Bump openbabel from 3.1.1.1 to 3.2.0 in /rdock-utils

[dependabot]

Bumps openbabel from 3.1.1.1 to 3.2.0.

Release notes

Sourced from openbabel's releases.

Open Babel 3.2.0

This release reflects the latest stable version, including multiple feature enhancements and many, many bug fixes. It is backwards 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).

... (truncated)

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