Open Babel has out-of-bounds write in PQS coord_file parserGHSA-f29h-2h58-48r7
HIGHFix: openbabel/openbabel@2a7d2cdGHSA-f29h-2h58-48r7 is a high-severity (CVSS 7.8) Buffer Overflow vulnerability in openbabel. 1 public exploit reference exists, so weaponization risk is real. A fix is available for openbabel — see the affected versions and patch details below.
Exploitation Status
No confirmed exploitation observed yet
- CISA assesses this as automatable — exploitation doesn’t require manual, per-target effort, which raises the odds of mass scanning and opportunistic attacks.
- A successful exploit gives an attacker total control of the affected component, not partial access.
- CISA’s own triage has not observed active exploitation or public proof-of-concept code for this CVE as of its last assessment.
Exploitation and automatability from CISA’s SSVC triage for GHSA-f29h-2h58-48r7.
EPSS Exploitation Probability
Probability of exploitation in the next 30 days, from FIRST.org EPSS.
How urgent is this, really
GHSA-f29h-2h58-48r7 by exploitation likelihood (EPSS) against impact (CVSS). Outside the shaded patch-first corner.
Where this sits among everything scored
Of 394,803 CVEs with a current EPSS score, this one falls in the < 10% band (highlighted). Counts from FIRST.org, log-scaled.
Real-World Exposure
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 PQS parser allowed an out-of-bounds write when reading a crafted input file.
Details
The flaw was in the coord_file parsing path of the PQS reader. A
malformed coord file specifier caused the parser to write past the
end of its destination buffer.
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 PQS 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/2a7d2cda
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 Cisco TALOS.
Affected Packages
| Ecosystem | Package | Vulnerable range | Fix |
|---|---|---|---|
| 🐍PyPI | openbabel | all versions | 3.2.0pip install --upgrade 'openbabel==3.2.0' |
Affected Products
open babelopenbabelResearch use only. For defensive security, authorized penetration testing, and academic research only. Never execute exploit code against systems without explicit written authorization.
Detection & mitigation playbook
Open-source dependencyDetect
Scan your dependency tree (package-lock.json, pnpm-lock.yaml, requirements.txt, go.sum, etc.) for openbabel, including transitive dependencies — a direct dependency you never call can still pull in a vulnerable version.
Fix
Update openbabel to 3.2.0 or later, then make sure no transitive (indirect) dependency still pins the vulnerable range — O3 confirms GHSA-f29h-2h58-48r7 is resolved across your whole dependency graph.
Workarounds
Stop feeding it untrusted input: reject or quarantine files and payloads from unverified sources until you can upgrade, restrict accepted formats to the ones you actually need, and run the parsing or decoding step in a least-privileged sandbox or short-lived worker so a crash or corrupted read cannot reach the rest of the process.
Frequently Asked Questions
Is GHSA-f29h-2h58-48r7 in your dependencies?
Find it across PyPI, including transitive dependencies.