natom: Number of Atoms in an Object Containing Atomic Coordinates

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

Number of Atoms in an Object Containing Atomic Coordinates

Description

Evaluates the number of atoms in an object containing atomic coordinates.

Usage

natom(x, ...)

## S3 method for class 'coords'
natom(x, factor = NULL, ...)

## S3 method for class 'atoms'
natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...)

## S3 method for class 'pdb'
natom(x, factor = NULL, ATOM = TRUE, HETATM = TRUE, ...)

Arguments

x	an R object containing atomic coordinates.
...	further arguments passed to or from other methods.
factor	a factor used to split the object and evaluate the number of atoms in each group.
ATOM	a single element logical vector indicating if ATOM records have to be considered or not.
HETATM	a single element logical vector indicating if HETATM records have to be considered or not.

Details

natom is a generic function to evalute the number of atom in an object containing atomic coordinates. The atomic coordinates of the object are first filtered to keep ATOM and/or HETATM records as indicated by the 'ATOM' and 'HETATM' arguments. Then, if factor is specify, the object is splitted to evalute the number of atoms in each group defined by factor. If factor is not specify then the total number of atoms in the object is return.

Value

Return an integer or a vector of integer of lenght equal to nlevels(factor) (if factor is specify) indication the number of atoms in the object or in the groups defined by factor.

See Also

coords, atoms, pdb, factor, split

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))

natom(x)
natom(x, x$atoms$resid)
natom(x, x$atoms$resname)
natom(x, HETATM = FALSE)
  

Rpdb documentation built on Sept. 28, 2023, 5:07 p.m.