GHSA-3f56-w4g2-mx64: Duplicate Advisory Open Babel Has NULL Pointer Vulnerability

LOW
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CVSS 4.3
CWE-119
Published
Advisory Summary

GHSA-3f56-w4g2-mx64 is a LOW (CVSS 4.3) open babel has null pointer vulnerability (CWE-119: Improper Restriction of Operations within the Bounds of a Memory Buffer) affecting Duplicate Advisory libraries in the PyPI ecosystem. The issue involves open babel has null pointer dereference in mol2 obatom::setformalcharge. Remediation is available by upgrading affected packages to version 3.2.0.

GHSA-3f56-w4g2-mx64 at a Glance

CVE Identifier N/A
GHSA Identifier GHSA-3f56-w4g2-mx64
Severity LOW
CVSS v3.1 Base Score 4.3
CWE Classification CWE-119: Improper Restriction of Operations within the Bounds of a Memory Buffer
Affected Product Duplicate Advisory
Package Ecosystem PyPI
Published Date
Last Updated

Security Impact

CVSS: 4.3

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

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

How to Fix GHSA-3f56-w4g2-mx64

To remediate this vulnerability, upgrade all affected Duplicate Advisory 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 GHSA-3f56-w4g2-mx64, inspect your installed packages using pip:

pip show openbabel

Analyze the terminal output to locate any version of Duplicate Advisory 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 Duplicate Advisory, 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

## Duplicate Advisory This advisory has been withdrawn because it is a duplicate of GHSA-4w5w-4fhm-q483. This link is maintained to preserve external references. ## Original Description A vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The project was informed of the problem early through an issue report but has not responded yet.

GHSA-3f56-w4g2-mx64 Affected Duplicate Advisory 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

NVD — GHSA-3f56-w4g2-mx64 NVD
https://nvd.nist.gov/vuln/detail/CVE-2026-2705
Duplicate Advisory Source Repository REPOSITORY
https://github.com/openbabel/openbabel/issues/2848
Duplicate Advisory Source Repository REPOSITORY
https://github.com/openbabel/openbabel/pull/2862
Security Fix Commit FIX COMMIT
https://github.com/VedantMadane/openbabel/commit/e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a
Duplicate Advisory Source Repository REPOSITORY
https://github.com/oneafter/0128/blob/main/ob2/repro.mol2
vuldb.com/ WEB
https://vuldb.com/?ctiid.346651
vuldb.com/ WEB
https://vuldb.com/?id.346651
vuldb.com/ WEB
https://vuldb.com/?submit.754379

Frequently Asked Questions

What is GHSA-3f56-w4g2-mx64?
GHSA-3f56-w4g2-mx64 is a security vulnerability in Duplicate Advisory involving Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge under CWE-119: Improper Restriction of Operations within the Bounds of a Memory Buffer.
Which Duplicate Advisory versions are affected?
Affected versions include releases prior to 3.2.0 across affected packages: openbabel.
What version fixes GHSA-3f56-w4g2-mx64?
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 GHSA-3f56-w4g2-mx64?
GHSA-3f56-w4g2-mx64 has a CVSS v3.1 base score of 4.3 (LOW) with vector string CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L.
What CWE is associated with GHSA-3f56-w4g2-mx64?
GHSA-3f56-w4g2-mx64 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 GHSA-3f56-w4g2-mx64?
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-3f56-w4g2-mx64",
  "modified" : "2026-06-30T18:46:54Z",
  "published" : "2026-02-19T18:31:51Z",
  "withdrawn" : "2026-06-30T18:46:53Z",
  "aliases" : [ ],
  "summary" : "Duplicate Advisory: Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge",
  "details" : "## Duplicate Advisory\nThis advisory has been withdrawn because it is a duplicate of GHSA-4w5w-4fhm-q483. This link is maintained to preserve external references.\n\n## Original Description\nA vulnerability was detected in Open Babel up to 3.1.1. The impacted element is the function OBAtom::SetFormalCharge in the library include/openbabel/atom.h of the component MOL2 File Handler. The manipulation results in out-of-bounds read. It is possible to launch the attack remotely. The exploit is now public and may be used. The project was informed of the problem early through an issue report but has not responded yet.",
  "severity" : [ {
    "type" : "CVSS_V3",
    "score" : "CVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L"
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    "type" : "CVSS_V4",
    "score" : "CVSS:4.0/AV:N/AC:L/AT:N/PR:N/UI:P/VC:N/VI:N/VA:L/SC:N/SI:N/SA:N/E:P/CR:X/IR:X/AR:X/MAV:X/MAC:X/MAT:X/MPR:X/MUI:X/MVC:X/MVI:X/MVA:X/MSC:X/MSI:X/MSA:X/S:X/AU:X/R:X/V:X/RE:X/U:X"
  } ],
  "affected" : [ {
    "package" : {
      "ecosystem" : "PyPI",
      "name" : "openbabel"
    },
    "ranges" : [ {
      "type" : "ECOSYSTEM",
      "events" : [ {
        "introduced" : "0"
      }, {
        "fixed" : "3.2.0"
      } ]
    } ]
  } ],
  "references" : [ {
    "type" : "ADVISORY",
    "url" : "https://nvd.nist.gov/vuln/detail/CVE-2026-2705"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/openbabel/openbabel/issues/2848"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/openbabel/openbabel/pull/2862"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/VedantMadane/openbabel/commit/e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a"
  }, {
    "type" : "WEB",
    "url" : "https://github.com/oneafter/0128/blob/main/ob2/repro.mol2"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?ctiid.346651"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?id.346651"
  }, {
    "type" : "WEB",
    "url" : "https://vuldb.com/?submit.754379"
  } ],
  "database_specific" : {
    "cwe_ids" : [ "CWE-119" ],
    "severity" : "LOW",
    "github_reviewed" : true,
    "github_reviewed_at" : "2026-06-30T18:46:53Z",
    "nvd_published_at" : "2026-02-19T07:17:49Z"
  }
}