> 1) there are structures that have information in labels. So sometimes the > stereochemistry at a particular center is is given by a dummy atom nearby > with a label 'R' or 'S'.
I think this is a perfect example of how "standard formats" quickly become complicated by "in practice usage." If you have some example files, we can probably code up a heuristic. > 2) the molecular formula has historically been entered independently of the > structure. When you check to see if you can get the molecular formula from > the structure, you get some inconsistencies. Some are pretty easy to figure > out (the difference between M.Cl, M.Cl- and M.HCl) and some that might take a > bit more thought. There are also cases that the counter-ion is left out of > the structure, but appears in the MF. > Of course all this is in addition to the kinds of chemistry and consistency > checks you talked about in the talk. If you or any other OpenBabel folks want > to help out, let me know. I'll prob have an sdf file with the raw database > extraction on our ftp site in the next few days. At the very least I expect I > will have some questions for the list. As you know, please feel free to post questions, concerns, bugs, etc. But I think we can definitely help out -- we've used the NCI databases as test sets, so it's only fair to return the favor. Best regards, -Geoff ------------------------------------------------------------------------------ EMC VNX: the world's simplest storage, starting under $10K The only unified storage solution that offers unified management Up to 160% more powerful than alternatives and 25% more efficient. Guaranteed. http://p.sf.net/sfu/emc-vnx-dev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
