Looks very good now. Nice work. On 21 September 2010 11:38, Noel O'Boyle <baoille...@gmail.com> wrote: > 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 >> >
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