minihf.molecule.molecule module

class minihf.molecule.molecule.Molecule(atoms=None, charge=0, multiplicity=1)[source]

Bases: object

Molecule class representing a collection of atoms

classmethod build(atoms, charge=0, multiplicity=1)[source]

Build a molecule from Atom objects.

Parameters:

atoms (list) – A list of Atom objects.
charge (int, optional) – Total molecular charge (default: 0)
multiplicity (int, optional) – Spin multiplicity (default: 1 for singlet)

add_atom(atom)[source]: Add an atom to the molecule

remove_atom(index)[source]: Remove atom at given index

get_atom(index)[source]: Get atom at given index

bond_length(i, j)[source]

Calculate the distance between atom i and j.

Parameters:

i (int) – Index of first atom.
j (int) – Index of second atom.

Returns:

Distance between atoms i and j

Return type:

float

bond_angle(i, j, k)[source]

Calculate the bond angle between atoms i,j,k.: Where atom j is the central atom.

Parameters:

i (int) – Index of first atom.
j (int) – Index of second atom.
k (int) – Index of third atom.
unit (str, optional) – Unit of the returned angle (‘rad’ or ‘deg’, default: ‘rad’)

Returns:

Bond angle between atoms i,j,k in specified unit

Return type:

float

dihedral_angle(i, j, k, l)[source]

Calculate dihedral angle for atom connectivity A,B,C,D.

Parameters:

i (int) – Index of first atom (atom A).
j (int) – Index of second atom (atom B).
k (int) – Index of third atom (atom C).
l (int) – Index of fourth atom (atom D).

Returns:

Dihedral angle in degrees (-180 to 180)

Return type:

float

Raises:

TypeError – If index of atom is not int.
ValueError – If index of atom is not zero or positive number. If index of atom is not smaller than number of atoms.

property nelec: Number of total electrons in the molecule.

property nalpha: Number of alpha electrons in the molecule.

property nbeta: Number of beta electrons in the molecule.

property energy_nuc

Nucelar repulsion energy.

Returns:: energy – Nuclear repulsion energy.
Return type:: float

property atom_coords: Get all atomic coordinates as Nx3 array

property atom_masses: Get all atomic masses as Nx1 array

property atom_numbers: Get all atomic numbers as Nx1 array

property atom_symbols: Get all atomic symbols as Nx1 array

property mass: Get total molecular mass

property center_of_mass

Calculate the center of mass for molecular.

Returns:: [x, y, z] coordinates of center of mass
Return type:: np.ndarray