molecular_simulations package

Subpackages

• molecular_simulations.analysis package
  • Submodules
    • molecular_simulations.analysis.autocluster module
      • AutoKMeans
      • Decomposition
      • GenericDataloader
      • PeriodicDataloader
    • molecular_simulations.analysis.cov_ppi module
      • PPInteractions
    • molecular_simulations.analysis.fingerprinter module
      • Fingerprinter
      • dist_mat()
      • electrostatic()
      • electrostatic_sum()
      • fingerprints()
      • lennard_jones()
      • lennard_jones_sum()
      • unravel_index()
    • molecular_simulations.analysis.interaction_energy module
      • DynamicInteractionEnergy
      • InteractionEnergy
      • InteractionEnergyFrame
      • StaticInteractionEnergy
    • molecular_simulations.analysis.ipSAE module
      • ModelParser
      • ScoreCalculator
      • ipSAE
    • molecular_simulations.analysis.sasa module
      • RelativeSASA
      • SASA
    • molecular_simulations.analysis.utils module
      • EmbedData
      • EmbedEnergyData
• molecular_simulations.build package
  • add_chains()
  • convert_cif_with_biopython()
  • convert_cif_with_gemmi()
  • Submodules
    • molecular_simulations.build.build_amber module
      • ExplicitSolvent
      • ImplicitSolvent
    • molecular_simulations.build.build_interface module
      • InterfaceBuilder
    • molecular_simulations.build.build_ligand module
      • ComplexBuilder
      • LigandBuilder
      • LigandError
      • PLINDERBuilder
• molecular_simulations.simulate package
  • Submodules
    • molecular_simulations.simulate.mmpbsa module
      • FileHandler
      • MMPBSA
      • MMPBSA_settings
      • OutputAnalyzer
    • molecular_simulations.simulate.omm_simulator module
      • CustomForcesSimulator
      • ImplicitSimulator
      • Minimizer
      • Simulator
    • molecular_simulations.simulate.parsl_settings module
      • AuroraSettings
      • BaseComputeSettings
      • BaseSettings
      • LocalSettings
      • PolarisSettings