is.distances(x)
distances(...)
"distances"(dx1 = numeric(0), dx2 = numeric(0), dx3 = numeric(0), basis = "xyz", ...)
"distances"(x, sel1, sel2, ...)
"distances"(x, sel1, sel2, ...)
"distances"(x, sel1, sel2, ...)
norm(...)
"norm"(x, type = "xyz", ...)
distance
function return an object of class ‘distances’ containing inter-atomic distance vectors.
The norm
function return an array, with the same dimensions as the dx1
, dx2
, dx3
components of the ‘distances’ object for which the norms have to be computed, containing the norm of the distance vectors.is.distances
returns TRUE if x is an object of class ‘distances’ and FALSE otherwise
distances
function is actually a builder allowing to create a ‘distances’ object from its different components, i.e.: dx1
, dx2
, dx3
, and basis
. All the arguments have to be specified except 'basis' which by default is set to "xyz" (Cartesian reference).For objects of class ‘coords’, ‘atoms’, ‘pdb’, two sets of atomic coordinates, defined by sel1
and sel2
, are extracted and inter-atomic distance vectors are computed between these two sets.
The method of the norm
function for objects of class ‘distances’ computes the norm of the distances vectors. type
specify how to project the distance vectors before computing the norms. By default no projection is perform. The three dx, dy, and dz components of the distance vectors are used to compute the norm. type
can take the following values:
is.distances
tests if x is an object of class ‘distances’, i.e. if x has a “class” attribute equal to distances
.
coords
, basis
, xyz2abc
, abc2xyz
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb")) is.DCB7 <- x$atoms$resname == "DCB" & x$atoms$resid == 7 is.DCB8 <- x$atoms$resname == "DCB" & x$atoms$resid == 8 d <- distances(x, is.DCB7, is.DCB8) norm(d, type = "xyz") norm(d, type = "xy") norm(d, type = "x")