Geoff, There's a problem in the current fragment making code (for the 3D builder) where the same fragment is generated several times, e.g. A1AA=AA1 and A1AAA=A1 are both generated in the case of the attached sdf file.
This occurs because the canonicalisation is based on the original fragment, which is different in each case (e.g. one could be a heterocycle, the other not). As a result the same canonical representation is only guaranteed if the original fragment is chemically identical. So I thought about changing the fragment to be composed of C atoms and using that to derive the canonical representation. However, this seems to be the method that you originally used and subsequently changed to the current method. Is there a major problem with that approach? (The most recent versions of the code can be found in SVN in contributed/c++/fragments) - Noel ------------------------------------------------------------------------------ Return on Information: Google Enterprise Search pays you back Get the facts. http://p.sf.net/sfu/google-dev2dev _______________________________________________ OpenBabel-Devel mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-devel
