I'm afraid I'm seeing problems with roundtripping from SMILES through 0D, 2D or 3D MDL.
If you run pytest_sym (e.g. "ctest -R pytest_sym -VV"), you should see several errors (http://my.cdash.org/testDetails.php?test=3025177&build=99128). As an example, one of the errors can be shown as follows: $ ./obabel -:"Cl[C@@](Br)(F)I" -osdf -Otmp.sdf ============================== *** Open Babel Warning in WriteMolecule No 2D or 3D coordinates exist. Any stereochemical information will be lost. To generate 2D or 3D coordinates use --gen2D or --gen3d. 1 molecule converted (tmp.sdf is correct) $ ./obabel tmp.sdf -osmi ClC(Br)(F)I # should be the starting SMILES with stereo Whatever you think of the merits of preserving chiral stereochemistry in a 0D mol file, this was working until the 31 file update on Sunday (http://my.cdash.org/index.php?project=Open+Babel&date=2010-09-19). - Noel On 20 September 2010 21:23, Tim Vandermeersch <tim.vandermeer...@gmail.com> wrote: > Hi, > > Here are some comments regarding my commits from yesterday. > > The type used to represent automorphisms has been changed from > std::vector< std::map<unsigned int, unsigned int> > to std::vector< > std::pair<unsigned int, unsigned int> >. This makes a huge difference > in performance but might require small changes in code using it (code > in svn is updated of course). When doing an automorphisms search for a > multiple fragment molecule, each fragment is treated separately and > the resulting set of automorphisms is simply the union of the > individual results. In other words, not all automorphisms will have > the same size and cover the whole molecule. Substructure search should > now also be much faster using OBIsomorphismMapper compared to smarts > although I haven't tested this yet. > > The canonical labeling code now uses memory more efficiently and also > treats connected fragments individually. Performance analysis shows > that precomputing and caching stereo descriptors would be the next > part to optimize and I'll do this tonight together with some other > smaller improvements. If anyone still encounters problematic cases > (now or later), they can always send me the cases. > > The canonical order is now "stable" and I'll add a unit test to check > this tonight. > > Still todo: Add square-planar stereochemistry + isotopes > > I've added a DataCache class to help with storing symmetry classes, > automorphisms and stereogenic units as generic data. The class uses > graph invariants and bitvec masks to check if the data needs to be > recalculated. I still need to document this although we might want to > keep this as private API? > > That's it for now, feel free to ask more questions... > > Tim > > ------------------------------------------------------------------------------ > Start uncovering the many advantages of virtual appliances > and start using them to simplify application deployment and > accelerate your shift to cloud computing. > http://p.sf.net/sfu/novell-sfdev2dev > _______________________________________________ > OpenBabel-Devel mailing list > OpenBabel-Devel@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-devel > ------------------------------------------------------------------------------ Start uncovering the many advantages of virtual appliances and start using them to simplify application deployment and accelerate your shift to cloud computing. http://p.sf.net/sfu/novell-sfdev2dev _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
