def _setup(self):
if len(self.dihedrals) != len(self.qm_results):
raise ValueError('The number of dihedral and QM result sets has to be the same!')
# Get dihedral names
self._names = ['-'.join(self.molecule.name[dihedral]) for dihedral in self.dihedrals]
# Get all equivalent dihedrals
all_equivalent_dihedrals = detectParameterizableDihedrals(self.molecule)
all_equivalent_dihedrals = {tuple(dihedrals[0]): dihedrals for dihedrals in all_equivalent_dihedrals}
# Choose the selected dihedrals
equivalent_dihedrals = []
for dihedral, name in zip(self.dihedrals, self._names):
if tuple(dihedral) not in all_equivalent_dihedrals:
raise ValueError('{} is not a parameterizable dihedral!'.format(name))
equivalent_dihedrals.append(all_equivalent_dihedrals[tuple(dihedral)])
# Get dihedral atom types
self._dihedral_atomtypes = [findDihedralType(tuple(self.molecule.atomtype[dihedral]), self.parameters) for dihedral in self.dihedrals]
# Get reference QM energies and rotamer coordinates
self._reference_energies = []
self._coords = []
for results in self.qm_results:
self._reference_energies.append(np.array([result.energy for result in results]))
self._coords.append([result.coords for result in results])
# Calculate dihedral angle values
# [# of scans, # of dihedrals, # of conformations, # of equivalents]
self._angle_values = []
for scan_coords in self._coords:
scan_angle_values = []
for equivalent_indices in equivalent_dihedrals:
angle_values = []
for coords in scan_coords:
angle_values.append([dihedralAngle(coords[indices, :, 0]) for indices in equivalent_indices])
scan_angle_values.append(np.array(angle_values))
self._angle_values.append(scan_angle_values)
# Calculated initial MM energies
ff = FFEvaluate(self.molecule, self.parameters)
self._initial_energies = []
for scan_coords in self._coords:
energies = [ff.calculateEnergies(coords[:, :, 0])['total'] for coords in scan_coords]
self._initial_energies.append(np.array(energies))
# Make result directories
os.makedirs(self.result_directory, exist_ok=True)
def _select_dihedrals(mol, args):
from htmd.parameterization.detect import detectParameterizableDihedrals
logger.info('=== Dihedral angles ===')
# Detect parameterizable dihedral angles
parameterizable_dihedrals = detectParameterizableDihedrals(mol)
logger.info('Parameterizable dihedral angles (and their equivalents):')
for i, equivalent_dihedrals in enumerate(parameterizable_dihedrals):
names = ['-'.join(mol.name[list(dihedral)]) for dihedral in equivalent_dihedrals]
line = ' {:2d}: {}'.format(i+1, names[0])
if names[1:]:
line += ' ({})'.format(', '.join(names[1:]))
logger.info(line)
# Print parameterize dihedral list to a file and exit
# TODO factor this out
if args.list:
dihedral_file = 'torsions.txt'
with open(dihedral_file, 'w') as file:
for dihedrals in parameterizable_dihedrals:
name = '-'.join(mol.name[list(dihedrals[0])])
file.write('{}\n'.format(name))
logger.info('Write the list of the parameterizable dihedral angles to {}'.format(dihedral_file))
sys.exit()
# Select dihedrals to parameterize
selected_dihedrals = []
if args.fit_dihedral:
if args.dihedral:
name2dihedral = {'-'.join(mol.name[list(dihedrals[0])]): dihedrals[0] for dihedrals in parameterizable_dihedrals}
for dihedral_name in args.dihedral:
if dihedral_name not in name2dihedral.keys():
raise ValueError('%s is not recognized as a rotatable dihedral angle' % dihedral_name)
selected_dihedrals.append(list(name2dihedral[dihedral_name]))
else:
# By default parameterize all the dihedrals
selected_dihedrals = [list(dihedrals[0]) for dihedrals in parameterizable_dihedrals]
if len(selected_dihedrals) > 0:
logger.info('Selected dihedral angles:')
for i, dihedral in enumerate(selected_dihedrals):
name = '-'.join(mol.name[list(dihedral)])
logger.info(' {:2d}: {}'.format(i+1, name))
else:
logger.info('No dihedral angles selected')
return selected_dihedrals
def getEquivalentsAndDihedrals(mol):
from htmd.molecule.util import guessAnglesAndDihedrals
from htmd.parameterization.detect import detectParameterizableDihedrals, detectEquivalentAtoms
mol = mol.copy()
# Guess bonds
if len(mol.bonds) == 0:
logger.warning('No bonds found! Guessing them...')
mol.bonds = mol._guessBonds()
mol.angles, mol.dihedrals = guessAnglesAndDihedrals(mol.bonds)
equivalents = detectEquivalentAtoms(mol)
all_dihedrals = detectParameterizableDihedrals(mol)
return mol, equivalents, all_dihedrals
def getEquivalentsAndDihedrals(mol):
from htmd.molecule.util import guessAnglesAndDihedrals
from htmd.parameterization.detect import detectParameterizableDihedrals, detectEquivalentAtoms
mol = mol.copy()
# Guess bonds
if len(mol.bonds) == 0:
logger.warning('No bonds found! Guessing them...')
mol.bonds = mol._guessBonds()
mol.angles, mol.dihedrals = guessAnglesAndDihedrals(mol.bonds)
equivalents = detectEquivalentAtoms(mol)
all_dihedrals = detectParameterizableDihedrals(mol)
return mol, equivalents, all_dihedrals