CVE-2025-10994: Openbabel :ReadMolecule Vulnerability

LOW
Advisory Identifier: GHSA-pp85-5j63-xpq3
Share
CVSS 7.8
CWE-119 CWE-416
Published
Advisory Summary

CVE-2025-10994 is a LOW (CVSS 7.8) :readmolecule vulnerability (CWE-119: Improper Restriction of Operations within the Bounds of a Memory Buffer) affecting Openbabel libraries in the PyPI ecosystem. The issue involves :readmolecule. Remediation is available by upgrading affected packages to version 3.2.0.

CVE-2025-10994 at a Glance

CVE Identifier CVE-2025-10994
GHSA Identifier GHSA-pp85-5j63-xpq3
Severity LOW
CVSS v3.1 Base Score 7.8
CWE Classification CWE-119: Improper Restriction of Operations within the Bounds of a Memory Buffer
Affected Product Openbabel
Package Ecosystem PyPI
Published Date
Last Updated

Security Impact

CVSS: 7.8

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:H/I:H/A:H).

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 High (C:H)
Integrity High (I:H)
Availability High (A:H)

How to Fix CVE-2025-10994

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-2025-10994, 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-119: Improper Restriction of Operations within the Bounds of a Memory Buffer, where the product performs operations on a memory buffer, but it reads from or writes to a memory location outside the buffer's intended boundary. this may result in read or write operations on unexpected memory locations that could be linked to other variables, data structures, or internal program data. 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 GAMESS output parser caused a use-after-free when reading a crafted input file. ### Details The flaw was in `GAMESSOutputFormat::ReadMolecule`. A malformed input caused the parser to dereference a stale pointer after the underlying object had been freed. ### 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 GAMESS output 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/95033d27 Originally reported as #2834; 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-2025-10994 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-pp85-5j63-xpq3
NVD — CVE-2025-10994 NVD
https://nvd.nist.gov/vuln/detail/CVE-2025-10994
Openbabel Source Repository REPOSITORY
https://github.com/openbabel/openbabel/issues/2834
Security Fix Commit FIX COMMIT
https://github.com/openbabel/openbabel/commit/95033d27d23c07f98daa92d3cd3ae5ea07594a91
Openbabel Source Repository REPOSITORY
https://github.com/openbabel/openbabel
Openbabel Source Repository REPOSITORY
https://github.com/user-attachments/files/22318611/poc.zip
vuldb.com/ WEB
https://vuldb.com/?ctiid.325922
vuldb.com/ WEB
https://vuldb.com/?id.325922
vuldb.com/ WEB
https://vuldb.com/?submit.654057

Frequently Asked Questions

What is CVE-2025-10994?
CVE-2025-10994 is a security vulnerability in Openbabel involving :ReadMolecule under CWE-119: Improper Restriction of Operations within the Bounds of a Memory Buffer.
Which Openbabel versions are affected?
Affected versions include releases prior to 3.2.0 across affected packages: openbabel.
What version fixes CVE-2025-10994?
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-2025-10994?
CVE-2025-10994 has a CVSS v3.1 base score of 7.8 (LOW) with vector string CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H.
What CWE is associated with CVE-2025-10994?
CVE-2025-10994 is classified under CWE-119: Improper Restriction of Operations within the Bounds of a Memory Buffer (The product performs operations on a memory buffer, but it reads from or writes to a memory location outside the buffer's intended boundary. This may result in read or write operations on unexpected memory locations that could be linked to other variables, data structures, or internal program data.).
How can I check PyPI dependencies for CVE-2025-10994?
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-pp85-5j63-xpq3",
  "modified" : "2026-06-30T18:48:57Z",
  "published" : "2026-06-30T18:48:57Z",
  "aliases" : [ "CVE-2025-10994" ],
  "summary" : "Open Babel has Use-after-free in GAMESS GAMESSOutputFormat::ReadMolecule",
  "details" : "### Summary\n\nA memory-safety vulnerability in Open Babel's GAMESS output parser\ncaused a use-after-free when reading a crafted input file.\n\n### Details\n\nThe flaw was in `GAMESSOutputFormat::ReadMolecule`. A malformed input\ncaused the parser to dereference a stale pointer after the underlying\nobject had been freed.\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 GAMESS output file with the\n`obabel` tool, the `OBConversion` API, or any of the language\nbindings (Python, Ruby, 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/95033d27\nOriginally reported as #2834; fixes 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:H/I:H/A:H"
  }, {
    "type" : "CVSS_V4",
    "score" : "CVSS:4.0/AV:L/AC:L/AT:N/PR:L/UI:N/VC:L/VI:L/VA:L/SC:N/SI:N/SA:N/E:P"
  } ],
  "affected" : [ {
    "package" : {
      "ecosystem" : "PyPI",
      "name" : "openbabel"
    },
    "ranges" : [ {
      "type" : "ECOSYSTEM",
      "events" : [ {
        "introduced" : "0"
      }, {
        "fixed" : "3.2.0"
      } ]
    } ]
  } ],
  "references" : [ {
    "type" : "WEB",
    "url" : "https://github.com/openbabel/openbabel/security/advisories/GHSA-pp85-5j63-xpq3"
  }, {
    "type" : "ADVISORY",
    "url" : "https://nvd.nist.gov/vuln/detail/CVE-2025-10994"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/openbabel/openbabel/issues/2834"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/openbabel/openbabel/commit/95033d27d23c07f98daa92d3cd3ae5ea07594a91"
  }, {
    "type" : "PACKAGE",
    "url" : "https://github.com/openbabel/openbabel"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/user-attachments/files/22318611/poc.zip"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?ctiid.325922"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?id.325922"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?submit.654057"
  } ],
  "database_specific" : {
    "cwe_ids" : [ "CWE-119", "CWE-416" ],
    "severity" : "LOW",
    "github_reviewed" : true,
    "github_reviewed_at" : "2026-06-30T18:48:57Z",
    "nvd_published_at" : null
  }
}