mirrorHelpers: Helper Functions for reflection of Atomic Coordinates

Description

Reflection of atomic coordinates with respect to a specific Cartesian plan or a plan defined by two lattice vectors.

Usage

Mxy(...)
# S3 method for coords
Mxy(x, mask = TRUE, cryst1 = NULL, ...)
# S3 method for pdb
Mxy(x, mask = TRUE, cryst1 = x$cryst1, ...)
Myz(...)
# S3 method for coords
Myz(x, mask = TRUE, cryst1 = NULL, ...)
# S3 method for pdb
Myz(x, mask = TRUE, cryst1 = x$cryst1, ...)
Mzx(...)
# S3 method for coords
Mzx(x, mask = TRUE, cryst1 = NULL, ...)
# S3 method for pdb
Mzx(x, mask = TRUE, cryst1 = x$cryst1, ...)
Mab(...)
# S3 method for coords
Mab(x, cryst1, mask = TRUE, ...)
# S3 method for pdb
Mab(x, cryst1 = x$cryst1, mask = TRUE, ...)
Mbc(...)
# S3 method for coords
Mbc(x, cryst1, mask = TRUE, ...)
# S3 method for pdb
Mbc(x, cryst1 = x$cryst1, mask = TRUE, ...)
Mca(...)
# S3 method for coords
Mca(x, cryst1, mask = TRUE, ...)
# S3 method for pdb
Mca(x, cryst1 = x$cryst1, mask = TRUE, ...)

Value

An object of the same class as x with reflected coordinates.

Arguments

...: further arguments passed to or from other methods.
x: an R object containing atomic coordinates.
mask: a logical vector indicating the set of coordinates to which to apply the reflection.
cryst1: an object of class ‘cryst1’ use to convert fractional into Cartesian coordinates when need.

Details

These functions are helper functions to perform a reflection with respect to a specific Cartesian plan or a plan defined by two lattice vectors. All of them call the mirror function.

Examples

Run this code

# First lets read a pdb file
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
visualize(x, mode = NULL)

# Mirror operation with respect to the ab-plane
visualize(Mab(x), mode = NULL)
# Mirror operation with respect to the ab-plane for residue 1
visualize(Mab(x, mask = x$atoms$resid == 1), mode = NULL)