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StructureFaces

StructureFaces[structure]⟹faces

given a nucleic acid structure, the function breaks down the structure into a list of faces, each face contains the corresponding loop type and start/end indices in the original structure.

Details

  • The decomposited faces of the structure plays a vital role in thermodynamics calculation, such as entropy/enthalpy/free energy calculation. Each face can be a type of StackingLoop|HairpinLoop|BulgeLoop|InternalLoop|MultipleLoop, more detailed description about the loop definitions can be found in Object[Report,Literature,"id:GmzlKjPkvDR4"]: SantaLucia Jr, J., & Hicks, D. (2004). The thermodynamics of DNA structural motifs. Annu. Rev. Biophys. Biomol. Struct., 33, 415-440.
    • Input
    Output

Examples

Basic Examples  (5)

Faces of simple single stranded structure:

Faces of a slightly more complicated single stranded structure:

Faces of a complicated single stranded structure with multiloops:

Faces of a simple multi-stranded structure:

Faces of a slightly more complicated multi stranded structure:

Additional Examples  (1)

Perfect Binding  (1)

Faces of two perfectly bound strands:

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