Stereochemistry

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Revision as of 11:37, 14 June 2009 by Baoilleach (Talk | contribs) (Initial creation)

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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.

Status

  • General stereochemistry framework: Done
  • 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 (?)

Bugs

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