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v0.2.8

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@github-actions github-actions released this 13 Apr 12:59
· 35 commits to main since this release
v0.2.8
8e52d97
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Added

  • SDF/MOL file support: New SDF parser supporting V2000 and V3000 formats. Calculate SASA for small molecules directly from SDF files (zsasa calc molecule.sdf) (#338)
  • --sdf option: Provide bond topology for CCD-unregistered compounds (e.g., Boltz-predicted ligands) via --sdf=ligand.sdf. Available in calc, batch, and traj subcommands (#338)
  • --mol option: Select a specific molecule from multi-molecule SDF by name or 1-based index (--mol=water or --mol=2) (#339)
  • Batch SDF expansion: Multi-molecule SDF files in batch mode are expanded into individual items, each molecule calculated independently (#339)

Changed

  • ProtOr is now an alias for CCD: --classifier=protor uses the same CCD bond-topology classifier. Default classifier for Python bindings changed from NACCESS to CCD (#335, #337)
  • Trajectory classifier default: traj subcommand defaults to NACCESS for MD trajectories (#337)

Fixed

  • SDF per-molecule SASA: Multi-molecule SDF files now calculate each molecule independently instead of combining them into one structure (#339)
  • Python classifier tests: Updated expected values for CCD default (ALA:O = 1.42 Å) (#338)
  • Memory safety: Fixed StoredComponent leaks on ComponentDict insertion failure, toAtomInput over-allocation with >26 molecules (#338, #339)

Documentation

  • CCD classifier documentation rewritten with accurate architecture details (#334, #336)
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