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GHSA-rj4c-r689-cm87 CVE-2022-46289 PYSEC-2026-2790

Open Babel has out-of-bounds write in ORCA nAtoms parser

High PyPI
Severity
7.8 / 10
High · CVSS 3.1
Exploit chance (EPSS)
0.80%
Chance of exploitation in the next 30 days. Higher than 56.73% of scored vulnerabilities.
Known exploited
No
Not in CISA's catalog
Weakness
CWE-122 Heap-based Buffer Overflow
CWE-787 Out-of-bounds Write
Fix
3.2.0
Upgrade openbabel to this version or later

Description

Summary

A memory-safety vulnerability in Open Babel's ORCA parser allowed an out-of-bounds write when reading a crafted input file.

Details

The flaw was in the nAtoms handling of the ORCA reader. A malformed input caused the parser to write past the end of its destination 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 ORCA 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/b239d06e

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 Cisco TALOS.

Affected versions

PyPI

PackageVulnerableFixed in
openbabel
< 3.2.0
3.2.0

How to fix

Move to the fixed version or later with your package manager, update the lockfile, and run your tests. If the package only arrives through another dependency, upgrade that dependency first. If none of its releases pulls a fixed version yet, force the version with your package manager's override.

openbabel PyPI → 3.2.0

pip
pip install --upgrade "openbabel>=3.2.0"
poetry
poetry add "openbabel>=3.2.0"
uv
uv add "openbabel>=3.2.0"

Severity breakdown

CVSS 3.1 7.8

CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:H/I:H/A:H

Attack vector
Local
Attack complexity
Low
Privileges required
None
User interaction
Required
Scope
Unchanged
Confidentiality
High
Integrity
High
Availability
High

Weakness

CWE-122: Heap-based Buffer Overflow

A heap overflow condition is a buffer overflow, where the buffer that can be overwritten is allocated in the heap portion of memory, generally meaning that the buffer was allocated using a routine such as malloc().

How to prevent it
  • Pre-design: Use a language or compiler that performs automatic bounds checking.
  • Architecture and Design: Use an abstraction library to abstract away risky APIs. Not a complete solution.
  • Operation, Build and Compilation: Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index checking. D3-SFCV (Stack Frame Canary Validation) from D3FEND [REF-1334] discusses canary-based detection in detail.
  • Operation, Build and Compilation: Run or compile the software using features or extensions that randomly arrange the positions of a program's executable and libraries in memory. Because this makes the addresses unpredictable, it can prevent an attacker from reliably jumping to exploitable code. Examples include Address Space Layout Randomization (ASLR) [REF-58] [REF-60] and Position-Independent Executables (PIE) [REF-64]. Imported modules may be similarly realigned if their default memory addresses conflict with other modules, in a process known as "rebasing" (for Windows) and "prelinking" (for Linux) [REF-1332] using randomly generated addresses. ASLR for libraries cannot be used in conjunction with prelink since it would require relocating the libraries at run-time, defeating the whole purpose of prelinking. For more information on these techniques see D3-SAOR (Segment Address Offset Randomization) from D3FEND [REF-1335].
  • Implementation: Implement and perform bounds checking on input.
  • Implementation: Do not use dangerous functions such as gets. Look for their safe equivalent, which checks for the boundary.
  • Operation: Use OS-level preventative functionality. This is not a complete solution, but it provides some defense in depth.

CWE-787: Out-of-bounds Write

The product writes data past the end, or before the beginning, of the intended buffer.

How to prevent it
  • Requirements: Use a language that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid. For example, many languages that perform their own memory management, such as Java and Perl, are not subject to buffer overflows. Other languages, such as Ada and C#, typically provide overflow protection, but the protection can be disabled by the programmer. Be wary that a language's interface to native code may still be subject to overflows, even if the language itself is theoretically safe.
  • Architecture and Design: Use a vetted library or framework that does not allow this weakness to occur or provides constructs that make this weakness easier to avoid. Examples include the Safe C String Library (SafeStr) by Messier and Viega [REF-57], and the Strsafe.h library from Microsoft [REF-56]. These libraries provide safer versions of overflow-prone string-handling functions.
  • Operation, Build and Compilation: Use automatic buffer overflow detection mechanisms that are offered by certain compilers or compiler extensions. Examples include: the Microsoft Visual Studio /GS flag, Fedora/Red Hat FORTIFY_SOURCE GCC flag, StackGuard, and ProPolice, which provide various mechanisms including canary-based detection and range/index checking. D3-SFCV (Stack Frame Canary Validation) from D3FEND [REF-1334] discusses canary-based detection in detail.
  • Implementation: Consider adhering to the following rules when allocating and managing an application's memory: Double check that the buffer is as large as specified. When using functions that accept a number of bytes to copy, such as strncpy(), be aware that if the destination buffer size is equal to the source buffer size, it may not NULL-terminate the string. Check buffer boundaries if accessing the buffer in a loop and make sure there is no danger of writing past the allocated space. If necessary, truncate all input strings to a reasonable length before passing them to the copy and concatenation functions.
  • Operation, Build and Compilation: Run or compile the software using features or extensions that randomly arrange the positions of a program's executable and libraries in memory. Because this makes the addresses unpredictable, it can prevent an attacker from reliably jumping to exploitable code. Examples include Address Space Layout Randomization (ASLR) [REF-58] [REF-60] and Position-Independent Executables (PIE) [REF-64]. Imported modules may be similarly realigned if their default memory addresses conflict with other modules, in a process known as "rebasing" (for Windows) and "prelinking" (for Linux) [REF-1332] using randomly generated addresses. ASLR for libraries cannot be used in conjunction with prelink since it would require relocating the libraries at run-time, defeating the whole purpose of prelinking. For more information on these techniques see D3-SAOR (Segment Address Offset Randomization) from D3FEND [REF-1335].
  • Operation: Use a CPU and operating system that offers Data Execution Protection (using hardware NX or XD bits) or the equivalent techniques that simulate this feature in software, such as PaX [REF-60] [REF-61]. These techniques ensure that any instruction executed is exclusively at a memory address that is part of the code segment. For more information on these techniques see D3-PSEP (Process Segment Execution Prevention) from D3FEND [REF-1336].
  • Implementation: Replace unbounded copy functions with analogous functions that support length arguments, such as strcpy with strncpy. Create these if they are not available.

References

Advisories

Packages

Other links

Timeline

  1. Published
  2. Last updated by the source
  3. Latest EPSS score
AdvisorySeverityWhy it's related
GHSA-55f6-pf8r-c2f4
Open Babel has out-of-bounds write in MOPAC translationVectors[] (UNIT CELL TRANSLATION)
High Also affects openbabel
GHSA-f8h2-c479-vqxf
Open Babel has out-of-bounds write in MSI translationVectors[]
High Also affects openbabel
GHSA-mjmg-352j-f456
Open Babel has out-of-bounds write in MOPAC IN translationVectors[] (Tv atom)
High Also affects openbabel
GHSA-7h6r-6p76-68c9
Open Babel has out-of-bounds write in MOPAC translationVectors[] (FINAL POINT)
High Also affects openbabel
GHSA-jg3h-pv7c-4f9c
Open Babel has out-of-bounds write in Gaussian translationVectors[]
High Also affects openbabel
GHSA-5rff-8f7c-8jmw
Open Babel has out-of-bounds write in ORCA nAtoms parser (second variant)
High Also affects openbabel
GHSA-8qxc-57hf-hc9j
Open Babel has uninitialized pointer dereference in PQS pFormat
High Also affects openbabel
GHSA-jr2x-6qf6-q5mc
Open Babel has uninitialized pointer dereference in MSI atom parser
High Also affects openbabel
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