Fig. 3
From: Numerical integration methods and layout improvements in the context of dynamic RNA visualization
The initial vertex layout process demonstrated using a sample theoretical RNA molecule. l 1, l 2, l 3, l 4, l 5, and l 6 represent loops while b 1, b 2, b 3, b 4, b 5, b 6, and b 7 represent base pairs. The loops and base pair vertexes are connected via black edges. a The RNA nucleotides are first laid out in a circle. b Each set of nucleotides has its average position calculated, and the vertex corresponding to that set is placed in that average position. Following this step, the iterative process of stabilization begins