molecular_simulations.analysis package

Submodules

• molecular_simulations.analysis.autocluster module
  • DataloaderProtocol
    • DataloaderProtocol.files
    • DataloaderProtocol.data
    • DataloaderProtocol.shape
    • DataloaderProtocol.__init__()
  • GenericDataloader
    • GenericDataloader.files
    • GenericDataloader.data_array
    • GenericDataloader.shapes
    • GenericDataloader.__init__()
    • GenericDataloader.data_array
    • GenericDataloader.shapes
    • GenericDataloader.load_data()
    • GenericDataloader.data
    • GenericDataloader.shape
  • PeriodicDataloader
    • PeriodicDataloader.__init__()
    • PeriodicDataloader.load_data()
    • PeriodicDataloader.remove_periodicity()
  • AutoKMeans
    • AutoKMeans.data
    • AutoKMeans.shape
    • AutoKMeans.reduced
    • AutoKMeans.centers
    • AutoKMeans.labels
    • AutoKMeans.cluster_centers
    • AutoKMeans.__init__()
    • AutoKMeans.dataloader
    • AutoKMeans.run()
    • AutoKMeans.reduce_dimensionality()
    • AutoKMeans.sweep_n_clusters()
    • AutoKMeans.map_centers_to_frames()
    • AutoKMeans.save_centers()
    • AutoKMeans.save_labels()
  • Decomposition
    • Decomposition.decomposer
    • Decomposition.__init__()
    • Decomposition.fit()
    • Decomposition.transform()
    • Decomposition.fit_transform()
• molecular_simulations.analysis.constant_pH_analysis module
  • UWHAMSolver
    • UWHAMSolver.__init__()
    • UWHAMSolver.load_data()
    • UWHAMSolver.solve()
    • UWHAMSolver.compute_log_weights()
    • UWHAMSolver.compute_expectation_at_pH()
    • UWHAMSolver.get_occupancy_for_resid()
  • TitrationCurve
    • TitrationCurve.__init__()
    • TitrationCurve.parse_log()
    • TitrationCurve.prepare()
    • TitrationCurve.compute_titrations_curvefit()
    • TitrationCurve.compute_titrations_weighted()
    • TitrationCurve.compute_titrations_bootstrap()
    • TitrationCurve.compute_titrations()
    • TitrationCurve.postprocess()
    • TitrationCurve.plot()
    • TitrationCurve.diagnose_residue()
    • TitrationCurve.hill_equation()
    • TitrationCurve.protonation_mapping
    • TitrationCurve.canonical_resname
    • TitrationCurve.compare_methods()
  • TitrationAnalyzer
    • TitrationAnalyzer.__init__()
    • TitrationAnalyzer.run()
    • TitrationAnalyzer.summary()
    • TitrationAnalyzer.get_results()
    • TitrationAnalyzer.plot_residue()
    • TitrationAnalyzer.plot_all()
    • TitrationAnalyzer.plot_summary()
    • TitrationAnalyzer.save_results()
    • TitrationAnalyzer.diagnose()
    • TitrationAnalyzer.recommend_protonation()
    • TitrationAnalyzer.get_protonation_string()
    • TitrationAnalyzer.export_protonation_states()
    • TitrationAnalyzer.plot_protonation_summary()
  • analyze_cph()
• molecular_simulations.analysis.cov_ppi module
  • PPInteractions
    • PPInteractions.u
    • PPInteractions.n_frames
    • PPInteractions.out
    • PPInteractions.mapping
    • PPInteractions.__init__()
    • PPInteractions.run()
    • PPInteractions.compute_interactions()
    • PPInteractions.get_covariance()
    • PPInteractions.res_map()
    • PPInteractions.interpret_covariance()
    • PPInteractions.identify_interaction_type()
    • PPInteractions.analyze_saltbridge()
    • PPInteractions.analyze_hbond()
    • PPInteractions.analyze_hydrophobic()
    • PPInteractions.survey_donors_acceptors()
    • PPInteractions.evaluate_hbond()
    • PPInteractions.save()
    • PPInteractions.plot_results()
    • PPInteractions.parse_results()
    • PPInteractions.make_plot()
• molecular_simulations.analysis.fingerprinter module
  • unravel_index()
  • dist_mat()
  • electrostatic()
  • electrostatic_sum()
  • lennard_jones()
  • lennard_jones_sum()
  • fingerprints()
  • Fingerprinter
    • Fingerprinter.topology
    • Fingerprinter.trajectory
    • Fingerprinter.target_selection
    • Fingerprinter.binder_selection
    • Fingerprinter.out
    • Fingerprinter.target_fingerprint
    • Fingerprinter.binder_fingerprint
    • Fingerprinter.__init__()
    • Fingerprinter.assign_nonbonded_params()
    • Fingerprinter.load_pdb()
    • Fingerprinter.assign_residue_mapping()
    • Fingerprinter.iterate_frames()
    • Fingerprinter.calculate_fingerprints()
    • Fingerprinter.run()
    • Fingerprinter.save()
• molecular_simulations.analysis.interaction_energy module
  • InteractionEnergy
    • InteractionEnergy.__init__()
    • InteractionEnergy.compute()
    • InteractionEnergy.energy()
    • InteractionEnergy.get_selection()
  • StaticInteractionEnergy
    • StaticInteractionEnergy.pdb
    • StaticInteractionEnergy.chain
    • StaticInteractionEnergy.platform
    • StaticInteractionEnergy.lj
    • StaticInteractionEnergy.coulomb
    • StaticInteractionEnergy.selection
    • StaticInteractionEnergy.__init__()
    • StaticInteractionEnergy.get_system()
    • StaticInteractionEnergy.compute()
    • StaticInteractionEnergy.get_selection()
    • StaticInteractionEnergy.fix_pdb()
    • StaticInteractionEnergy.interactions
    • StaticInteractionEnergy.energy()
  • InteractionEnergyFrame
    • InteractionEnergyFrame.__init__()
    • InteractionEnergyFrame.get_system()
  • DynamicInteractionEnergy
    • DynamicInteractionEnergy.system
    • DynamicInteractionEnergy.coordinates
    • DynamicInteractionEnergy.stride
    • DynamicInteractionEnergy.energies
    • DynamicInteractionEnergy.IE
    • DynamicInteractionEnergy.__init__()
    • DynamicInteractionEnergy.compute_energies()
    • DynamicInteractionEnergy.build_system()
    • DynamicInteractionEnergy.load_traj()
    • DynamicInteractionEnergy.setup_pbar()
• molecular_simulations.analysis.ipSAE module
  • ipSAE
    • ipSAE.parser
    • ipSAE.plddt_file
    • ipSAE.pae_file
    • ipSAE.path
    • ipSAE.scores
    • ipSAE.__init__()
    • ipSAE.parse_structure_file()
    • ipSAE.prepare_scorer()
    • ipSAE.run()
    • ipSAE.save_scores()
    • ipSAE.load_pLDDT_file()
    • ipSAE.load_PAE_file()
  • ScoreCalculator
    • ScoreCalculator.chains
    • ScoreCalculator.unique_chains
    • ScoreCalculator.chain_pair_type
    • ScoreCalculator.n_res
    • ScoreCalculator.permuted
    • ScoreCalculator.scores
    • ScoreCalculator.__init__()
    • ScoreCalculator.compute_scores()
    • ScoreCalculator.compute_pDockQ_scores()
    • ScoreCalculator.compute_LIS()
    • ScoreCalculator.compute_ipTM_ipSAE()
    • ScoreCalculator.get_max_values()
    • ScoreCalculator.permute_chains()
    • ScoreCalculator.pDockQ_score()
    • ScoreCalculator.pDockQ2_score()
    • ScoreCalculator.compute_pTM()
    • ScoreCalculator.compute_d0()
    • ScoreCalculator.compute_d0_array()
  • ModelParser
    • ModelParser.structure
    • ModelParser.protein_token_indices
    • ModelParser.residues
    • ModelParser.chains
    • ModelParser.chain_types
    • ModelParser.__init__()
    • ModelParser.parse_structure_file()
    • ModelParser.build_protein_token_indices()
    • ModelParser.classify_chains()
    • ModelParser.NUCLEIC_ACIDS
    • ModelParser.STANDARD_RESIDUES
    • ModelParser.parse_pdb_line()
    • ModelParser.parse_cif_line()
    • ModelParser.package_line()
• molecular_simulations.analysis.sasa module
  • SASA
    • SASA.ag
    • SASA.probe_radius
    • SASA.n_points
    • SASA.radii
    • SASA.max_radii
    • SASA.results.sasa
    • SASA.__init__()
    • SASA.get_sphere()
    • SASA.measure_sasa()
  • RelativeSASA
    • RelativeSASA.results.sasa
    • RelativeSASA.results.relative_area
    • RelativeSASA.__init__()
• molecular_simulations.analysis.utils module
  • EmbedData
    • EmbedData.pdb
    • EmbedData.embeddings
    • EmbedData.out
    • EmbedData.u
    • EmbedData.__init__()
    • EmbedData.embed()
    • EmbedData.embed_selection()
    • EmbedData.write_new_pdb()
  • EmbedEnergyData
    • EmbedEnergyData.__init__()
    • EmbedEnergyData.preprocess()
    • EmbedEnergyData.sanitize_data()