GHSA-p594-7xw4-g76p CVE-2022-41793 PYSEC-2026-2788
Open Babel has out-of-bounds write in CSR PadString (title field)
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 56.66% of scored vulnerabilities.
- Known exploited
- No
- Not in CISA's catalog
- Weakness
- CWE-120 Buffer Copy without Checking Size of Input ('Classic 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 CSR parser allowed an out-of-bounds write when reading a crafted input file.
Details
The flaw was in the PadString helper used to handle the CSR title
field. A title longer than the fixed destination buffer caused the
parser to write past the end of the 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 CSR 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/528c142f
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
| 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 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-120: Buffer Copy without Checking Size of Input ('Classic Buffer Overflow')
The product copies an input buffer to an output buffer without verifying that the size of the input buffer is less than the size of the output 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 your buffer is as large as you specify. 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.
- Implementation: Assume all input is malicious. Use an "accept known good" input validation strategy, i.e., use a list of acceptable inputs that strictly conform to specifications. Reject any input that does not strictly conform to specifications, or transform it into something that does. When performing input validation, consider all potentially relevant properties, including length, type of input, the full range of acceptable values, missing or extra inputs, syntax, consistency across related fields, and conformance to business rules. As an example of business rule logic, "boat" may be syntactically valid because it only contains alphanumeric characters, but it is not valid if the input is only expected to contain colors such as "red" or "blue." Do not rely exclusively on looking for malicious or malformed inputs. This is likely to miss at least one undesirable input, especially if the code's environment changes. This can give attackers enough room to bypass the intended validation. However, denylists can be useful for detecting potential attacks or determining which inputs are so malformed that they should be rejected outright.
- Architecture and Design: For any security checks that are performed on the client side, ensure that these checks are duplicated on the server side, in order to avoid CWE-602. Attackers can bypass the client-side checks by modifying values after the checks have been performed, or by changing the client to remove the client-side checks entirely. Then, these modified values would be submitted to the server.
- 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].
- Build and Compilation, Operation: Most mitigating technologies at the compiler or OS level to date address only a subset of buffer overflow problems and rarely provide complete protection against even that subset. It is good practice to implement strategies to increase the workload of an attacker, such as leaving the attacker to guess an unknown value that changes every program execution.
- Implementation: Replace unbounded copy functions with analogous functions that support length arguments, such as strcpy with strncpy. Create these if they are not available.
- Architecture and Design: When the set of acceptable objects, such as filenames or URLs, is limited or known, create a mapping from a set of fixed input values (such as numeric IDs) to the actual filenames or URLs, and reject all other inputs.
- Architecture and Design, Operation: Run your code using the lowest privileges that are required to accomplish the necessary tasks [REF-76]. If possible, create isolated accounts with limited privileges that are only used for a single task. That way, a successful attack will not immediately give the attacker access to the rest of the software or its environment. For example, database applications rarely need to run as the database administrator, especially in day-to-day operations.
- Architecture and Design, Operation: Run the code in a "jail" or similar sandbox environment that enforces strict boundaries between the process and the operating system. This may effectively restrict which files can be accessed in a particular directory or which commands can be executed by the software. OS-level examples include the Unix chroot jail, AppArmor, and SELinux. In general, managed code may provide some protection. For example, java.io.FilePermission in the Java SecurityManager allows the software to specify restrictions on file operations. This may not be a feasible solution, and it only limits the impact to the operating system; the rest of the application may still be subject to compromise. Be careful to avoid CWE-243 and other weaknesses related to jails.
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
- Published
- Last updated by the source
- Latest EPSS score
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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