def __init__(self, complex_data=None, molecules_data=None):
if complex_data is None: complex_data = {'name': None}
if molecules_data is None: molecules_data = []
GroupOfSites.__init__(self, name=complex_data['name'])
self.qm_energy = None
self.molecules = []
# load molecules
num_extra = 0
num_atoms = 0
for mol_data in molecules_data:
natoms = mol_data['num atoms']
mol_name = mol_data['name']
sym = mol_data['symmetry']
atoms = []
try:
atoms_order = mol_data['atoms order']
except KeyError:
atoms_order = [a+1+num_atoms for a in range(natoms)]
for i in atoms_order:
index, elem, crds, q = complex_data['atoms'][i-1] # indices start with 1
index += num_extra
atom = (index, elem, crds, q)
atoms.append(atom)
d = {
'name': mol_name,
'atoms': atoms,
'symmetry': sym,
}
m = Molecule(data=d)
self.add_molecule(m)
num_extra += len(m.extra_sites)
num_atoms += len(m.atoms)
self.decomposition = {
'electrostatic': None,
'dispersion': None,
'exchange': None,
}
def __init__(self, mol1, mol2):
name = '%s-%s' % (mol1.name, mol2.name)
GroupOfSites.__init__(self, name)
AtomsInMolecule.__init__(self, name)
self.mol1 = mol1
self.mol2 = mol2
self.molecules = (mol1, mol2)
iatom = 1
isite = 1
for m in self.molecules:
for site in m.sites:
site.set_index(isite)
self.add_site(site)
isite += 1
for atom in m.atoms:
atom.set_index(iatom)
self.add_atom(atom)
iatom += 1
self.decomposition = {
'electrostatic': None,
'6': None,
'12': None,
'LJ': None,
}