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Organise atom data in a standard format for later use

standardise_sdata.Rd

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)
#> $a
#> [1] 20
#> 
#> $SG
#> [1] "P1"
#> 
#> $x0
#> [1]  2 11 16 19
#> 
#> $Z
#> [1]  6  6 16  8
#> 
#> $B
#> [1] 13 14  5 10
#> 
#> $occ
#> [1] 1 1 1 1
#>