Structure object

$ Structure(coordinates=None,

internal=None, z_matrix=None, int_label=None, atom_types=None, atomic_elements=None, atomic_numbers=None, connectivity=None, file_name=None, charge=0, multiplicity=1, int_weights=None):

Methods

def get_coordinates():

return self._coordinates.copy()

def set_coordinates(self, coordinates):

self._coordinates = coordinates self._number_of_atoms = None self._energy = None

def get_internal():

return self._internal.copy()

def set_internal(internal):

self._internal = internal

def get_full_z_matrix():

return self._full_z_matrix

def get_z_matrix():

return self._z_matrix

def set_z_matrix(z_matrix):

self._z_matrix = z_matrix

def get_int_label():

return self._int_label

def set_int_label(int_label):

self._int_label = int_label

def get_int_dict():

self._internal_dict = {} for i, label in enumerate(self.get_int_label()[:,0]):

self._internal_dict.update({label:self.get_internal()[i, 0]})

return self._internal_dict

def get_int_weights():

return self._int_weights

def set_int_weights(int_weights):

self._int_weights = int_weights

def get_atomic_elements_with_dummy():

return self._atomic_elements

def get_atom_types():

return self._atom_types

def set_atom_types(atom_types):

self._atom_types = atom_types

def get_atomic_numbers():

return self._atomic_numbers

def set_atomic_numbers(atomic_numbers):

def get_atomic_elements(self):

return np.array([i for i in self._atomic_elements if i != “X”], dtype=str)

def set_atomic_elements(atomic_elements):

def get_connectivity():

return self._connectivity

def set_connectivity(connectivity):

def get_number_of_atoms():

return self._number_of_atoms

def get_number_of_internal():

return self._number_of_internal

def get_energy(method=None):

return self._energy

def get_modes(method=None):

return self._modes

def get_atomic_masses(self):

return self._atomic_masses

Properties

@property def charge(self):

return self._charge

@property def multiplicity(self):

return self._multiplicity

example

initial_coordinates = [[ 0.5784585,  0.7670811,  1.3587379],
                       [-1.7015514, -0.0389921, -0.0374715],
                       [ 0.5784290, -1.6512236, -0.0374715],
                       [ 0.5784585,  0.7670811, -1.4336809],
                       [ 0.0000000,  0.0000000,  0.0000000]]
initial_coordinates = np.array(initial_coordinates)

atomic_elements = ['O', 'O', 'O', 'O', 'P']
atomic_elements = np.array(atomic_elements)[None].T

molecule = Structure(coordinates=initial_coordinates,
                       atomic_elements=atomic_elements)

molecule.charge = 0
molecule.multiplicity = 1