R/read.crd.amber.R

In bio3d: Biological Structure Analysis

read.crd.amber <- function(file, ...) {
  cl <- match.call()

  if(missing(file)) {
    stop("read.pdb: please specify a PDB 'file' for reading")
  }
  
  ##- Check if file exists locally or on-line
  if(!file.exists(file)) {
    stop("No input PDB file found: check filename")
  }
  
  ## parse CRD file with cpp function
  crd <- .read_crd(file)
  if(!is.null(crd$error))
    stop(paste("Could not read", file))
  else
    class(crd) <- c("amber", "crd")

  if(is.na(crd$time))
    crd$time <- NULL
  
  if(!length(crd$velocities)>0)
    crd$velocities <- NULL

  if(!length(crd$box)>0)
    crd$box <- NULL
  
  crd$xyz <- as.xyz(crd$xyz)
  crd$call <- cl
  
  ## finished
  return(crd)
}