
    • PredictionRMSD
      • PredictionRMSD.forward()
  • Module contents

Submodules

bindingrmsd.inference module

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

bindingrmsd.inference.main()

Main entry point for the command line interface.

Module contents