AlphaFoldFetch¶

AlphaFoldFetch is a command-line tool for downloading AlphaFold structure files from UniProt IDs and UniProt FASTA files.

It is meant for fast batch workflows:

• download one or many structure in one command
• choose any combination of PDB, CIF, or gzipped outputs
• tune concurrency for larger downloads

CLI Summary¶

affetch [OPTIONS] UNIPROT...

Arguments:

• UNIPROT...: UniProt IDs, FASTA files, or - for stdin

Options:

• --output, -o: output directory
• --file-type, -f: any combination of p, c, and z
• --model, -m: AlphaFold model version 1 through 6
• --n-sync: concurrent download requests
• --n-save: file writes submitted per batch

Input Rules¶

AlphaFoldFetch accepts:

• raw UniProt accessions like P11388
• text that contains a valid UniProt accession
• FASTA files ending in .fasta, .fas, .fa, or .faa
• - to read whitespace-separated input from stdin

FASTA parsing only keeps validated UniProt IDs from header lines.

Output Rules¶

The default file-type value is pcz, which means:

• p: PDB output
• c: CIF output
• z: gzip compression

So the default behavior downloads both PDB and CIF files as gzip outputs.

Examples¶

Single AlphaFold structure

affetch P11388

Multiple AlphaFold structures

affetch P11388 Q01320 P41516

Structures from a single UniProt FASTA file

affetch UP000005640_9606.fasta

Multiple UniProt FASTA files

affetch UP000007305_4577.fasta UP000005640_9606.fasta UP000000625_83333.fasta

Multiple custom FASTA files

affetch plant_pgks.fasta mammalian_pgks.fasta bacterial_pgks.fasta

Unzipped PDB file

affetch -f p P11388

Redirect output to a directory

mkdir human_top2a && affetch -o ./human_top2a P11388

EBI AlphaFold Download data - Search Results CSV File

tail -n +2 results-csv.csv | while IFS='-' read -r f1 f2 f3; do echo $f2; done | affetch -

Don't know the UniProt ID? Use getSequence and pipe into affetch

getseq human top2a, mouse top2a, rat top2a | affetch -