molecular-simulations
molecular_simulations.simulate package¶
Subpackages¶
Submodules¶
- molecular_simulations.simulate.cph_simulation module
- molecular_simulations.simulate.free_energy module
PMFResultConvergenceResultConvergenceResult.window_idxConvergenceResult.mean_rcConvergenceResult.semConvergenceResult.n_blocksConvergenceResult.block_meansConvergenceResult.is_convergedConvergenceResult.window_idxConvergenceResult.mean_rcConvergenceResult.semConvergenceResult.n_blocksConvergenceResult.block_meansConvergenceResult.is_convergedConvergenceResult.__init__()
OverlapResultEquilibrationResultEquilibrationResult.window_idxEquilibrationResult.t0EquilibrationResult.gEquilibrationResult.n_effectiveEquilibrationResult.fraction_discardedEquilibrationResult.window_idxEquilibrationResult.t0EquilibrationResult.gEquilibrationResult.n_effectiveEquilibrationResult.fraction_discardedEquilibrationResult.__init__()
EVBAnalysisResultEVBAnalysisResult.pmfEVBAnalysisResult.convergenceEVBAnalysisResult.overlapEVBAnalysisResult.equilibrationEVBAnalysisResult.rc_dataEVBAnalysisResult.temperatureEVBAnalysisResult.k_umbrellaEVBAnalysisResult.pmfEVBAnalysisResult.convergenceEVBAnalysisResult.overlapEVBAnalysisResult.equilibrationEVBAnalysisResult.rc_dataEVBAnalysisResult.temperatureEVBAnalysisResult.k_umbrellaEVBAnalysisResult.__init__()
EVBAnalyzerEVBAnalyzer.__init__()EVBAnalyzer.from_metadata()EVBAnalyzer.from_evb_instance()EVBAnalyzer.save_metadata()EVBAnalyzer.load_rc_data()EVBAnalyzer.get_available_windows()EVBAnalyzer.check_run_status()EVBAnalyzer.detect_equilibration()EVBAnalyzer.check_convergence()EVBAnalyzer.analyze_overlap()EVBAnalyzer.compute_pmf()EVBAnalyzer.run_full_analysis()EVBAnalyzer.save_analysis_results()
EVBEVB.__init__()EVB.prepare_inputs()EVB.construct_rc()EVB.initialize()EVB.shutdown()EVB.run_evb()EVB.process_evb_run()EVB.load_rc_data()EVB.detect_equilibration()EVB.check_convergence()EVB.analyze_overlap()EVB.compute_pmf()EVB.run_full_analysis()EVB.save_analysis_results()EVB.save_metadata()EVB.get_analyzer()EVB.umbrellaEVB.morse_bond
EVBCalculation
- molecular_simulations.simulate.mmpbsa module
MMPBSASettingsMMPBSASettings.topMMPBSASettings.dcdMMPBSASettings.selectionsMMPBSASettings.first_frameMMPBSASettings.last_frameMMPBSASettings.strideMMPBSASettings.n_cpusMMPBSASettings.outMMPBSASettings.solvent_probeMMPBSASettings.offsetMMPBSASettings.gb_surftenMMPBSASettings.gb_surfoffMMPBSASettings.topMMPBSASettings.dcdMMPBSASettings.selectionsMMPBSASettings.first_frameMMPBSASettings.last_frameMMPBSASettings.strideMMPBSASettings.n_cpusMMPBSASettings.outMMPBSASettings.solvent_probeMMPBSASettings.offsetMMPBSASettings.gb_surftenMMPBSASettings.gb_surfoffMMPBSASettings.__init__()
MMPBSAOutputAnalyzerOutputAnalyzer.pathOutputAnalyzer.surftenOutputAnalyzer.offsetOutputAnalyzer.free_energyOutputAnalyzer.gbOutputAnalyzer.pbOutputAnalyzer.__init__()OutputAnalyzer.parse_outputs()OutputAnalyzer.read_sasa()OutputAnalyzer.read_GB()OutputAnalyzer.read_PB()OutputAnalyzer.parse_energy_file()OutputAnalyzer.check_bonded_terms()OutputAnalyzer.generate_summary()OutputAnalyzer.compute_dG()OutputAnalyzer.pretty_print()OutputAnalyzer.parse_line()
FileHandlerFileHandler.topFileHandler.trajFileHandler.pathFileHandler.selectionsFileHandler.topologiesFileHandler.trajectoriesFileHandler.pdbsFileHandler.trajectory_chunksFileHandler.__init__()FileHandler.prepare_topologies()FileHandler.prepare_trajectories()FileHandler.filesFileHandler.files_chunkedFileHandler.write_file()
- molecular_simulations.simulate.multires_simulator module
- molecular_simulations.simulate.omm_simulator module
SimulatorSimulator.pathSimulator.top_fileSimulator.coor_fileSimulator.temperatureSimulator.simulationSimulator.__init__()Simulator.setup_barostat()Simulator.load_system()Simulator.load_amber_files()Simulator.load_charmm_files()Simulator.setup_sim()Simulator.run()Simulator.equilibrate()Simulator.production()Simulator.load_checkpoint()Simulator.attach_reporters()Simulator.get_restraint_indices()Simulator.check_num_steps_left()Simulator.add_backbone_posres()
ImplicitSimulatorCustomForcesSimulatorMinimizer
- molecular_simulations.simulate.reporters module