wrap: Wrap Atomic Coordinates

In Rpdb: Read, Write, Visualize and Manipulate PDB Files

Wrap Atomic Coordinates

Description

Wraps atomic coordinates using periodic boundary conditions.

Usage

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, ...)

Arguments

x	an R object containing atomic coordinates to be wrapped.
...	further arguments passed to or from other methods.
cryst1	an object of class ‘cryst1’ containing periodic boundary conditions used for wrapping.
factor	a factor used to wrap the atoms by groups.

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.

Value

Return an object of class ‘pdb’ with wrapped atomic coordinates.

See Also

coords, atoms, pdb, cryst1, centres.pdb, xyz2abc

Examples

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)

Rpdb documentation built on Sept. 28, 2023, 5:07 p.m.