basis: The Basis of an Object

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

The Basis of an Object

Description

Functions to get or set the basis of an object containing atomic coordinates.

Usage

basis(x)

## Default S3 method:
basis(x)

basis(x) <- value

## Default S3 replacement method:
basis(x) <- value

## S3 method for class 'pdb'
basis(x)

## S3 replacement method for class 'pdb'
basis(x) <- value

Arguments

x	an R object containing atomic coordinates.
value	a single element character vector use to set the basis of x.

Details

basis and basis<- are respectively generic accessor and replacement functions. The default methods get and set the basis attribute of an object containing atomic coordinates. This attribute indicate the type basis vector used to express atomic coordinates.
value must be equal to "xyz", for Cartesian, or "abc", for fractional coordinates.
The methods for objects of class ‘pdb’ get and set the basis attribute of its atoms component.

Value

For basis:

NULL or a single element character vector. (NULL is given if the object has no basis attribute.)

For basis<-:

the updated object. (Note that the value of basis(x) <- value is that of the assignment, value, not the return value from the left-hand side.)

See Also

coords, atoms, pdb

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
basis(x)
x <- xyz2abc(x)
basis(x)

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