Looks up a protein name in the RCSB PDB search API and downloads the best matching legacy PDB file. A 4-character PDB ID can also be supplied directly.
download_pdb(
protein,
out_dir = ".",
filename = NULL,
overwrite = FALSE,
max_results = 10L,
verbose = FALSE
)Arguments
- protein
Protein name or 4-character PDB ID.
- out_dir
Default `"."`. Directory where the PDB file will be written.
- filename
Default `NULL`. Optional output file name. If `NULL`, the downloaded file is named with the matched PDB ID.
- overwrite
Default `FALSE`. Whether to overwrite an existing file.
- max_results
Default `10L`. Maximum number of RCSB search matches to try when downloading a legacy PDB file.
- verbose
Default `FALSE`. If `TRUE`, report the matched PDB ID and destination path.
Value
Path to the downloaded PDB file.
Examples
# Start with a direct PDB ID download. A temporary directory, custom
# filename, overwrite flag, and verbose output make the file handling clear.
pdb_file = download_pdb(
"4fsp",
out_dir = tempdir(),
filename = "outer-membrane-barrel.pdb",
overwrite = TRUE,
verbose = TRUE
)
#> Downloaded RCSB PDB 4FSP for '4fsp' to /tmp/Rtmp0RXH6o/outer-membrane-barrel.pdb
read_pdb(pdb_file, verbose = TRUE) |>
generate_ribbon_scene() |>
render_model(
pathtrace = FALSE,
width = 800,
height = 800,
background = "grey12"
)
#> Read CRYSTAL STRUCTURE OF PSEUDOMONAS AERUGINOSA OCCK11 (OPDR) PDB models [1]
#> PDB ID: 4FSP
#> Experiment: X-RAY DIFFRACTION
#> Parsed: 3135 atoms, 364 residues, 1 chains, 192 bonds
# Protein-name lookup searches RCSB and tries up to three legacy PDB matches.
hemoglobin_file = download_pdb(
"hemoglobin",
out_dir = tempdir(),
max_results = 3L
)
read_pdb(hemoglobin_file, verbose = TRUE) |>
generate_ribbon_scene() |>
render_model(
pathtrace = FALSE,
width = 800,
height = 800,
background = "grey12"
)
#> Read CRYSTAL STRUCTURE OF DOG (CANIS FAMILIARIS) HEMOGLOBIN PDB models [1]
#> PDB ID: 3GOU
#> Experiment: X-RAY DIFFRACTION
#> Parsed: 4618 atoms, 574 residues, 4 chains, 416 bonds
