Eric Rawdon's Triangle Matrix Software Page

Download the code. Also, you need to download key.colors and keyfixed.colors.

This software is written in perl and is released under the GNU General Public License (version 3) as published by the Free Software Foundation.

The usage is: ./squarev4.prl -f rstatsfile -v vertices -o svgoutputfile

You will need to download key.colors and keyfixed.colors. You can put these in the directory from which you run the program or you can put them in your executable folder. If you put everything in an executable folder, change $bindir (near the top of the program) to wherever you place these files, including roundv4.prl. These files define the colors that are used and in that order. You can certainly mess with them. The keyfixed.colors is only useful if you are using very simple knots. Of course, you can hack it to do whatever.

You will need to input the information in what I call an rstats file, an example of which I've included here. The format should be easy to discern. Note that the first two numbers need to be in order. The program only uses the first four columns. The fourth column determines the opacity of the cell coloring.

This program outputs an svg file. I like them because they scale well, seem to be easily converted to other (less space demanding) image formats, and they are human readable. The cells are all labeled by an id which has the information from the first two columns, so it's easy to go find certain cells and change the color or whatever you might want to mess with.

To create the image above (which is for the protein 3bjx), you need 3bjx.rstats and 3bjx.info. Then use
./squarev4.prl -f 3bjx.rstats -v 311 -o 3bjx.svg -i 3bjx.info
That will give you the file 3bjx.svg, which should look like my 3bjx.svg file. You can open this svg file in a text editor and mess around if you wish.

There are a number of other flags that let you mess with the picture.

• -w cutoff
  If you set the cutoff to say 0.4, then any fourth column value under 0.4 will show up as white instead of being colored.
• -i infofile
  I use this mainly for proteins and the data from the PDB oftentimes doesn't start at 1. The infofile is a one line file that says simply what the first vertex (amino acid) number is. An example of an info file is 3bjx.info.
• -t
  Changes the axis labels to "N-terminal aa" and "C-terminal aa".
• -x xaxislabel
  Changes the x-axis label to xaxislabel.
• -y yaxislabel
  Changes the y-axis label to yaxislabel.
• -d edgesperdash
  Changes the number of edges per dash on the x and y axes.
• -b
  Adds a border around the image matrix.
• -h
  Adds a hovering feature. Sometimes I want to see what arc is related to a given cell. With the right browser (which seems to change, used to be chrome, now seems to be firefox), if you open the image and hover or click on a cell, you should see the arc and percentage shown above the graph. You might need to zoom out on your browser to see everything at once. This makes the svg file huger, but can be helpful if you are trying to track down information about a sector.
• -a
  In some versions of my programs, the short data (for subarcs from length 1 to 5 (or 6, can't remember)) aren't in the rstats files. So this is just a way to get those autofilled as unknots. You probably won't need to use this.
• -c
  Uses keyfixed.colors instead of key.colors.
• -n
  Normalizes the data so the opacity is (fourth column)/(maximum value in the fourth column).

The program will create a key on the right. In the svg file, this is near the bottom. You can change information there as needed. You might also need to change the size of the canvas to tighten up or loosen up space on the right side.

This work has been supported by NFS DMS grant numbers 0074315, 0296098, 0311010, 0621903, 0810415, 1115722, and 1418869. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation.