# Open Babel NULL pointer dereference in CDXML File Handler

Source: https://junglewise.ai/threats/open-babel-null-pointer-dereference-in-cdxml-file-handler-5a967b79  
Publisher: Junglewise Threat Intelligence, https://junglewise.ai/threats  
Published: 2026-03-02. Updated: 2026-06-30  
License: CC BY 4.0 with a link back

Severity: medium · CVSS 4.3 · Published 2026-03-02

Open Babel, a chemical toolbox used to search, convert, and analyze data from molecular modeling and chemistry, is vulnerable to a crash when processing certain chemical data files. By providing a specially crafted CDXML file, an attacker could cause the software to crash, leading to a denial of service. This could disrupt laboratory workflows or automated chemical data processing pipelines.

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?** Medium severity, with a CVSS score of 4.3, published 2 March 2026.

**Which products and versions are affected?** openbabel (PyPI) < 3.2.0.

**Is there a fix for This vulnerability?** No fixed version is recorded yet. Check the vendor's advisory in the references below. If you run it, Junglewise drafts a mitigation that fits your setup and applies it once you approve, with senior security engineers behind it.

**How is This vulnerability attacked?** It is attacked over the network, 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.

## Technical details

A NULL pointer dereference exists in Open Babel versions up to 3.1.1 within the OBAtom::GetExplicitValence function in src/atom.cpp. The vulnerability is triggered during the parsing of malformed CDXML files via the CDXML File Handler. An attacker can exploit this by providing a crafted file to be processed by the library, leading to an application crash (denial of service). While the attack vector is network-based (remote), it typically requires user interaction to open or process the malicious file. A patch (commit e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a) is available and the issue is addressed in version 3.2.0.

## Affected products

- Open Babel openbabel <= 3.1.1

## Timeline

- 2026-03-02: disclosed: Initial disclosure and NVD publication
- 2026-06-30: advisory: GitHub advisory withdrawn as duplicate of GHSA-rxpr-wq63-jr7p

## References

- [https://github.com/openbabel/openbabel/issues/2848](https://github.com/openbabel/openbabel/issues/2848)
- [https://github.com/openbabel/openbabel/pull/2862](https://github.com/openbabel/openbabel/pull/2862)
- [https://github.com/VedantMadane/openbabel/commit/e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a](https://github.com/VedantMadane/openbabel/commit/e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a)
- [https://github.com/oneafter/0128/blob/main/ob3/repro.cdxml](https://github.com/oneafter/0128/blob/main/ob3/repro.cdxml)
- [https://vuldb.com/?ctiid.348303](https://vuldb.com/?ctiid.348303)

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