On Fri, Feb 13, 2009 at 11:21 PM, Andrew Dalke <da...@dalkescientific.com> wrote: > On Feb 13, 2009, at 9:14 PM, TJ O'Donnell wrote: >> Yes, INnChI is unique across different packages. This is because >> there is one definitive source for the code and algorithm. This was >> a design goal of InChI. > > > Or to twist TJ's words around .. it's exactly the same as with > canonical SMILES - every implementation of InChI does it a different > way. It's just that there's only one InChI implementation.
And since IUPAC has not only done an open implementation with a reasonable license, but also trademarked the name and placed the restriction on its use that you can't call it InChI unless you pass their validate suite, InChI will hopefully remain a "portable" canonical identifier. >> in this case probably to do with which branch to deal with first) > > > As I recall when trying to implement the algorithm, the ambiguity is > in dealing with ties. The algorithm assigns a unique ordering to the > atoms, up to symmetry, but it's defined at the atom level. Given an > atom A bonded to atoms B1 and B2, it's possible for B1 and B2 to be > in the same symmetry class, but with different bond types going to B1 > and B2. > > I asked Weininger about it and he said "choose the highest order bond > first", which mostly works but I think can be ambiguous for a few > rare cases. I don't recall any. The decision about which bond to follow first at a branch is really the big one. > There may be other under-specified aspects. I haven't looked at the > paper in 10 years. stereochemistry is one that immediately comes to mind -greg
