qp.protonate.fix.adjust_activesites

qp.protonate.fix.adjust_activesites(path, center_residue: CenterResidue)[source]

Deprotonate metal-coordinating residues incorrectly protonated by Protoss.

Removes hydrogens from residues coordinating to metal centers:

  • Tyrosine OH groups within 3 A of a metal

  • Cysteine SG groups within 3 A of a metal

  • Backbone N atoms within 3 A of a metal

  • All hydrogens on NO ligands (protonated as hydroxylamine by Protoss)

  • Any ligand H atoms within 1.5 A of a metal

Also flips incorrectly oriented histidine rings and adds hydrogens to CSO (cysteine sulfenic acid) residues.

Parameters:

  • path (str) – Path to the Protoss output PDB file (modified in place).

  • center_residue (CenterResidue) – Center residue definition identifying metal atoms.

Notes

The file at path is overwritten with the corrected structure.