# Open Babel out-of-bounds read in CIF transform3d

Source: https://junglewise.ai/threats/open-babel-out-of-bounds-read-in-cif-transform3d-917f633e  
Publisher: Junglewise Threat Intelligence, https://junglewise.ai/threats  
Published: 2026-02-19. Updated: 2026-09-26  
License: CC BY 4.0 with a link back

Severity: low · CVSS 3.1 · Published 2026-02-19

Open Babel is a widely-used chemistry file format converter shipped by Linux distributions and embedded in many scientific software tools. A flaw in its CIF file parser allows an attacker to craft a malicious chemistry data file that, when opened by the obabel tool or used through the library API, can cause the application to read beyond its internal memory buffer. This could expose sensitive data in memory or crash the application, disrupting chemistry data processing workflows.

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

## Quick answers

**Is This vulnerability exploited in the wild?** No. Junglewise Threat Intelligence has no report of This vulnerability being exploited in the wild.

**How severe is This vulnerability?** Low severity, with a CVSS score of 3.1, published 19 February 2026.

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

**Is there a fix for This vulnerability?** 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 This vulnerability attacked?** It is attacked with local access, in a software library.

**Am I affected?** 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

The vulnerability is an out-of-bounds read (CWE-125) in the OpenBabel::transform3d::DescribeAsString function within the CIF file format handler (src/math/transform3d.cpp). A malformed symmetry-operation string in a crafted CIF file causes the parser to read past the end of its internal buffer during string formatting. The attack requires local network access and user interaction (opening the malicious file with obabel or through the OBConversion API). An attacker can trigger memory disclosure or application denial of service. The vulnerability affects all versions up to and including 3.1.1; it was fixed in version 3.2.0 released May 2026.

## Affected products

- Open Babel Open Babel up to and including 3.1.1

## Timeline

- 2026-02-19: disclosed: Publicly disclosed
- 2026-05-26: patched: Fixed in version 3.2.0

## References

- [https://github.com/openbabel/openbabel/security/advisories/GHSA-6xw4-2g22-26h8](https://github.com/openbabel/openbabel/security/advisories/GHSA-6xw4-2g22-26h8)

## 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)