Skip to main content

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

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?
Rich Apodaca said…
Interesting idea - what would be some applications?
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.
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.
gilleain said…
See this gist : https://gist.github.com/1023824 for the ring equivalence class code...

Popular posts from this blog

How many isomers of C4H11N are there?

One of the most popular queries that lands people at this blog is about the isomers of C4H11N - which I suspect may be some kind of organic chemistry question on student homework. In any case, this post will describe how to find all members of a small space like this by hand rather than using software.

Firstly, lets connect all the hydrogens to the heavy atoms (C and N, in this case). For example:


Now eleven hydrogens can be distributed among these five heavy atoms in various ways. In fact this is the problem of partitioning a number into a list of other numbers which I've talked about before. These partitions and (possible) fragment lists are shown here:


One thing to notice is that all partitions have to have 5 parts - even if one of those parts is 0. That's not strictly a partition anymore, but never mind. The other important point is that some of the partitions lead to multiple fragment lists - [3, 3, 2, 2, 1] could have a CH+NH2 or an NH+CH2.

The final step is to connect u…

Havel-Hakimi Algorithm for Generating Graphs from Degree Sequences

A degree sequence is an ordered list of degrees for the vertices of a graph. For example, here are some graphs and their degree sequences:



Clearly, each graph has only one degree sequence, but the reverse is not true - one degree sequence can correspond to many graphs. Finally, an ordered sequence of numbers (d1 >= d2 >= ... >= dn > 0) may not be the degree sequence of a graph - in other words, it is not graphical.

The Havel-Hakimi (HH) theorem gives us a way to test a degree sequence to see if it is graphical or not. As a side-effect, a graph is produced that realises the sequence. Note that it only produces one graph, not all of them. It proceeds by attaching the first vertex of highest degree to the next set of high-degree vertices. If there are none left to attach to, it has either used up all the sequence to produce a graph, or the sequence was not graphical.



The image above shows the HH algorithm at work on the sequence [3, 3, 2, 2, 1, 1]. Unfortunately, this produce…

Generating Dungeons With BSP Trees or Sliceable Rectangles

So, I admit that the original reason for looking at sliceable rectangles was because of this gaming stackoverflow question about generating dungeon maps. The approach described there uses something called a binary split partition tree (BSP Tree) that's usually used in the context of 3D - notably in the rendering engine of the game Doom. Here is a BSP tree, as an example:



In the image, we have a sliced rectangle on the left, with the final rectangles labelled with letters (A-E) and the slices with numbers (1-4). The corresponding tree is on the right, with the slices as internal nodes labelled with 'h' for horizontal and 'v' for vertical. Naturally, only the leaves correspond to rectangles, and each internal node has two children - it's a binary tree.

So what is the connection between such trees and the sliceable dual graphs? Well, the rectangles are related in exactly the expected way:


Here, the same BSP tree is on the left (without some labels), and the slicea…