GHSA-4w5w-4fhm-q483
MEDIUMOpen Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge
Blast Radius
openbabelReal-time download stats are indexed for npm and PyPI packages. This vulnerability affects PyPI packages — download data is not available via public APIs for these ecosystems.
Description
Summary
A memory-safety vulnerability in Open Babel's MOL2 file format parser caused a NULL pointer dereference when reading a crafted input file.
Details
The flaw was in OBAtom::SetFormalCharge as called from the MOL2
parser. A malformed atom record caused the parser to call the method
on a NULL atom pointer.
Impact
Open Babel is a C++ library and CLI used to read and write chemistry
file formats; it is shipped by Linux distributions and embedded in
services that may parse untrusted input. Triggering this vulnerability
requires the victim to open a malicious MOL2 file with the obabel
tool, the OBConversion API, or any of the language bindings (Python,
Ruby, Java, R, Perl, C#, PHP).
Affected versions
All releases up to and including 3.1.1.
Patched version
3.2.0 (released 2026-05-26).
Patch
Fix commit: https://github.com/openbabel/openbabel/commit/e23a224b Tracked in #2862.
A minimized reproducer for this CVE is checked in under
test/files/fuzz_regress/ and is exercised on every CI build under
ASAN+UBSAN by the fuzzregresstest harness.
Credit
Reported by Vedant Madane (@VedantMadane) via VulDB.
Affected Packages
| Ecosystem | Package | Vulnerable range | Fix |
|---|---|---|---|
| 🐍PyPI | openbabel | all versions | 3.2.0 |
Detection & mitigation playbook
Open-source dependencyDetect
Scan your dependency tree (package-lock.json, pnpm-lock.yaml, requirements.txt, go.sum, etc.) for openbabel. O3's reachability analysis confirms whether the vulnerable code path is actually invoked in your application, so you act on real exposure instead of every transitive match.
Fix
Update openbabel to 3.2.0 or later, then make sure no transitive (indirect) dependency still pins the vulnerable range — O3 confirms GHSA-4w5w-4fhm-q483 is resolved across your whole dependency graph.
Workarounds
If you can't upgrade right away: gate or disable the affected feature, validate untrusted input at the boundary, and avoid passing attacker-controlled data into the vulnerable path. O3's runtime protection blocks exploitation in production as an interim safeguard until the upgrade lands.
How O3 protects you
O3 pinpoints whether GHSA-4w5w-4fhm-q483 is reachable in your code and exactly where to fix it, then blocks exploitation in production at runtime until the patched version is deployed.
Tailored to GHSA-4w5w-4fhm-q483. Runtime protection reduces exposure until a permanent patch is applied and verified — it complements patching, it doesn't replace it.
Frequently Asked Questions
Is GHSA-4w5w-4fhm-q483 in your dependencies?
O3 detects GHSA-4w5w-4fhm-q483 across PyPI dependencies and uses function-level reachability to confirm whether the vulnerable code path is actually reachable — not just present. No false positives.