GHSA-m982-7q3h-r784 CVE-2025-11000 PYSEC-2026-2785
Open Babel has out-of-bounds read in PQS lowerit (pre-buffer read)
- Severity
- 1.9 / 10
- Low · CVSS 4.0
- Exploit chance (EPSS)
- 0.25%
- Chance of exploitation in the next 30 days. Higher than 15.91% of scored vulnerabilities.
- Known exploited
- No
- Not in CISA's catalog
- Fix
3.2.0- Upgrade openbabel to this version or later
Description
Summary
A memory-safety vulnerability in Open Babel's PQS parser caused an out-of-bounds (pre-buffer) read when reading a crafted input file.
Details
The flaw was in the lowerit helper used by the PQS parser. A
malformed input caused the helper to read one or more bytes before
the start of its input 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 PQS 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/f4a5ebae Fixes consolidated in #2913.
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 via OSS-Fuzz.
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 4.0 1.9
CVSS:4.0/AV:L/AC:L/AT:N/PR:L/UI:N/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
- Attack vector
- Local
- Attack complexity
- Low
- Attack requirements
- None
- Privileges required
- Low
- User interaction
- None
- Confidentiality (vulnerable system)
- None
- Integrity (vulnerable system)
- None
- Availability (vulnerable system)
- Low
- Confidentiality (subsequent systems)
- None
- Integrity (subsequent systems)
- None
- Availability (subsequent systems)
- None
- Exploit maturity
- Proof of concept
- Scope
- X
CVSS 3.1 4.4
CVSS:3.1/AV:L/AC:L/PR:N/UI:R/S:U/C:L/I:N/A:L
- Attack vector
- Local
- Attack complexity
- Low
- Privileges required
- None
- User interaction
- Required
- Scope
- Unchanged
- Confidentiality
- Low
- Integrity
- None
- Availability
- Low
Weakness
CWE-125: Out-of-bounds Read
The product reads data past the end, or before the beginning, of the intended buffer.
How to prevent it
- 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. To reduce the likelihood of introducing an out-of-bounds read, ensure that you validate and ensure correct calculations for any length argument, buffer size calculation, or offset. Be especially careful of relying on a sentinel (i.e. special character such as NUL) in untrusted inputs.
- Architecture and Design: Use a language that provides appropriate memory abstractions.
CWE-404: Improper Resource Shutdown or Release
The product does not release or incorrectly releases a resource before it is made available for re-use.
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, languages such as Java, Ruby, and Lisp perform automatic garbage collection that releases memory for objects that have been deallocated.
- Implementation: It is good practice to be responsible for freeing all resources you allocate and to be consistent with how and where you free memory in a function. If you allocate memory that you intend to free upon completion of the function, you must be sure to free the memory at all exit points for that function including error conditions.
- Implementation: Memory should be allocated/freed using matching functions such as malloc/free, new/delete, and new[]/delete[].
- Implementation: When releasing a complex object or structure, ensure that you properly dispose of all of its member components, not just the object itself.
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 |
MergeHarbor checks every repository's dependencies against this database, ranks what matters by exploitability and reachability, routes it to the owning team and opens the fix pull request.
Check your repos with MergeHarbor