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