xyz2abc: From Cartesian to Fractional Coordinates and Vice Versa

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

From Cartesian to Fractional Coordinates and Vice Versa

Description

Converts Cartesian coordinates into fractional coordinates and vice versa.

Usage

xyz2abc(...)

## S3 method for class 'coords'
xyz2abc(x, crystal, ...)

## S3 method for class 'atoms'
xyz2abc(x, crystal, ...)

## S3 method for class 'pdb'
xyz2abc(x, crystal = x$crystal, ...)

## S3 method for class 'distances'
xyz2abc(x, crystal, ...)

abc2xyz(...)

## S3 method for class 'coords'
abc2xyz(x, crystal, ...)

## S3 method for class 'atoms'
abc2xyz(x, crystal, ...)

## S3 method for class 'pdb'
abc2xyz(x, crystal = x$crystal, ...)

## S3 method for class 'distances'
abc2xyz(x, crystal, ...)

Arguments

...	arguments passed to methods.
x	an R object containing atomic coordinates.
crystal	an object of class crystal.

Details

For atoms and pdb objects, the atomic coordinates are first extracted from x using the coords function. Then, the aforementioned functions convert the coordinates using the periodic boundary conditions stored into the crystal field, as follows: The xyz2abc function converts the coordinates from Cartesian to fractional, while abc2xyz function from fractional to Cartesian coordinates. Finally, for atoms and pdb objects, the new atomic coordinates are reassigned to the original x object using the coords<- function, returning this new x.

Value

Return an object of the same class as x, with atomic coordinates expressed in a different basis set.

See Also

basis, coords, atoms, pdb, crystal

Examples

x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
basis(x)
x <- xyz2abc(x)
basis(x)
x <- abc2xyz(x)
basis(x)


  
  # This example returns an error because the coordinates stored
  # into the PDB file are already Cartesian coordinates.
  x <- read.pdb(system.file("examples/PCBM_ODCB.pdb", package="Rpdb"))
  try(x <- abc2xyz(x))

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