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FREENRG_INTEGRATION.md

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FreeNRG Integration

This branch adds the FreeNRG unified free energy framework that bridges FlexAID-deltaS entropy-aware docking with NRGRank virtual screening.

FreeNRG Repository

The FreeNRG Python package is maintained at: https://github.com/lmorency/FreeNRG

What FreeNRG Provides

FreeNRG is a Python package that ports key FlexAID-deltaS thermodynamic components into a reusable library:

  • StatMechEngine - Python port of statmech.cpp (partition functions, WHAM, TI)
  • ShannonThermoStack - Python port of ShannonThermoStack.cpp (Shannon entropy)
  • TorsionalENM - Python port of tencm.cpp (backbone flexibility)
  • CFScorer - Python port of cffunction.cpp (complementarity scoring)
  • FlexAIDBridge - Subprocess wrapper for the FlexAID C++ binary
  • NRGRankBridge - Direct Python integration with NRGRank

Usage with FlexAID

from freenrg.pipeline import FreeNRGPipeline, FreeNRGConfig, DockingMode

config = FreeNRGConfig(
    mode=DockingMode.FLEXAID,
    flexaid_binary="/path/to/FlexAID",
    receptor_pdb="receptor.inp.pdb",
    ligand_inp="ligand.inp",
    binding_site="cleft.pdb",
)

pipeline = FreeNRGPipeline()
result = pipeline.run(config)
print(f"deltaG = {result.delta_G:.2f} kcal/mol")

Install

pip install freenrg