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Filter Data by Wyckoff Symbol

filter_by_wyckoff_symbol.Rd

Filters a data table (e.g., bonds or angles) to include only entries where a specified atom occupies one of the given Wyckoff sites.

Usage

filter_by_wyckoff_symbol(
  data_table,
  atomic_coordinates,
  atom_col,
  wyckoff_symbols
)

Arguments

data_table

A data.table object, such as one produced by minimum_distance or calculate_angles.

atomic_coordinates

A data.table from extract_atomic_coordinates containing WyckoffMultiplicity and WyckoffSymbol columns.

atom_col

A character string specifying the column in data_table that contains the atom labels to filter by (e.g., "Atom1", "CentralAtom").

wyckoff_symbols

A character vector of the full Wyckoff symbols to keep (e.g., c("4c") or c("6c", "16i", "24k")).

Value

A data.table filtered to include only rows where the specified atom occupies one of the desired Wyckoff sites.

Details

This function is designed to facilitate analysis based on crystallographic site symmetry. It is particularly useful for analyzing complex structures like clathrates where different atoms perform distinct structural roles based on their site symmetry.

The function works by:

  1. Creating a full Wyckoff label (e.g., "4c", "24k") by combining the WyckoffMultiplicity and WyckoffSymbol columns from the atomic_coordinates table.

  2. Identifying the parent atom for each entry in the data_table.

  3. Merging this Wyckoff information into the results table.

  4. Filtering to keep only rows where the atom's full Wyckoff label matches one of the symbols provided in the wyckoff_symbols vector.

See also

Other property calculators: calculate_angles(), calculate_distances(), calculate_neighbor_counts(), calculate_weighted_neighbor_counts(), filter_atoms_by_symbol(), filter_by_elements()

Examples

cif_file <- system.file("extdata", "1590946.cif", package = "crystract")
if (file.exists(cif_file)) {
  # 1. Perform a standard analysis to get bond and coordinate tables
  cif_content <- read_cif_files(cif_file)[[1]]
  atoms <- extract_atomic_coordinates(cif_content)
  metrics <- extract_unit_cell_metrics(cif_content)
  sym_ops <- extract_symmetry_operations(cif_content)
  full_cell <- apply_symmetry_operations(atoms, sym_ops, metrics)
  super_cell <- expand_transformed_coords(full_cell)
  dists <- calculate_distances(atoms, super_cell, metrics)
  bonds <- minimum_distance(dists)

  # 2. Mock Wyckoff sites since 1590946 doesn't explicitly declare them
  atoms[, WyckoffSymbol := "c"]
  atoms[, WyckoffMultiplicity := 4]

  print("Original atomic coordinates showing Wyckoff sites:")
  print(atoms[, .(Label, WyckoffSymbol, WyckoffMultiplicity)])

  filtered_bonds <- filter_by_wyckoff_symbol(
    data_table = bonds,
    atomic_coordinates = atoms,
    atom_col = "Atom1",
    wyckoff_symbols = "4c"
  )

  cat("\nNumber of bonds in original table:", nrow(bonds), "\n")
  cat("Number of bonds after filtering for '4c' site:", nrow(filtered_bonds), "\n")
}
#> [1] "Original atomic coordinates showing Wyckoff sites:"
#>     Label WyckoffSymbol WyckoffMultiplicity
#>    <char>        <char>               <num>
#> 1:    Sr1             c                   4
#> 2:    Sr2             c                   4
#> 3:    Si1             c                   4
#> 
#> Number of bonds in original table: 14 
#> Number of bonds after filtering for '4c' site: 14