cellProperties: Properties of a Unit Cell

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

Properties of a Unit Cell

Description

Compute the Cartesian coordinates of lattice vectors, the volume or the density of a unit cell.

Usage

cell.coords(...)

## Default S3 method:
cell.coords(abc, abg = c(90, 90, 90), digits = 3, ...)

## S3 method for class 'cryst1'
cell.coords(x, digits = 3, ...)

## S3 method for class 'pdb'
cell.coords(x, digits = 3, ...)

cell.volume(...)

## S3 method for class 'cryst1'
cell.volume(x, ...)

## S3 method for class 'pdb'
cell.volume(x, ...)

cell.density(...)

## Default S3 method:
cell.density(masses, volume, ...)

## S3 method for class 'pdb'
cell.density(x, ...)

Arguments

...	further arguments passed to or from other methods.
abc	a length 3 numeric vector containing the length of the a, b and c lattice vectors.
abg	a length 3 numeric vector containing the angles (degrees) between the a, b and c lattice vectors (alpha, beta, gamma).
digits	an integer used to round the lattice vectors coordinates.
x	an R object containing lattice parameters.
masses	a numeric vector containing atomic masses.
volume	a single element numeric vector containing the volume of the unit cell in Angstrom cube.

Details

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’, the unit cell parameters are directly used to compute the volume. For objects of class ‘pdb’, their cryst1 component is used.

cell.density is a generic function to compute the density of a unit cell. For objects of class ‘pdb’: First the volume of the unit cell is calculated by calling the cell.volume function on the cryst1 component of the ‘pdb’ object. Then the element names are converted into element symbols using 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.

Value

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.

See Also

cryst1, pdb, xyz2abc

Examples

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

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