rdkit.Ched.rdFMCS.FindMCS generates invalid smarts

[luancarvalhomartins]

Configuration:

• RDKit Version: 2019.09.1
• Operating system: Linux laptop 5.0.0-36-generic Support turning off sanitization for GetMolFrags() from python. #39-Ubuntu SMP Tue Nov 12 09:46:06 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
• Python version (if relevant): 3.6
• Are you using conda? Yes
• If you are using conda, which channel did you install the rdkit from? conda install rdkit -c rdkit

Description:

rdkit.Ched.rdFMCS.FindMCS generates invalid SMARTS if ringMatchesRingOnly = True and the MCS contains a query atom bonded through an "any bond" type bond. This is irrespective of the molecule bearing a ring.

import rdkit.Chem, rdkit.Chem.rdFMCS

mol = rdkit.Chem.MolFromSmarts('*~CCC')

# Works
args = {'ringMatchesRingOnly': False}
rdkit.Chem.MolFromSmarts(rdkit.Chem.rdFMCS.FindMCS([mol, mol], **args).smartsString)

# SMARTS Parse Error: Failed parsing SMARTS '[#0&!R]&!@[#6&!R]-&!@[#6&!R]-&!@[#6&!R]' for input: '[#0&!R]&!@[#6&!R]-&!@[#6&!R]-&!@[#6&!R]'
args = {'verbose': False, 'ringMatchesRingOnly': True}
rdkit.Chem.MolFromSmarts(rdkit.Chem.rdFMCS.FindMCS([mol, mol], **args).smartsString)

[ptosco]

@luancarvalhomartins thanks for reporting this bug. Tomorrow I'll commit the fix together with a new unit test.