def test_ammonium_formal_charge(objkey, request):
mol = request.getfixturevalue(objkey)
mdt.assign_formal_charges(mol)
assert mol.charge == 1 * u.q_e
for atom in mol.atoms:
if atom.atnum == 7:
assert atom.formal_charge == 1 * u.q_e
else:
assert atom.atnum == 1
assert atom.formal_charge == 0 * u.q_e
def test_ammonium_formal_charge(objkey, request):
mol = request.getfixturevalue(objkey)
mdt.assign_formal_charges(mol)
assert mol.charge == 1 * u.q_e
for atom in mol.atoms:
if atom.atnum == 7:
assert atom.formal_charge == 1 * u.q_e
else:
assert atom.atnum == 1
assert atom.formal_charge == 0 * u.q_e
def set_protonation(mol, ph=7.4):
""" Adjust protonation according to the OpenBabel pka model.
This routine will return a copy of the molecule with the new protonation state and adjusted
formal charges
Args:
mol (moldesign.Molecule): Molecule to adjust
ph (float): assign protonation state for this pH value
Returns:
moldesign.Molecule: New molecule with adjusted protonation
"""
# TODO: this doesn't appear to do anything for most molecules!!!
# TODO: this renames hydrogens!!!
pbmol = mol_to_pybel(mol)
pbmol.OBMol.AddHydrogens(False, True, ph)
newmol = pybel_to_mol(pbmol, reorder_atoms_by_residue=True)
mdt.helpers.assign_unique_hydrogen_names(newmol)
mdt.assign_formal_charges(newmol, ignore_nonzero=False)
return newmol
def set_protonation(mol, ph=7.4):
""" Adjust protonation according to the OpenBabel pka model.
This routine will return a copy of the molecule with the new protonation state and adjusted
formal charges
Args:
mol (moldesign.Molecule): Molecule to adjust
ph (float): assign protonation state for this pH value
Returns:
moldesign.Molecule: New molecule with adjusted protonation
"""
# TODO: this doesn't appear to do anything for most molecules!!!
# TODO: this renames hydrogens!!!
pbmol = mol_to_pybel(mol)
pbmol.OBMol.AddHydrogens(False, True, ph)
newmol = pybel_to_mol(pbmol, reorder_atoms_by_residue=True)
mdt.helpers.assign_unique_hydrogen_names(newmol)
mdt.assign_formal_charges(newmol, ignore_nonzero=False)
return newmol