standardise_sdata: Organise atom data in a standard format for later use

In jfoadi/crone: Structural Crystallography in 1d

Organise atom data in a standard format for later use

Description

Function to put any group consisting of cell size a, space group SG, atom coordinates x0, atomic numbers Z, atomic B factors B and atomic occupancies occ, into a named list with 6 fields. This is then used as standard input/output format throughout the crone package.

Usage

standardise_sdata(a, SG, x0, Z, B, occ)

Arguments

a	Real numeric. Unit cell length in angstroms.
SG	SG 2-letters character string. There are only two symmetries possible when working within 1D crystallography, P1 (no symmetry) and P-1 (inversion through the origin). SG can be either "P1" or "P-1".
x0	Vector of real numerics indicating the expanded atomic positions in the unit cell.
Z	Vector of integers indicating the expanded atomic numbers for all atoms in the unit cell.
B	Vector of real numerics indicating the expanded B factors for all atoms in the unit cell.
occ	Vector of real numerics indicating the expanded occupancies for all atoms in the unit cell.

Value

A named list with the following elements:

• a. Real numeric. Unit cell length in angstroms.

• SG. SG 2-letters character string. There are only two symmetries possible when working within 1D crystallography, P1 (no symmetry) and P-1 (inversion through the origin). SG can be either "P1" or "P-1".

• x0. Vector of real numerics indicating the expanded atomic positions in the unit cell.

• Z. Vector of integers indicating the expanded atomic numbers for all atoms in the unit cell.

• B. Vector of real numerics indicating the expanded B factors for all atoms in the unit cell.

• occ. Vector of real numerics indicating the expanded occupancies for all atoms in the unit cell.

Examples

# Create standard format for an arbitrary structure in P1
a <- 20
SG <- "P1"
x0 <- c(2,11,16,19)
Z <- c(6,6,16,8)
B <- c(13,14,5,10)
occ <- c(1,1,1,1)
sdata <- standardise_sdata(a,SG,x0,Z,B,occ)
print(sdata)

jfoadi/crone documentation built on Sept. 10, 2022, 4:34 p.m.