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CVE-2026-3408

Open Babel CDXML File atom.cpp GetExplicitValence null pointer dereference

5.3 MediumFix available

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Attack profile

How easy it is to exploit

Attack vector
Network
Complexity
Low
Privileges needed
None
User interaction
Passive

What an attacker can affect

Confidentiality
None
Integrity
None
Availability
Low

Exploit likelihood

0.56%Up 0.5 points since Mar 2, 2026
90%50%10%1%

What each source reports

CVE List Score used 5.3

Open Babel CDXML File atom.cpp GetExplicitValence null pointer dereference

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
CVE-2026-3408
CVSS 4.0
5.3 MediumCVSS: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
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L/E:P/RL:O/RC:C
CVSS 3.0
4.3 MediumCVSS:3.0/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L/E:P/RL:O/RC:C
CVSS 2.0
5.0 AV:N/AC:L/Au:N/C:N/I:N/A:P/E:POC/RL:OF/RC:C
Weakness
CWE-476, CWE-404
Updated
2026-11-02
EUVDEUVD-2026-9141 5.3

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
EUVD-2026-9141
CVSS 4.0
5.3 MediumCVSS: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
Updated
2026-11-02
GitHub AdvisoriesGHSA-fg6r-xgp8-x64r 2.1

Duplicate Advisory: Open Babel has a NULL pointer dereference in CDXML OBAtom::GetExplicitValence

Duplicate Advisory

This advisory has been withdrawn because it is a duplicate of GHSA-rxpr-wq63-jr7p. This link is maintained to preserve external references.

Original Description

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
GHSA-fg6r-xgp8-x64r
CVSS 4.0
2.1 LowCVSS: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
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
Weakness
CWE-404, CWE-787
Updated
2026-11-02
GitHub AdvisoriesGHSA-rxpr-wq63-jr7p 2.1

Open Babel has a NULL pointer dereference in CDXML OBAtom::GetExplicitValence

Summary

A memory-safety vulnerability in Open Babel's CDXML file format parser caused a NULL pointer dereference when reading a crafted input file.

Details

The flaw was in OBAtom::GetExplicitValence as called from the CDXML parser. A malformed fragment caused the parser to invoke the method on a NULL atom pointer.

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 CDXML 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/e23a224b Tracked in #2862.

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 by Vedant Madane (@VedantMadane) via VulDB.

Record
GHSA-rxpr-wq63-jr7p
CVSS 4.0
2.1 LowCVSS: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
CVSS 3.1
5.5 MediumCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
Weakness
CWE-476
Updated
2026-11-02
NVD 2.1

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
CVE-2026-3408
CVSS 4.0
2.1 LowCVSS: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
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
CVSS 3.1
6.5 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
CVSS 2.0
5.0 MediumAV:N/AC:L/Au:N/C:N/I:N/A:P
Weakness
CWE-404, CWE-476, CWE-787
Updated
2026-11-02
OSV 2.1

Open Babel CDXML File atom.cpp GetExplicitValence null pointer dereference

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
CVE-2026-3408
CVSS 4.0
2.1 LowCVSS: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
Weakness
CWE-404, CWE-476
Updated
2026-11-02
Show 7 moreShow less
OSVDEBIAN-CVE-2026-3408 6.5

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
DEBIAN-CVE-2026-3408
CVSS 3.1
6.5 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
Updated
2026-11-07
OSVGHSA-fg6r-xgp8-x64r 2.1

Duplicate Advisory: Open Babel has a NULL pointer dereference in CDXML OBAtom::GetExplicitValence

Duplicate Advisory

This advisory has been withdrawn because it is a duplicate of GHSA-rxpr-wq63-jr7p. This link is maintained to preserve external references.

Original Description

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
GHSA-fg6r-xgp8-x64r
CVSS 4.0
2.1 LowCVSS: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
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
Weakness
CWE-404, CWE-787
Updated
2026-11-02
OSVGHSA-rxpr-wq63-jr7p 2.1

Open Babel has a NULL pointer dereference in CDXML OBAtom::GetExplicitValence

Summary

A memory-safety vulnerability in Open Babel's CDXML file format parser caused a NULL pointer dereference when reading a crafted input file.

Details

The flaw was in OBAtom::GetExplicitValence as called from the CDXML parser. A malformed fragment caused the parser to invoke the method on a NULL atom pointer.

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 CDXML 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/e23a224b Tracked in #2862.

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 by Vedant Madane (@VedantMadane) via VulDB.

Record
GHSA-rxpr-wq63-jr7p
CVSS 4.0
2.1 LowCVSS: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
CVSS 3.1
5.5 MediumCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
Weakness
CWE-476
Updated
2026-11-02
OSVPYSEC-2026-2791 2.1

Open Babel has a NULL pointer dereference in CDXML OBAtom::GetExplicitValence

Summary

A memory-safety vulnerability in Open Babel's CDXML file format parser caused a NULL pointer dereference when reading a crafted input file.

Details

The flaw was in OBAtom::GetExplicitValence as called from the CDXML parser. A malformed fragment caused the parser to invoke the method on a NULL atom pointer.

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 CDXML 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/e23a224b Tracked in #2862.

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 by Vedant Madane (@VedantMadane) via VulDB.

Record
PYSEC-2026-2791
CVSS 4.0
2.1 LowCVSS: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
CVSS 3.1
5.5 MediumCVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
Updated
2026-11-02
OSVUBUNTU-CVE-2026-3408 2.1

A vulnerability was identified in Open Babel up to 3.1.1. This impacts the function OBAtom::GetExplicitValence of the file isrc/atom.cpp of the component CDXML File Handler. Such manipulation leads to null pointer dereference. The attack can be launched remotely. The exploit is publicly available and might be used. The name of the patch is e23a224b8fd9d7c2a7cde9ef4ec6afb4c05aa08a. It is best practice to apply a patch to resolve this issue.

Record
UBUNTU-CVE-2026-3408
CVSS 4.0
2.1 LowCVSS: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
CVSS 3.1
6.5 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:H
CVSS 3.1
4.3 MediumCVSS:3.1/AV:N/AC:L/PR:N/UI:R/S:U/C:N/I:N/A:L
Updated
2026-11-02
OSVopenSUSE-SU-2026:11096-1 No score

libopenbabel8-3.2.0-2.1 on GA media

These are all security issues fixed in the libopenbabel8-3.2.0-2.1 package on the GA media of openSUSE Tumbleweed.

Record
openSUSE-SU-2026:11096-1
Updated
2026-11-02
OSVopenSUSE-SU-2026:21190-1 No score

Security update for openbabel

This update for openbabel fixes the following issues:

Changes in openbabel:

  • Update to version 3.2.0:
    • Add an L-BFGS optimizer, used by default for gen3d and conformer searches
    • New macrocycle ring builder (Dale codes) for better initial 3D geometry of large rings
    • Add KET (Ketcher JSON) and ChemicalJSON (.cjson) format support
    • Drop Python 2 support; Python 3.13 supported
    • Faster, vectorized distance-geometry implementation
    • Full CMake 4 compatibility and modernized build
    • Backwards compatible with 3.0 and 3.1
    • Fix many crash and memory-safety bugs found via OSS-Fuzz and TALOS, including the following security issues: CVE-2022-37331 (boo#1217676), CVE-2022-41793, CVE-2022-42885, CVE-2022-43467, CVE-2022-43607, CVE-2022-44451, CVE-2022-46280, CVE-2022-46289, CVE-2022-46290, CVE-2022-46291, CVE-2022-46292, CVE-2022-46294, CVE-2022-46295, CVE-2025-10994, CVE-2025-10995, CVE-2025-10996, CVE-2025-10997, CVE-2025-10998, CVE-2025-10999, CVE-2025-11000, CVE-2026-2704 (boo#1258501), CVE-2026-2705 (boo#1258507) and CVE-2026-3408 (boo#1259041)
Record
openSUSE-SU-2026:21190-1
Updated
2026-11-02

Affected products

Affected packages

Affected packages
PackageAffectedFixed
openbabel
PyPI
 before 3.2.0
3.2.0
openbabel
Debian:12
 All versions, plus listed versions
3.1.1+dfsg-103.1.1+dfsg-113.1.1+dfsg-123.1.1+dfsg-133.1.1+dfsg-14
Show 5 moreShow less
3.1.1+dfsg-15~exp3.1.1+dfsg-93.2.0+dfsg-13.2.0+dfsg-1~exp3.2.0+dfsg-2
 None known
openbabel
Debian:13
 All versions, plus listed versions
3.1.1+dfsg-123.1.1+dfsg-133.1.1+dfsg-143.1.1+dfsg-15~exp3.2.0+dfsg-13.2.0+dfsg-1~exp3.2.0+dfsg-2
 None known
openbabel
Debian:14
 before 3.2.0+dfsg-1, plus listed versions
3.1.1+dfsg-123.1.1+dfsg-133.1.1+dfsg-143.1.1+dfsg-15~exp3.2.0+dfsg-1~exp
3.2.0+dfsg-1
openbabel
PyPI
 before 3.2.0, plus listed versions
1.81.8.11.8.21.8.31.8.4
Show 6 moreShow less
2.4.02.4.13.0.03.0.0a13.1.13.1.1.1
3.2.0
openbabel
Ubuntu:16.04:LTS
 All versions, plus listed versions
2.3.2+dfsg-2.22.3.2+dfsg-2.2build1
 None known
openbabel
Ubuntu:18.04:LTS
 All versions, plus listed versions
2.3.2+dfsg-3build1
 None known
openbabel
Ubuntu:20.04:LTS
 All versions, plus listed versions
2.4.1+dfsg-32.4.1+dfsg-3build12.4.1+dfsg-5.12.4.1+dfsg-63.0.0+dfsg-33.0.0+dfsg-3ubuntu3
 None known
openbabel
Ubuntu:22.04:LTS
 All versions, plus listed versions
3.1.1+dfsg-6ubuntu13.1.1+dfsg-6ubuntu5
 None known
openbabel
Ubuntu:24.04:LTS
 All versions, plus listed versions
3.1.1+dfsg-9build23.1.1+dfsg-9ubuntu13.1.1+dfsg-9ubuntu23.1.1+dfsg-9ubuntu43.1.1+dfsg-9ubuntu5
 None known
Show 5 moreShow less
Affected packages
PackageAffectedFixed
openbabel
Ubuntu:25.10
 All versions, plus listed versions
3.1.1+dfsg-11ubuntu33.1.1+dfsg-11ubuntu4
 None known
openbabel
Ubuntu:26.10
 All versions, plus listed versions
3.1.1+dfsg-11ubuntu53.1.1+dfsg-14ubuntu2
 None known
openbabel
Ubuntu:26.04:LTS
 All versions, plus listed versions
3.1.1+dfsg-11ubuntu43.1.1+dfsg-11ubuntu5
 None known
openbabel
openSUSE:Tumbleweed
From an advisory covering 2 CVEs
 before 3.2.0-2.1
3.2.0-2.1
openbabel
openSUSE:Leap 16.0
From an advisory covering 23 CVEs
 before 3.2.0-bp160.1.1
3.2.0-bp160.1.1

History

History
RecordedChangedSources
affectedOSV
affected, facts
affected
first indexedCVE List, EUVD, GitHub Advisories, NVD, OSV

Dates are when Every CVE recorded each change. Upstream dates may differ.

In short

CVE-2026-3408 is a medium vulnerability (CVSS 5.3) in Openbabel Open Babel, published March 2, 2026. No source lists public exploit code. EPSS puts the chance of exploitation in the next 30 days at 0.56%, the 46th percentile. Fixed in openbabel 3.2.0.

References

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