download_structures¶

Download PDB files from RCSB for a list of PDB codes.

Synopsis¶

python scripts/download_structures.py [OPTIONS]

Description¶

Reads a list of four-character PDB codes and fetches the corresponding .pdb files from https://files.rcsb.org/download/. Files that already exist in the output directory are skipped unless --overwrite is set. A configurable delay between requests avoids overloading the RCSB servers.

Options¶

Flag	Default	Description
`--codes-file PATH`	`data/structures/pdb_codes.txt`	Text file with one PDB code per line. Lines beginning with `#` are ignored. Mutually exclusive with `--codes`.
`--codes CODE [CODE ...]`	—	One or more PDB codes supplied directly on the command line. Mutually exclusive with `--codes-file`.
`--output-dir DIR`	`data/structures`	Directory in which to save `.pdb` files. Created automatically if it does not exist.
`--overwrite`	off	Re-download files that already exist.
`--delay SECONDS`	`0.5`	Pause between HTTP requests (seconds).

Examples¶

Download all LeuT transporters to input directory¶

python scripts/download_structures.py \
    --codes-file data/protein_families/LeuT_transporters.txt \
    --output-dir input

Download specific structures¶

python scripts/download_structures.py \
    --codes 3F3A 3F3C 3F3D 3F3E \
    --output-dir input

Re-download with overwrite¶

python scripts/download_structures.py \
    --codes-file data/protein_families/LeuT_transporters.txt \
    --output-dir input \
    --overwrite

Faster downloads (no delay between requests)¶

python scripts/download_structures.py \
    --codes-file data/protein_families/LeuT_transporters.txt \
    --output-dir input \
    --delay 0

Output¶

.pdb files saved to --output-dir with names matching their PDB codes (uppercase)
Example: downloading PDB code 3F3A creates input/3F3A.pdb
Console output reports: success count, failed codes (if any), and HTTP/network errors
Existing files are reported as “skipped” (unless --overwrite is used)

Notes¶

PDB codes are normalized to uppercase internally
Default delay of 0.5 seconds between requests respects RCSB rate limits
Failed downloads are reported at the end but do not stop execution
Files are downloaded from https://files.rcsb.org/download/{CODE}.pdb