# CVE-2026-2705: Open Babel NULL pointer dereference in MOL2 OBAtom::SetFormalCharge

Source: https://junglewise.ai/threats/cve-2026-2705-open-babel-null-pointer-dereference-in-mol2-obatom-setformalcharge  
Publisher: Junglewise Threat Intelligence, https://junglewise.ai/threats  
Published: 2026-06-30. Updated: 2026-06-30  
License: CC BY 4.0 with a link back

CVE-2026-2705 · Severity: medium · CVSS 5.5 · Published 2026-06-30

Open Babel is a software library used to process and convert chemistry data files. A vulnerability in its file parser allows a specially crafted chemistry file to crash the application. This could lead to a service outage or application failure if a user or automated system attempts to process a malicious file.

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

## Quick answers

**Is CVE-2026-2705 exploited in the wild?** No. Junglewise Threat Intelligence has no report of CVE-2026-2705 being exploited in the wild.

**How severe is CVE-2026-2705?** Medium severity, with a CVSS score of 5.5, published 30 June 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-2026-2705?** 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-2026-2705 attacked?** It is attacked with local access, in a software library.

**Am I affected by CVE-2026-2705?** 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 memory-safety vulnerability exists in Open Babel's MOL2 file format parser due to a NULL pointer dereference in the `OBAtom::SetFormalCharge` function. The flaw is triggered when the parser encounters a malformed atom record in a MOL2 file, causing it to call the method on a NULL atom pointer. An attacker can exploit this by providing a crafted MOL2 file to the `obabel` CLI tool, the `OBConversion` API, or any of its language bindings (Python, Java, etc.). This results in a denial-of-service (application crash). The issue is fixed in version 3.2.0.

## Affected products

- Open Babel openbabel <= 3.1.1

## Identifiers

- CVE-2026-2705
- GHSA-4w5w-4fhm-q483
- PYSEC-2026-2770

## Timeline

- 2026-05-26: patched: Version 3.2.0 released
- 2026-06-30: advisory: GitHub Advisory published

## References

- [https://api.github.com/users/VedantMadane](https://api.github.com/users/VedantMadane)
- [https://github.com/VedantMadane](https://github.com/VedantMadane)
- [https://api.github.com/users/VedantMadane/gists%7B/gist_id%7D](https://api.github.com/users/VedantMadane/gists%7B/gist_id%7D)
- [https://api.github.com/users/VedantMadane/repos](https://api.github.com/users/VedantMadane/repos)
- [https://avatars.githubusercontent.com/u/6527493?v=4](https://avatars.githubusercontent.com/u/6527493?v=4)
- [https://api.github.com/users/VedantMadane/events%7B/privacy%7D](https://api.github.com/users/VedantMadane/events%7B/privacy%7D)

## 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)