miniworld package

Subpackages

• miniworld.feature package
  • Submodules
  • miniworld.feature.MiniWorld_featuring_species module
    • MSA_block_deletion()
    • MSA_featurize_wo_statistics()
    • MSA_featurize_wo_statistics_by_chain()
    • center_and_realign_missing()
    • chain_break_cropping()
    • cluster_sum()
    • cutoff_chain_num()
    • display_top()
    • find_chain_combinations()
    • generate_combinations()
    • get_STRING_crop()
    • get_complex_crop()
    • get_crop()
    • get_same_crop_idx()
    • get_spatial_crop()
    • getsize()
    • permute_label()
    • random_split()
    • template_featurize()
  • Module contents
• miniworld.models_MiniWorld_v1_5_use_interaction package
  • Submodules
  • miniworld.models_MiniWorld_v1_5_use_interaction.Attention_module module
    • Attention
      • Attention.forward()
      • Attention.reset_parameter()
    • AttentionWithBias
      • AttentionWithBias.forward()
      • AttentionWithBias.reset_parameter()
    • BiasedAxialAttention
      • BiasedAxialAttention.forward()
      • BiasedAxialAttention.reset_parameter()
    • FeedForwardLayer
      • FeedForwardLayer.forward()
      • FeedForwardLayer.reset_parameter()
    • GraphTriangleAttention
      • GraphTriangleAttention.apply_RT()
      • GraphTriangleAttention.forward()
      • GraphTriangleAttention.gather_edges()
      • GraphTriangleAttention.gather_edges_3d()
      • GraphTriangleAttention.reset_parameter()
    • MSAColAttention
      • MSAColAttention.forward()
      • MSAColAttention.reset_parameter()
    • MSAColGlobalAttention
      • MSAColGlobalAttention.forward()
      • MSAColGlobalAttention.reset_parameter()
    • MSARowAttentionWithBias
      • MSARowAttentionWithBias.forward()
      • MSARowAttentionWithBias.reset_parameter()
    • SequenceWeight
      • SequenceWeight.forward()
      • SequenceWeight.reset_parameter()
    • StateAttentionGate
      • StateAttentionGate.forward()
      • StateAttentionGate.reset_parameter()
    • TriangleMultiplication
      • TriangleMultiplication.forward()
      • TriangleMultiplication.reset_parameter()
  • miniworld.models_MiniWorld_v1_5_use_interaction.AuxiliaryPredictor module
    • BinderNetwork
      • BinderNetwork.forward()
      • BinderNetwork.reset_parameter()
    • DistanceNetwork
      • DistanceNetwork.forward()
      • DistanceNetwork.reset_parameter()
    • ExpResolvedNetwork
      • ExpResolvedNetwork.forward()
      • ExpResolvedNetwork.reset_parameter()
    • LDDTNetwork
      • LDDTNetwork.forward()
      • LDDTNetwork.reset_parameter()
    • MaskedTokenNetwork
      • MaskedTokenNetwork.forward()
      • MaskedTokenNetwork.reset_parameter()
    • PAENetwork
      • PAENetwork.forward()
      • PAENetwork.reset_parameter()
  • miniworld.models_MiniWorld_v1_5_use_interaction.Embeddings module
    • Extra_emb
      • Extra_emb.forward()
      • Extra_emb.reset_parameter()
    • InteractionEmb
      • InteractionEmb.forward()
    • MSA_emb
      • MSA_emb.forward()
      • MSA_emb.reset_parameter()
    • PositionalEncoding2D
      • PositionalEncoding2D.forward()
      • PositionalEncoding2D.get_chain_break_from_mask()
      • PositionalEncoding2D.get_chain_embedding()
    • Recycling
      • Recycling.forward()
    • Species_emb
      • Species_emb.forward()
      • Species_emb.reset_parameter()
    • Templ_emb
      • Templ_emb.forward()
      • Templ_emb.reset_parameter()
    • TemplatePairStack
      • TemplatePairStack.forward()
    • TemplateTorsionStack
      • TemplateTorsionStack.forward()
      • TemplateTorsionStack.reset_parameter()
  • miniworld.models_MiniWorld_v1_5_use_interaction.MiniWorld module
    • MiniWorldModule
      • MiniWorldModule.forward()
      • MiniWorldModule.update_value_net()
  • miniworld.models_MiniWorld_v1_5_use_interaction.Track_module module
    • IPA
      • IPA.apply_RT()
      • IPA.forward()
      • IPA.gather_edges()
      • IPA.gather_edges_3d()
      • IPA.inverse_RT()
      • IPA.reset_parameter()
    • IterBlock
      • IterBlock.forward()
    • IterativeSimulator
      • IterativeSimulator.forward()
      • IterativeSimulator.reset_parameter()
    • MSA2Pair
      • MSA2Pair.forward()
      • MSA2Pair.reset_parameter()
    • MSAPairStr2MSA
      • MSAPairStr2MSA.forward()
      • MSAPairStr2MSA.reset_parameter()
    • PairStr2Pair
      • PairStr2Pair.forward()
      • PairStr2Pair.subblock()
    • SCPred
      • SCPred.forward()
      • SCPred.reset_parameter()
    • SeqSep
      • SeqSep.forward()
    • Str2Chain_IPA
      • Str2Chain_IPA.forward()
      • Str2Chain_IPA.reset_parameter()
    • Str2Residue_IPA
      • Str2Residue_IPA.forward()
      • Str2Residue_IPA.reset_parameter()
    • UpdatePairByValue
      • UpdatePairByValue.forward()
      • UpdatePairByValue.reset_parameter()
    • update_symm_Rs()
    • update_symm_subs()
  • miniworld.models_MiniWorld_v1_5_use_interaction.value_network module
    • MPNN_block
      • MPNN_block.forward()
      • MPNN_block.reset_parameter()
    • PositionWiseFeedForward
      • PositionWiseFeedForward.forward()
      • PositionWiseFeedForward.reset_parameter()
    • StrSeqValueNet
      • StrSeqValueNet.forward()
      • StrSeqValueNet.reset_parameter()
      • StrSeqValueNet.turnoff()
      • StrSeqValueNet.turnon()
    • cat_neighbors_nodes()
    • gather_edges()
    • gather_nodes()
  • Module contents
• miniworld.utils package
  • Submodules
  • miniworld.utils.DataClass module
    • MiniWorldBatchedDataClass
    • MiniWorldDataClass
    • MiniWorldLabelClass
    • MiniWorldMSAClass
    • MiniWorldTemplateClass
    • MiniWorldWrongDataClass
  • miniworld.utils.My_mistake module
    • MSA_change_idx()
    • MSA_change_idx_v2()
  • miniworld.utils.ProteinClass module
    • PDB_parsing()
    • Protein
      • Protein.get_sequence_by_chain_ID()
      • Protein.get_structure_by_chain_ID()
      • Protein.get_symmetry_related_info()
      • Protein.save()
    • ProteinMSA
      • ProteinMSA.from_a3m_file_path()
      • ProteinMSA.from_msa_tensor()
      • ProteinMSA.print_query()
      • ProteinMSA.save()
    • ProteinSequence
      • ProteinSequence.get_sequence_by_chain_ID()
      • ProteinSequence.get_sequence_length()
    • ProteinStructure
      • ProteinStructure.get_chain_length_by_ID()
      • ProteinStructure.get_chain_structure_by_ID()
      • ProteinStructure.get_structure_by_model()
    • ProteinTemplate
      • ProteinTemplate.from_dict()
      • ProteinTemplate.from_dict2()
    • ProteinTemplates
      • ProteinTemplates.filter_template_by_sequence_identity()
      • ProteinTemplates.from_hhr_file()
      • ProteinTemplates.from_pdb_file()
      • ProteinTemplates.save()
  • miniworld.utils.arguments_MiniWorld module
    • get_args()
  • miniworld.utils.chemical module
  • miniworld.utils.data_refactoring module
    • AF_Results_filtering()
    • AF_Results_json_filtering()
    • AF_Results_json_viewer()
    • PDB_parsing_from_pt()
    • STRING_refactoring()
    • a3m_pickling()
    • check_hhr_loaded()
    • get_ID_to_source_dict()
    • get_csv()
    • get_hash_dict()
    • get_query_from_a3m()
    • gzip_files()
    • hhr_dir_rerefactoring()
    • hhr_file_rerefactoring()
    • hhr_refactoring()
    • mmcif_Full_sequence_parsing()
    • mmcif_full_sequence()
    • mmcif_line_parser()
    • mmcif_loop_parser()
    • mmcif_parsing()
    • mmcif_pickling()
    • pdb_Sampling()
    • pdb_pickling()
    • print_hhr_pt()
    • protein_to_template()
    • refactoring_hhr_file()
    • test_a3m()
    • test_a3m_file()
  • miniworld.utils.ffindex module
    • FFindexEntry
      • FFindexEntry.length
      • FFindexEntry.name
      • FFindexEntry.offset
    • finish_db()
    • get_entry_by_name()
    • read_data()
    • read_entry_data()
    • read_entry_lines()
    • read_index()
    • write_entries_to_db()
    • write_entry()
    • write_entry_with_file()
  • miniworld.utils.hhpred_parser module
    • hhpred_parser()
    • parse_segment()
  • miniworld.utils.kalign_mapping module
    • kalign_mapping()
  • miniworld.utils.kinematics module
    • Qs2Rs()
    • Rs2Qs()
    • avgQ()
    • c6d_to_bins()
    • c6d_to_bins2()
    • dist_to_bins()
    • dist_to_onehot()
    • get_ang()
    • get_dih()
    • get_pair_dist()
    • normQ()
    • xyz_to_bbtor()
    • xyz_to_c6d()
    • xyz_to_chi1()
    • xyz_to_t2d()
  • miniworld.utils.output_visualize module
    • TMalign()
    • align_two_protein()
    • atom_to_pdb_line()
    • output_to_pdb()
    • protein_to_pdb()
    • tensor_to_pdb()
    • visualize_2D_heatmap()
    • visualize_2D_heatmaps()
    • visualize_2D_tensor()
    • visualize_t_map()
  • miniworld.utils.parser_util module
    • center_and_realign_missing()
    • cross_product_matrix()
    • donorHs()
    • get_Cb()
    • make_frame()
    • random_rot_trans()
    • rigid_from_3_points()
    • th_ang_v()
    • th_dih()
    • th_dih_v()
    • writepdb()
  • miniworld.utils.template_parser module
    • get_args()
    • parse_a3m()
    • parse_pdb()
    • parse_pdb_lines()
    • parse_pdb_lines_w_seq()
    • parse_pdb_w_seq()
    • parse_templates_raw()
    • read_template_pdb()
    • read_templates()
  • miniworld.utils.util module
    • cal_integrated_frame()
    • center_and_realign_missing()
    • centering_RT()
    • cross_product_matrix()
    • donorHs()
    • draw_attn()
    • draw_attn_multirow()
    • draw_pae()
    • extract_tip_atom_xyz()
    • generate_initial_xyz()
    • generate_random_xyz()
    • generate_symmetric_operation()
    • generate_symmetric_xyz()
    • get_Cb()
    • get_train_valid_data_dir_dictionary()
    • make_frame()
    • random_rot_trans()
    • rigid_from_3_points()
    • rigid_from_3_points_v2()
    • th_ang_v()
    • th_dih()
    • th_dih_v()
    • writepdb()
  • miniworld.utils.util_module module
    • ComputeAllAtomCoords
      • ComputeAllAtomCoords.forward()
    • Dropout
      • Dropout.forward()
    • XYZConverter
      • XYZConverter.compute_all_atom()
      • XYZConverter.get_tor_mask()
      • XYZConverter.get_torsions()
    • create_custom_forward()
    • get_clones()
    • get_seqsep()
    • get_topk()
    • init_lecun_normal()
    • init_lecun_normal_param()
    • make_rotX()
    • make_rotZ()
    • make_rot_axis()
    • rbf()
  • Module contents

Submodules

miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction module

class miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.EMA(model, decay)

Bases: Module

forward(*args, **kwargs)

Define the computation performed at every call.

Should be overridden by all subclasses.

Note

Although the recipe for forward pass needs to be defined within this function, one should call the Module instance afterwards instead of this since the former takes care of running the registered hooks while the latter silently ignores them.

update()

class miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.ModelVisulizer(saved_model_path, saving_dir, device, model_param={}, input_param={}, batch_size=1, maxcycle=4)

Bases: object

ATOM_REPR(atom)

draw_distogram(logit_s, saving_path)

get_fasta(fasta_path)

Input : a3m_file_path (.a3m or .a3m.gz)

get_msa(a3m_path)

inference_from_raw_data(raw_file_dict, template_mode='use_hhr', a3m_mode='use_raw_a3m', saving_dir=None, saving_intermediate=False, only_structure=True, symmetry=None, msa_save_path=None)

load_initial_xyz(initial_xyz_path, is_protein=True)

load_model(model, saved_model_path)

model_inference(inputs, device, saving_dir=None, saving_intermediate=False, only_structure=True)

save_clean_msa(msa, symmetry, save_path)

symmetric_a3m_to_diagonal_a3m(a3m_file_path, fasta_file_path, saving_path)

symmetric_a3m_to_full_a3m(a3m_file_path, fasta_file_path, saving_path)

write_pae_plddt(save_path, ID, pae, plddt)

write_pdb(pred_crds_list, seq_list, ID_list, lddt_list, idx_to_chain_list, crop_idx, File_suffix, saving_dir=None)

miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.a3m_parse(a3m_file_path)

Input : a3m_file_path (.a3m or .a3m.gz)

miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.add_weight_decay(model, l2_coeff)

miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.count_parameters(model)

miniworld.MiniWorld_train_multi_deep_v1_5_use_interaction.visualize_2D_tensor(tensor, sav_dir='permutation_test/', name='test')

Module contents