Wraps atomic coordinates using periodic boundary conditions.
Usage
wrap(x, ...)
"wrap"(x, cryst1, factor = NULL, ...)
"wrap"(x, cryst1, factor = NULL, ...)
"wrap"(x, cryst1 = x$cryst1, factor = NULL, ...)
Arguments
x
an R object containing atomic coordinates to be wrapped.
cryst1
an object of class ‘cryst1’ containing periodic boundary conditions used for wrapping.
factor
a factor used to wrap the atoms by groups
...
further arguments passed to or from other methods.
Value
‘pdb’ with wrapped atomic coordinates.
Details
The wrap function translates all atoms out of the unit cell back into the unit cell
using periodic boundary conditions. To do so, the wrap function first converts Cartesian
into fractional coordinates. Then atoms with fractional coordinates greater than 1 or lower
than 0 are respectively translated by -1 or +1. Finally, if the original atomic coordinates
were Cartesian coordinates their are reconverted into Cartesian coordinates.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
# Translation of the atoms along x-axisx$atoms$x1 <- x$atoms$x1 + 10# Wrapping the structurey <- wrap(x)