Wrap Atomic Coordinates
Wraps atomic coordinates using periodic boundary conditions.
wrap(x, ...) ## S3 method for class 'coords' wrap(x, cryst1 = NULL, factor = NULL, ...) ## S3 method for class 'atoms' wrap(x, cryst1 = NULL, factor = NULL, ...) ## S3 method for class 'pdb' wrap(x, cryst1 = x$cryst1, factor = NULL, ...)
x |
an R object containing atomic coordinates to be wrapped. |
cryst1 |
an object of class ‘cryst1’ containing periodic boundary conditions used for wrapping. |
factor |
a factor used to wrap the atoms by groups |
... |
further arguments passed to or from other methods. |
The wrap function translates all atoms out of the unit cell back into
the unit cell using periodic boundary conditions. To do so, the wrap
function first converts Cartesian into fractional coordinates. Then atoms
with fractional coordinates greater than 1 or lower than 0 are respectively
translated by -1 or +1. Finally, if the original atomic coordinates were
Cartesian coordinates their are reconverted into Cartesian coordinates.
Return a object of class ‘pdb’ with wrapped atomic coordinates.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
# Translation of the atoms along x-axis
x$atoms$x1 <- x$atoms$x1 + 10
# Wrapping the structure
y <- wrap(x)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.