From Cartesian to Fractional Coordinates and Vis Versa
Converts Cartesian coordinates into fractional coordinates and vice versa.
xyz2abc(...) ## S3 method for class 'coords' xyz2abc(x, cryst1, ...) ## S3 method for class 'atoms' xyz2abc(x, cryst1, ...) ## S3 method for class 'pdb' xyz2abc(x, cryst1 = x$cryst1, ...) ## S3 method for class 'distances' xyz2abc(x, cryst1, ...) abc2xyz(...) ## S3 method for class 'coords' abc2xyz(x, cryst1, ...) ## S3 method for class 'atoms' abc2xyz(x, cryst1, ...) ## S3 method for class 'pdb' abc2xyz(x, cryst1 = x$cryst1, ...) ## S3 method for class 'distances' abc2xyz(x, cryst1, ...)
x |
an R object containing atomic coordinates. |
cryst1 |
an object of class |
... |
arguments passed to methods. |
For atoms and pdb objects, the atomic coordinates
are first extracted from x using the coords function.
Then, using the periodic boundary conditions stored into cryst1, the
coordinates are converted from Cartesian to fractional (for the
xyz2abc functions) or from fractional to Cartesian (for the
abc2xyz functions) coordinates. Finally, for atoms and
pdb objects, the new atomic coordinates are reassigned to the
original x object using the coords<- function and
x is returned.
Return an object of the same class as x, with atomic
coordinates expressed in a different basis set.
x <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
basis(x)
x <- xyz2abc(x)
basis(x)
x <- abc2xyz(x)
basis(x)
## Not run:
# This example return 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"))
x <- abc2xyz(x)
## End(Not run)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.