INNER CODE UNIT · Python
initialize_full_optimization
Electrostatics/pdb2pqr · pdb2pqr/hydrogens/__init__.py:335
def initialize_full_optimization(self):
"""Initialize the full optimization.
Detects all optimizeable donors and acceptors and sets the internal
optlist.
"""
# Do some setup
self.debumper.cells = cells.Cells(5)
self.debumper.cells.assign_cells(self.biomolecule)
self.biomolecule.calculate_dihedral_angles()
self.biomolecule.set_donors_acceptors()
self.biomolecule.update_internal_bonds()
self.biomolecule.set_reference_distance()
self.optlist = []
self.atomlist = []
# First initialize the various types
for residue in self.biomolecule.residues:
optinstance = self.is_optimizeable(residue)