def __init__(self, at_type, at_coords, at_charge, at_ro, at_eps, at_mass):
self.attype = at_type
self.element = at_type[0].capitalize()
self.coords = at_coords
self.charge = at_charge
self.ro = at_ro
self.eps = at_eps
self.sreps = math.sqrt(self.eps)
self.mass = at_mass
self.covrad = param.get_cov_rad(self.element)
self.e_nonbonded = 0.0
self.e_bonded = 0.0
self.g_nonbonded = np.zeros(3)
self.g_bonded = np.zeros(3)
def __init__(self, at_type, at_coords, at_charge, at_ro, at_eps, at_mass):
self.attype = at_type
self.element = at_type[0].capitalize()
self.coords = at_coords
self.charge = at_charge
self.ro = at_ro
self.eps = at_eps
self.sreps = math.sqrt(self.eps)
self.mass = at_mass
self.covrad = param.get_cov_rad(self.element)
self.e_nonbonded = 0.0
self.e_bonded = 0.0
self.g_nonbonded = np.zeros(3)
self.g_bonded = np.zeros(3)
def get_geom(mol):
infile_array = get_file_string_array(mol.infile)
mol.n_atoms = int(infile_array[0][0])
for i in range(mol.n_atoms):
at_type = infile_array[i+2][0]
at_coords = np.zeros(3)
for j in range(3):
at_coords[j] = float(infile_array[i+2][j+1])
at_charge = float(infile_array[i+2][4])
at_element = at_type[0].capitalize()
at_mass = param.get_at_mass(at_element)
at_ro, at_eps = param.get_vdw_param(at_type)
new_atom = molecule.atom(at_type, at_coords, at_charge, at_ro, at_eps, at_mass)
new_atom.set_covrad(param.get_cov_rad(at_element))
mol.atoms.append(new_atom)