| mirror {Rpdb} | R Documentation |
Reflexion of Atomic Coordinates
Description
Perform a reflexion (or mirror) operation on atomic coordinates with respect to a given reflexion plane.
Usage
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$cryst1, ...)
Arguments
... |
further arguments passed to or from other methods. |
x |
an R object containing atomic coordinates. |
p1 |
a numeric vector of length 3 containing the coordinates of the
first point defining the reflexion plan. Can also be a 3x3 matrix or
data.frame containing by row |
p2 |
a numeric vector of length 3 containing the coordinates of the second point defining the reflexion plane. |
p3 |
a numeric vector of length 3 containing the coordinates of the third point defining the reflexion plane. |
mask |
a logical vector indicating the set of coordinates to which to apply the reflexion. |
cryst1 |
an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need. |
Details
mirror is a generic function. Method for objects of class
‘coords’ first convert the coordinates into Cartesian coordinates
using cryst1 if needed. Once reflected, the coordinates are
reconverted back to the orginal basis set using again cryst1. Method
for objects of class ‘pdb’ first extract coordinates from the object
using the function coords, perform the reflection, and update the
coordinates of the ‘pdb’ object using the function coords<-.
Value
An object of the same class as x with reflected coordinates.
See Also
Helper functions for reflection with respect to a given Cartesian
plane or a plane defined by two lattice vectors:
Mxy,
Myz, Mzx, Mab, Mbc,
Mca
Passing from Cartesian to fractional coordinates (or Vis
Versa):
xyz2abc, abc2xyz
Examples
# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
cell <- cell.coords(x)
visualize(x, mode = NULL)
# Mirror operation with respect to the ab-plane
visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"]), mode = NULL)
# Mirror operation with respect to the ab-plane for residue 1
visualize(mirror(x, rep(0,3), p1=cell[, "a"], p2=cell[, "b"],
mask = x$atoms$resid == 1), mode = NULL)