def test_to_adjacency_list_for_non_integer_bonds(self):
"""
Test the adjacency list can be created for molecules with bond orders
that don't fit into single, double, triple, or benzene
"""
from rmgpy.molecule.molecule import Atom, Bond, Molecule
atom1 = Atom(element='H', lone_pairs=0)
atom2 = Atom(element='H', lone_pairs=0)
bond = Bond(atom1, atom2, 0.5)
mol = Molecule(multiplicity=1)
mol.add_atom(atom1)
mol.add_atom(atom2)
mol.add_bond(bond)
adjlist = mol.to_adjacency_list()
self.assertIn('H', adjlist)
self.assertIn('{1,0.5}', adjlist)
def get_resonance_hybrid(self):
"""
Returns a molecule object with bond orders that are the average
of all the resonance structures.
"""
# get labeled resonance isomers
self.generate_resonance_structures(keep_isomorphic=True)
# only consider reactive molecules as representative structures
molecules = [mol for mol in self.molecule if mol.reactive]
# return if no resonance
if len(molecules) == 1:
return molecules[0]
# create a sorted list of atom objects for each resonance structure
cython.declare(
atomsFromStructures=list,
oldAtoms=list,
newAtoms=list,
numResonanceStructures=cython.short,
structureNum=cython.short,
oldBondOrder=cython.float,
index1=cython.short,
index2=cython.short,
newMol=Molecule,
oldMol=Molecule,
atom1=Atom,
atom2=Atom,
bond=Bond,
atoms=list,
)
atoms_from_structures = []
for new_mol in molecules:
new_mol.atoms.sort(key=lambda atom: atom.id)
atoms_from_structures.append(new_mol.atoms)
num_resonance_structures = len(molecules)
# make original structure with no bonds
new_mol = Molecule()
original_atoms = atoms_from_structures[0]
for atom1 in original_atoms:
atom = new_mol.add_atom(Atom(atom1.element))
atom.id = atom1.id
new_atoms = new_mol.atoms
# initialize bonds to zero order
for index1, atom1 in enumerate(original_atoms):
for atom2 in atom1.bonds:
index2 = original_atoms.index(atom2)
bond = Bond(new_atoms[index1], new_atoms[index2], 0)
new_mol.add_bond(bond)
# set bonds to the proper value
for structureNum, oldMol in enumerate(molecules):
old_atoms = atoms_from_structures[structureNum]
for index1, atom1 in enumerate(old_atoms):
# make bond orders average of resonance structures
for atom2 in atom1.bonds:
index2 = old_atoms.index(atom2)
new_bond = new_mol.get_bond(new_atoms[index1],
new_atoms[index2])
old_bond_order = oldMol.get_bond(
old_atoms[index1], old_atoms[index2]).get_order_num()
new_bond.apply_action(
('CHANGE_BOND', None,
old_bond_order / num_resonance_structures / 2))
# set radicals in resonance hybrid to maximum of all structures
if atom1.radical_electrons > 0:
new_atoms[index1].radical_electrons = max(
atom1.radical_electrons,
new_atoms[index1].radical_electrons)
new_mol.update_atomtypes(log_species=False, raise_exception=False)
return new_mol