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This page describes progress on the new stereochemistry framework in OpenBabel. This framework will be included in OpenBabel versions from OpenBabel 3.0 onwards.


  • General stereochemistry framework: Done (advanced 2D coords -> OBStereo still needs some work)
  • Symmetry handling: Need to cache symmetry_classes
  • SMILES format: Done
  • MDL format: 2D to be completed (possibly port from RDKit)
  • InChI format: Done
  • SMARTS: Update to use facade (?)


stereo branch: this branch contains the new stereo code... (50.000 molecules from PubMed < 5 errors)

2D branch: contains some code to improve 2D coords -> OBStereo objects conversion (needs debugging)

openbabel-2-2x: contains some bug fixes using parts of new stereo code


Loss of aromaticity

This bug occurs only on the obsym branch (compared to ob22x). c12c(Cc3c1cccc3)cccc2C is written out as canonical SMILES C[[email protected]?H]1CCC[[email protected]?H]2C[[email protected]?H]3CCCC[[email protected]?H]3[[email protected]?H]12