Null Atomtypes in PDB Het Dictionary now in some sort of RDF thing

This blog post won "Best Title" in the award for "Random Combinations of Words" category.

Anyway, the atomtypes that were not found by the CDKAtomMatcher are now down to just 1,400. There were various errors on my part (such as using element symbols like "CL" rather than "Cl') and CIF files are trickier to parse than I thought (an atom name can be "HOH'" or 'P"' - look closely!).

Just to make life even harder, and because Egon suggested it, I tried to get the output in some kind of RDF using Jena. In practice, this seems to mean a sort of vague tree of nodes, some of which are data and some are types.

Well, its in the same repository as before, with source code. Although looking at the N3 file it still looks like it would be impossible to work out which atom belongs to which hetgroup...

Comments

chalky

I wanted to show something that hints at the things that the new architecture can afford us: This is using a Java2D graphics Paint object to make it look like chalk...kindof. It's a very simplistic way of doing it by making a small image with a random number of white, gray, lightgray, and black pixels. edit: it doesn't look so good at small scales some tweaking of stroke widths and so on is essential.

The Gale-Ryser Theorem

This is a small aside. While reading a paper by Grüner, Laue, and Meringer on generation by homomorphism they mentioned the Gale-Ryser (GR) theorem. As it turns out, this is a nice small theorem closely related to the better known Erdős-Gallai (EG). So, GR says that given two partitions of an integer ( p and q) there exists a (0, 1) matrix A iff p* dominates q such that the row sum vector r(A) = p and the column sum vector c(A) = q . As with most mathematics, that's quite terse and full of terminology like 'dominates' : but it's relatively simple. Here is an example: The partitions p and q are at the top left, they both sum to 10. Next, p is transposed to get p* = [5, 4, 1] and this is compared to q at the bottom left. Since the sum at each point in the sequence is greater (or equal) for p* than q , the former dominates. One possible matrix is at the top left with the row sum vector to the right, and th...

1,2-dichlorocyclopropane and a spiran

As I am reading a book called "Symmetry in Chemistry" (H. H. Jaffé and M. Orchin) I thought I would try out a couple of examples that they use. One is 1,2-dichlorocylopropane : which is, apparently, dissymmetric because it has a symmetry element (a C2 axis) but is optically active. Incidentally, wedges can look horrible in small structures - this is why: The box around the hydrogen is shaded in grey, to show the effect of overlap. A possible fix might be to shorten the wedge, but sadly this would require working out the bounds of the text when calculating the wedge, which has to be done at render time. Oh well. Another interesting example is this 'spiran', which I can't find on ChEBI or ChemSpider: Image again courtesy of JChempaint . I guess the problem marker (the red line) on the N suggests that it is not a real compound? In any case, some simple code to determine potential chiral centres (using signatures) finds 2 in the cyclopropane structure, and 4 in the ...

Some Stuff

Search This Blog