| #' 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") | |