Some molecules fail isomorphism check #1740
Description
Bug Description
I'm checking isomorphism between a molecule generated from xyz. When generated in the same atom order, the isomorphism check returns True. When generated in a different atom order (changing C and Cl), the isomorphism check returns False.
How To Reproduce
Run the following script:
from rmgpy.molecule.molecule import Atom, Molecule
import numpy as np
def s_bonds_mol_from_xyz(xyz):
mol = Molecule()
for symbol, coord in zip(xyz['symbols'], xyz['coords']):
atom = Atom(element=symbol)
atom.coords = np.array([coord[0], coord[1], coord[2]], np.float64)
mol.add_atom(atom)
mol.connect_the_dots()
return mol
xyz1 = {'symbols': ('Cl', 'F', 'C', 'O', 'O', 'H'),
'isotopes': (35, 19, 12, 16, 16, 1),
'coords': ((3.09727149, -1.18647281, -0.9370755),
(0.27568368, 0.01156702, -0.4122491),
(1.50048866, -0.50848248, -0.64006761),
(1.93561914, 0.7474161, -1.16759033),
(2.33727805, 1.9067071, -1.65453438),
(3.25580294, 1.83954553, -1.92546105))}
xyz2 = {'symbols': ('C', 'F', 'Cl', 'O', 'O', 'H'), # this is xyz1 with C and Cl replaced
'isotopes': (12, 19, 35, 16, 16, 1),
'coords': ((1.50048866, -0.50848248, -0.64006761),
(0.27568368, 0.01156702, -0.4122491),
(3.09727149, -1.18647281, -0.9370755),
(1.93561914, 0.7474161, -1.16759033),
(2.33727805, 1.9067071, -1.65453438),
(3.25580294, 1.83954553, -1.92546105))}
xyz3 = {'symbols': ('C', 'F', 'Cl', 'O', 'O', 'H'), # identical to xyz2
'isotopes': (12, 19, 35, 16, 16, 1),
'coords': ((1.50048866, -0.50848248, -0.64006761),
(0.27568368, 0.01156702, -0.4122491),
(3.09727149, -1.18647281, -0.9370755),
(1.93561914, 0.7474161, -1.16759033),
(2.33727805, 1.9067071, -1.65453438),
(3.25580294, 1.83954553, -1.92546105))}
mol1 = s_bonds_mol_from_xyz(xyz1)
mol2 = s_bonds_mol_from_xyz(xyz2)
mol3 = s_bonds_mol_from_xyz(xyz3)
print(mol2.is_isomorphic(mol1)) # gives False
print(mol2.is_isomorphic(mol3)) # gives True
print(mol1.to_adjacency_list())
print(mol2.to_adjacency_list())
print(mol3.to_adjacency_list())Expected Behavior
If I understand correctly, the isomorphism check should not care about atom order, and should return a consistent answer, hopefully the correct one (True in this case)
Installation Information
master branches (ce53e34 for RMG-Py)