R/mirrorHelpers.R

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

#' Helper Functions for reflection of Atomic Coordinates
#' 
#' Reflection of atomic coordinates with respect to a specific Cartesian plan or
#' a plan defined by two lattice vectors.
#' 
#' 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 \code{mirror} function.
#' 
#' @return An object of the same class as \code{x} with reflected coordinates.
#'   
#' @param x an R object containing atomic coordinates.
#' @param mask a logical vector indicating the set of coordinates to which to
#'   apply the reflection.
#' @param cryst1 an object of class \sQuote{cryst1} use to convert fractional
#'   into Cartesian coordinates when need.
#' @param \dots further arguments passed to or from other methods.
#'   
#' @seealso \code{\link{mirror}} and \code{\link{xyz2abc}},
#' \code{\link{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)
#' 
#' @keywords manip
#' 
#' @name mirrorHelpers
#' @export
Mxy <- function(...)
  UseMethod("Mxy")

#' @rdname mirrorHelpers
#' @export
Mxy.coords <- function(x, mask = TRUE, cryst1 = NULL, ...)
  mirror(x, c(0,0,0), c(1,0,0), c(0,1,0), mask=mask, cryst1=cryst1)

#' @rdname mirrorHelpers
#' @export
Mxy.pdb <- function(x, mask = TRUE, cryst1 = x$cryst1, ...)
  mirror(x, c(0,0,0), c(1,0,0), c(0,1,0), mask=mask, cryst1=cryst1)

#' @rdname mirrorHelpers
#' @export
Myz <- function(...)
  UseMethod("Myz")

#' @rdname mirrorHelpers
#' @export
Myz.coords <- function(x, mask = TRUE, cryst1 = NULL, ...)
  mirror(x, c(0,0,0), c(0,1,0), c(0,0,1), mask=mask, cryst1=cryst1)

#' @rdname mirrorHelpers
#' @export
Myz.pdb <- function(x, mask = TRUE, cryst1 = x$cryst1, ...)
  mirror(x, c(0,0,0), c(0,1,0), c(0,0,1), mask=mask, cryst1=cryst1)

#' @rdname mirrorHelpers
#' @export
Mzx <- function(...)
  UseMethod("Mzx")

#' @rdname mirrorHelpers
#' @export
Mzx.coords <- function(x, mask = TRUE, cryst1 = NULL, ...)
  mirror(x, c(0,0,0), c(0,0,1), c(1,0,0), mask=mask, cryst1=cryst1)

#' @rdname mirrorHelpers
#' @export
Mzx.pdb <- function(x, mask = TRUE, cryst1 = x$cryst1, ...)
  mirror(x, c(0,0,0), c(0,0,1), c(1,0,0), mask=mask, cryst1=cryst1)


#' @rdname mirrorHelpers
#' @export
Mab <- function(...)
  UseMethod("Mab")

#' @rdname mirrorHelpers
#' @export
Mab.coords <- function(x, cryst1, mask = TRUE, ...){
  if(missing(cryst1))
    stop("'cryst1' is required to defined the mirror plan")
  cell <- cell.coords(x, cryst1=cryst1)
  mirror(x, c(0,0,0), cell[,"a"], cell[,"b"], mask=mask, cryst1=cryst1)
}
  
#' @rdname mirrorHelpers
#' @export
Mab.pdb <- function(x, cryst1 = x$cryst1, mask = TRUE, ...){
  if(is.null(cryst1))
    stop("'cryst1' is required to defined the mirror plan")
  cell <- cell.coords(x, cryst1=cryst1)
  mirror(x, c(0,0,0), cell[,"a"], cell[,"b"], mask=mask, cryst1=cryst1)
}

#' @rdname mirrorHelpers
#' @export
Mbc <- function(...)
  UseMethod("Mbc")

#' @rdname mirrorHelpers
#' @export
Mbc.coords <- function(x, cryst1, mask = TRUE, ...){
  if(missing(cryst1))
    stop("'cryst1' is required to defined the mirror plan")
  cell <- cell.coords(x, cryst1=cryst1)
  mirror(x, c(0,0,0), cell[,"b"], cell[,"c"], mask=mask, cryst1=cryst1)
}

#' @rdname mirrorHelpers
#' @export
Mbc.pdb <- function(x, cryst1 = x$cryst1, mask = TRUE, ...){
  if(is.null(cryst1))
    stop("'cryst1' is required to defined the mirror plan")
  cell <- cell.coords(x, cryst1=cryst1)
  mirror(x, c(0,0,0), cell[,"b"], cell[,"c"], mask=mask, cryst1=cryst1)
}

#' @rdname mirrorHelpers
#' @export
Mca <- function(...)
  UseMethod("Mca")

#' @rdname mirrorHelpers
#' @export
Mca.coords <- function(x, cryst1, mask = TRUE, ...){
  if(missing(cryst1))
    stop("'cryst1' is required to defined the mirror plan")
  cell <- cell.coords(x, cryst1=cryst1)
  mirror(x, c(0,0,0), cell[,"c"], cell[,"a"], mask=mask, cryst1=cryst1)
}

#' @rdname mirrorHelpers
#' @export
Mca.pdb <- function(x, cryst1 = x$cryst1, mask = TRUE, ...){
  if(is.null(cryst1))
    stop("'cryst1' is required to defined the mirror plan")
  cell <- cell.coords(x, cryst1=cryst1)
  mirror(x, c(0,0,0), cell[,"c"], cell[,"a"], mask=mask, cryst1=cryst1)
}