def _analyse(self, mol, pdb, rtf, prm, traj, ftraj):
t = Molecule(pdb)
t.read(traj)
t.filter('not water')
t.write(ftraj)
m = FFMolecule(filename=mol, rtf=rtf, prm=prm)
m.read(ftraj)
torsions = m.getRotatableDihedrals()
# For each torsion
for i in range(len(torsions)):
# Create title
title = '{}-{}-{}-{}'.format(m.name[torsions[i][0]], m.name[torsions[i][1]], m.name[torsions[i][2]],
m.name[torsions[i][3]])
# Measure
(r, theta) = self._measure_torsion(torsions[i], m.coords)
self._plot_scatter(r, theta, title)
self._plot_hist(theta, title)
def main_parameterize(arguments=None):
args = getArgumentParser().parse_args(args=arguments)
if not os.path.exists(args.filename):
raise ValueError('File %s cannot be found' % args.filename)
method_map = {'GAFF': FFTypeMethod.GAFF, 'GAFF2': FFTypeMethod.GAFF2, 'CGENFF': FFTypeMethod.CGenFF_2b6}
methods = [method_map[method] for method in args.forcefield] # TODO: move into FFMolecule
# Get RTF and PRM file names
rtf, prm = None, None
if args.rtf_prm:
rtf, prm = args.rtf_prm
# Create a queue for QM
if args.queue == 'local':
queue = LocalCPUQueue()
elif args.queue == 'Slurm':
queue = SlurmQueue(_configapp=args.code.lower())
elif args.queue == 'LSF':
queue = LsfQueue(_configapp=args.code.lower())
elif args.queue == 'PBS':
queue = PBSQueue() # TODO: configure
elif args.queue == 'AceCloud':
queue = AceCloudQueue() # TODO: configure
else:
raise NotImplementedError
# Override default ncpus
if args.ncpus:
logger.info('Overriding ncpus to {}'.format(args.ncpus))
queue.ncpu = args.ncpus
# Create a QM object
if args.code == 'Psi4':
qm = Psi4()
elif args.code == 'Gaussian':
qm = Gaussian()
else:
raise NotImplementedError
# This is for debugging only!
if args.fake_qm:
qm = FakeQM()
logger.warning('Using FakeQM')
# Set up the QM object
qm.theory = args.theory
qm.basis = args.basis
qm.solvent = args.environment
qm.queue = queue
# List rotatable dihedral angles
if args.list:
mol = FFMolecule(args.filename, method=methods[0], netcharge=args.charge, rtf=rtf, prm=prm, qm=qm,
outdir=args.outdir)
print('\n === Parameterizable dihedral angles of %s ===\n' % args.filename)
with open('torsions.txt', 'w') as fh:
for dihedral in mol.getRotatableDihedrals():
dihedral_name = '%s-%s-%s-%s' % tuple(mol.name[dihedral])
print(' '+dihedral_name)
fh.write(dihedral_name+'\n')
print()
sys.exit(0)
# Print arguments
print('\n === Arguments ===\n')
for key, value in vars(args).items():
print('{:>12s}: {:s}'.format(key, str(value)))
print('\n === Parameterizing %s ===\n' % args.filename)
for method in methods:
print(" === Fitting for %s ===\n" % method.name)
# Create the molecule
mol = FFMolecule(args.filename, method=method, netcharge=args.charge, rtf=rtf, prm=prm, qm=qm,
outdir=args.outdir)
mol.printReport()
# Copy the molecule to preserve initial coordinates
mol_orig = mol.copy()
# Update B3LYP to B3LYP-D3
# TODO: this is silent and not documented stuff
if qm.theory == 'B3LYP':
qm.correction = 'D3'
# Update basis sets
# TODO: this is silent and not documented stuff
if mol.netcharge < 0 and qm.solvent == 'vacuum':
if qm.basis == '6-31G*':
qm.basis = '6-31+G*'
if qm.basis == 'cc-pVDZ':
qm.basis = 'aug-cc-pVDZ'
logger.info('Changing basis sets to %s' % qm.basis)
# Minimize molecule
if args.minimize:
print('\n == Minimizing ==\n')
mol.minimize()
# Fit ESP charges
if args.fit_charges:
print('\n == Fitting ESP charges ==\n')
# Set random number generator seed
if args.seed:
np.random.seed(args.seed)
# Select the atoms with fixed charges
fixed_atom_indices = []
for fixed_atom_name in args.fix_charge:
if fixed_atom_name not in mol.name:
raise ValueError('Atom %s is not found. Check --fix-charge arguments' % fixed_atom_name)
for aton_index in range(mol.numAtoms):
if mol.name[aton_index] == fixed_atom_name:
fixed_atom_indices.append(aton_index)
logger.info('Charge of atom %s is fixed to %f' % (fixed_atom_name, mol.charge[aton_index]))
# Fit ESP charges
score, qm_dipole = mol.fitCharges(fixed=fixed_atom_indices)
# Print results
mm_dipole = mol.getDipole()
score = np.sum((qm_dipole[:3] - mm_dipole[:3])**2)
print('Charge fitting score: %f\n' % score)
print('QM dipole: %f %f %f; %f' % tuple(qm_dipole))
print('MM dipole: %f %f %f; %f' % tuple(mm_dipole))
print('Dipole Chi^2 score: %f\n' % score)
# Fit dihedral angle parameters
if args.fit_dihedral:
print('\n == Fitting dihedral angle parameters ==\n')
# Set random number generator seed
if args.seed:
np.random.seed(args.seed)
# Get all rotatable dihedrals
all_dihedrals = mol.getRotatableDihedrals()
# Choose which dihedrals to fit
dihedrals = []
all_dihedral_names = ['-'.join(mol.name[dihedral]) for dihedral in all_dihedrals]
for dihedral_name in args.dihedral:
if dihedral_name not in all_dihedral_names:
raise ValueError('%s is not recognized as a rotatable dihedral angle' % dihedral_name)
dihedrals.append(all_dihedrals[all_dihedral_names.index(dihedral_name)])
dihedrals = dihedrals if len(dihedrals) > 0 else all_dihedrals # Set default to all dihedral angles
# Fit the parameters
mol.fitDihedrals(dihedrals, args.optimize_dihedral)
# Output the FF parameters
print('\n == Writing results ==\n')
mol.writeParameters(mol_orig)
# Write energy file
energyFile = os.path.join(mol.outdir, 'parameters', method.name, mol.output_directory_name(), 'energies.txt')
printEnergies(mol, energyFile)
logger.info('Write energy file: %s' % energyFile)
def main_parameterize(arguments=None):
args = getArgumentParser().parse_args(args=arguments)
if not os.path.exists(args.filename):
raise ValueError('File %s cannot be found' % args.filename)
method_map = {
'GAFF': FFTypeMethod.GAFF,
'GAFF2': FFTypeMethod.GAFF2,
'CGENFF': FFTypeMethod.CGenFF_2b6
}
methods = [method_map[method]
for method in args.forcefield] # TODO: move into FFMolecule
# Get RTF and PRM file names
rtf, prm = None, None
if args.rtf_prm:
rtf, prm = args.rtf_prm
# Create a queue for QM
if args.queue == 'local':
queue = LocalCPUQueue()
elif args.queue == 'Slurm':
queue = SlurmQueue(_configapp=args.code.lower())
elif args.queue == 'LSF':
queue = LsfQueue(_configapp=args.code.lower())
elif args.queue == 'PBS':
queue = PBSQueue() # TODO: configure
elif args.queue == 'AceCloud':
queue = AceCloudQueue() # TODO: configure
queue.groupname = args.groupname
queue.hashnames = True
else:
raise NotImplementedError
# Override default ncpus
if args.ncpus:
logger.info('Overriding ncpus to {}'.format(args.ncpus))
queue.ncpu = args.ncpus
if args.memory:
logger.info('Overriding memory to {}'.format(args.memory))
queue.memory = args.memory
# Create a QM object
if args.code == 'Psi4':
qm = Psi4()
elif args.code == 'Gaussian':
qm = Gaussian()
else:
raise NotImplementedError
# This is for debugging only!
if args.fake_qm:
qm = FakeQM2()
logger.warning('Using FakeQM')
# Set up the QM object
qm.theory = args.theory
qm.basis = args.basis
qm.solvent = args.environment
qm.queue = queue
# List rotatable dihedral angles
if args.list:
mol = FFMolecule(args.filename,
method=methods[0],
netcharge=args.charge,
rtf=rtf,
prm=prm,
qm=qm,
outdir=args.outdir)
print('\n === Parameterizable dihedral angles of %s ===\n' %
args.filename)
with open('torsions.txt', 'w') as fh:
for dihedral in mol.getRotatableDihedrals():
dihedral_name = '%s-%s-%s-%s' % tuple(mol.name[dihedral])
print(' ' + dihedral_name)
fh.write(dihedral_name + '\n')
print()
sys.exit(0)
# Print arguments
print('\n === Arguments ===\n')
for key, value in vars(args).items():
print('{:>12s}: {:s}'.format(key, str(value)))
print('\n === Parameterizing %s ===\n' % args.filename)
for method in methods:
print(" === Fitting for %s ===\n" % method.name)
# Create the molecule
mol = FFMolecule(args.filename,
method=method,
netcharge=args.charge,
rtf=rtf,
prm=prm,
qm=qm,
outdir=args.outdir)
mol.printReport()
# Copy the molecule to preserve initial coordinates
mol_orig = mol.copy()
# Update B3LYP to B3LYP-D3
# TODO: this is silent and not documented stuff
if qm.theory == 'B3LYP':
qm.correction = 'D3'
# Update basis sets
# TODO: this is silent and not documented stuff
if mol.netcharge < 0 and qm.solvent == 'vacuum':
if qm.basis == '6-31G*':
qm.basis = '6-31+G*'
if qm.basis == 'cc-pVDZ':
qm.basis = 'aug-cc-pVDZ'
logger.info('Changing basis sets to %s' % qm.basis)
# Minimize molecule
if args.minimize:
print('\n == Minimizing ==\n')
mol.minimize()
# Fit ESP charges
if args.fit_charges:
print('\n == Fitting ESP charges ==\n')
# Set random number generator seed
if args.seed:
np.random.seed(args.seed)
# Select the atoms with fixed charges
fixed_atom_indices = []
for fixed_atom_name in args.fix_charge:
if fixed_atom_name not in mol.name:
raise ValueError(
'Atom %s is not found. Check --fix-charge arguments' %
fixed_atom_name)
for aton_index in range(mol.numAtoms):
if mol.name[aton_index] == fixed_atom_name:
fixed_atom_indices.append(aton_index)
logger.info('Charge of atom %s is fixed to %f' %
(fixed_atom_name, mol.charge[aton_index]))
# Fit ESP charges
_, qm_dipole = mol.fitCharges(fixed=fixed_atom_indices)
# Copy the new charges to the original molecule
mol_orig.charge[:] = mol.charge
# Print dipoles
logger.info('QM dipole: %f %f %f; %f' % tuple(qm_dipole))
mm_dipole = mol.getDipole()
if np.all(np.isfinite(mm_dipole)):
logger.info('MM dipole: %f %f %f; %f' % tuple(mm_dipole))
else:
logger.warning(
'MM dipole cannot be computed. Check if elements are detected correctly.'
)
# Fit dihedral angle parameters
if args.fit_dihedral:
print('\n == Fitting dihedral angle parameters ==\n')
# Set random number generator seed
if args.seed:
np.random.seed(args.seed)
# Get all rotatable dihedrals
all_dihedrals = mol.getRotatableDihedrals()
# Choose which dihedrals to fit
dihedrals = []
all_dihedral_names = [
'-'.join(mol.name[dihedral]) for dihedral in all_dihedrals
]
for dihedral_name in args.dihedral:
if dihedral_name not in all_dihedral_names:
raise ValueError(
'%s is not recognized as a rotatable dihedral angle' %
dihedral_name)
dihedrals.append(
all_dihedrals[all_dihedral_names.index(dihedral_name)])
dihedrals = dihedrals if len(
dihedrals
) > 0 else all_dihedrals # Set default to all dihedral angles
# Fit the parameters
mol.fitDihedrals(dihedrals, args.optimize_dihedral)
# Output the FF parameters
print('\n == Writing results ==\n')
mol.writeParameters(mol_orig)
# Write energy file
energyFile = os.path.join(mol.outdir, 'parameters', method.name,
mol.output_directory_name(), 'energies.txt')
printEnergies(mol, energyFile)
logger.info('Write energy file: %s' % energyFile)
