Rpdb (version 2.2)

cryst1: Create ‘cryst1’ Object

Description

Create an object of class ‘cryst1’ containing the unit cell parameters and the name of the space group to associate with an object of class ‘pdb’.

Usage

cryst1(...)
"cryst1"(abc, abg = c(90, 90, 90), sgroup = "P1", ...)
is.cryst1(x)

Arguments

...

further arguments passed to or from other methods.

abc

a numeric vector of length 3 containing the norms of the lattice vectors a, b and c.

abg

a numeric vector of length 3 containing the angles between the lattice vectors $\alpha$, $\beta$ and $\gamma$.

sgroup

a character string giving the Hermann-Mauguin symbol of the space group.

x

an R obecjt to be tested.

Value

cryst1 returns a list of class ‘cryst1’ with the following components:

abc

a numeric vector of length 3 containing the norms of the lattice vectors a, b and c.

abg

a numeric vector of length 3 containing the angles between the lattice vectors $\alpha$, $\beta$ and $\gamma$.

sgroup

a character string giving the Hermann-Mauguin symbol of the space group.

is.Cryst1 returns TRUE if x is an object of class ‘cryst1’ and FALSE otherwise.

Details

cryst1 is a generic function to create objects of class ‘cryst1’. The purpose of this class is to store CRYST1 records from PDB files which contain the unit cell parameters and the name of the space group of a molecular system stored in a PDB file. The default method of the cryst1 function create an object of class ‘cryst1’ from its different components, i.e.: abc, abg and sgroup. At least abc has to be specified.

is.cryst1 tests if an object of class ‘cryst1’, i.e. if it has a “class” attribute equal to cryst1.

See Also

cell.coords, pdb

Examples

x <- cryst1(abc = c(10, 10, 10), abg = c(90,90,90), sgroup = "P1")
is.cryst1(x)