Open Babel 3.2.0#

Released on 2026-05-26.

This release reflects the latest stable version, including multiple feature enhancements and many, many bug fixes. It is API compatible with 3.0 and 3.1.

We anticipate more bug-fix releases over the course of 2026 and appreciate the many contributions and reports from everyone.

Major Features and Fixes#

  • Many memory and crash bugs fixed, thanks to OSS-Fuzz (Google) for infrastructure, including Cisco TALOS, Trail of Bits, ADA Logics, and Claude Mythos for bug reports. At the moment, all reported bugs are fixed.

  • L-BFGS optimizer added to OBForceField (internal LBFGS.h); gen3d and conformer search now use L-BFGS by default (with CG fallback when Eigen is unavailable). @ghutchis (#2933)

  • New macrocycle ring builder with Dale codes for cycloalkanes with n > 24, plus a post-pass crown builder for unmatched rings up to n ≤ 24. Substantially improves initial 3D geometry for macrocycles. @ghutchis (#2923)

  • Distance-geometry improvements: faster, vectorized implementation ensuring stereochemistry is preserved @ghutchis (#2896, #2897)

  • KET format (Ketcher JSON) read/write, including aromatic-bond preservation and alias expansion for clean round-trip. @romanbsd (#2909)

  • ChemicalJSON (``.cjson``) format support — Avogadro’s native format — with rich metadata: total charge & spin multiplicity, NMR and electronic spectra, conformer energies, unit-cell vectors, and space-group info. @ghutchis (#2486, #2491, #2516, #2640, #2654)

  • InChI bumped to 1.07.5; library version now reported in the format description. @e-kwsm @ghutchis (#2857, #2947)

  • Python 2 dropped; Python 3.13 supported (distutils removed). @e-kwsm @chrisjonesBSU (#2924, #2809) Integrated PyPI binary wheels @njzjz #2925

  • CMake 4 compatibility, FindPython refactor, Eigen 2 dropped, Eigen3::Eigen imported target adopted. @PPN-SD @e-kwsm (#2784, #2753, #2858)

  • OBRandomMT: new std::mt19937_64-based PRNG wrapper (opt-in via USE_RANDOMMT, default on); OB_RANDOM_SEED environment variable documented for reproducibility. @e-kwsm (#2241)

New Features and Improvements#

  • WLN (Wiswesser Line Notation) reader additions. @baoilleach @michaelblakey (#2510)

  • PDBQT: Meeko-compatible VDW radii @bmp192529 (#2798); data-block output @dkoes (#2796); implicit H assignment on read @fredrikw (#2553); partial-charge column alignment fix @flatstik (#2601).

  • PDB: segment-name parsing/retention @dkoes (#2637); more robust reading @dkoes (#2395).

  • Tinker: custom atom-class read @mquevill (#2355); multi-word titles and optional comment line @mquevill (#2354).

  • ORCA: retain all conformers on read @ghutchis (#2922); ORCA 5 vibration header handled @ghutchis (#2521).

  • xtb: handle “Gaussian”-style vibration output (Raman = 0.0). @ghutchis (#2653)

  • Turbomole: write $lattice block when a unit cell is present. @e-kwsm (#2823)

  • CIF: atomic coordinates are no longer wrapped into the unit cell by default. @ghutchis (#2629)

  • COF: new version-numbering scheme (old files still readable). @pbecherer (#2840)

  • CML/CMLR: support conversion to CMLR @romanbsd (#2694); dangling-reference fix in the reaction writer @romanbsd (#2926).

  • STL: bond visualization, improved color export, -s scale option, modernized source. @TheRealSami (#2814)

  • FASTA: actually connect atoms on conversion @fredrikw (#2371); retain chains/residues @ghutchis (#2734).

  • Ruby SWIG wrapper: reactions @romanbsd (#2748) and tautomers @romanbsd (#2943) now supported.

  • obrms: parameter docs added to help text and man page; length-of-RMSDs sanity check @e-kwsm (#2942); improvements @dkoes (#2608).

  • ``obabel``: --separate no longer breaks on EOL when reading from stdin. @matterhorn103 (#2721)

  • ``CorrectForPH`` now respects perceived chains. @fredrikw (#2648)

  • C++ syntax: OBAtom::GetNbrs() and range-based for loops @timvdm (#2635); override annotations @e-kwsm (#2175); noexcept for deprecated throw() @e-kwsm (#2859); OB_DEPRECATED macros @e-kwsm (#2002).

Bug Fixes#

  • Stereo leak in SMILES parser @ghutchis (#2908); tautomer assertion / code bugs.

  • Canonical-label generation now has a 5-second timeout to avoid hangs on pathological inputs. @ghutchis (#2921)

  • CDXML: clear ImplicitHydrogens between fragments (fixes segfault, #2696) @fredrikw (#2697); implicit-H handling generally improved (#2416) @StashOfCode (#2400).

  • CDJSON: implicit-valence handling on read; "l" field deserialization; "h" field respected. @gregmagdits (#2769)

  • libxml2 ≥ 2.12.7 compatibility. @merkys (#2702)

  • InChI: memory leaks @romanbsd (#2706, #2772) and crashes @romanbsd (#2717, #2747) fixed; crash converting some bad CML → InChI fixed.

  • CML parsing crash on specific inputs. @romanbsd (#2705)

  • AOFORCE parser memory issues. @tyler92 (#2749)

  • SSSR/RingSearch: ring-pruning bug @fredrikw (#2684); ring iteration with no rings @dkoes (#2295).

  • pybel: missing atom properties @dkoes (#2293); pybel.draw file-write check; removed _png2 requirement for coordinate generation.

  • SMILES: H-suppression bug when specifying output atom order. @baoilleach (#2287)

  • SMILES crashes from malformed input. @tyler92 (#2746)

  • obthermo crash from pointgroup code. @dspoel (#2285)

  • GRO format: first residue index 0 no longer crashes. @DStarEpoch (#2598)

  • VASP and Turbomole format fixes. @e-kwsm (#2563)

  • obminimize help text and docs. (#2519)

  • CopySubstructure segfault with option 2. @baoilleach (#2449)

  • Bond perception of ring nitrogens @dkoes (Nbondfix branch); azete bond order @dkoes (#2379); ammonium XYZ parsing @dkoes (#2380).

  • MDL v3000 coordinate rounding (%.4f 2D, %.6f 3D). @ghutchis (#2929)

  • Uninitialized arrays / infinite-loop fixes. @Crivella (#2850, #2851)

  • Big-endian / s390x portability fixes. @pranavkaruvally (#2816)

  • PQR debug output cleanup. @crabby-rathbun (#2854)

  • Examples build fix for GCC / libstdc++ 8.3. @jcbollinger (#2235)

  • Misc undefined-behavior and memory leak fixes. @jcbollinger (#2224, #2227, #2228), @afonari (#2220, #2225, #2226, #2232, #2233)

  • Initialize allocated memory to zero. @afonari (#2248)

  • OBMol::NumHvyAtoms() const + OBResidue::GetNumHvyAtoms(). (#2300, #2299)

Security and Fuzz Hardening#

  • CVE-2022 (Cisco TALOS): 14 CVEs across MOL2 (CVE-2022-43607), CSR, GRO, PQS, MSI, ORCA, Gaussian, and MOPAC formats — including 5 translationVectors[] OOB writes. @ghutchis (#2883, #2884, #2885, #2886, #2887)

  • CVE-2026 batch: CIF transform3d::DescribeAsString OOB read, MOL2 SetFormalCharge NULL deref, CDXML NULL deref. @VedantMadane (#2862)

  • CVE-2025: GAMESS use-after-free (CVE-2025-10994), zipstream overlapping memcpy (CVE-2025-10995), SMILES heap-buffer-overflow (CVE-2025-10996), ChemKin (CVE-2025-10997/10998), CACAO (CVE-2025-10999), PQS (CVE-2025-11000). @ghutchis (#2913)

  • OSS-Fuzz / Trail of Bits / ADA Logics / Claude Mythos / TALOS: dozens of fixes across MCDL, ChemDraw CDX, Chemkin, abinit, cacao, Gaussian (incl. z-matrix and cube), Molpro, POV-Ray, Tinker, SMARTS, MDL V3000, SDF, CIF, and the SMILES canonicalizer (OOM on hypervalent / high-permutation molecules). @ghutchis (#2891, #2910, #2916–#2918, #2921, #2928, #2937, #2938, #2939, #2944, #2948, #2949, #2950, #2954)

  • Hardening: stack-smashing recursion in FindRings converted to an iterative loop; bond-loop and atom-count bounds checks; charge bounds (±999); rejection of recursive SMARTS (( depth > 1000; bound on heavy atoms (MCDL > 200); guards on tokenize/vs access; rejection of elements > 118; std::unique_ptr adoption to fix leaks/use-after-free.

  • MCDL hardening (Arthur Chan / ADA Logics report). @ghutchis (#2883)

  • ``SECURITY`` policy and fuzz regression tests added. @ghutchis (#2882)

  • New fuzz harnesses: three new harnesses by @DavidKorczynski (#2874), plus fuzz_convert by @tyler92 (#2737). Initial OSS-Fuzz integration by @catenacyber (#2342).

Build Improvements#

  • CI: CIFuzz GitHub Action @DavidKorczynski (#2551); CodeQL workflow @lgtm-migrator (#2546); Dependabot for GitHub Actions @ghutchis (#2739); cibuildwheel workflow producing relocatable Python wheels for Windows / macOS / Linux / Linux ARM64 @ghutchis (#2946); Linux ARM64 ASAN+UBSAN test build @ghutchis (#2898); Python lint with safety policy.

  • CMake 4 compatibility end-to-end @PPN-SD (#2784); replaced deprecated exec_program and other modernization @e-kwsm (#2507); OpenBabel3Config.cmake retains include info @e-kwsm (#2802); public/private include-dir hygiene @pinotree (#2315); Windows config-install location fix @nicolasfella (#2463); CMake-version bumps for Python @chrisjonesBSU (#2809).

  • ``FindPython`` adopted; Python install path/prefix modernized @e-kwsm (#2753, #2927); per-language *_INSTDIR variables (Python, Java, R, Perl, Ruby, C#, PHP) made configurable @cygwin-lem (#2289).

  • Eigen: drop Eigen 2; find Eigen3 in config mode and link Eigen3::Eigen; ensure HAVE_EIGEN3 is set at configure @e-kwsm (#2858).

  • Dependencies: InChI 1.07.5 @e-kwsm (#2857); maeparser 1.3.3 @e-kwsm (#2899); coordgen pinned to v3.0.2-10-gd20e735 @e-kwsm (#2901), with template-file lookup removed @bsiegert (#2297).

  • Compiler/portability: include <ctime> for GCC 12+/C++17 @KunhuanLiu (#2844); CMake time-check typo for GCC 12 @thesamesam (#2493); drop register @e-kwsm (#2920); drop deprecated <ciso646> @e-kwsm (#2860); replace std::random_shuffle with std::shuffle @e-kwsm (#2931); remove deprecated C headers @e-kwsm (#2388); MSVC2015 back_inserter include @baoilleach (#2230); Intel build uses IPO and strip at link in Release; big-endian / s390x fixes @pranavkaruvally (#2816).

  • Modernization: SWIG 4.x support and Javadoc/Pydoc bindings @baoilleach (#2242, #2243); std::unordered_map adoption @e-kwsm (#2500); always use std::shared_ptr (#2501); remove deprecated std::bind1st/bind2nd/binary_function @e-kwsm (#2569, #2001, #2464); replace deprecated throw spec with noexcept @e-kwsm (#2859); IOError → OSError in Python tests @e-kwsm (#2466).

  • Misc.: .gitattributes + EOL renormalization @e-kwsm (#2489); updated built-in data files @dkoes (#2328); debug/sanitizer build variants skip slow tests @ghutchis (#2907); many internal deprecation warnings removed in a final refactor @ghutchis (#2937).

Contributors#

Many thanks to everyone who contributed code, bug reports, and reviews for 3.2. Full shortlog: git shortlog -sn openbabel-3-1-1..openbabel-3-2-0.

Top contributors by commit count: @ghutchis, @e-kwsm, @fredrikw, @romanbsd, @dkoes, @baoilleach, @afonari, @cygwin-lem, @chrisjonesBSU, @jcbollinger, @pinotree, @TheRealSami, @timvdm, @yishutu, @szlepermarcin, @mquevill, @tyler92, @Crivella, @DavidKorczynski, @VedantMadane, @bmp192529, @pbecherer, @matterhorn103, @merkys, @StashOfCode, @gregmagdits, @PPN-SD, @pranavkaruvally, @dspoel, @bsiegert, @KunhuanLiu, @thesamesam, @nicolasfella, @flatstik, @crabby-rathbun, @catenacyber, @njzjz-bot.

Also via fuzzing reports: OSS-Fuzz, Cisco TALOS, Trail of Bits, ADA Logics (Arthur Chan), and Claude Mythos / Claude Security.

New Contributors#

Full Changelog: https://github.com/openbabel/openbabel/compare/openbabel-3-1-1…openbabel-3-2-0