angles.plot | R Documentation |
Given an object of class 'structure' and names of dihedral angles, creates plots of the dihedral angles as a function of frames in a pdf file.
angles.plot(dynamic_structure, angles, filepathroot=NULL)
dynamic_structure |
Dihedral angle structure, result of the |
angles |
A vector containing the names of the dihedral angles to be visualized.Default is NULL (all the torsional angles of the dynamic_structure object are taken into account). |
filepathroot |
Root of the full path name for the output file. Default is NULL. In this case, the output file is named "ANGLES.pdf". When filepathroot is not NULL, a "_ANGLES.pdf" extention is added to the filepathroot name. |
The object of class 'structure' contains the side chain dihedral angles (between -180 and 180) for each residue in the protein, for each frame of the molecular simulations. This function allows visualisation of the evolution of selected angles.
returns a pdf file containing the plots of the frame dependance of each element included in argument angles
.
Antoine GARNIER and Marie CHABBERT
#Indicating file path for output files wd <- tempdir() #wd <- getwd() file <- file.path(wd,"test_dyn1") #Reading pdb and dcd files pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor") trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor") #Creating dynamic_structure object for wanted frames wanted_frames <- seq(from= 1, to= 40, by= 2) dynamic_structure <- dynamic_structure(pdb, trj, wanted_frames) #Calculating circular correlation between dihedral angles of selected residues wanted_residues <- c("H","N","Q","F","Y","W") dihed_corr <- dynamic_circular(dynamic_structure, wanted_residues) #Selecting a correlation matrix dihed_corr <- dihed_corr$Zscore #Selecting angles of interest (here from the "top_pairs_analysis" function) top_angles <- top_pairs_analysis(dihed_corr, top= 25, file) my_angles <- unlist(top_angles$positions) #Creating plots of the time evolution of the dihedral angles evol_angles <- angles.plot(dynamic_structure, my_angles, file)
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