ToDo

  • improve generation of coordinates (when reading SMILES for example)
  • implement CIP for stereochemistry detection
  • read stereochemistry from InChI
  • isotopes – there is already isotope_database.py, add support to periodic_table (counting of mw, display), molfile, cairo_out, BKChem, many other modules
    ** isotop will not be visible in summary formula, but will show in molecular weight
  • have a look at ring search for fullerene – there might be some error
  • when CID_5006.sdf is read it will create Pr with 3 hydrogens, but there should be none. It would be best to have a look at the molecule on reading and if there are already some hydrogens present not add any implicit ones
  • have a look at the strange InChI for Br- (InChI=1/BrH/h1H/p-1/fBr/h1h/q-1)
  • implement search for rings according to http://pubs.acs.org/doi/full/10.1021/ci960322f – it’s done, but it is neccessary to switch to edge based algorithm, not vertex based
  • when PubChem SDF file 000000-25000 testovacim skriptem (in tests.py) is processed, it crashes with “fuck, how comes?!” somewhere. Have a look at it.
  • read metadata from SDF
  • OASA does not properly read CDML (BKChem’s internal format) with more than one molecule