# CVE-2025-11000: Open Babel out-of-bounds read in PQS parser lowerit helper

Source: https://junglewise.ai/threats/cve-2025-11000-open-babel-out-of-bounds-read-in-pqs-parser-lowerit-helper  
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-2025-11000 · Severity: medium · CVSS 4.4 · Published 2026-07-01

Open Babel, a software library used for processing chemistry data files, contains a memory-safety flaw in its PQS file parser. If a user opens a specially crafted, malicious PQS file using an application or service built with Open Babel, it could cause the program to crash or potentially expose small amounts of memory. This affects various programming language interfaces including Python, Java, and C#.

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

## Quick answers

**Is CVE-2025-11000 exploited in the wild?** No. Junglewise Threat Intelligence has no report of CVE-2025-11000 being exploited in the wild.

**How severe is CVE-2025-11000?** Medium severity, with a CVSS score of 4.4, 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-2025-11000?** 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-2025-11000 attacked?** It is attacked with local access, in a software library.

**Am I affected by CVE-2025-11000?** 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

An out-of-bounds (pre-buffer) read vulnerability exists in Open Babel versions up to 3.1.1 within the PQS parser. The flaw is located in the `lowerit` helper function used by `PQSFormat::ReadMolecule` in `src/formats/PQSformat.cpp`. When processing a malformed PQS input file, the helper may attempt to read memory bytes preceding the start of the allocated input buffer. This can lead to application crashes (denial of service) or limited information disclosure. The vulnerability can be triggered via the `obabel` CLI tool, the `OBConversion` API, or any language bindings (Python, Ruby, Java, etc.). The issue was addressed in version 3.2.0.

## Affected products

- Open Babel openbabel All releases up to and including 3.1.1

## Identifiers

- CVE-2025-11000
- GHSA-m982-7q3h-r784
- PYSEC-2026-2785

## Timeline

- 2025-09-14: disclosed: Initial bug report on GitHub
- 2026-05-26: patched: Version 3.2.0 released
- 2026-07-01: advisory: GHSA advisory published

## References

- [https://github.com/openbabel/openbabel/security/advisories/GHSA-m982-7q3h-r784](https://github.com/openbabel/openbabel/security/advisories/GHSA-m982-7q3h-r784)
- [https://github.com/openbabel/openbabel/issues/2826](https://github.com/openbabel/openbabel/issues/2826)
- [https://github.com/openbabel/openbabel/commit/f4a5ebae](https://github.com/openbabel/openbabel/commit/f4a5ebae)
- [https://github.com/user-attachments/files/22318474/poc.zip](https://github.com/user-attachments/files/22318474/poc.zip)
- [https://vuldb.com/?ctiid.325928](https://vuldb.com/?ctiid.325928)

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