Nothing
##get.bond.order <- function(bond) {
## stop("Doesn't work at this point")
## if (is.null(attr(bond, 'jclass')) ||
## attr(bond, "jclass") != "org/openscience/cdk/interfaces/IBond") {
## stop("Must supply an IBond object")
## }
##
## bo <- .jcall(bond, "Lorg/openscience/cdk/interfaces/IBond.Order;", "getBondOrder")
## bo
##}
##
#' Get the atom connected to an atom in a bond.
#'
#' This function returns the atom that is connected to a
#' specified in a specified bond. Note that this function assumes
#' 2-atom bonds, mainly because the CDK does not currently
#' support other types of bonds
#'
#' @param bond A \code{jObjRef} representing an `IBond` object
#' @param atom A \code{jObjRef} representing an `IAtom` object
#' @return A \code{jObjRef} representing an `IAtom`` object
#' @seealso \code{\link{get.atoms}}
#' @export
#' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com})
get.connected.atom <- function(bond, atom) {
if (is.null(attr(bond,"jclass")) || is.null(attr(atom,"jclass")))
stop("Must supply an IBond object or Bond")
if (!.check.class(bond, "org/openscience/cdk/interfaces/IBond") &&
!.check.class(bond, "org/openscience/cdk/Bond"))
stop("Must supply an IBond or Bond object")
if (.check.class(bond, "org/openscience/cdk/Bond"))
bond <- .jcast(bond, "org/openscience/cdk/interfaces/IBond")
if (!.check.class(atom, "org/openscience/cdk/interfaces/IAtom") &&
!.check.class(atom, "org/openscience/cdk/Atom"))
stop("Must supply an IAtom or Atom object")
if (.check.class(atom, "org/openscience/cdk/Atom"))
atom <- .jcast(atom, "org/openscience/cdk/interfaces/IAtom")
.jcall(bond, "Lorg/openscience/cdk/interfaces/IAtom;", "getConnectedAtom", atom);
}
#' Get an object representing bond order
#'
#' This function returns a Java enum representing a
#' bond order. This can be used to modify the order
#' of pre-existing bonds
#'
#' @param order A character vector that can be one of single, double, triple,
#' quadruple, quintuple, sextuple or unset. Case is ignored
#' @return A \code{jObjRef} representing an `Order` enum object
#' @export
#' @author Rajarshi Guha (\email{rajarshi.guha@@gmail.com})
#' @examples
#' \dontrun{
#' m <- parse.smiles('CCN')[[1]]
#' b <- get.bonds(m)[[1]]
#' b$setOrder(get.bond.order("double"))
#' }
get.bond.order <- function(order = 'single') {
switch(tolower(order),
single = get("BOND_ORDER_SINGLE", envir = .rcdk.GlobalEnv),
double = get("BOND_ORDER_DOUBLE", envir = .rcdk.GlobalEnv),
triple = get("BOND_ORDER_TRIPLE", envir = .rcdk.GlobalEnv),
quadruple = get("BOND_ORDER_QUADRUPLE", envir = .rcdk.GlobalEnv),
quintuple = get("BOND_ORDER_QUINTUPLE", envir = .rcdk.GlobalEnv),
sextuple = get("BOND_ORDER_SEXTUPLE", envir = .rcdk.GlobalEnv),
unset = get("BOND_ORDER_UNSET", envir = .rcdk.GlobalEnv),
)
}
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