Description:
ops::hydro::construct_n_term_hydrogens treats every N-terminal protein residue as a primary amine, ignoring that PRO's backbone nitrogen is a secondary amine (N–CA + N–CD). For any structure where PRO occupies the N-terminus, this over-places hydrogens by +1 in both protonated and neutral conditions and distributes them without constraining the N–CD ring bond direction.
Tasks:
Description:
ops::hydro::construct_n_term_hydrogenstreats every N-terminal protein residue as a primary amine, ignoring that PRO's backbone nitrogen is a secondary amine (N–CA + N–CD). For any structure where PRO occupies the N-terminus, this over-places hydrogens by +1 in both protonated and neutral conditions and distributes them without constraining the N–CD ring bond direction.Tasks:
residue.standard_name == Some(StandardResidue::PRO)residue.atom("CD")and construct H positions from the N–CA and N–CD vectors (anti-bisector + cross-product tetrahedral geometry)