Get or set the atomic coordinates (either Cartesian or fractional coordinates) of an object.
coords(...)coords(x) <- value
# S3 method for default
coords(x1, x2, x3, basis = "xyz", ...)
# S3 method for data.frame
coords(x, basis = NULL, ...)
# S3 method for matrix
coords(x, basis = NULL, ...)
# S3 method for atoms
coords(x, ...)
# S3 method for atoms
coords(x) <- value
# S3 method for pdb
coords(x, ...)
# S3 method for pdb
coords(x) <- value
is.coords(x)
The accessor function returns a data.frame of class ‘coords’
whose columns contain the three coordinates of the atoms of a molecular
system. The coordinates can either be Cartesian (basis attribute equal
to "xyz") or fractional coordinates (basis attribute equal to
"abc").
The replacement function returns an object of the same
class as x with updated coordinates.
is.coords returns
TRUE if x is an object of class ‘coords’ and FALSE otherwise
further arguments passed to or from other methods.
an R object containing atomic coordinates.
an object of class ‘coords’ used for replacement
numeric vectors containing the first, second and third coordinates.
a single element character vector indicating the type of basis vector used to express the atomic coordinates.
The purpose of the ‘coords’ class is to store the coordinates of a
molecular system and facilitate their manipulation when passing from the
Cartesian to fractional coordinates and vice versa.
coords and
coords<- are generic accessor and replacement functions.
The
default method of the coords function is actually a builder allowing
to create a ‘coords’ object from its different components, i.e.:
x1, x2, x3, and basis. All the arguments have to
be specified except 'basis' which by default is set to "xyz" (Cartesian
coordinates).
For an object of class ‘atoms’, the accessor
function extracts its x1, x2 and x3 components as well
as its basis attribute to create a ‘coords’ object. The
replacement function set its x1, x2 and x3 components as
well as its basis attribute.
For an object of class
‘pdb’, the accessor function extracts the x1, x2 and
x3 components as well as the basis attribute of its
atoms component to create a ‘coords’ object. The replacement
function set the x1, x2 and x3 components as well as the
basis attribute of its atoms component.
For
‘matrix’ and ‘data.frame’ objects, when basis==NULL this
function search x, y, z or a, b, c columns in x.
If x, y, z columns
are found they are used to a set the first, second and third coordinates of
the returned ‘coords’ object. In that case the basis set of x
is set to "xyz".
If a, b, c columns are found they are used to a
set the first, second and third coordinates of the returned ‘coords’
object. In that case the basis set of x is set to "abc".
If
the function doesn't found neither the x, y, z nor the a, b, c columns an
error is returned.
When basis!=NULL it has to be equal to
"xyz" or "abc" and x must have exactly 3 columns.
is.coords tests if x is an object of class ‘coords’, i.e. if x
has a “class” attribute equal to coords.
basis
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
is.coords(x)
is.coords(x$atoms)
## Replace the coordinates of x by translated coordinates
coords(x) <- coords(Tz(x, 10))
coords(x)
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