Bug
AllChem.AddHs() in schema.py (line ~1243) can crash the process with SIGSEGV (exit -11) or SIGILL (exit -4) on certain valid-looking SMILES inputs.
Root cause
AddHs() internally calls getNumImplicitHs(), which requires calcImplicitValence() to have run successfully for all atoms. While MolFromSmiles() with default sanitization catches most problems, some molecules with problematic valence states (hypervalent atoms, certain organometallics) pass sanitization but still crash in AddHs().
Location
# src/boltz/data/parse/schema.py, ligand SMILES processing
mol = AllChem.MolFromSmiles(seq)
mol = AllChem.AddHs(mol) # <-- can SIGSEGV here
Fix
Add UpdatePropertyCache(strict=True) between MolFromSmiles() and AddHs(). This replicates the implicit valence calculation and raises a clean ValueError for molecules that would otherwise crash:
mol = AllChem.MolFromSmiles(seq)
if mol is None:
raise ValueError(f"Failed to parse SMILES: {seq}")
mol.UpdatePropertyCache(strict=True)
mol = AllChem.AddHs(mol)We encountered this in production and fixed it in volgin/boltz-community@b555625.
Bug
AllChem.AddHs()inschema.py(line ~1243) can crash the process with SIGSEGV (exit -11) or SIGILL (exit -4) on certain valid-looking SMILES inputs.Root cause
AddHs()internally callsgetNumImplicitHs(), which requirescalcImplicitValence()to have run successfully for all atoms. WhileMolFromSmiles()with default sanitization catches most problems, some molecules with problematic valence states (hypervalent atoms, certain organometallics) pass sanitization but still crash inAddHs().Location
Fix
Add
UpdatePropertyCache(strict=True)betweenMolFromSmiles()andAddHs(). This replicates the implicit valence calculation and raises a cleanValueErrorfor molecules that would otherwise crash:We encountered this in production and fixed it in volgin/boltz-community@b555625.