Analyze the Content of a Single CIF File — analyze_single

The core worker function that orchestrates the analysis pipeline for a single crystal structure's data. It dynamically adjusts supercell size and coordinate sets based on the requested bonding algorithms. For geometric algorithms (Voronoi/CrystalNN), it automatically merges atoms occupying the same site to ensure mathematical validity.

Usage

analyze_single_cif(
  cif_content,
  file_name = NULL,
  perform_extraction = TRUE,
  perform_calcs_and_transforms = TRUE,
  bonding_algorithms = c("minimum_distance"),
  calculate_bond_angles = TRUE,
  perform_error_propagation = TRUE,
  tolerance = 1e-04,
  minimum_distance_delta = 0.1
)

Arguments

cif_content: Either a data.table containing the lines of a CIF file, OR a character string specifying the file path to a CIF file.
file_name: The name of the original CIF file, used for labeling output.
perform_extraction: Logical. If TRUE, extracts all metadata.
perform_calcs_and_transforms: Logical. If TRUE, generates unit cell and supercell.
bonding_algorithms: Character vector. Options: "minimum_distance", "brunner", "econ", "crystal_nn", "voronoi".
calculate_bond_angles: Logical.
perform_error_propagation: Logical.
tolerance: Numeric. Cutoff for floating-point noise and atom merging (default 1e-4).
minimum_distance_delta: Numeric. Tolerance for min-dist algorithm.

Value

A one-row data.table with results.

Examples

cif_path <- system.file("extdata", "1590946.cif", package = "crystract")
if (file.exists(cif_path)) {
  res <- analyze_single_cif(cif_path, perform_error_propagation = FALSE)
}