INNER CODE UNIT · Python
set_optimizeable_hydrogens
Electrostatics/pdb2pqr · pdb2pqr/hydrogens/__init__.py:316
def set_optimizeable_hydrogens(self):
"""Set any hydrogen listed in HYDROGENS.xml that is optimizeable.
Used BEFORE hydrogen optimization to label atoms so that they won't be
debumped - i.e. if SER HG is too close to another atom, don't debump
but wait for optimization.
.. note::
This function should not be used if full optimization is not taking
place.
"""
for residue in self.biomolecule.residues:
optinstance = self.is_optimizeable(residue)
if optinstance is None:
continue
for atom in residue.atoms:
if atom.name in optinstance.map:
atom.optimizeable = 1