Some Stuff

A quick example of a mini-application made using the new JChempaint renderer: the picture is of an isomer space (C 3 H 7 NO), with compact mode on and atoms rendered as circles. The code is here, for now: http://gist.github.com/70342 which is a kind of dumb way to achieve this, as it creates an instance of a renderer for each molecule, instead of adding them to a molecule set, and then laying that out... edit: just realised; it's rendering the hydrogens as compact black circles :( edit2: Ahhh. that's better: edit3: Ha! This was a mistake, but it looks kind of cool:

JCP now has minimal lone pair display. I would prefer the layout to be at the corners of a square, rather than on the edges. Videlicet, they are currently only at N, W, S, E; I think that NW, SW, SW, and NE would be better. Strangely lone pairs don't seem to appear in CML files when written out, but Egon says he will look at this. Perhaps I should file a bug report... Oh, and radicals are implemented too, but I don't have a picture of that  (see right). They are in different generators, but I guess a single 'DotGenerator' could do both :)

So, all of the isomers of C4H11O are in NMRShiftDB  and here are all the experimental and predicted carbon spectra: It's not obvious from this picture, but not all of the predicted spectra are unique matches for their experimental partners. In other words, you could not pick out the right molecule by comparing the predicted and experimental spectra. The situation is more difficult still for larger isomer spaces, where the predicted spectra may be exactly the same for sub-sets of the isomers. There are still many with unique predictions, but the rest follow a sort of power-law distribution of spectral-equivalent sets. EDIT: As per a suggestion by egon, here is a table of top hits (a yellow square indicates the top match):

A really tiny isomer set, with a particularly regular network: Nicely enough, all 8 of these structures are in NMRShiftDB, so it will be possible to compare all against all.

Slightly more useful/comprehensible. Also, this is a more interesting isomer space (C3H7ON) which is more fragmented at a 50% similarity cutoff.

C8H16 this time. The central bridge has split into two parts, it seems. The clustering is somewhat artificial, I suppose... An example from one of these is C=C(C(C)C)C(C)C, and from the other is C=CC(CC)CCC. Hmmm.

Another one (C7H14 this time): It's a bit cumbersome, but I managed to get smiles strings to show as tooltip text. This tells me that the three vertices in the center of this picture (the bridging ones) are C=C(C)CCCC, C=C(CC)C(C)C, and C=C(CC)CCC. Not sure why. Oh, and the 'lobe' on the left seem to be (all?) non-cyclic, while the ones on the right seem to be cyclic, which makes sense.