Summary:

Corrected the behavior of the flat-bottom potential functions (apply_flat_bottom_vdw and apply_flat_bottom_hbond) to prevent them from incorrectly softening the energy of severe atomic clashes. The previous implementation applied the softening delta parameter across the entire repulsive region, which could lead to an underestimation of steric penalties. This fix introduces a "hardcore" repulsive boundary, ensuring that only the raw, unsoftened potential is used for very short inter-atomic distances.

Changes:

• Introduced Hardcore Repulsive Core:

  • Added a REPULSIVE_CORE_SCALE_FACTOR to both apply_flat_bottom_vdw and apply_flat_bottom_hbond.
  • If the inter-atomic distance is less than this fraction of the ideal distance, the flat-bottom softening logic is now bypassed, applying the full repulsive penalty.
  • This ensures the potential correctly models severe steric clashes while still softening the energy landscape for near-native conformations.

• Updated and Added Unit Tests:

  • Refined existing test cases to accurately reflect the three distinct regions of the potential: hardcore repulsion, soft repulsion (flat-bottom), and the attractive tail.
  • Added new tests specifically to verify that the softening effect is correctly disabled within the new hardcore boundary.