fix(ops): Correct N-Terminal Proline Hydrogen Geometry

[TKanX]

Summary:

Fixed a bug where N-terminal Proline residues were incorrectly assigned three hydrogens (H1, H2, H3) with a standard primary amine sp³ geometry. Proline has a secondary amine due to its pyrrolidine ring, so its N-terminus should only receive two hydrogens (H2, H3) when protonated, and one (H2) when deprotonated. The geometry calculation has been updated to correctly place these hydrogens based on the angle bisector of the CA-N-CD bonds, respecting the ring structure.

Changes:

• Updated construct_n_term_hydrogens in ops/hydro.rs:

  • Added a specific branch for StandardResidue::PRO.
  • For N-terminal Proline, the code now calculates the direction for H2 and H3 using the bisector and perpendicular vectors of the N-CA and N-CD bonds.
  • H1 is never added to Proline.
  • H3 is only added if the terminus is protonated (pH < 8.0).

• Added Validation Tests:

  • Introduced n_terminal_pro_residue helper for generating test cases.
  • Added tests to verify correct protonation states for N-term PRO with and without specified pH (pro_n_terminal_defaults_to_protonated_without_ph, pro_n_terminal_remains_protonated_below_pka, pro_n_terminal_deprotonates_above_pka).
  • Added geometric validation tests (pro_n_terminal_h_has_tetrahedral_bond_lengths, pro_n_terminal_h_has_tetrahedral_bond_angles) to ensure the newly placed hydrogens satisfy the expected 1.01 Å bond length and ~109.5° tetrahedral angles relative to the CA and CD atoms.

[Copilot]

Pull request overview

Fixes N-terminal Proline hydrogen reconstruction so PRO (secondary amine) no longer receives an invalid third N–H and uses ring-aware geometry for placed hydrogens.

Changes:

• Added a PRO-specific branch in construct_n_term_hydrogens to place only H2 (neutral) or H2+H3 (protonated), never H1.
• Updated N-terminal hydrogen placement for PRO to use CA–N–CD bisector/perpendicular directions rather than the generic sp³ frame.
• Added targeted tests covering PRO N-terminus protonation behavior and geometric sanity checks (bond lengths/angles).

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