Open Babel NULL pointer dereference in CDXML File Handler

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). 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  • 2026-06-30: advisory: GitHub advisory withdrawn as duplicate of GHSA-rxpr-wq63-jr7p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

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