cell.coords(...)
## S3 method for class 'default':
cell.coords(abc, abg = c(90, 90, 90), digits = 3, ...)
## S3 method for class 'cryst1':
cell.coords(x, digits = 3, \dots)
## S3 method for class 'pdb':
cell.coords(x, digits = 3, \dots)cell.volume(...)
## S3 method for class 'cryst1':
cell.volume(x, ...)
## S3 method for class 'pdb':
cell.volume(x, ...)
cell.density(...)
## S3 method for class 'default':
cell.density(masses, volume, ...)
## S3 method for class 'pdb':
cell.density(x, ...)
cell.coords returns a 3x3 matrix containing the Cartesian coordinates of lattice vectors arranged by columns.
cell.volume returns a single element numeric vector containing the volume of the unit cell in Angstrom cube.
cell.density returns a single element numeric vector containing the density of the unit cell in g.cm-3.cell.coords is a generic function which computes a 3x3 matrix whose columns contrain the Cartesian coordinates of lattice vectors.
The 'a' and 'b' vectors are assumed to be respectively along the x-axis and in the xy-plane.
The default method takes directly the lattice parameters as arguments.
For objects of class cryst1 the lattice parameters are first extracted from the object and then the default method is called.
For objects of class pdb the lattice parameters are extracted from their cryst1 component and the default method is called.cell.volume is a generic function to compute the volume of a unit cell.
For objects of class cryst1 component is used.
cell.density is a generic function to compute the density of a unit cell.
For objects of class cell.volume function on the cryst1 component of the toSymbols function and their masses are taken from the elements data set.
Finally the density is calculated using the sum of the atomic masses and the volume of the unit cell.
cryst1, pdb, xyz2abcx <- read.pdb(system.file("examples/PCBM_ODCB.pdb",package="Rpdb"))
cell.volume(x)
cell.density(x)
cell.coords(x)Run the code above in your browser using DataLab