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[DRAFT] Schrodinger solvation shell extraction #23

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@jeevster jeevster commented Jul 2, 2024

Simplified solvation shell extraction using the schrodinger Python API. This is a unified procedure for low and high concentration simulations.
Main points:

  1. Instead of using solvation analysis to find solvation shell radii from the RDF, just pick system-agnostic, heuristic radii for solvation shell extraction (e.g 3 and 6 Angstroms).
  2. For each solute molecule, extract solvation shells, bin by composition, and extract top n most diverse by RMSD from each bin. When extracting shells around a solute molecule, if we run into another solute molecule, recursively expand around that one too.
  3. To capture solvent-solvent interactions, pick random solvent molecules and expand shells around them which have no solutes (only do for low concentration simulations).

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