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The vulnerability resides in the CSR (Chemical Structure Response) format parser of Open Babel, a widely used cheminformatics C++ library and command‑line tool. CSR is a text‑based format that includes a field, which the parser processes through a helper function named `PadString`. This function is responsible for copying the string into a fixed‑size destination buffer. The flaw arises because `PadString` performs no validation on the length of the input before copying. When a maliciously crafted CSR file contains a that exceeds the buffer’s capacity, the copy operation writes past the end of the buffer, corrupting adjacent memory.
This out‑of‑bounds write is a classic buffer overflow (CWE‑120) that can be triggered simply by convincing a victim to open a tainted CSR file. The attack surface is broad: the vulnerable code is reachable via the `obabel` command‑line tool, the `OBConversion` API, and all language bindings (Python, Ruby, Java, R, Perl, C, PHP). Because Open Babel is shipped by Linux distributions and embedded in services that may parse untrusted chemical data, this memory‑safety bug represents a significant security risk.
The vulnerable versions include all releases up to and including 3.1.1, as well as master commit 530dbfa3. The issue was addressed in commit `528c142f`, which was included in version 3.2.0 released on 2026‑05‑26. A minimized reproducer is checked into the `test/files/fuzz_regress/` directory and is automatically exercised under ASAN+UBSAN by the `fuzzregresstest` harness. The vulnerability was reported by Cisco TALOS (TALOS‑2022‑1667).
An attacker can exploit this by supplying a specially crafted CSR file with an overly long . When parsed, the uncontrolled write can overwrite critical memory structures, potentially leading to arbitrary code execution with the privileges of the process that opened the file. The CVSS v3 base score is 7.8 (High) per NIST, and 9.8 (Critical) per Talos, reflecting the ease of exploitation and the severe impact on confidentiality, integrity, and availability.
<h2 style="color: blue;">DailyCVE Form:</h2>
Platform: Open Babel
Version: 3.1.1 and earlier
Vulnerability: Out‑of‑bounds write
Severity: High
date: 2023‑07‑21
<h2 style="color: blue;">Prediction: 2026‑05‑26</h2>
<h2 style="color: blue;">What Undercode Say:</h2>
Trigger the vulnerability with a malicious CSR file obabel -icsr malicious.csr -osmi Build with AddressSanitizer to observe the out‑of‑bounds write mkdir build && cd build cmake -DCMAKE_CXX_FLAGS="-fsanitize=address -g" .. make ./bin/obabel -icsr ../test/files/fuzz_regress/csr__overflow.csr -osmi The fix commit that prevents the overflow git show 528c142f
<h2 style="color: blue;">Exploit:</h2>
The exploitation vector is straightforward: an attacker crafts a CSR file whose field contains a string longer than the fixed internal buffer. When `PadString` copies this string without length checking, it overflows the buffer. The corrupted memory can be used to overwrite function pointers, saved return addresses, or other critical data, ultimately allowing the attacker to execute arbitrary shellcode. Because the vulnerability is reachable from multiple language bindings and automated conversion pipelines, it can be triggered in both interactive and headless environments.
Protection:
- Upgrade to Open Babel 3.2.0 or later, which includes the patched commit
528c142f. - Apply the patch manually if upgrading is not immediately possible: backport the changes from `528c142f` to your local source tree.
- Validate input at the application level: reject CSR files with lengths exceeding a safe threshold before passing them to Open Babel.
- Run with sanitizers (ASAN/UBSAN) in development and testing to catch similar memory errors early.
- Restrict file sources – avoid opening untrusted CSR files, especially from unknown or unauthenticated origins.
Impact:
Successful exploitation leads to memory corruption that can be leveraged for arbitrary code execution. An attacker could gain full control over the affected process, which may run with elevated privileges in server‑side or automated conversion services. This could result in data theft, system compromise, or denial of service. The vulnerability affects all deployments of Open Babel up to 3.1.1, including those in Linux distributions, scientific computing environments, and web‑based chemistry platforms that rely on the library for file parsing.
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Sources:
Reported By: github.com
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