# CVE-2025-10999: Open Babel NULL pointer dereference in CacaoFormat::SetHilderbrandt

Source: https://junglewise.ai/threats/cve-2025-10999-open-babel-null-pointer-dereference-in-cacaoformat  
Publisher: Junglewise Threat Intelligence, https://junglewise.ai/threats  
Published: 2026-07-01. Updated: 2026-07-01  
License: CC BY 4.0 with a link back

CVE-2025-10999 · Severity: medium · CVSS 5.5 · Published 2026-07-01

Open Babel is a widely used software library for processing chemical data and file formats. A vulnerability in its CACAO file parser allows an attacker to crash applications using the library by providing a specially crafted chemistry file. This could lead to a denial-of-service, affecting researchers and automated chemical analysis services that process untrusted data.

Technologies: [openbabel (PyPI)](https://junglewise.ai/threats/technologies/openbabel). Vendors: [PyPI](https://junglewise.ai/threats/vendors/pypi).

## Quick answers

**Is CVE-2025-10999 exploited in the wild?** No. Junglewise Threat Intelligence has no report of CVE-2025-10999 being exploited in the wild.

**How severe is CVE-2025-10999?** Medium severity, with a CVSS score of 5.5, published 1 July 2026.

**Which products and versions are affected?** openbabel (PyPI) < 3.2.0, ECOSYSTEM:introduced=0,fixed=3.2.0.

**Is there a fix for CVE-2025-10999?** Yes. openbabel (PyPI): upgrade to 3.2.0 or later. Junglewise finds every place you run it, drafts the upgrade and applies it once you approve.

**How is CVE-2025-10999 attacked?** It is attacked with local access, in a software library.

**Am I affected by CVE-2025-10999?** Check whether you run openbabel (PyPI) at an affected version. Junglewise does that check for you around the clock: connect your code, cloud and domains, and it matches new vulnerabilities like this one against what you actually run and tells you when one reaches you.

## How to fix

- openbabel (PyPI): upgrade to 3.2.0 or later

  ```sh
  pip install "openbabel>=3.2.0"
  ```


## Technical details

A NULL pointer dereference exists in the CacaoFormat::SetHilderbrandt function within src/formats/cacaoformat.cpp. The vulnerability is triggered when the parser applies the Hilderbrandt transformation to a malformed CACAO input file that contains invalid internal coordinate references. Specifically, the code assumes all OBAtom pointers in the internal coordinate list are valid; a crafted file can provide null or corrupted pointers, leading to a crash (SEGV) when OBAtom::GetIdx() is called. This affects the obabel CLI tool, the OBConversion API, and all language bindings. The issue is fixed in version 3.2.0.

## Affected products

- Open Babel Open Babel <= 3.1.1

## Identifiers

- CVE-2025-10999
- GHSA-55j6-rjhx-hwfh
- PYSEC-2026-2772

## Timeline

- 2025-09-14: disclosed: Initial bug report via OSS-Fuzz/GitHub issues
- 2026-05-26: patched: Version 3.2.0 released
- 2026-07-01: advisory: GitHub Advisory published

## References

- [https://github.com/openbabel/openbabel/security/advisories/GHSA-55j6-rjhx-hwfh](https://github.com/openbabel/openbabel/security/advisories/GHSA-55j6-rjhx-hwfh)
- [https://github.com/openbabel/openbabel/issues/2827](https://github.com/openbabel/openbabel/issues/2827)
- [https://github.com/openbabel/openbabel/commit/ecaed96f](https://github.com/openbabel/openbabel/commit/ecaed96f)
- [https://github.com/user-attachments/files/22318503/poc.zip](https://github.com/user-attachments/files/22318503/poc.zip)
- [https://vuldb.com/?ctiid.325927](https://vuldb.com/?ctiid.325927)

## Related threats

- [Open Babel out-of-bounds write in MOPAC output parser](https://junglewise.ai/threats/cve-2022-46292-open-babel-out-of-bounds-write-in-mopac-output-parser)
- [Open Babel out-of-bounds write in MSI parser translationVectors](https://junglewise.ai/threats/cve-2022-46295-open-babel-out-of-bounds-write-in-msi-parser-translationvectors)
- [Open Babel out-of-bounds write in MOPAC input parser](https://junglewise.ai/threats/cve-2022-46294-open-babel-out-of-bounds-write-in-mopac-input-parser)
- [Open Babel out-of-bounds write in MOPAC output parser](https://junglewise.ai/threats/cve-2022-46293-open-babel-out-of-bounds-write-in-mopac-output-parser)
- [Open Babel out-of-bounds write in Gaussian translationVectors](https://junglewise.ai/threats/cve-2022-46291-open-babel-out-of-bounds-write-in-gaussian-translationvectors)