CVE-2025-11000: Openbabel Open Babel Has Out-of-bounds Read Vulnerability

MODERATE
Advisory Identifier: GHSA-m982-7q3h-r784
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CVSS 4.4
CWE-125 CWE-404
Published
Advisory Summary

CVE-2025-11000 is a MODERATE (CVSS 4.4) open babel has out-of-bounds read vulnerability (CWE-125: Out-of-bounds Read) affecting Openbabel libraries in the PyPI ecosystem. The issue involves open babel has out-of-bounds read in pqs lowerit (pre-buffer read). Remediation is available by upgrading affected packages to version 3.2.0.

CVE-2025-11000 at a Glance

CVE Identifier CVE-2025-11000
GHSA Identifier GHSA-m982-7q3h-r784
Severity MODERATE
CVSS v3.1 Base Score 4.4
CWE Classification CWE-125: Out-of-bounds Read
Affected Product Openbabel
Package Ecosystem PyPI
Published Date
Last Updated

Security Impact

CVSS: 4.4

The security impact metrics below are parsed directly from the CVSS v3.1 vector string (CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:L/I:N/A:L).

Attack Vector Local (AV:L)
Attack Complexity Low (AC:L)
Privileges Required None (PR:N)
User Interaction Required (UI:R)
Scope Unchanged (S:U)
Confidentiality Low (C:L)
Integrity None (I:N)
Availability Low (A:L)

How to Fix CVE-2025-11000

To remediate this vulnerability, upgrade all affected Openbabel dependencies to a patched release. Both direct and transitive dependencies should be checked, as frameworks or security libraries may pull in vulnerable versions transitively.

openbabel fixed: 3.2.0 
pip install openbabel>=3.2.0
Verify Direct and Transitive Dependencies

Run the following command in your project directory to verify that all resolved dependencies use the patched release: 

pip show openbabel

How to Check if You Are Affected

To determine whether your Python environment is affected by CVE-2025-11000, inspect your installed packages using pip:

pip show openbabel

Analyze the terminal output to locate any version of Openbabel in your dependency tree. If any resolved version matches the vulnerable ranges listed in the table below (for example, versions earlier than 3.2.0), your application is affected.

Note: The pip show openbabel command checks currently installed packages in your active Python environment.

Technical Details

Vulnerability Mechanism & Technical Analysis

This vulnerability is classified under CWE-125: Out-of-bounds Read, where the product reads data past the end, or before the beginning, of the intended buffer. In Openbabel, software state validation or input boundaries are circumvented during processing. Review the official source advisory statement below for specific affected components, classes, and reproduction details.

Source Advisory Statement

### Summary 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. ### 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). ### Affected versions All releases up to and including 3.1.1. ### Patched version 3.2.0 (released 2026-05-26). ### Patch Fix commit: https://github.com/openbabel/openbabel/commit/f4a5ebae Fixes consolidated in #2913. A minimized reproducer for this CVE is checked in under `test/files/fuzz_regress/` and is exercised on every CI build under ASAN+UBSAN by the `fuzzregresstest` harness. ### Credit Reported via OSS-Fuzz.

CVE-2025-11000 Affected Openbabel Versions

1 component(s)
Fixed Versions:
3.2.0
Product / Package Ecosystem Affected Versions Fixed Version
openbabel
pypi/openbabel
PyPI
< 3.2.0
3.2.0

References

GitHub Advisory / Wiki ADVISORY
https://github.com/openbabel/openbabel/security/advisories/GHSA-m982-7q3h-r784
NVD — CVE-2025-11000 NVD
https://nvd.nist.gov/vuln/detail/CVE-2025-11000
Openbabel Source Repository REPOSITORY
https://github.com/openbabel/openbabel/issues/2826
Security Fix Commit FIX COMMIT
https://github.com/openbabel/openbabel/commit/f4a5ebae
Openbabel Source Repository REPOSITORY
https://github.com/openbabel/openbabel
Openbabel Source Repository REPOSITORY
https://github.com/user-attachments/files/22318474/poc.zip
vuldb.com/ WEB
https://vuldb.com/?ctiid.325928
vuldb.com/ WEB
https://vuldb.com/?id.325928
vuldb.com/ WEB
https://vuldb.com/?submit.654066

Frequently Asked Questions

What is CVE-2025-11000?
CVE-2025-11000 is a security vulnerability in Openbabel involving Open Babel has out-of-bounds read in PQS lowerit (pre-buffer read) under CWE-125: Out-of-bounds Read.
Which Openbabel versions are affected?
Affected versions include releases prior to 3.2.0 across affected packages: openbabel.
What version fixes CVE-2025-11000?
Upgrading to 3.2.0 (or the latest patched release for your respective branch) resolves the vulnerability.
Is openbabel affected?
Yes, openbabel is affected in releases prior to 3.2.0. Upgrade your dependency to 3.2.0 or later.
What is the CVSS score of CVE-2025-11000?
CVE-2025-11000 has a CVSS v3.1 base score of 4.4 (MODERATE) with vector string CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:L/I:N/A:L.
What CWE is associated with CVE-2025-11000?
CVE-2025-11000 is classified under CWE-125: Out-of-bounds Read (The product reads data past the end, or before the beginning, of the intended buffer.).
How can I check PyPI dependencies for CVE-2025-11000?
Run the dependency tree command: 'pip show openbabel'. This command lists direct and transitive dependencies in your build configuration so you can verify if a vulnerable version is resolved.
Machine-readable OSV JSON OSV v1.5 Schema
Normalized schema output
View Raw JSON 
{
  "schema_version" : "1.4.0",
  "id" : "GHSA-m982-7q3h-r784",
  "modified" : "2026-07-01T17:42:20Z",
  "published" : "2026-07-01T17:42:20Z",
  "aliases" : [ "CVE-2025-11000" ],
  "summary" : "Open Babel has out-of-bounds read in PQS lowerit (pre-buffer read)",
  "details" : "### Summary\n\nA memory-safety vulnerability in Open Babel's PQS parser caused an\nout-of-bounds (pre-buffer) read when reading a crafted input file.\n\n### Details\n\nThe flaw was in the `lowerit` helper used by the PQS parser. A\nmalformed input caused the helper to read one or more bytes before\nthe start of its input buffer.\n\n### Impact\n\nOpen Babel is a C++ library and CLI used to read and write chemistry\nfile formats; it is shipped by Linux distributions and embedded in\nservices that may parse untrusted input. Triggering this vulnerability\nrequires the victim to open a malicious PQS file with the `obabel`\ntool, the `OBConversion` API, or any of the language bindings (Python,\nRuby, Java, R, Perl, C#, PHP).\n\n### Affected versions\n\nAll releases up to and including 3.1.1.\n\n### Patched version\n\n3.2.0 (released 2026-05-26).\n\n### Patch\n\nFix commit: https://github.com/openbabel/openbabel/commit/f4a5ebae\nFixes consolidated in #2913.\n\nA minimized reproducer for this CVE is checked in under\n`test/files/fuzz_regress/` and is exercised on every CI build under\nASAN+UBSAN by the `fuzzregresstest` harness.\n\n### Credit\n\nReported via OSS-Fuzz.",
  "severity" : [ {
    "type" : "CVSS_V3",
    "score" : "CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:L/I:N/A:L"
  } ],
  "affected" : [ {
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      "ecosystem" : "PyPI",
      "name" : "openbabel"
    },
    "ranges" : [ {
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      "events" : [ {
        "introduced" : "0"
      }, {
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      } ]
    } ]
  } ],
  "references" : [ {
    "type" : "WEB",
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  }, {
    "type" : "ADVISORY",
    "url" : "https://nvd.nist.gov/vuln/detail/CVE-2025-11000"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/openbabel/openbabel/issues/2826"
  }, {
    "type" : "WEB",
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    "url" : "https://github.com/user-attachments/files/22318474/poc.zip"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?ctiid.325928"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?id.325928"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?submit.654066"
  } ],
  "database_specific" : {
    "cwe_ids" : [ "CWE-125", "CWE-404" ],
    "severity" : "MODERATE",
    "github_reviewed" : true,
    "github_reviewed_at" : "2026-07-01T17:42:20Z",
    "nvd_published_at" : null
  }
}