mdigest package

Subpackages

• mdigest.core package
  • Subpackages
    • mdigest.core.plots package
      • Submodules
      • mdigest.core.plots.dim_reduction_plots module
      • mdigest.core.plots.general_plots module
      • mdigest.core.plots.plot_correlation module
      • Module contents
  • Submodules
  • mdigest.core.analysis module
    • MDS_analysis
      • MDS_analysis.align_traj()
      • MDS_analysis.calc_NH_order_params()
      • MDS_analysis.calc_chi1()
      • MDS_analysis.calc_rms_quant()
      • MDS_analysis.compute_radius_of_gyration()
      • MDS_analysis.do_dihedral_calcs()
      • MDS_analysis.do_ss_calculation()
      • MDS_analysis.get_universe()
      • MDS_analysis.load_class_from_file()
      • MDS_analysis.load_system()
      • MDS_analysis.save_class()
      • MDS_analysis.set_NH_selections()
      • MDS_analysis.set_node_type_sele()
      • MDS_analysis.set_num_replicas()
      • MDS_analysis.set_selection()
      • MDS_analysis.stride_trajectory()
  • mdigest.core.auxiliary module
    • compute_DCC()
    • compute_DCC_matrix()
    • compute_distance_matrix()
    • compute_eigenvector_centrality()
    • compute_generalized_correlation_coefficients()
    • coordinate_reshape()
    • corr()
    • create_graph()
    • evaluate_covariance_matrix()
    • filter_adjacency()
    • filter_adjacency_inv()
    • get_centrality_df()
    • linfit()
    • prune_adjacency()
    • reduce_trajectory()
    • sorted_eig()
    • to_pickle()
    • vec_query()
  • mdigest.core.correlation module
    • DynCorr
      • DynCorr.edge_exclusion()
      • DynCorr.parse_dynamics()
      • DynCorr.save_class()
  • mdigest.core.dcorrelation module
    • DihDynCorr
      • DihDynCorr.parse_dih_dynamics()
      • DihDynCorr.save_class()
  • mdigest.core.imports module
  • mdigest.core.kscorrelation module
    • KS_Box
    • KS_Energy
      • KS_Energy.KS_pipeline()
      • KS_Energy.compute_EEC()
      • KS_Energy.compute_KS_energy()
      • KS_Energy.compute_distances_parallel()
      • KS_Energy.prepare_kabsch_sander_arrays()
      • KS_Energy.save_class()
      • KS_Energy.set_backbone_dictionary()
      • KS_Energy.set_charges_array()
      • KS_Energy.set_offset()
      • KS_Energy.set_selection()
  • mdigest.core.networkcanvas module
    • ProcCorr
      • ProcCorr.corrNetworkPymol()
      • ProcCorr.filter_by_distance()
      • ProcCorr.get_selection_fromMDS()
      • ProcCorr.load_matrix_dictionary()
      • ProcCorr.populate_attributes()
      • ProcCorr.select_frame_coordinates()
      • ProcCorr.set_outputparams()
      • ProcCorr.set_selection()
      • ProcCorr.set_thresholds()
      • ProcCorr.source_universe()
      • ProcCorr.to_df()
      • ProcCorr.writePDBforframe()
    • display_community()
    • draw_electrostatic_network()
    • ss_network()
  • mdigest.core.networkcommunities module
    • CMTY
      • CMTY.assign_filters()
      • CMTY.best_iteration_louvain()
      • CMTY.calculate_betweenness()
      • CMTY.community_data()
      • CMTY.compute_optimal_paths()
      • CMTY.create_matrix_dict()
      • CMTY.get_degree()
      • CMTY.girvannewman()
      • CMTY.load_graph()
      • CMTY.most_valuable_edge()
      • CMTY.most_valuable_edge_fw()
      • CMTY.populate_filters()
      • CMTY.retrieve_path()
      • CMTY.run_cmty_louvain()
      • CMTY.run_cmtys_louvain()
      • CMTY.save_class()
      • CMTY.set_parameters()
      • CMTY.sort_cmty()
    • display_shortes_path()
  • mdigest.core.parsetrajectory module
    • MDS
      • MDS.align_traj()
      • MDS.get_universe()
      • MDS.load_system()
      • MDS.set_num_replicas()
      • MDS.set_selection()
      • MDS.source_system()
      • MDS.stride_trajectory()
  • mdigest.core.savedata module
    • MDSdata
      • MDSdata.load_from_file()
      • MDSdata.save_to_file()
  • mdigest.core.toolkit module
    • dict2list()
    • dump()
    • file_exists()
    • folder_exists()
    • get_NGLselection_from_node()
    • get_or_minus1()
    • get_path()
    • get_selection_from_node()
    • intersection()
    • keywithmaxval()
    • list2dict()
    • log_progress()
    • normalize()
    • normalize_array()
    • partition2dict()
    • retrieve()
  • Module contents
• mdigest.utils package
  • Submodules
  • mdigest.utils.imports module
  • mdigest.utils.pdbhandler module
    • center_pdb()
    • df_to_pdb()
    • fill_topology_df()
    • mdatopology_to_dataframe()
    • read_pdb_file()
    • select_frame()
  • mdigest.utils.simulation module
    • MDAUniverse
      • MDAUniverse.align_traj()
      • MDAUniverse.compute_rmsd()
      • MDAUniverse.find_shift()
      • MDAUniverse.load_universe()
      • MDAUniverse.set_name()
      • MDAUniverse.set_selection()
      • MDAUniverse.set_selection_ref()
      • MDAUniverse.set_selection_rmsd()
      • MDAUniverse.source_universe()
    • MDTUniverse
      • MDTUniverse.adjust_topology()
      • MDTUniverse.align_md_traj()
      • MDTUniverse.calc_rmsd_2frames()
      • MDTUniverse.centroid()
      • MDTUniverse.compute_angles()
      • MDTUniverse.compute_dihed()
      • MDTUniverse.compute_distances()
      • MDTUniverse.find_shift()
      • MDTUniverse.load_universe()
      • MDTUniverse.set_distances_cache()
      • MDTUniverse.set_logfile()
      • MDTUniverse.set_mapping_chainid()
      • MDTUniverse.set_mapping_segid()
      • MDTUniverse.set_name()
      • MDTUniverse.set_selection()
      • MDTUniverse.set_selection_alignment()
      • MDTUniverse.set_selection_alignment_ref()
      • MDTUniverse.set_use_frame()
      • MDTUniverse.source_universe()
    • pkl_dump()
  • mdigest.utils.toolkit module
    • print_screen_logfile()
    • reduce_mdt_trajectory()
    • reduce_trajectory()
    • write_universe()
  • Module contents

Module contents