Error in Reaction Template Matching for a custom made family during model generation

[akashg08]

Bug Description

For the family H_Abs_through_Rad_recombination, RMG is violating the groups' reaction sites, when implementing the reaction recipe. The following is the error produced:

Adding rate rules from training set in kinetics families...
Traceback (most recent call last):
  File "/home/akash-g/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 308, in main
    python(**vars(ns))
  File "/home/akash-g/miniconda3/envs/rmg_env/lib/python3.7/site-packages/julia/pseudo_python_cli.py", line 59, in python
    scope = runpy.run_path(script, run_name="__main__")
  File "/home/akash-g/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 263, in run_path
    pkg_name=pkg_name, script_name=fname)
  File "/home/akash-g/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 96, in _run_module_code
    mod_name, mod_spec, pkg_name, script_name)
  File "/home/akash-g/miniconda3/envs/rmg_env/lib/python3.7/runpy.py", line 85, in _run_code
    exec(code, run_globals)
  File "rmg.py", line 118, in <module>
    main()
  File "rmg.py", line 112, in main
    rmg.execute(**kwargs)
  File "/home/akash-g/RMG/RMG-Py/rmgpy/rmg/main.py", line 785, in execute
    self.initialize(**kwargs)
  File "/home/akash-g/RMG/RMG-Py/rmgpy/rmg/main.py", line 556, in initialize
    self.load_database()
  File "/home/akash-g/RMG/RMG-Py/rmgpy/rmg/main.py", line 475, in load_database
    family.add_rules_from_training(thermo_database=self.database.thermo)
  File "/home/akash-g/RMG/RMG-Py/rmgpy/data/kinetics/family.py", line 1273, in add_rules_from_training
    template = self.get_reaction_template(item)
  File "/home/akash-g/RMG/RMG-Py/rmgpy/data/kinetics/family.py", line 2514, in get_reaction_template
    return self.groups.get_reaction_template(reaction)
  File "/home/akash-g/RMG/RMG-Py/rmgpy/data/kinetics/groups.py", line 199, in get_reaction_template
    raise UndeterminableKineticsError(reaction, message=msg)
rmgpy.exceptions.UndeterminableKineticsError: (TemplateReaction(reactants=[Molecule(smiles="[H]"), Molecule(smiles="C[CH2]")], products=[Molecule(smiles="[CH3]"), Molecule(smiles="[CH3]")]), 'Kinetics could not be determined. Unable to find matching template for reaction <Molecule "[H]"> + <Molecule "C[CH2]"> <=> <Molecule "[CH3]"> + <Molecule "[CH3]"> in reaction family <KineticsGroups "H_Abs_through_Rad_recombination/groups">.Trying to match [<Entry index=0 label="R1_rad">, <Entry index=25 label="R2_rad">, <Entry index=26 label="[H]">] but matched [<Entry index=26 label="[H]">]')

How To Reproduce

Attached below are the libraries, families and the input file.

Expected Behavior

The reactants have to be matched with the groups where *1 site is always H. The above groups of reactants are NOT supposed to react.

Installation Information

• OS : Ubuntu 24.04.1
• Installation method: By Source Using Anaconda Environment for Unix-based Systems
• RMG version information: RMG 3.2.0

data.zip