molecular_simulations.simulate package

Submodules

• molecular_simulations.simulate.mmpbsa module
  • FileHandler
    • FileHandler.files
    • FileHandler.prepare_topologies()
    • FileHandler.prepare_trajectories()
    • FileHandler.write_file()
  • MMPBSA
    • MMPBSA.calculate_energy()
    • MMPBSA.calculate_sasa()
    • MMPBSA.run()
    • MMPBSA.write_mdins()
  • MMPBSA_settings
    • MMPBSA_settings.dcd
    • MMPBSA_settings.first_frame
    • MMPBSA_settings.gb_surfoff
    • MMPBSA_settings.gb_surften
    • MMPBSA_settings.last_frame
    • MMPBSA_settings.n_cpus
    • MMPBSA_settings.offset
    • MMPBSA_settings.out
    • MMPBSA_settings.selections
    • MMPBSA_settings.solvent_probe
    • MMPBSA_settings.stride
    • MMPBSA_settings.top
  • OutputAnalyzer
    • OutputAnalyzer.check_bonded_terms()
    • OutputAnalyzer.compute_dG()
    • OutputAnalyzer.generate_summary()
    • OutputAnalyzer.parse_energy_file()
    • OutputAnalyzer.parse_line()
    • OutputAnalyzer.parse_outputs()
    • OutputAnalyzer.pretty_print()
    • OutputAnalyzer.read_GB()
    • OutputAnalyzer.read_PB()
    • OutputAnalyzer.read_sasa()
• molecular_simulations.simulate.omm_simulator module
  • CustomForcesSimulator
    • CustomForcesSimulator.add_forces()
    • CustomForcesSimulator.load_amber_files()
  • ImplicitSimulator
    • ImplicitSimulator.equilibrate()
    • ImplicitSimulator.load_amber_files()
  • Minimizer
    • Minimizer.load_amber()
    • Minimizer.load_files()
    • Minimizer.load_gromacs()
    • Minimizer.load_pdb()
    • Minimizer.minimize()
  • Simulator
    • Simulator.add_backbone_posres()
    • Simulator.attach_reporters()
    • Simulator.check_num_steps_left()
    • Simulator.equilibrate()
    • Simulator.get_restraint_indices()
    • Simulator.load_amber_files()
    • Simulator.load_checkpoint()
    • Simulator.production()
    • Simulator.run()
    • Simulator.setup_sim()
• molecular_simulations.simulate.parsl_settings module
  • AuroraSettings
    • AuroraSettings.account
    • AuroraSettings.available_accelerators
    • AuroraSettings.config_factory()
    • AuroraSettings.cpus_per_node
    • AuroraSettings.label
    • AuroraSettings.model_config
    • AuroraSettings.num_nodes
    • AuroraSettings.queue
    • AuroraSettings.retries
    • AuroraSettings.scheduler_options
    • AuroraSettings.strategy
    • AuroraSettings.walltime
    • AuroraSettings.worker_init
  • BaseComputeSettings
    • BaseComputeSettings.config_factory()
    • BaseComputeSettings.model_config
  • BaseSettings
    • BaseSettings.dump_yaml()
    • BaseSettings.from_yaml()
    • BaseSettings.model_config
  • LocalSettings
    • LocalSettings.available_accelerators
    • LocalSettings.config_factory()
    • LocalSettings.label
    • LocalSettings.model_config
    • LocalSettings.retries
    • LocalSettings.worker_port_range
  • PolarisSettings
    • PolarisSettings.account
    • PolarisSettings.available_accelerators
    • PolarisSettings.config_factory()
    • PolarisSettings.cpus_per_node
    • PolarisSettings.label
    • PolarisSettings.model_config
    • PolarisSettings.num_nodes
    • PolarisSettings.queue
    • PolarisSettings.scheduler_options
    • PolarisSettings.strategy
    • PolarisSettings.walltime
    • PolarisSettings.worker_init