Undesirable behavior of to_smiles

[IannLiu]

@lily90502

Bug Description

Getting wrong SMILES of oxygen atom when loading data from database.kinetics.families

How To Reproduce

Here is the code:

from rmgpy import settings
from rmgpy.data.rmg import RMGDatabase

families = []
libraries = []
database = RMGDatabase()
database.load(
    path = settings['database.directory'],
    thermo_libraries = ['primaryThermoLibrary'], 
    kinetics_families = families or 'default',
    reaction_libraries = libraries,
    kinetics_depositories = ['training'],
)
family = database.kinetics.families['1+2_Cycloaddition']
all_entries = family.get_training_depository().entries

for num, reaction_entry in all_entries.items():
    # To find out the reactants and products
    rs = reaction_entry.item.reactants
    ps = reaction_entry.item.products
    r_smiles = [s.molecule[0].to_smiles() for s in rs]
    p_smiles = [s.molecule[0].to_smiles() for s in ps]
        
    print(r_smiles)
    print(p_smiles)

I tried the following code as well:

from rmgpy.molecule.molecule import Molecule
m = Molecule().from_adjacency_list("""
                                   O
                                   1 O u0 p3 c0
                                   """)
m_smiles = m.to_smiles()
print(m_smiles)

However, the oxygen atom SMILES is 'O' rather than '[O]'

Expected Behavior

Get the correct SMILES of oxygen atom

Installation Information

• OS (include version if known): Ubuntu 18
• Installation method: (Installation from binary, with anaconda)
• RMG version
  • RMG-Py: 3.1.0
  • RMG-database: 3.1.0

[xiaoruiDong]

@lily90502, this looks similar to what you recently encountered. Can you take a look?

[lily90502]

The issue occurs due to radical electron not updated to be 2 It will pass the radical electron = 0 to rdkit which will make rdkit automatically saturate with H (this does not change even with Chem.RemoveHs(rdkitmol)) The next thing to check is where the molecule information such as radical electron and lone pairs should be corrected (update_atomtypes or update_atoms or other functions)

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