molecular_simulations.analysis package

Submodules

• molecular_simulations.analysis.autocluster module
  • AutoKMeans
    • AutoKMeans.map_centers_to_frames()
    • AutoKMeans.reduce_dimensionality()
    • AutoKMeans.run()
    • AutoKMeans.save_centers()
    • AutoKMeans.save_labels()
    • AutoKMeans.sweep_n_clusters()
  • Decomposition
    • Decomposition.fit()
    • Decomposition.fit_transform()
    • Decomposition.transform()
  • GenericDataloader
    • GenericDataloader.data
    • GenericDataloader.load_data()
    • GenericDataloader.shape
  • PeriodicDataloader
    • PeriodicDataloader.load_data()
    • PeriodicDataloader.remove_periodicity()
• molecular_simulations.analysis.cov_ppi module
  • PPInteractions
    • PPInteractions.analyze_hbond()
    • PPInteractions.analyze_hydrophobic()
    • PPInteractions.analyze_saltbridge()
    • PPInteractions.compute_interactions()
    • PPInteractions.evaluate_hbond()
    • PPInteractions.get_covariance()
    • PPInteractions.identify_interaction_type()
    • PPInteractions.interpret_covariance()
    • PPInteractions.make_plot()
    • PPInteractions.parse_results()
    • PPInteractions.plot_results()
    • PPInteractions.res_map()
    • PPInteractions.run()
    • PPInteractions.save()
    • PPInteractions.survey_donors_acceptors()
• molecular_simulations.analysis.fingerprinter module
  • Fingerprinter
    • Fingerprinter.assign_nonbonded_params()
    • Fingerprinter.assign_residue_mapping()
    • Fingerprinter.calculate_fingerprints()
    • Fingerprinter.iterate_frames()
    • Fingerprinter.load_pdb()
    • Fingerprinter.run()
    • Fingerprinter.save()
  • dist_mat()
  • electrostatic()
  • electrostatic_sum()
  • fingerprints()
  • lennard_jones()
  • lennard_jones_sum()
  • unravel_index()
• molecular_simulations.analysis.interaction_energy module
  • DynamicInteractionEnergy
    • DynamicInteractionEnergy.build_system()
    • DynamicInteractionEnergy.compute_energies()
    • DynamicInteractionEnergy.load_traj()
    • DynamicInteractionEnergy.setup_pbar()
  • InteractionEnergy
    • InteractionEnergy.compute()
    • InteractionEnergy.energy()
    • InteractionEnergy.get_selection()
  • InteractionEnergyFrame
    • InteractionEnergyFrame.get_system()
  • StaticInteractionEnergy
    • StaticInteractionEnergy.compute()
    • StaticInteractionEnergy.energy()
    • StaticInteractionEnergy.fix_pdb()
    • StaticInteractionEnergy.get_selection()
    • StaticInteractionEnergy.get_system()
    • StaticInteractionEnergy.interactions
• molecular_simulations.analysis.ipSAE module
  • ModelParser
    • ModelParser.classify_chains()
    • ModelParser.nucleic_acids
    • ModelParser.package_line()
    • ModelParser.parse_cif_line()
    • ModelParser.parse_pdb_line()
    • ModelParser.parse_structure_file()
  • ScoreCalculator
    • ScoreCalculator.compute_LIS()
    • ScoreCalculator.compute_d0()
    • ScoreCalculator.compute_ipTM_ipSAE()
    • ScoreCalculator.compute_pDockQ_scores()
    • ScoreCalculator.compute_pTM
    • ScoreCalculator.compute_scores()
    • ScoreCalculator.get_max_values()
    • ScoreCalculator.pDockQ2_score()
    • ScoreCalculator.pDockQ_score()
    • ScoreCalculator.permute_chains()
  • ipSAE
    • ipSAE.load_PAE_file()
    • ipSAE.load_pLDDT_file()
    • ipSAE.parse_structure_file()
    • ipSAE.prepare_scorer()
    • ipSAE.run()
    • ipSAE.save_scores()
• molecular_simulations.analysis.sasa module
  • RelativeSASA
  • SASA
    • SASA.get_sphere()
    • SASA.measure_sasa()
• molecular_simulations.analysis.utils module
  • EmbedData
    • EmbedData.embed()
    • EmbedData.embed_selection()
    • EmbedData.write_new_pdb()
  • EmbedEnergyData
    • EmbedEnergyData.preprocess()
    • EmbedEnergyData.sanitize_data()