Reflexion of Atomic Coordinates
Perform a reflexion (or mirror) operation on atomic coordinates with respect to a given reflexion plan.
mirror(...) ## S3 method for class 'coords' mirror(x, p1, p2 = NULL, p3 = NULL, mask = TRUE, cryst1 = NULL, ...) ## S3 method for class 'pdb' mirror(x, p1, p2 = NULL, p3 = NULL, mask = TRUE, cryst1 = x$cryst1, ...)
x |
an R object containing atomic coordinates. |
p1 |
a numeric vector of length 3 containing the coordinates of the
first point defining the reflexion plan. Can also be a 3x3 matrix or
data.frame containing by row |
p2 |
a numeric vector of length 3 containing the coordinates of the second point defining the reflexion plan. |
p3 |
a numeric vector of length 3 containing the coordinates of the thrid point defining the reflexion plan. |
mask |
a logical vector indicating the set of coordinates to which to apply the reflexion. |
cryst1 |
an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need. |
... |
further arguments passed to or from other methods. |
mirror is generic functions. Method for objects of class
‘coords’ first convert the coordinates into Cartesian coordinates
using cryst1 if needed. Once reflected, the coordinates are
reconverted back to the orginal basis set using again cryst1. Method
for objects of class ‘pdb’ first extract coordinates from the object
using the function coords, perform the reflection, and update the
coordinates of the ‘pdb’ object using the function coords<-.
An object of the same class as x with reflected coordinates.
# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
cell <- cell.coords(x)
visualize(x, mode = NULL)
# Mirror operation with respect to the ab-plan
visualize(mirror(x, rep(0,3), p1=cell[,"a"], p2=cell[,"b"]), mode = NULL)
# Mirror operation with respect to the ab-plan for residue 1
visualize(mirror(x, rep(0,3), p1=cell[,"a"], p2=cell[,"b"], mask=x$atoms$resid==1), mode = NULL)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.