molecular_simulations package

Subpackages

• molecular_simulations.analysis package
  • Submodules
    • molecular_simulations.analysis.autocluster module
      • DataloaderProtocol
      • GenericDataloader
      • PeriodicDataloader
      • AutoKMeans
      • Decomposition
    • molecular_simulations.analysis.constant_pH_analysis module
      • UWHAMSolver
      • TitrationCurve
      • TitrationAnalyzer
      • analyze_cph()
    • molecular_simulations.analysis.cov_ppi module
      • PPInteractions
    • molecular_simulations.analysis.fingerprinter module
      • unravel_index()
      • dist_mat()
      • electrostatic()
      • electrostatic_sum()
      • lennard_jones()
      • lennard_jones_sum()
      • fingerprints()
      • Fingerprinter
    • molecular_simulations.analysis.interaction_energy module
      • InteractionEnergy
      • StaticInteractionEnergy
      • InteractionEnergyFrame
      • DynamicInteractionEnergy
    • molecular_simulations.analysis.ipSAE module
      • ipSAE
      • ScoreCalculator
      • ModelParser
    • molecular_simulations.analysis.sasa module
      • SASA
      • RelativeSASA
    • molecular_simulations.analysis.utils module
      • EmbedData
      • EmbedEnergyData
• molecular_simulations.build package
  • convert_cif_with_biopython()
  • convert_cif_with_gemmi()
  • add_chains()
  • Submodules
    • molecular_simulations.build.build_amber module
      • ImplicitSolvent
      • ExplicitSolvent
    • molecular_simulations.build.build_calvados module
    • molecular_simulations.build.build_interface module
      • InterfaceBuilder
    • molecular_simulations.build.build_ligand module
      • LigandError
      • LigandBuilder
      • PLINDERBuilder
      • ComplexBuilder
• molecular_simulations.data package
  • Submodules
    • molecular_simulations.data.constant_ph_reference_energies module
      • get_ref_energies()
• molecular_simulations.simulate package
  • Subpackages
    • molecular_simulations.simulate.constantph namespace
      • Submodules
  • Submodules
    • molecular_simulations.simulate.cph_simulation module
    • molecular_simulations.simulate.free_energy module
      • PMFResult
      • ConvergenceResult
      • OverlapResult
      • EquilibrationResult
      • EVBAnalysisResult
      • EVBAnalyzer
      • EVB
      • EVBCalculation
    • molecular_simulations.simulate.mmpbsa module
      • MMPBSASettings
      • MMPBSA
      • OutputAnalyzer
      • FileHandler
    • molecular_simulations.simulate.multires_simulator module
    • molecular_simulations.simulate.omm_simulator module
      • Simulator
      • ImplicitSimulator
      • CustomForcesSimulator
      • Minimizer
    • molecular_simulations.simulate.reporters module
      • RCReporter
• molecular_simulations.utils package
  • Submodules
    • molecular_simulations.utils.amber_utils module
      • assign_chainids()
    • molecular_simulations.utils.mda_utils module
      • trim_trajectory()
    • molecular_simulations.utils.parsl_settings module
      • BaseSettings
      • BaseComputeSettings
      • LocalSettings
      • LocalCPUSettings
      • HeterogeneousSettings
      • PolarisSettings
      • AuroraSettings

Submodules

• molecular_simulations.logging_config module
  • configure_logging()