def format_coords(geo):
""" format the coords section
"""
# Get the number of atoms
natoms = len(geo)
# Get the geometry information
symbols = geom.symbols(geo)
coordinates = geom.coordinates(geo)
masses = [int(ptab.to_mass(symbol)) for symbol in symbols]
# Build a string with the formatted coordinates string
if geom.is_atom(geo):
geo_str = '{0:<4s}{1:<6d}'.format(symbols[0], masses[0])
else:
geo_str = ''
for symbol, mass, coords in zip(symbols, masses, coordinates):
coords = [coord * BOHR2ANG for coord in coords]
coords_str = '{0:>14.8f}{1:>14.8f}{2:>14.8f}'.format(
coords[0], coords[1], coords[2])
geo_str += '{0:<4s}{1:<6d}{2}\n'.format(symbol, mass, coords_str)
# Remove final newline character from the string
geo_str = geo_str.rstrip()
return natoms, geo_str
def sample_normal_modes(conformer, n_samples, temperature):
"""
Take a conformer and return randomly sampled geometries by applying
random displacements according to the normal modes of the molecule
"""
atoms = conformer.atoms
n_atoms = atoms.shape[0]
original_xyz = conformer.xyz
masses = [periodictable.to_mass(atom) for atom in atoms.tolist()]
normal_modes = conformer.labels['normal modes']
force_constants = conformer.labels['force constants']
n_modes = len(normal_modes)
kb = physical_constants.pc['boltzmann constant']
new_coords = []
for sample in range(n_samples):
cis = torch.rand(n_modes)
c_scale = torch.rand(1)
cis = c_scale * cis / cis.sum()
displacement_scalars = (
((torch.bernoulli(torch.fill(n_modes, 0.5)) - 0.5) * 2.0) *
torch.sqrt(
3.0 * cis * n_atoms * kb * temperature / force_constants))
displacements = [
mode * displacement_scalars[i]
for i, mode in enumerate(normal_modes)
]
def to_mass(atom):
""" Obtain the atomic mass for a given atom (in amu).
:param atom: atom representation (symbol, number, mass)
:type atom: str/int
:rtype: float
"""
return periodictable.to_mass(atom)
def atom_mass(har_min_cnf_locs, har_cnf_save_fs):
""" write the atom string
"""
har_geo = har_cnf_save_fs.leaf.file.geometry.read(har_min_cnf_locs)
return ptab.to_mass(har_geo[0][0])
def atom_to_mass(atom: Union[str, int]) -> float:
"""Give back the mass of a given element."""
return periodictable.to_mass(atom)