RDKit test failure

[RMeli]

RDKit test failures started to show up in CI:

>               Chem.AssignStereochemistryFrom3D(mol)
E               RuntimeError: Cannot normalize a zero length vector

A new version of RDKit landed a couple of days ago: https://github.com/rdkit/rdkit/releases.

[RMeli]

I can reproduce it locally (macOS 15) with rdkit==2024.9.3 but it works with rdkit==2024.9.2.

[RMeli]

Reproducer:

import rdkit.Chem as Chem
import MDAnalysis as mda
from io import StringIO

mol = Chem.MolFromSmiles("O=S(C)(C)=NC")
mol = Chem.AddHs(mol)
pdb = Chem.MolToPDBBlock(mol)
print(pdb)
u = mda.Universe(StringIO(pdb), format="PDB")
ag = u.select_atoms("all")
conf = Chem.Conformer(mol.GetNumAtoms())
for atom in mol.GetAtoms():
    idx = atom.GetIdx()
    xyz = ag.positions[idx].astype(float)
    print(xyz)
    conf.SetAtomPosition(idx, xyz)
mol.AddConformer(conf)
Chem.AssignStereochemistryFrom3D(mol)

The positions are all zero in the PDB file, and therefore the same is true for the coordinates of the conformer. Something must have changed within AssignStereochemistryFrom3D where a normalization (on distances?) has been added.

[RMeli]

@cbouy do you have any idea of what changed? Something definitely changed in RDKit, but I feel we are hitting an issue because we were relying on a bug/implementation detail of RDKit: the function AssignStereochemistryFrom3D is expected to user 3D information to assign the stereochemistry, while all coordinates of the conformer are [0., 0., 0.].