boyquotes / aurisim Goto Github PK

This is going to be a simulator for 2d folding RNA transcripts. As of now the GUI works as follows. 
Mouse wheel zooms, dragging moves the canvas.
If the mouse cursor is over a position on the grid where a bead can be added, a colored circle appears.

Double clicking adds a bead of the type which is selected in the Bead type drop down list. If there was a bead there already, its 
type is changed.

If the Delete check-button is on, double clicking an existing bead deletes it.

If Follow button is on and a bead is placed, it will be added into a path following the last double clicked bead.

If Bond button is on, then double click adds a bond between the last two beads which were double clicked.

If Fold button is on then double clicking a bead starts to fold the transcript given in the textbox starting from the bead
which was clicked. The transcript has to start with the type of the bead we double click as starting point 
(so, usually, this would mean it starts with the last bead of the seed).

If the Stepwise button is on when folding starts, then beads are placed one-by-one every time the Step button is pressed.
One of the most stable elongations fixing the current bead is drawn with different color.

Load OS loads up a file containing all necessary parameters of an OS. As demo, two files are included, a pyramid construction
and a glider. After selecting the file, the seed is drawn on canvas. Folding the transcript is then done as above.

The Clear canvas button clears all beads, transcript edges and bonds from the canvas.

# Acknowledgment

This work was supported by JSPS Kakenhi Grant Number 18K19779.