stacker.residue_movement.calculate_bottaro_values_for_frame#
- calculate_bottaro_values_for_frame(perspective_base_coords, viewed_midpoint)[source]#
Calculates the r, rho, and theta values as expressed in the Bottaro paper.
Calculates the r, rho, and theta values between two nucleotides in a single frame as presented in Figure 1 of Bottaro et. al (https://doi.org/10.1093/nar/gku972).
- Parameters:
- perspective_base_coordsBase
List of the x, y, z coords of C2, C4, C6 and their midpoint for the perspective residue in a single frame.
- viewed_midpointVector
x, y, z position of the midpoint of the viewed nucleotide at the same frame.
- Returns:
- list
A list containing 3 floats from Bottaro; structure: [r_dist, rho_dist, theta].
References
[1] Sandro Bottaro, Francesco Di Palma, Giovanni Bussi, The role of nucleobase interactions in RNA structure and dynamics, Nucleic Acids Research, Volume 42, Issue 21, 1 December 2014, Pages 13306–13314, https://doi.org/10.1093/nar/gku972