FindAtomEnvironmentOfRadiusN error for small molecules

[Arch4ngel21]

When using rdkit.Chem.rdmolops.FindAtomEnvironmentOfRadiusN with small molecules like LiF or LiCl, this function returns ValueError for atom index 0. Found it while reimplementing MAP4 fingerprint.

Code to reproduce:

from rdkit.Chem.rdmolops import FindAtomEnvironmentOfRadiusN
from rdkit.Chem import MolFromSmiles

radius = 2
mol = MolFromSmiles("[Li]F")

assert mol is not None

for atom in mol.GetAtoms():
    idx = atom.GetIdx()
    for r in range(1, radius + 1):
        env = FindAtomEnvironmentOfRadiusN(mol, idx, r)

Returns:

ValueError: bad atom index

Configuration:

• RDKit version: 2022.09.5
• OS: Windows 10
• Python version: 3.9.7
• rdkit installed through pip

[j-adamczyk]

Root cause: this error happens because there is no radius N for atoms in a molecule with diameter lower than N. This function returns an environment of radius exactly N, not up to N. This is not stated anywhere in the docs, which should be fixed.

[greglandrum]

This should definitely have a better error message

[github-actions[bot]]

This issue was marked as stale because it has been open for 90 days with no activity.