Extract Atomic Coordinates

Parses atomic site info, including labels, fractional coordinates, occupancies, oxidation states, and thermal parameters. It includes logic to extract oxidation states from both site tags and type loops.

Usage

extract_atomic_coordinates(cif_content, chemical_formula = NA)

Arguments

cif_content

A data.table containing the lines of a CIF file.

chemical_formula

The chemical formula string for validation.

Value

A data.table with atomic coordinate data, or NULL if not found.

See also

Other extractors: extract_chemical_formula(), extract_database_code(), extract_space_group_name(), extract_space_group_number(), extract_structure_type(), extract_symmetry_operations(), extract_unit_cell_metrics()

Examples

cif_path <- system.file("extdata", "1590946.cif", package = "crystract")
if (file.exists(cif_path)) {
  cif_content <- read_cif_files(cif_path)[[1]]
  extract_atomic_coordinates(cif_content)
}
#>     Label TypeSymbol WyckoffSymbol WyckoffMultiplicity OxidationState
#>    <char>     <char>        <char>               <num>          <num>
#> 1:    Sr1       Sr0+          <NA>                  NA             NA
#> 2:    Sr2       Sr0+          <NA>                  NA             NA
#> 3:    Si1       Si0+          <NA>                  NA             NA
#>    ThermalParam Occupancy OccupancyError    x_a   y_b    z_c x_error y_error
#>           <num>     <num>          <num>  <num> <num>  <num>   <num>   <num>
#> 1:           NA         1             NA 0.6529  0.25 0.0769       0       0
#> 2:           NA         1             NA 0.5192  0.25 0.6748       0       0
#> 3:           NA         1             NA 0.2539  0.25 0.1028       0       0
#>    z_error
#>      <num>
#> 1:       0
#> 2:       0
#> 3:       0