TemplateReactions not isomorphic to normal Reaction?

[nateharms]

Bug Description

When trying to create an isomorphic template reaction, RMG's generate_reactions generates reactions from a KineticFamily, it creates template reactions which are not isomorphic to the input reaction of interest

How To Reproduce

In:

import rmgpy
from rmgpy.molecule import Molecule
from rmgpy.reaction import Reaction
from rmgpy.data.rmg import RMGDatabase

rmg_database = RMGDatabase()
database_path = rmgpy.settings['database.directory']
rmg_database.load(
    database_path,
    kinetics_families=["H_Abstraction"],
    transport_libraries=[],
    reaction_libraries=[],
    seed_mechanisms=[],
    thermo_libraries=[
        'primaryThermoLibrary',
        'thermo_DFT_CCSDTF12_BAC',
        'CBS_QB3_1dHR'],
    solvation=False,
)
family = rmg_database.kinetics.families["H_Abstraction"]

r1 = Reaction(reactants=[Molecule(smiles="[CH2]"), Molecule(smiles="[H]")], products=[Molecule(smiles="[H][H]"), Molecule(smiles="[CH]")])

print("Initial reactions is: {}".format(r1))
print("")
for i, r2 in enumerate(family.generate_reactions(r1.reactants)):
    print("The {}th generated reaction is {}".format(i, r2))
    print("Isomorphic?: {}".format(r2.is_isomorphic(r1)))
    for sp in r2.reactants + r2.products:
        sp.clear_labeled_atoms()

Out:

Initial reactions is: <Molecule "[CH2]"> + <Molecule "[H]"> <=> <Molecule "[H][H]"> + <Molecule "[CH]">

The 0th generated reaction is <Molecule "[H]"> + <Molecule "[CH2]"> <=> <Molecule "[H][H]"> + <Molecule "[CH]">
Isomorphic?: False
The 1th generated reaction is <Molecule "[H]"> + <Molecule "[CH2]"> <=> <Molecule "[H][H]"> + <Molecule "[CH]">
Isomorphic?: False

Expected Behavior

We expect one result to be True. However all are False. Also, I would only expect one reaction, however family.generate_reaction(r1.reactants) is list of length 2 of seemingly identical reactions but I'm guessing they are labeled differently.

Installation Information

Describe your installation method and system information.

• OS (include version if known): macOS 10.15.2
• Installation method: From source
• RMG version information:
  • RMG-Py: latest master
  • RMG-database: latest master

[amarkpayne]

I need to test this out, but I wonder if the fact that one of the species is a carbene is relevant. Are there differences in the [CH] molecules in the three reactions? Check the multiplicity and number of paired/unpaired electrons.

[nateharms]

Oy vey... that'll do it... Not a bug, just me having a brain fart 🙃