Rpdb (version 2.0)

cell.density: Density of a Unit Cell

Description

Compute the density of a unit cell.

Usage

cell.density(...)
## S3 method for class 'default':
cell.density(masses, volume, ...)
## S3 method for class 'pdb':
cell.density(x, ...)

Arguments

...

further arguments passed to or from other methods.

masses

a numeric vector containing atomic masses.

volume

a single element numeric vector containing the volume of the unit cell in Angstrom cube.

x

an object of class pdb containing a cryst1 componant.

Value

• Return a single element numeric vector containing the density of the unit cell in g.cm-3.

Details

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 thecell.volumefunction on thecryst1component of thepdbobject.
• Then the element names are converted into element symbols using thetoSymbolsfunction and their masses are taken from theelementsdata set.
• Finally the density is calculated using the sum of the atomic masses and the volume of the unit cell.

See Also

cryst1, pdb, cell.volume

Examples

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