def _get_neighbor_coeffs(self, mol: Molecule) -> Counter:
"""
Get a counter containing the coefficients for the gamma
(bond_corr_neighbor) variables.
Args:
mol: RMG-Py molecule.
Returns:
Counter containing gamma coefficients.
"""
if hasattr(mol, 'id') and mol.id is not None:
if mol.id in self._gamma_coeffs:
return self._gamma_coeffs[mol.id]
coeffs = Counter()
for bond in mol.get_all_edges():
atom1 = bond.atom1
atom2 = bond.atom2
# Atoms adjacent to atom1
counts1 = Counter(a.element.symbol for a, b in atom1.bonds.items() if b is not bond)
counts1[atom1.element.symbol] += max(0, len(atom1.bonds) - 1)
# Atoms adjacent to atom2
counts2 = Counter(a.element.symbol for a, b in atom2.bonds.items() if b is not bond)
counts2[atom2.element.symbol] += max(0, len(atom2.bonds) - 1)
coeffs += counts1 + counts2
if hasattr(mol, 'id'):
self._gamma_coeffs[mol.id] = coeffs
return coeffs
def _get_length_coeffs(self, mol: Molecule) -> defaultdict:
"""
Get a dictionary containing the coefficients for the beta
(bond_corr_length) variables. There is one coefficient per atom
type and an additional coefficient for each combination of atom
types.
Example: If the atoms are H, C, and O, there are (at most)
coefficients for H, C, O, (C, H), (H, O), and (C, O).
Args:
mol: RMG-Py molecule.
Returns:
Defaultdict containing beta coefficients.
"""
if hasattr(mol, 'id') and mol.id is not None:
if mol.id in self._beta_coeffs:
return self._beta_coeffs[mol.id]
coeffs = defaultdict(float)
for bond in mol.get_all_edges():
atom1 = bond.atom1
atom2 = bond.atom2
symbol1 = atom1.element.symbol
symbol2 = atom2.element.symbol
c = np.exp(-self.exp_coeff * np.linalg.norm(atom1.coords - atom2.coords))
k = symbol1 if symbol1 == symbol2 else tuple(sorted([symbol1, symbol2]))
coeffs[k] += c
if hasattr(mol, 'id'):
self._beta_coeffs[mol.id] = coeffs
return coeffs
def test_molecule(self):
"""
Test that a Molecule contains the `id` attribute.
"""
rmg_mol = RMGMolecule(smiles='C')
mol = Molecule(smiles='C')
self.assertIsInstance(mol, RMGMolecule)
self.assertTrue(hasattr(mol, 'id'))
self.assertFalse(hasattr(rmg_mol, 'id'))
def test_geo_to_mol(self):
"""
Test that a geometry can be converted to an RMG molecule.
"""
# Hydrogen
nums = (1, 1)
coords = np.array([[0, 0, 0], [0, 0, 0.74]])
mol = geo_to_mol(coords, nums=nums)
self.assertIsInstance(mol, Molecule)
self.assertTrue(mol.to_single_bonds().is_isomorphic(
Molecule(smiles='[H][H]').to_single_bonds()))
# Methane
symbols = ('H', 'C', 'H', 'H', 'H')
coords = np.array([[0.5288, 0.1610, 0.9359], [0.0000, 0.0000, 0.0000],
[0.2051, 0.8240, -0.6786],
[0.3345, -0.9314, -0.4496],
[-1.0685, -0.0537, 0.1921]])
mol = geo_to_mol(coords, symbols=symbols)
self.assertIsInstance(mol, Molecule)
self.assertTrue(mol.to_single_bonds().is_isomorphic(
Molecule(smiles='C').to_single_bonds()))