Measures a "dynamic entropy" or variability score of each dihedral angle based on the number of rotameric changes during the molecular dynamics trajectory.
A character matrix of type 'rotamers' that is produced by the
The "dynamic entropy" score S is computed by summing the number of rotameric changes over all frames, normalized to the number of frames. It is not a "true entropy" score but gives usefull information on variability of the dihedral angle during the MD simulation.
A numeric vector containing a "dynamic entropy" score for each side chain dihedral angle during the trajectory. The score is comprised between 0 (no change in the rotameric state during the trajectory) and 1 (rotameric change for every frame of the trajectory).
Antoine GARNIER, Lea BELLENGER and Marie CHABBERT
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#Reading pdb and dcd files pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor") trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor") #Reading conversion file conversion_file <- system.file("rotamer/dynameomics_rotamers.csv", package= "Bios2cor") #Creating the dynamic_structure and rotamers objects wanted_frames <- seq(from = 1, t = 40, by = 5) dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames) rotamers <- angle2rotamer(dynamic_structure, conversion_file) #creating the dynamic_entropy object dynamic_entropy <- dynamic_entropy(rotamers)
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