Stereochemistry

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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 (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 (?)

Code

stereo branch: this branch contains the new stereo code... (50.000 molecules from PubMed < 5 errors) http://github.com/timvdm/openbabel/commits/stereo

2D branch: contains some code to improve 2D coords -> OBStereo objects conversion (needs debugging) http://github.com/timvdm/openbabel/commits/2D

openbabel-2-2x: contains some bug fixes using parts of new stereo code http://openbabel.svn.sourceforge.net/viewvc/openbabel/openbabel/branches/openbabel-2-2-x/

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