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 htmd.charge import fitGasteigerCharges
from htmd.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)
# 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)))
charge = int(round(np.sum(mol.charge)))
if args.charge != charge:
raise RuntimeError(
'Molecular charge is set to {}, but Gasteiger atomic charges add up to {}.'
.format(args.charge, 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 htmd.charge import fitGasteigerCharges, fitChargesWithAntechamber, fitESPCharges, symmetrizeCharges
from htmd.parameterization.util import guessBondType, getFixedChargeAtomIndices, getDipole, _qm_method_name
from htmd.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:
raise RuntimeError(
'Molecular charge is set to {}, but Gasteiger atomic charges add up to {}.'
.format(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