def from_molecule(cls, molecule, model, points):
r"""
Initialize class from `Molecule` object(s).
Parameters
----------
molecule : Molecule or Sequence of Molecule
Instance of Molecule class, or sequence of Molecule class instances.
model : str
Energy model used to calculate local reactivity descriptors.
Available models are "linear" and "quadratic".
points : np.array
Coordinates of points on which the local properties are evaluated given as a 2D
array with 3 columns.
"""
# check molecule
molecule = check_arg_molecule(molecule)
# if points is None:
# # make molecular grid which also checks for matching atomic numbers & coordinates
# grid = get_molecular_grid(molecule, grid=None)
# points, numbers, coords = grid.points, grid.numbers, grid.centers
numbers = get_matching_attr(molecule, "numbers", 1.e-8)
coords = get_matching_attr(molecule, "coordinates", 1.e-4)
dict_dens = get_dict_density(molecule, points)
return cls(dict_dens, model, coords, numbers)
def from_molecule(cls, molecule, model, approach="FMR", scheme="h", **kwargs):
r"""
Initialize class from `Molecule` object(s).
Parameters
----------
molecule : Molecule or Sequence of Molecule
Instance of Molecule class, or sequence of Molecule class instances.
model : str
Energy model used to calculate condensed reactivity descriptors.
Available models are "linear" and "quadratic".
approach : str, optional
Choose between "FMR" (fragment of molecular response) or "RMF"
(response of molecular fragment).
scheme : str, optional
Partitioning scheme. Options: "h", "hi", "mbis".
kwargs : dict, optional
Extra keyword arguments required for partitioning, like 'grid' and 'proatomdb'.
"""
# check molecule
molecule = check_arg_molecule(molecule)
# check type of grid
if "grid" in list(kwargs.keys()) and not isinstance(kwargs["grid"], MolecularGrid):
raise ValueError("Currently, only 'MolecularGrid' is supported for condensing!")
# get atomic number, coordinates, N_max, and global softness
gcdft = GlobalConceptualDFT.from_molecule(molecule, model)
coords, nums, n_max, s = gcdft.coordinates, gcdft.numbers, gcdft.n_max, gcdft.softness
# get dictionary of populations
dict_pops = get_dict_population(molecule, approach, scheme, **kwargs)
return cls(dict_pops, model, coords, nums, n_max, s)
def from_molecule(cls, molecule, model):
r"""
Initialize class from `Molecule` object(s).
Parameters
----------
molecule : Molecule or Sequence of Molecule
Instance of Molecule class, or sequence of Molecule class instances.
model : str
Energy model used to calculate global reactivity descriptors.
"""
# check molecule
molecule = check_arg_molecule(molecule)
# get atomic number and atomic coordinates
number = get_matching_attr(molecule, "numbers", 1.e-8)
coords = get_matching_attr(molecule, "coordinates", 1.e-4)
dict_energy = get_dict_energy(molecule)
return cls(dict_energy, model, coords, number)