Fig. 5

Implementing the ideal position attraction forces causes the stems to align with their ideal layout. a Originally, attraction forces were acting between base pairs, and the loops, attracting the centres of the vertexes directly. b The resulting layout contained artefacts of distorted stems, since base-pairs were unaware of their positions relative to loops. c The idealized attraction forces employ the ideal positions (purple circles) of the stems to attract the base-pair vertexes. d The resulting layout when employing the ideal positions is aware of the position stems should take relative to their parent loops