#' Assemble PDBs
#'
#' @param data_path character directory .pdb.gz files are located
#' @param output_path character output .parquet path
#'
#' Write output_path .parquet file with columns
#'   <id> <pdb>
assemble_models <- function(
    data_path,
    output_path) {

    cat(
        "data path: ", data_path, "\n",
        "output path: ", output_path, "\n",
        sep = "")

    file_index <- 1
    models <- list.files(
        path = data_path,
        full.names = TRUE,
        pattern = "*.pdb",
        recursive = TRUE) |>
        purrr::map_dfr(.f = function(path) {
            file_handle <- path |>
                file(open = "rb") |>
                gzcon()

            if( file_index %% 20 == 0) {
                cat("Reading  '", path, "' ", file_index, "\n", sep = "")
            }
            file_index <<- file_index + 1

            lines <- file_handle |> readLines()
            file_handle |> close()

            data.frame(
                name = path |>
                    basename() |>
                    stringr::str_replace("[:]", "|"),
                pdb = lines |> paste0(collapse = "\n"))
        })
    models |> arrow::write_parquet(output_path)
    models
}


assemble_models(
    data_path = "data/AlphaFold_model_PDBs",
    output_path = "intermediate/AlphaFold_model_PDBs.parquet")