qp.protonate.fix.add_hydrogen_CSO¶
- qp.protonate.fix.add_hydrogen_CSO(res, structure)[source]¶
Add hydrogens to cysteine sulfenic acid (CSO) residues.
CSO is a post-translational modification not recognized by Protoss. This function adds hydrogens to CA (HA), CB (HB1, HB2), and the hydroxyl oxygen (HD) using ideal geometry. The hydroxyl hydrogen is omitted if a TAN (2,3,3-trichloroallyl alcohol) ligand is covalently bonded to the OD atom.
- Parameters:
res (Bio.PDB.Residue.Residue) – A CSO residue (modified in place).
structure (Bio.PDB.Structure.Structure) – The full protein structure (used to detect TAN–CSO bonds).
Notes
The residue is modified in place. Existing hydrogens are not replaced.