CodeEntropy package

CodeEntropy

CodeEntropy is a Python package for computing the configurational entropy of macromolecular systems using forces sampled from molecular dynamics (MD) simulations. It implements the multiscale cell correlation method to provide accurate and efficient entropy estimates, supporting a wide range of applications in molecular simulation and statistical mechanics.

Subpackages

• CodeEntropy.config package
  • Submodules
    • CodeEntropy.config.argparse module
      • ArgSpec
      • ConfigResolver
    • CodeEntropy.config.runtime module
      • CodeEntropyRunner
• CodeEntropy.core package
  • Submodules
    • CodeEntropy.core.logging module
      • ErrorFilter
      • LoggingConfig
• CodeEntropy.entropy package
  • Subpackages
    • CodeEntropy.entropy.nodes package
      • Submodules
  • Submodules
    • CodeEntropy.entropy.configurational module
      • ConformationalEntropy
    • CodeEntropy.entropy.graph module
      • EntropyGraph
      • NodeSpec
    • CodeEntropy.entropy.orientational module
      • OrientationalEntropy
      • OrientationalEntropyResult
    • CodeEntropy.entropy.vibrational module
      • VibrationalEntropy
      • VibrationalEntropyResult
    • CodeEntropy.entropy.water module
      • WaterEntropy
      • WaterEntropyInput
    • CodeEntropy.entropy.workflow module
      • EntropyWorkflow
• CodeEntropy.levels package
  • Subpackages
    • CodeEntropy.levels.nodes package
      • Submodules
  • Submodules
    • CodeEntropy.levels.axes module
      • AxesCalculator
    • CodeEntropy.levels.dihedrals module
      • ConformationStateBuilder
    • CodeEntropy.levels.forces module
      • ForceTorqueCalculator
      • TorqueInputs
    • CodeEntropy.levels.frame_dag module
      • FrameContext
      • FrameGraph
    • CodeEntropy.levels.hierarchy module
      • HierarchyBuilder
    • CodeEntropy.levels.level_dag module
      • LevelDAG
    • CodeEntropy.levels.linalg module
      • MatrixUtils
    • CodeEntropy.levels.neighbors module
      • Neighbors
    • CodeEntropy.levels.search module
      • Search
• CodeEntropy.molecules package
  • Submodules
    • CodeEntropy.molecules.grouping module
      • GroupingConfig
      • MoleculeGrouper
• CodeEntropy.results package
  • Submodules
    • CodeEntropy.results.reporter module
      • ResultsReporter
• CodeEntropy.trajectory package
  • Submodules
    • CodeEntropy.trajectory.frames module
      • FrameSelection
    • CodeEntropy.trajectory.mda module
      • UniverseOperations
    • CodeEntropy.trajectory.source module
      • FrameSource

Submodules

• CodeEntropy.cli module
  • main()