distances: Inter-Atomic Distances

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

Inter-Atomic Distances

Description

Computes inter-atomic distance vectors.

Usage

distances(...)

dist.point(...)

## Default S3 method:
distances(
  dx1 = numeric(0),
  dx2 = numeric(0),
  dx3 = numeric(0),
  basis = "xyz",
  ...
)

## S3 method for class 'coords'
distances(x, sel1, sel2, ...)

## S3 method for class 'atoms'
distances(x, sel1, sel2, ...)

## S3 method for class 'connect'
distances(x, data, ...)

## S3 method for class 'pdb'
distances(x, sel1, sel2, ...)

## Default S3 method:
dist.point(data, x, y = NULL, z = NULL, subset = NULL, ...)

is.distances(x)

norm(...)

## S3 method for class 'distances'
norm(x, type = "xyz", ...)

## S3 method for class 'connect'
norm(x, data, type = "xyz", ...)

Arguments

...	further arguments passed to or from other methods.
dx1, dx2, dx3	numeric arrays containing the first, second and third components of the distance vectors.
basis	a single element character vector indicating the type of basis vector used to express the coordinates.
x, y, z	an R object containing atomic coordinates, or a a connect object (for the corresponding method);
sel1, sel2	integer or logical vectors defining two atomic selections between which the distance vectors are computed.
data	an object of type pdb, atoms or coords, containing atomic coordinates.
subset	enables sub-setting the coords object;
type	a single element character vector indicating how to project the distances vectors before computing the norms. See details.

Details

The purpose of the ‘distances’ class is to store the inter-atomic distance vectors and facilitate their manipulation when passing from the Cartesian to fractional references and vice versa.
The default method of the 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. For objects of class ‘connect’, distances are computed for the atoms specified by the ‘connect’ object.

The method for the ‘dist.point’ function computes the inter-atomic distances between the atoms and a specified point.

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:

• x: The distance vectors are projected over x.

• y: The distance vectors are projected over y.

• z: The distance vectors are projected over z.

• xy: The distance vectors are projected in the xy-plan.

• yz: The distance vectors are projected in the yz-plan.

• zx: The distance vectors are projected in the zx-plan.

• xyz: The distance vectors are not projected (The three components of the distance vectors are used to compute the norm).

is.distances tests if x is an object of class ‘distances’; the test is limited to the class attribute.

Value

The distances and dist.point functions 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 been computed, containing the norm of the distance vectors.

is.distances returns TRUE if x is an object of class ‘distances’ and FALSE otherwise.

See Also

coords, basis, xyz2abc, abc2xyz

Examples

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")
d <- dist.point(x, c(0,0,0), subset = is.DCB7)
norm(d, type = "xyz")

Rpdb documentation built on May 12, 2026, 5:06 p.m.