API Documentation

Here is the API Documentation.

The following API represents the MoleculeVisualizer, which is responsible for the display of the molecule in IPywidgets.

OpenMMDL Analysis API

OpenMMDL Analysis consists of analysis, core and visualization modules.

Here is the API of the analysis modules:

API Analysis Modules:

• API Documentation for bindingmodes
  • BindingModeProcesser
    • BindingModeProcesser._gather_interactions()
    • BindingModeProcesser._process_interaction_wraper()
    • BindingModeProcesser._filtering_values()
    • BindingModeProcesser._unique_data_generation()
    • BindingModeProcesser._df_iteration_numbering()
• API Documentation for interactions
  • InteractionAnalyzer
    • InteractionAnalyzer._retrieve_plip_interactions()
    • InteractionAnalyzer._retrieve_plip_interactions_peptide()
    • InteractionAnalyzer._create_df_from_binding_site()
    • InteractionAnalyzer._change_lig_to_residue()
    • InteractionAnalyzer._process_frame()
    • InteractionAnalyzer._process_frame_special()
    • InteractionAnalyzer._process_frame_wrapper()
    • InteractionAnalyzer._process_trajectory()
• API Documentation for markovchains
  • MarkovChainAnalysis
    • MarkovChainAnalysis.generate_transition_graph()
    • MarkovChainAnalysis._calculate_min_transitions()
• API Documentation for rmsd
  • RMSDAnalyzer
    • RMSDAnalyzer.rmsd_for_atomgroups()
    • RMSDAnalyzer.rmsd_dist_frames()
    • RMSDAnalyzer.calculate_distance_matrix()
    • RMSDAnalyzer.calculate_representative_frame()
    • RMSDAnalyzer._calc_rmsd_2frames()
  • calc_rmsd_2frames_jit()
• API Documentation for stablewaters
  • StableWaters
    • StableWaters.stable_waters_pipeline()
    • StableWaters.analyze_protein_and_water_interaction()
    • StableWaters._trace_waters()
    • StableWaters._perform_clustering_and_writing()
    • StableWaters._write_pdb_clusters_and_representatives()
    • StableWaters._find_interacting_residues()

Here is the API of the core modules:

API Core Modules:

• API Documentation for Preprocessing
  • Preprocessing
    • Preprocessing.renumber_protein_residues()
    • Preprocessing.increase_ring_indices()
    • Preprocessing.process_pdb_file()
    • Preprocessing.extract_and_save_ligand_as_sdf()
    • Preprocessing.renumber_atoms_in_residues()
    • Preprocessing.replace_atom_type()
    • Preprocessing.process_pdb()
• API Documentation for TrajectorySaver
  • TrajectorySaver
    • TrajectorySaver.save_interacting_waters_trajectory()
    • TrajectorySaver.save_frame()
• API Documentation for utils
  • update_dict()
  • combine_subdict_values()
  • update_values()
  • remove_duplicate_values()
  • read_pdb_as_dataframe()
  • filter_and_parse_pdb()

Here is the API of the visualization modules:

API Visualization Modules:

• API Documentation for barcodes
  • BarcodeGenerator
    • BarcodeGenerator.generate_barcode()
    • BarcodeGenerator.interacting_water_ids()
    • BarcodeGenerator._generate_waterids_barcode()
    • BarcodeGenerator._gather_interactions()
  • BarcodePlotter
    • BarcodePlotter.plot_waterbridge_piechart()
    • BarcodePlotter.plot_barcodes_grouped()
    • BarcodePlotter._plot_barcodes()
• API Documentation for figures
  • FigureMerger
    • FigureMerger.create_and_merge_images()
  • FigureArranger
    • FigureArranger.arranged_figure_generation()
• API Documentation for highlighting
  • FigureHighlighter
    • FigureHighlighter.split_interaction_data()
    • FigureHighlighter.highlight_numbers()
    • FigureHighlighter.generate_interaction_dict()
  • LigandImageGenerator
    • LigandImageGenerator.generate_image()
• API Documentation for pharmacophore
  • PharmacophoreGenerator
    • PharmacophoreGenerator.to_dict()
    • PharmacophoreGenerator.generate_md_pharmacophore_cloudcenters()
    • PharmacophoreGenerator.generate_point_cloud_pml()
    • PharmacophoreGenerator.generate_bindingmode_pharmacophore()
    • PharmacophoreGenerator._generate_clouds()
    • PharmacophoreGenerator._format_clouds()
    • PharmacophoreGenerator._generate_pharmacophore_centers()
    • PharmacophoreGenerator._generate_pharmacophore_vectors()
    • PharmacophoreGenerator._generate_pharmacophore_centers_all_points()
• API Documentation for visualization
  • Visualizer
    • Visualizer._load_cloud()
    • Visualizer.visualize()
  • run_visualization()