def __init__(self, dihedral, molecule=None, top_indexes=None, potential=None):
"""
Arguments
| ``dihedral`` -- the index of the atoms that define the dihedral
angle
Optional arguments
| ``molecule`` -- a molecule object. required when top_indexes is not
given
| ``top_indexes`` -- a list of atom indexes involved in the rotor.
required when molecule is not given
| ``potential`` -- rotational potential info (if this is a hindered
rotor). must be a two-tuple containing the angles
and the corresponding energies.
"""
self.dihedral = dihedral
if top_indexes is None:
# try to deduce the top indexes
if molecule is None:
raise ValueError("missing arguemt: top_indexes or molecule from which top_indexes can be derived")
atom0, atom1 = dihedral[1:3]
graph = MolecularGraph.from_geometry(molecule)
half0, half1 = graph.get_halfs(atom0, atom1)
if len(half1) > len(half0):
top_indexes = half0
top_indexes.discard(atom0)
else:
top_indexes = half1
top_indexes.discard(atom1)
top_indexes = tuple(top_indexes)
self.top_indexes = top_indexes
self.potential = potential
def __init__(self,
dihedral,
molecule=None,
top_indexes=None,
potential=None):
"""
Arguments
| ``dihedral`` -- the index of the atoms that define the dihedral
angle
Optional arguments
| ``molecule`` -- a molecule object. required when top_indexes is not
given
| ``top_indexes`` -- a list of atom indexes involved in the rotor.
required when molecule is not given or when the
top_indexes can not be derived automatically.
| ``potential`` -- rotational potential info (if this is a hindered
rotor). must be a two-tuple containing the angles
and the corresponding energies.
"""
self.dihedral = dihedral
if top_indexes is None:
# try to deduce the top indexes
if molecule is None:
raise ValueError(
"missing arguemt: top_indexes or molecule from which top_indexes can be derived"
)
atom0, atom1 = dihedral[1:3]
graph = MolecularGraph.from_geometry(molecule)
half0, half1 = graph.get_halfs(atom0, atom1)
if (len(half0) + len(half1) !=
molecule.size) or len(half0) == 1 or len(half1) == 1:
raise ValueError(
"The rotating top could not be assigned properly. Specify the top_indexes manually."
)
if len(half1) > len(half0):
top_indexes = half0
top_indexes.discard(atom0)
else:
top_indexes = half1
top_indexes.discard(atom1)
top_indexes = tuple(top_indexes)
else:
# check the sanity of the top indexes
if not ((self.dihedral[0] in top_indexes) ^
(self.dihedral[3] in top_indexes)):
raise ValueError(
'The top must contain either first or the last atom of the dihedral angle.'
)
if ((self.dihedral[1] in top_indexes) |
(self.dihedral[2] in top_indexes)):
raise ValueError(
'The top may not contain atoms from the central bond of the dihedral angle.'
)
self.top_indexes = top_indexes
self.potential = potential
def get_precursor_model():
m = XYZFile("test/input/mfi_precursor.xyz").get_molecule()
mgraph = MolecularGraph.from_geometry(m)
connect_masks = np.array([
number == 8 and len(mgraph.neighbors[index]) == 1
for index, number in enumerate(m.numbers)
], bool)
radii = np.array([
periodic[number].vdw_radius * {True: 0.3, False: 1.0}[connect_mask]
for number, connect_mask in zip(m.numbers, connect_masks)
], float)
radii += np.random.uniform(0, 0.1, radii.shape)
return m.coordinates, connect_masks, radii
def __init__(self, dihedral, molecule=None, top_indexes=None, potential=None):
"""
Arguments
| ``dihedral`` -- the index of the atoms that define the dihedral
angle
Optional arguments
| ``molecule`` -- a molecule object. required when top_indexes is not
given
| ``top_indexes`` -- a list of atom indexes involved in the rotor.
required when molecule is not given or when the
top_indexes can not be derived automatically.
| ``potential`` -- rotational potential info (if this is a hindered
rotor). must be a two-tuple containing the angles
and the corresponding energies.
"""
self.dihedral = dihedral
if top_indexes is None:
# try to deduce the top indexes
if molecule is None:
raise ValueError("missing arguemt: top_indexes or molecule from which top_indexes can be derived")
atom0, atom1 = dihedral[1:3]
graph = MolecularGraph.from_geometry(molecule)
half0, half1 = graph.get_halfs(atom0, atom1)
if (len(half0) + len(half1) != molecule.size) or len(half0) == 1 or len(half1) == 1:
raise ValueError("The rotating top could not be assigned properly. Specify the top_indexes manually.")
if len(half1) > len(half0):
top_indexes = half0
top_indexes.discard(atom0)
else:
top_indexes = half1
top_indexes.discard(atom1)
top_indexes = tuple(top_indexes)
else:
# check the sanity of the top indexes
if not ((self.dihedral[0] in top_indexes) ^ (self.dihedral[3] in top_indexes)):
raise ValueError('The top must contain either first or the last atom of the dihedral angle.')
if ((self.dihedral[1] in top_indexes) | (self.dihedral[2] in top_indexes)):
raise ValueError('The top may not contain atoms from the central bond of the dihedral angle.')
self.top_indexes = top_indexes
self.potential = potential