Summary
Open Babel has out-of-bounds read in PQS lowerit (pre-buffer read)
A memory-safety vulnerability in Open Babel's PQS parser caused an
out-of-bounds (pre-buffer) read when reading a crafted input file.
Details
The flaw was in the lowerit helper used by the PQS parser. A
malformed input caused the helper to read one or more bytes before
the start of its input buffer.
Affected versions
All releases up to and including 3.1.1.
Patched version
3.2.0 (released 2026-05-26).
Credit
Reported via OSS-Fuzz.
Impact
Open Babel is a C++ library and CLI used to read and write chemistry
file formats; it is shipped by Linux distributions and embedded in
services that may parse untrusted input. Triggering this vulnerability
requires the victim to open a malicious PQS file with the obabel
tool, the OBConversion API, or any of the language bindings (Python,
Ruby, Java, R, Perl, C#, PHP).
A read operation accesses a memory location beyond the intended buffer boundary. Typical impact: sensitive data disclosure or crash.
CVE-2025-11000 has a CVSS score of 4.4 (Medium). The vector is requires local access, no privileges required, and user interaction required. A CVSS score reflects the worst-case severity of the vulnerability, not your specific exposure. Whether this affects your application depends on whether the vulnerable code is present and reachable in your environment. A fixed version is available (3.2.0); upgrading removes the vulnerable code path.
Affected versions
Security releases
Kodem intelligence
Severity tells you how bad this could be in the worst case. It does not tell you whether you are exposed. Exploitability and impact are functions of runtime truth: whether the vulnerable code is present, reachable, and actually executes in your application. A vulnerable package can sit in your dependency tree and never run.
Kodem, an Intelligent Application Security platform, uses runtime intelligence to reveal which vulnerabilities actually execute in production, so teams prioritize the ones that genuinely matter. Kodem's runtime-powered SCA identifies whether this CVE is reachable in your applications.
Already deployed Kodem?
See it in your environmentNew to Kodem? Get a demo →Remediation advice
Fix commit: https://github.com/openbabel/openbabel/commit/f4a5ebae
Fixes consolidated in #2913.
A minimized reproducer for this CVE is checked in undertest/files/fuzz_regress/ and is exercised on every CI build under
ASAN+UBSAN by the fuzzregresstest harness.
Frequently Asked Questions
- What is CVE-2025-11000? CVE-2025-11000 is a medium-severity out-of-bounds read vulnerability in openbabel (pip), affecting versions < 3.2.0. It is fixed in 3.2.0. A read operation accesses a memory location beyond the intended buffer boundary.
- How severe is CVE-2025-11000? CVE-2025-11000 has a CVSS score of 4.4 (Medium). This score reflects the worst-case severity of the vulnerability, not your specific exposure. Whether it represents real risk in your environment depends on whether the vulnerable code is present and reachable.
- Which versions of openbabel are affected by CVE-2025-11000? openbabel (pip) versions < 3.2.0 is affected.
- Is there a fix for CVE-2025-11000? Yes. CVE-2025-11000 is fixed in 3.2.0. Upgrade to this version or later.
- Is CVE-2025-11000 exploitable, and should I be worried? Whether CVE-2025-11000 is exploitable in your environment depends on whether the vulnerable code is present and reachable. A CVSS score is a worst-case rating; it does not account for your specific deployment, configuration, or usage patterns. Kodem, an Intelligent Application Security platform, uses runtime intelligence to show which vulnerabilities actually execute in production, so you can focus on the ones that represent real risk. Get a demo
- What actually determines whether CVE-2025-11000 is exploitable, and how bad it is? Exploitability and impact are not fixed properties of a CVE. They depend on runtime truth: whether the vulnerable code is present, reachable, and actually executes in your application. A high CVSS score on a dependency that never runs is not the same as real risk. Kodem, an Intelligent Application Security platform, uses runtime intelligence to reveal which vulnerabilities actually execute in production, so teams prioritize the ones that genuinely matter.
- How do I fix CVE-2025-11000? Upgrade
openbabelto 3.2.0 or later.