xyz2torsion | R Documentation |
Convert cartesian coordinate matrix to torsion angles with
function torsion.pdb
.
xyz2torsion(pdb, xyz, tbl = c("basic", "mainchain", "sidechain", "all", "phi", "psi", paste("chi", 1:5, sep="")), ncore = NULL)
pdb |
A PDB structure object as obtained from |
xyz |
Cartesian coordinates as a Mx(3N) matrix. |
tbl |
Names of torsion angles to calculate. |
ncore |
Number of CPU cores used to do the calculation. By default (NULL), use all detected CPU cores. |
Available values for the argument ‘tbl’ include:
Basic: "phi", "psi", "chi1".
Mainchain: "phi", "psi".
Sidechain: "chi1", "chi2", "chi3", "chi4", "chi5".
All: all of the above.
Each individual angle.
Returns a MxP matrix, where M is the number of frames and P the number of valid torsion angles.
New function from the bio3d package, available at <https://github.com/Grantlab/bio3d/blob/master/new_funs/xyz2torsion.R>
Xin-Qiu Yao
Grant, B.J. et al. (2006) Bioinformatics 22, 2695–2696.
torsion.xyz
, torsion.pdb
pdb <- system.file("rotamer/toy_coordinates.pdb", package= "Bios2cor") trj <- system.file("rotamer/toy_dynamics.dcd", package= "Bios2cor") pdb <- read.pdb(pdb) trj <- read.dcd(trj) #Selecting only "CA" atoms ca.inds <- atom.select(pdb, elety = "CA") #Getting xyz coordinates using fit.xyz form bio3d package xyz <- fit.xyz(fixed = pdb$xyz, mobile = trj,fixed.inds=ca.inds$xyz,mobile.inds=ca.inds$xyz) frames <- seq(from= 1, to= 40, by= 2) #Creating torsion object for side chains using xyz2torsion function from bio3d package tor <- xyz2torsion(pdb, xyz[frames,], tbl = "sidechain", ncore= 1)
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