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files.\n\nIt is meant for fast batch workflows:\n\n- download one or many structure in one command\n- choose any combination of PDB, CIF, or gzipped outputs\n- tune concurrency for larger downloads\n\n## Install\n\nRun it without installing:\n\n```bash\nuvx --from AlphaFoldFetch affetch P11388\n```\n\nInstall the CLI with `uv`:\n\n```bash\nuv tool install AlphaFoldFetch\n```\n\n## CLI Summary\n\n```bash\naffetch [OPTIONS] UNIPROT...\n```\n\nArguments:\n\n- `UNIPROT...`: UniProt IDs, FASTA files, or `-` for stdin\n\nOptions:\n\n- `--output`, `-o`: output directory\n- `--file-type`, `-f`: any combination of `p`, `c`, and `z`\n- `--model`, `-m`: AlphaFold model version `1` through `6`\n- `--n-sync`: concurrent download requests\n- `--n-save`: file writes submitted per batch\n\n## Input Rules\n\nAlphaFoldFetch accepts:\n\n- raw UniProt accessions like `P11388`\n- text that contains a valid UniProt accession\n- FASTA files ending in `.fasta`, `.fas`, `.fa`, or `.faa`\n- `-` to read whitespace-separated input from stdin\n\nFASTA parsing only keeps validated UniProt IDs from header lines.\n\n## Output Rules\n\nThe default file-type value is `pcz`, which means:\n\n- `p`: PDB output\n- `c`: CIF output\n- `z`: gzip compression\n\nSo the default behavior downloads both PDB and CIF files as gzip outputs.\n\n### Examples\n\nSingle AlphaFold structure\n```bash\naffetch P11388\n```\n\nMultiple AlphaFold structures\n```bash\naffetch P11388 Q01320 P41516\n```\n\nStructures from a single UniProt FASTA file\n```bash\naffetch UP000005640_9606.fasta\n```\n\nMultiple UniProt FASTA files\n```bash\naffetch UP000007305_4577.fasta UP000005640_9606.fasta UP000000625_83333.fasta\n```\n*First obtain these FASTA files from UniProt*\n\nMultiple custom FASTA files\n```bash\naffetch plant_pgks.fasta mammalian_pgks.fasta bacterial_pgks.fasta\n```\n*Input files must be in the UniProt FASTA file format*\n\nUnzipped PDB file\n```bash\naffetch -f p P11388\n```\n*Default will dowload zipped PDB and CIF files for all entries*\n\nRedirect output to a directory\n```bash\nmkdir human_top2a \u0026\u0026 affetch -o ./human_top2a P11388\n```\n\nEBI AlphaFold Download data - Search Results CSV File\n```bash\ntail -n +2 results-csv.csv | while IFS='-' read -r f1 f2 f3; do echo $f2; done | affetch -\n```\n\nDon't know the UniProt ID? Use [getSequence] and pipe into `affetch`\n```bash\ngetseq human top2a, mouse top2a, rat top2a | affetch -\n```\n*Pipe input arguments must be indicated with a dash `-`*\n\n\nFor more information, read the [docs](https://mansanlab.github.io/alphafoldfetch/)\n\n## Credits\n\nInspired by [getSequence](https://github.com/alexholehouse/getSequence).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmansanlab%2Falphafoldfetch","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmansanlab%2Falphafoldfetch","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmansanlab%2Falphafoldfetch/lists"}