mirrorHelpers: Helper Functions for reflection of Atomic Coordinates

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

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 class 'coords'
Mxy(x, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Mxy(x, mask = TRUE, cryst1 = x$cryst1, ...)

Myz(...)

## S3 method for class 'coords'
Myz(x, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Myz(x, mask = TRUE, cryst1 = x$cryst1, ...)

Mzx(...)

## S3 method for class 'coords'
Mzx(x, mask = TRUE, cryst1 = NULL, ...)

## S3 method for class 'pdb'
Mzx(x, mask = TRUE, cryst1 = x$cryst1, ...)

Mab(...)

## S3 method for class 'coords'
Mab(x, cryst1, mask = TRUE, ...)

## S3 method for class 'pdb'
Mab(x, cryst1 = x$cryst1, mask = TRUE, ...)

Mbc(...)

## S3 method for class 'coords'
Mbc(x, cryst1, mask = TRUE, ...)

## S3 method for class 'pdb'
Mbc(x, cryst1 = x$cryst1, mask = TRUE, ...)

Mca(...)

## S3 method for class 'coords'
Mca(x, cryst1, mask = TRUE, ...)

## S3 method for class 'pdb'
Mca(x, cryst1 = x$cryst1, mask = TRUE, ...)

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.

Value

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

See Also

mirror and xyz2abc, abc2xyz for passing from Cartesian to fractional coordinates (or Vis Versa).

Examples

# 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)

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