def _run(self, molName):
self.molName = molName
logger.info("Molecule: {}".format(self.molName))
molFile = os.path.join(home("test-charge"), self.molName + ".mol2")
self.mol = Molecule(molFile)
self.new_mols = {}
self.extras = {}
self.new_mols["Gasteiger"] = fitGasteigerCharges(self.mol)
try:
self.new_mols["AM1-BCC"] = fitChargesWithAntechamber(self.mol,
type="bcc")
except:
pass
qm = Psi4()
qm.theory = "B3LYP"
qm.basis = "6-311++G**"
workDir = os.path.join("tmp", self.molName)
os.makedirs(workDir, exist_ok=True)
for factor in [-10, -5, -4, -3, -2, -1]:
logger.info("Factor: {}".format(factor))
key = "ESP b {}".format(factor)
np.random.seed(20181114) # Make ESP grid generation deterministic
self.new_mols[key], self.extras[key] = fitESPCharges(
self.mol, qm, workDir, restraint_factor=10**factor)
def _fit_initial_charges(mol, args, atom_types):
from parameterize.charge import fitGasteigerCharges
from parameterize.parameterization.util import guessBondType
logger.info("=== Initial atomic charge fitting ===")
if args.charge_type == "None":
logger.info("Initial atomic charges are taken from {}".format(
args.filename))
elif args.charge_type in ("Gasteiger", "AM1-BCC", "ESP"):
if args.min_type == "mm":
logger.info("Method: Gasteiger")
# TODO move to _prepare_molecule
if np.any(mol.bondtype == "un"):
logger.info("Guessing bond types")
mol = guessBondType(mol)
mol = fitGasteigerCharges(mol, atom_types=atom_types)
charge = int(round(np.sum(mol.charge)))
if args.charge != charge:
logger.warning(
f"Molecular charge is {args.charge}, but Gasteiger atomic charges add up to {charge}!"
)
args.charge = charge
# Print the initial charges
logger.info("Initial atomic charges:")
for name, charge in zip(mol.name, mol.charge):
logger.info(" {:4s}: {:6.3f}".format(name, charge))
logger.info("Molecular charge: {:6.3f}".format(np.sum(mol.charge)))
elif args.min_type in ("None", "qm"):
logger.info("Initial atomic charges are not required")
else:
raise AssertionError()
else:
raise AssertionError()
return mol
def _fit_charges(mol, args, qm, atom_types):
from parameterize.charge import (
fitGasteigerCharges,
fitChargesWithAntechamber,
fitESPCharges,
symmetrizeCharges,
)
from parameterize.parameterization.util import (
guessBondType,
getFixedChargeAtomIndices,
getDipole,
_qm_method_name,
)
from parameterize.parameterization.detect import detectEquivalentAtoms
logger.info("=== Atomic charge fitting ===")
logger.info("Method: {}".format(args.charge_type))
if args.charge_type == "None":
# TODO move to argument validation
if len(args.fix_charge) > 0:
logger.warning("Flag --fix-charge does not have effect!")
logger.info("Atomic charges are taken from {}".format(args.filename))
elif args.charge_type == "Gasteiger":
# TODO move to argument validation
if len(args.fix_charge) > 0:
logger.warning("Flag --fix-charge does not have effect!")
# TODO move to _prepare_molecule
if np.any(mol.bondtype == "un"):
logger.info("Guessing bond types")
mol = guessBondType(mol)
mol = fitGasteigerCharges(mol, atom_types=atom_types)
charge = int(round(np.sum(mol.charge)))
if args.charge != charge:
logger.warning(
f"Molecular charge is {args.charge}, but Gasteiger atomic charges add up to {charge}!"
)
args.charge = charge
elif args.charge_type == "AM1-BCC":
# TODO move to argument validation
if len(args.fix_charge) > 0:
logger.warning("Flag --fix-charge does not have effect!")
mol = fitChargesWithAntechamber(mol, type="bcc", molCharge=args.charge)
mol = symmetrizeCharges(mol)
elif args.charge_type == "ESP":
# Detect equivalent atom groups
logger.info("Equivalent atom groups:")
atom_groups = [
group for group in detectEquivalentAtoms(mol)[0] if len(group) > 1
]
for atom_group in atom_groups:
logger.info(" {}".format(", ".join(mol.name[list(atom_group)])))
# Select the atoms with fixed charges
fixed_atom_indices = getFixedChargeAtomIndices(mol, args.fix_charge)
# Create an ESP directory
espDir = os.path.join(args.outdir, "esp", _qm_method_name(qm))
os.makedirs(espDir, exist_ok=True)
charge = int(round(np.sum(mol.charge)))
if args.charge != charge:
logger.warning(
"Molecular charge is set to {}, but atomic charges add up to {}"
"".format(args.charge, charge))
if len(args.fix_charge) > 0:
raise RuntimeError(
"Flag --fix-charge cannot be used when atomic charges are inconsistent with passed "
"molecular charge {}".format(args.charge))
mol.charge[:] = args.charge / mol.numAtoms
# Set random number generator seed
if args.seed:
np.random.seed(args.seed)
# Fit ESP charges
mol, extra = fitESPCharges(mol, qm, espDir, fixed=fixed_atom_indices)
# Print QM dipole
logger.info(
"QM dipole: {:6.3f} {:6.3f} {:6.3f}; total: {:6.3f}".format(
*extra["qm_dipole"]))
else:
raise ValueError()
# Print MM dipole
mm_dipole = getDipole(mol)
logger.info("MM dipole: {:6.3f} {:6.3f} {:6.3f}; total: {:6.3f}".format(
*mm_dipole))
# Print the new charges
logger.info("Atomic charges:")
for name, charge in zip(mol.name, mol.charge):
logger.info(" {:4s}: {:6.3f}".format(name, charge))
logger.info("Molecular charge: {:6.3f}".format(np.sum(mol.charge)))
return mol