GHSA-vx29-rwgr-834p
Duplicate Advisory: Open Babel has out-of-bounds write in PQS coord_file parser
Critical
Withdrawn Jul 1, 2026
PyPI
Description
Duplicate Advisory
This advisory has been withdrawn because it is a duplicate of GHSA-f29h-2h58-48r7. This link is maintained to preserve external references.
Original Description
An out-of-bounds write vulnerability exists in the PQS format coord_file functionality of Open Babel 3.1.1 and master commit 530dbfa3. A specially crafted malformed file can lead to arbitrary code execution. An attacker can provide a malicious file to trigger this vulnerability.
Affected versions
PyPI
| Package | Vulnerable | Fixed 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 9.8
CVSS:3.1/AV:N/AC:L/PR:N/UI:N/S:U/C:H/I:H/A:H
- Attack vector
- Network
- Attack complexity
- Low
- Privileges required
- None
- User interaction
- None
- Scope
- Unchanged
- Confidentiality
- High
- Integrity
- High
- Availability
- High
Weakness
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 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.
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
Other links
Timeline
- Published
- Withdrawn
- Last updated by the source
Related advisories
| Advisory | Severity | Why 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-rj4c-r689-cm87 Open Babel has out-of-bounds write in ORCA nAtoms parser | High | Also affects openbabel |
| GHSA-8qxc-57hf-hc9j Open Babel has uninitialized pointer dereference in PQS pFormat | High | Also affects openbabel |
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