Open Babel has NULL pointer dereference in MOL2 OBAtom::SetFormalCharge

Summary

A memory-safety vulnerability in Open Babel's MOL2 file format parser
caused a NULL pointer dereference when reading a crafted input file.

Details

The flaw was in OBAtom::SetFormalCharge as called from the MOL2
parser. A malformed atom record caused the parser to call 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 MOL2 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.