Ring Plate Visualisation

One diagram I've often wanted to make was filled-in rings in molecules :

Mainly for the purposes of highlighting rings without highlighting the atoms involved. This image was made using the CDK renderbasic module, and a small toy AWTRenderingVisitor that fills in paths. I'm not sure if the current one does this...

The gist for the main drawing method is here but is really just stuff seen before. The custom generator for rings is probably more interesting - if very simple - and is here. Note that it doesn't look too nice with inner-ring double bonds:

and would look nicer if the double bonds were symmetric.

EDIT : Coloring by ring equivalence classes didn't do what I expected...

Shouldn't all the outer rings be in the same class? Steran is how I expect, though:

Comments

Egon Willighagen said…

Nice!

It makes me think, despite that Margin bug, maybe there is enough new stuff here to write up that paper... what do you think?

13 June 2011 at 05:18

Rich Apodaca said…

Interesting idea - what would be some applications?

13 June 2011 at 15:38

gilleain said…

Egon: Margin bug? This:

http://sourceforge.net/tracker/index.php?func=detail&aid=3062137&group_id=20024&atid=120024

or? If so, this is the two-pass system, which is more than just a bug :)

If we can find a way of unit-testing graphics, then that could definitely be publishable, as I think that a tested chemical graphics library would be of interest.

13 June 2011 at 22:39

gilleain said…

Rich : Well, for any ring-finding algorithm, I suppose. I don't know what it would look like if you filled in a large ring that had smaller ones inside it.

A simple extension of the code I posted might color different ring equivalence classes (the SSSRFinder calculates these).

In general, you can highlight a set of atoms in a ring without confusion. Something like coronene could have all the outer rings highlighted, without the inner one.

13 June 2011 at 22:42

gilleain said…

See this gist : https://gist.github.com/1023824 for the ring equivalence class code...

13 June 2011 at 22:59

Adamantane, Diamantane, Twistane

After cubane, the thought occurred to look at other regular hydrocarbons. If only there was some sort of classification of chemicals that I could use look up similar structures. Oh wate, there is . Anyway, adamantane is not as regular as cubane, but it is highly symmetrical, looking like three cyclohexanes fused together. The vertices fall into two different types when colored by signature: The carbons with three carbon neighbours (degree-3, in the simple graph) have signature (a) and the degree-2 carbons have signature (b). Atoms of one type are only connected to atoms of another - the graph is bipartite . Adamantane connects together to form diamondoids (or, rather, this class have adamantane as a repeating subunit). One such is diamantane , which is no longer bipartite when colored by signature: It has three classes of vertex in the simple graph (a and b), as the set with degree-3 has been split in two. The tree for signature (c) is not shown. The graph is still bipartite accordin...

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 ...

General Graph Layout : Putting the Parts Together

An essential tool for graph generation is surely the ability to draw graphs. There are, of course, many methods for doing so along with many implementations of them. This post describes one more (or perhaps an existing method - I haven't checked). Firstly, lets divide a graph up into two parts; a) the blocks, also known as ' biconnected components ', and b) trees connecting those blocks. This is illustrated in the following set of examples on 6 vertices: Trees are circled in green, and blocks in red; the vertices in the overlap between two circles are articulation points. Since all trees are planar, a graph need only have planar blocks to be planar overall. The layout then just needs to do a tree layout on the tree bits and some other layout on the embedding of the blocks. One slight wrinkle is shown by the last example in the image above. There are three parts - two blocks and a tree - just like the one to its left, but sharing a single articulation point. I had...

Some Stuff

Search This Blog