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CLI Reference

This section documents all available CLI commands.

protein-quest COMMAND

Protein Quest CLI

Table of Contents

Commands:

protein-quest --install-completion

protein-quest --install-completion [OPTIONS]

Install shell completion for this application.

This command generates and installs the completion script to the appropriate location for your shell. After installation, you may need to restart your shell or source your shell configuration file.

Parameters:

  • --shell: Shell type for completion. If not specified, attempts to auto-detect current shell. [choices: zsh, bash, fish]
  • --output, -o: Output path for the completion script. If not specified, uses shell-specific default.

Search data sources

protein-quest search uniprot

protein-quest search uniprot [OPTIONS] OUTPUT

Search for UniProt accessions.

Search for UniProt accessions based on various criteria in the Uniprot SPARQL endpoint.

Arguments:

  • OUTPUT: Output text file for UniProt accessions (one per line). Use - for stdout. [required]

Parameters:

  • --taxon-id: NCBI Taxon ID to filter results by organism (for example 9606 for human).
  • --reviewed, --no-reviewed: Whether to filter results by reviewed status (True for reviewed, False for unreviewed).
  • --subcellular-location-uniprot: Subcellular location in UniProt format (for example "nucleus").
  • --subcellular-location-go: Subcellular location in GO format. Can be a single GO term (for example, ["GO:0005634"]) or a collection of GO terms (for example, ["GO:0005634", "GO:0005737"]), which are searched with OR logic.
  • --molecular-function-go: Molecular function in GO format. Can be a single GO term (for example, ["GO:0003674"]) or a collection of GO terms (for example, ["GO:0003674", "GO:0008150"]), which are searched with OR logic.
  • --min-sequence-length: Minimum length of the canonical sequence.
  • --max-sequence-length: Maximum length of the canonical sequence.
  • --limit: Maximum number of uniprot accessions to return. [default: 10000]
  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search pdbe

protein-quest search pdbe [OPTIONS] UNIPROT_ACCESSIONS OUTPUT_CSV

Search for PDB structures of given UniProt accessions.

Search for PDB structures of given UniProt accessions in the Uniprot SPARQL endpoint.

Arguments:

  • UNIPROT_ACCESSIONS: Text file with UniProt accessions (one per line). Use - for stdin. [required]
  • OUTPUT_CSV: Output CSV with following columns: uniprot_accession, pdb_id, method, resolution, uniprot_chains, chain, chain_length. Where uniprot_chains is the raw UniProt chain string, for example A=1-100. And where chain is the first chain from uniprot_chains, for example A. And chain_length is the length of the chain, for example 100 or '' if it could not be determined. Use - for stdout. The chain ids returned are in 'auth' chain id system. [required]

Parameters:

  • --limit: Maximum number of PDB uniprot accessions combinations to return. [default: 10000]
  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]
  • --min-residues: Minimum number of residues required in the chain mapped to the UniProt accession.
  • --max-residues: Maximum number of residues allowed in chain mapped to the UniProt accession.
  • --keep-invalid: Keep PDB results when chain length could not be determined. [default: False]
  • --top-resolution-per-uniprot-accession: Retain the top N PDB entries per UniProt accession, ranked by best (lowest) resolution first, then by highest residue count. For example use --top-resolution-per-uniprot-accession 3 to keep only the best 3 PDB entries per UniProt accession.

  • --top-clustered-resolution-per-uniprot-accession: Retain the top N PDB entries per UniProt accession cluster. Uses clustering to give better coverage.

    See clustering documentation for details on the clustering and ordering criteria.

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search pdbe-quality

protein-quest search pdbe-quality [OPTIONS] PDBE_CSV QUALITY_JSON

Search for quality scores of PDBe entries.

Search for validation summary quality scores of PDBe entries in the PDBe REST API.

Arguments:

  • PDBE_CSV: CSV file with a pdb_id column, or with model_provider and model_identifier columns. When using model_provider, only rows with model_provider == 'pdbe' are used. Single-column CSV files are also accepted, and the first row is treated as an ID. Use - for stdin. [required]
  • QUALITY_JSON: Output JSON file with quality scores for PDBe entries. Use - for stdout. [required]

Parameters:

  • --batch-size: Number of PDB IDs to query in each batch request to the PDBe REST API. [default: 100]
  • --timeout: Maximum seconds to wait for single batch request. [default: 1800]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search alphafold

protein-quest search alphafold [OPTIONS] UNIPROT_ACCESSIONS OUTPUT_CSV

Search for AlphaFold structures of given UniProt accessions.

Search for AlphaFold structures of given UniProt accessions in the Uniprot SPARQL endpoint.

Arguments:

  • UNIPROT_ACCESSIONS: Text file with UniProt accessions (one per line). Use - for stdin. [required]
  • OUTPUT_CSV: Output CSV with AlphaFold IDs per UniProt accession. CSV has columns: uniprot_accession, af_id. Use - for stdout. [required]

Parameters:

  • --min-sequence-length: Minimum length of the canonical sequence.
  • --max-sequence-length: Maximum length of the canonical sequence.
  • --limit: Maximum number of Alphafold entry identifiers to return. [default: 10000]
  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search structure

protein-quest search structure [OPTIONS] UNIPROT_ACCESSIONS OUTPUT_CSV

Search for experimentally determined and predicted structures.

Search for experimentally determined and predicted structures of given UniProt accessions in the 3D Beacons Network API.

Arguments:

  • UNIPROT_ACCESSIONS: Text file with UniProt accessions (one per line). Use - for stdin. [required]
  • OUTPUT_CSV: Output CSV with following columns: uniprot_accession, provider, model_identifier, model_url, model_format, chain, residue_count. The chain values are in 'auth' chain id system. Use - for stdout. [required]

Parameters:

  • --source: Source of the structures to search for. Default pdbe and alphafold. Multiple sources can be given by repeating the --source parameter. Use 'all' to search all sources. [choices: pdbe, ped, swissmodel, alphafold, sasbdb, alphafill, hegelab, modelarchive, isoformio, levylab, all]
  • --min-residues: Minimum number of residues required in the chain mapped to the UniProt accession.
  • --max-residues: Maximum number of residues allowed in the chain mapped to the UniProt accession.
  • --limit: Maximum number of structures per uniprot accession per source to return. [default: 10000]
  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]
  • --raw: Path to write raw 3D beacon summaries as JSON.

  • --top-clustered-resolution-per-uniprot-accession: Retain the top N PDBe entries per UniProt accession cluster. Uses clustering to give better coverage. Non-PDBe structures (e.g. AlphaFold, SWISS-MODEL) are always retained..

    See clustering documentation for details on the clustering and ordering criteria.

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search emdb

protein-quest search emdb [OPTIONS] UNIPROT_ACCESSIONS OUTPUT_CSV

Search for EMDB identifiers of given UniProt accessions.

Search for Electron Microscopy Data Bank (EMDB) identifiers of given UniProt accessions in the Uniprot SPARQL endpoint.

Arguments:

  • UNIPROT_ACCESSIONS: Text file with UniProt accessions (one per line). Use - for stdin. [required]
  • OUTPUT_CSV: Output CSV with EMDB IDs per UniProt accession. CSV has columns: uniprot_accession, emdb_id. Use - for stdout. [required]

Parameters:

  • --limit: Maximum number of EMDB entry identifiers to return. [default: 10000]
  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search go

protein-quest search go [OPTIONS] TERM OUTPUT_CSV

Search for Gene Ontology (GO) terms.

Search for Gene Ontology (GO) terms in the EBI QuickGO API.

Arguments:

  • TERM: GO term to search for. For example apoptosome. [required]
  • OUTPUT_CSV: Output CSV with GO term results. CSV has columns: term, id, name, aspect, definition. Use - for stdout. [required]

Parameters:

  • --aspect: Filter on aspect. [choices: cellular_component, biological_process, molecular_function]
  • --limit: Maximum number of GO term results to return. [default: 100]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search taxonomy

protein-quest search taxonomy [OPTIONS] QUERY OUTPUT_CSV

Search for taxon information in UniProt.

Search for taxon information in UniProt. Uses https://www.uniprot.org/taxonomy?query=*.

Arguments:

  • QUERY: Search query for the taxon. Surround multiple words with quotes. [required]
  • OUTPUT_CSV: Output CSV with taxonomy results. CSV has columns: tax_id, name, rank, parent_tax_id, parent_tax_name. Use - for stdout. [required]

Parameters:

  • --field: Field to search in. If not given then searches all fields. If "tax_id" then searches by taxon ID. If "parent" then given a parent taxon ID returns all its children. [choices: tax_id, scientific, common, parent]
  • --limit: Maximum number of results to return. [default: 100]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search interaction-partners

protein-quest search interaction-partners [OPTIONS] UNIPROT_ACCESSION OUTPUT_CSV

Search for interaction partners of given UniProt accession.

Search for interaction partners of given UniProt accession in the Uniprot SPARQL endpoint and Complex Portal.

Arguments:

  • UNIPROT_ACCESSION: UniProt accession (for example P12345). [required]
  • OUTPUT_CSV: Output CSV with interaction partners per UniProt accession. CSV has columns: uniprot_accession. Use - for stdout. [required]

Parameters:

  • --exclude: UniProt accessions to exclude from the results. Multiple accessions can be given by repeating the --exclude option.
  • --limit: Maximum number of interaction partner uniprot accessions to return. [default: 10000]
  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search complexes

protein-quest search complexes [OPTIONS] UNIPROT_ACCESSIONS OUTPUT_CSV

Search for complexes in the Complex Portal.

Search for complexes in the Complex Portal (https://www.ebi.ac.uk/complexportal/).

The output CSV file has the following columns:

  • query_protein: UniProt accession used as query
  • complex_id: Complex Portal identifier
  • complex_url: URL to the Complex Portal entry
  • complex_title: Title of the complex
  • members: Semicolon-separated list of UniProt accessions of complex members

Arguments:

  • UNIPROT_ACCESSIONS: Text file with UniProt accessions (one per line) as query. Use - for stdin. [required]
  • OUTPUT_CSV: Output CSV file with complex results. Use - for stdout. [required]

Parameters:

  • --limit: Maximum number of complex results to return. [default: 100]
  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest search uniprot-details

protein-quest search uniprot-details [OPTIONS] UNIPROT_ACCESSIONS OUTPUT_CSV

Search for UniProt details for given UniProt accessions from the UniProt SPARQL endpoint.

The output CSV file has the following columns:

  • uniprot_accession: UniProt accession.
  • uniprot_id: UniProt ID (mnemonic).
  • sequence_length: Length of the canonical sequence.
  • reviewed: Whether the entry is reviewed (Swiss-Prot) or unreviewed (TrEMBL).
  • protein_name: Recommended protein name.
  • taxon_id: NCBI Taxonomy ID of the organism.
  • taxon_name: Scientific name of the organism.

The order of the output CSV can be different from the input order.

Arguments:

  • UNIPROT_ACCESSIONS: Text file with UniProt accessions (one per line). Use - for stdin. [required]
  • OUTPUT_CSV: Output CSV with UniProt details. CSV has columns: uniprot_accession, uniprot_id, sequence_length, reviewed, protein_name, taxon_id, taxon_name. Use - for stdout. [required]

Parameters:

  • --timeout: Maximum seconds to wait for query to complete. [default: 1800]
  • --batch-size: Number of accessions to query per batch. [default: 1000]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest retrieve

Retrieve structure files

protein-quest retrieve pdbe

protein-quest retrieve pdbe [OPTIONS] PDBE_CSV OUTPUT_DIR

Retrieve mmCIF files from PDBe for PDB IDs in CSV.

Retrieve mmCIF files from Protein Data Bank in Europe Knowledge Base (PDBe) website for unique PDB IDs listed in a CSV file.

Arguments:

  • PDBE_CSV: CSV file with a pdb_id column, or with model_provider and model_identifier columns. When using model_provider, only rows with model_provider == 'pdbe' are used. Single-column CSV files are also accepted, and the first row is treated as an ID. Use - for stdin. [required]
  • OUTPUT_DIR: Directory to store downloaded PDBe mmCIF files. [required]

Parameters:

  • --archived: Retrieve archived versions. By default downloads an updated version of the PDB archive mmCIF format file. The updated version is generated with standardisation of vocabularies, and addition of connectivity information for every chemical compound present in the PDB entry. [default: False]
  • --max-parallel-downloads: Maximum number of parallel downloads. [default: 5]

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest retrieve alphafold

protein-quest retrieve alphafold [OPTIONS] ALPHAFOLD_CSV OUTPUT_DIR

Retrieve AlphaFold files for IDs in CSV.

Retrieve AlphaFold files from the AlphaFold Protein Structure Database.

Arguments:

  • ALPHAFOLD_CSV: CSV file with an af_id column, or with model_provider and model_identifier columns. When using model_provider, only rows with model_provider == 'alphafold' are used. Single-column CSV files are also accepted, and the first row is treated as an ID. Use - for stdin. [required]
  • OUTPUT_DIR: Directory to store downloaded AlphaFold files. [required]

Parameters:

  • --format: Formats to retrieve. Defaults to [cif]. Repeat parameter for multiple formats, for example --format cif --format pdb. [choices: summary, bcif, cif, pdb, paeDoc, amAnnotations, amAnnotationsHg19, amAnnotationsHg38, msa, plddtDoc]
  • --db-version: AlphaFold database version.
  • --gzip-files: Gzip downloaded files. [default: False]
  • --all-isoforms: Return all isoforms. [default: False]
  • --max-parallel-downloads: Maximum number of parallel downloads. [default: 5]

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest retrieve emdb

protein-quest retrieve emdb [OPTIONS] EMDB_CSV OUTPUT_DIR

Retrieve EMDB volume files for EMDB IDs in CSV.

Retrieve volume files from Electron Microscopy Data Bank (EMDB) website for unique EMDB IDs listed in a CSV file.

Arguments:

  • EMDB_CSV: CSV file with emdb_id column. Other columns are ignored. Single-column CSV files are also accepted, and the first row is treated as an ID. Use - for stdin. [required]
  • OUTPUT_DIR: Directory to store downloaded EMDB volume files. [required]

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest retrieve structure

protein-quest retrieve structure [OPTIONS] STRUCTURES_CSV OUTPUT_DIR

Retrieve structure files from search structure CSV output.

Retrieve structure files from model URLs listed in search structure CSV output.

Arguments:

  • STRUCTURES_CSV: CSV file with provider, model_identifier, model_url, and model_format columns. Use - for stdin. [required]
  • OUTPUT_DIR: Directory to store retrieved structure files. [required]

Parameters:

  • --raw: Download in native format from CSV. [default: False]
  • --max-parallel-downloads: Maximum number of parallel downloads. [default: 5]

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest filter

Filter files

protein-quest filter confidence

protein-quest filter confidence [OPTIONS] INPUT_DIR OUTPUT_DIR

Filter AlphaFold mmcif/PDB files by confidence (plDDT).

Filter AlphaFold mmcif/PDB files by confidence (plDDT). Passed files are written with residues below threshold removed.

Arguments:

  • INPUT_DIR: Directory with AlphaFold mmcif/PDB files. [required]
  • OUTPUT_DIR: Directory to write filtered mmcif/PDB files. [required]

Parameters:

  • --confidence: The confidence threshold for filtering residues. Residues with a pLDDT (b-factor) above this value are considered high confidence. [default: 70.0]
  • --min-residues: The minimum number of high-confidence residues required to keep the structure. [default: 0]
  • --max-residues: The maximum number of high-confidence residues required to keep the structure. [default: 10000000]
  • --write-stats: Write filter statistics to file. In CSV format with <input_file>,<residue_count>,<passed>,<output_file> columns. Use - for stdout.
  • --scheduler-address: Address of the Dask scheduler to connect to. If not provided, will create a local cluster. If set to sequential will run tasks sequentially.

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest filter chain

protein-quest filter chain [OPTIONS] CHAINS INPUT_DIR OUTPUT_DIR

Filter on chain.

For each input PDB/mmCIF and chain combination write a PDB/mmCIF file with just the given chain and rename it to chain A. Filtering is done in parallel using a Dask cluster.

Arguments:

  • CHAINS: CSV file with pdb_id and chain columns. Other columns are ignored. [required]
  • INPUT_DIR: Directory with PDB/mmCIF files. Expected filenames are {pdb_id}.cif.gz, {pdb_id}.cif, {pdb_id}.pdb.gz or {pdb_id}.pdb. [required]
  • OUTPUT_DIR: Directory to write the single-chain PDB/mmCIF files. Output files are in same format as input files. [required]

Parameters:

  • --chain-system: System of chain ids in the input CSV. Set to 'label' to use chain ids assigned by PDB. See docs for more information on chain id system. [choices: auth, label] [default: auth]
  • --scheduler-address: Address of the Dask scheduler to connect to. If not provided, will create a local cluster. If set to sequential will run tasks sequentially.
  • --force: If not set and given chain exists and is only one, then file is copied unchanged. If set always rewrites and overwrites output files. [default: False]

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest filter residue

protein-quest filter residue [OPTIONS] INPUT_DIR OUTPUT_DIR

Filter PDB/mmCIF files by number of residues in chain A.

Filter PDB/mmCIF files by number of residues in chain A.

Arguments:

  • INPUT_DIR: Directory with PDB/mmCIF files (for example from 'filter chain'). [required]
  • OUTPUT_DIR: Directory to write filtered PDB/mmCIF files. Files are copied without modification. [required]

Parameters:

  • --min-residues: Min residues in chain A. [default: 0]
  • --max-residues: Max residues in chain A. [default: 10000000]
  • --write-stats: Write filter statistics to file. In CSV format with <input_file>,<residue_count>,<passed>,<output_file> columns. Use - for stdout.

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest filter resolution

protein-quest filter resolution [OPTIONS] INPUT_DIR OUTPUT_DIR

Filter structure files by best resolution.

  • Structures with no resolution and no Uniprot accession are discarded.
  • Structures with lower resolution are preferred.
  • If resolution is the same, structures with more residues are preferred.
  • If resolution is missing, those structures are undesirable.
  • Structures with low sequence identity (smaller than 1) are undesirable.
  • Structures are grouped by Uniprot accession and then clustered by their coverage of the Uniprot sequence (can be disabled with --no-group-by-uniprot-accession and --no-coverage).

To see how clustering was done use protein-quest convert clusters command.

Arguments:

  • INPUT_DIR: Directory structure files. [required]
  • OUTPUT_DIR: Directory to write the selected structure files. [required]

Parameters:

  • --no-group-by-uniprot-accession: Disable grouping by Uniprot accession and use global top-N ranking across all files. [default: False]
  • --top: Maximum number of files to keep. [default: 1000]
  • --no-coverage: If not set, will take top by first grouping by uniprot accession and then clustering files by their coverage and then take the top. See clustering documentation for details on the clustering and ordering criteria. If set will sort files per Uniprot accession by just their resolution. [default: False]
  • --min-sequence-identity: Minimum sequence identity ratio to the Uniprot sequence for a structure to be passed. If not set then discards structures that are not fully identical to the Uniprot sequence. For example if set to 0.8 then structures that have sequence identity below 0.8 are discarded. [default: 1.0]
  • --lax: If set will passthrough files that do not have valid resolution, regardless of other flags like --top. By default filter is applied strictly and those files are discarded. Useful if you have a directory with files from different sources/methods and want to call multiple filters sequentially to discard files gradually. [default: False]
  • --scheduler-address: Address of the Dask scheduler to connect to. If not provided, will create a local cluster. If set to sequential will run tasks sequentially.
  • --write-stats: Write filter statistics to file. In CSV format with columns: <input_file>,<id>,<uniprot_accession>,<resolution>,<total_residue_count>,<is_alphafold>,<uniprot_start>,<uniprot_end>,<sequence_identity>,<chain_length>,<passed>,<output_file>,<discard_reason>,<discard_reason_type>. Use - for stdout.

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest filter pdbe-quality

protein-quest filter pdbe-quality [OPTIONS] INPUT_DIR QUALITY_JSON OUTPUT_DIR

Filter PDB/mmCIF files by PDBe quality scores.

Arguments:

  • INPUT_DIR: Directory with PDB/mmCIF files. [required]
  • QUALITY_JSON: JSON file with PDBe quality scores. Can be made with protein-quest search pdbe-quality command. [required]
  • OUTPUT_DIR: Directory to write filtered PDB/mmCIF files. Files are copied without modification. [required]

Parameters:

  • --minimal-geometry-quality: Minimal geometry quality score to pass the filter. [default: 50.0]
  • --top: Maximum number of structures to keep, ranked by geometry quality (best first). When used with --cluster-by-uniprot-accession-and-coverage, applies only to structures without a UniProt accession; the per-cluster limit is controlled separately by --cluster-by-uniprot-accession-and-coverage. If not given, all structures that meet the quality threshold are kept.
  • --cluster-by-uniprot-accession-and-coverage: Number of top structures to keep per UniProt cluster. Structures are grouped by UniProt accession, then clustered by residue-range overlap. [default: 0]
  • --pass-given-resolution: If set will passthrough files that have a valid resolution. [default: False]
  • --scheduler-address: Address of the Dask scheduler to connect to. If not provided, will create a local cluster. If set to sequential will run tasks sequentially.
  • --write-stats: Write filter statistics to file. In CSV format with columns: <pdb_id>,<input_file>,<geometry_quality>,<passed>,<output_file>,<reason>. Use - for stdout.

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest filter secondary-structure

protein-quest filter secondary-structure [OPTIONS] INPUT_DIR OUTPUT_DIR

Filter PDB/mmCIF files by secondary structure.

Filter PDB/mmCIF files by secondary structure.

Arguments:

  • INPUT_DIR: Directory with PDB/mmCIF files. [required]
  • OUTPUT_DIR: Directory to write filtered PDB/mmCIF files. Files are copied without modification. [required]

Parameters:

  • --abs-min-helix-residues: Minimum number of residues in helices (absolute).
  • --abs-max-helix-residues: Maximum number of residues in helices (absolute).
  • --abs-min-sheet-residues: Minimum number of residues in sheets (absolute).
  • --abs-max-sheet-residues: Maximum number of residues in sheets (absolute).
  • --ratio-min-helix-residues: Minimum helix residue ratio (fraction from 0 to 1).
  • --ratio-max-helix-residues: Maximum helix residue ratio (fraction from 0 to 1).
  • --ratio-min-sheet-residues: Minimum sheet residue ratio (fraction from 0 to 1).
  • --ratio-max-sheet-residues: Maximum sheet residue ratio (fraction from 0 to 1).
  • --write-stats: Write filter statistics to file. In CSV format with columns: <input_file>,<nr_residues>,<nr_helix_residues>,<nr_sheet_residues>, <helix_ratio>,<sheet_ratio>,<passed>,<output_file>. Use - for stdout.

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest filter combined

protein-quest filter combined [OPTIONS] INPUT_DIR QUALITY_JSON OUTPUT_DIR

Filter PDB/mmCIF files using a combination of filters.

This command is a combination of the protein-quest filter confidence, protein-quest filter residue, protein-quest filter resolution, and protein-quest filter pdbe-quality commands. As each of those commands accepts a certain source/method of structures. This command accepts all sources/methods of structures and applies the appropriate filters to each.

For details about filtering see the documentation.

Arguments:

  • INPUT_DIR: Directory with PDB/mmCIF files. [required]
  • QUALITY_JSON: JSON file with PDBe quality scores. Can be made with protein-quest search pdbe-quality command. [required]
  • OUTPUT_DIR: Directory to write filtered PDB/mmCIF files. Files are copied without modification. [required]

Parameters:

  • --min-confidence: Minimal confidence (plDDT) for AlphaFold structures to pass the filter. [default: 70.0]
  • --min-residues: Min residues in chain A. [default: 0]
  • --max-residues: Max residues in chain A. [default: 10000000]
  • --min-geometry-quality: Minimal geometry quality score to pass the filter. [default: 50.0]
  • --min-sequence-identity: Minimum sequence identity ratio to the Uniprot sequence for a structure to be passed. If not set then discards structures that are not fully identical to the Uniprot sequence. For example if set to 0.8 then structures that have sequence identity below 0.8 are discarded. [default: 1.0]
  • --top-uniprot-cluster: Maximum number of files to keep for structures per cluster per Uniprot accession. Alphafold structures are excluded from this limit. [default: 1000]
  • --top-non-uniprot: Maximum number of files to keep for structures without Uniprot accession. [default: 0]
  • --write-stats: Write filter statistics to file. In CSV format with columns: <input_file>,<pdb_id>,<uniprot_accession>,<resolution>,<high_confidence_residues_count>,<total_residue_count>, <method>,<is_alphafold>,<uniprot_start>,<uniprot_end>,<sequence_identity>,<chain_length> ,<geometry_quality>,<passed>,<output_file>,<reason> columns for resolution filtering. Depending on filter way some column can be empty. Use - for stdout.
  • --scheduler-address: Address of the Dask scheduler to connect to. If not provided, will create a local cluster. If set to sequential will run tasks sequentially.

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest convert

Convert files between formats

protein-quest convert uniprot

protein-quest convert uniprot [OPTIONS] INPUT_DIR OUTPUT

Convert structure files to list of UniProt accessions.

UniProt accessions are read from database reference of each structure.

Arguments:

  • INPUT_DIR: Directory with structure files. Supported extensions are .cif, .cif.gz, .pdb, .pdb.gz. [required]
  • OUTPUT: Output text file with UniProt accessions (one per line). Use '-' for stdout. [required]

Parameters:

  • --grouped: Whether to group accessions by structure file. If set output changes to <structure_file1>,<acc1>\n<structure_file1>,<acc2> format. [default: False]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest convert structures

protein-quest convert structures [OPTIONS] INPUT_DIR

Convert structure files between formats.

Convert structure files between formats.

Arguments:

  • INPUT_DIR: Directory with structure files. Supported extensions are .pdb, .pdb.gz, .ent, .ent.gz, .cif, .cif.gz, .bcif, .bcif.gz. [required]

Parameters:

  • --output-dir: Directory to write converted structure files. If not given, files are written to input_dir.
  • --output-format: Output format for converted files. Supported values are .cif and .cif.gz. [choices: .cif, .cif.gz] [default: .cif.gz]
  • --uniprots: Supply Uniprot to PDB id and chain mappings. Adds UniProt accessions to structures that are missing them based on the provided mapping. The supplied file must be in CSV format with 3 columns: pdb_id,uniprot_accession,uniprot_chains. (column order does not matter) This CSV file can be generated with protein-quest search pdbe ....
  • --chain-system: System of chain ids in the input CSV. Set to 'label' to use chain ids assigned by PDB. See docs for more information on chain id system. [choices: auth, label] [default: auth]

Cache:

  • --no-cache: Disable caching of files to central location. [default: False]
  • --cache-dir: Directory to use as cache for files. [default: /home/runner/.cache/protein-quest]
  • --copy-method: How to make target file be same file as source file. By default uses hardlinks to save disk space. Note that hardlinks only work within the same filesystem and are harder to track. If you want to track cached files easily then use 'symlink'. On Windows you need developer mode or admin privileges to create symlinks. [choices: copy, symlink, hardlink] [default: hardlink]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest convert clusters

protein-quest convert clusters [OPTIONS] INPUT_DIR OUTPUT_FILE

Group structures per UniProt accession and cluster based on coverage.

Always writes one CSV file:

  • output_file: one row per structure with cluster assignment.

Can be used to investigate why protein-quest filter resolution ... or protein-quest search pdbe --top_clustered_resolution_per_uniprot_accession ... or protein-quest search structure --top_clustered_resolution_per_uniprot_accession ... keeps or discards certain structures by checking their intermediate cluster assignments and statistics.

See clustering documentation for details on the clustering and ordering criteria.

Arguments:

  • INPUT_DIR: Directory with structure files. [required]
  • OUTPUT_FILE: Output CSV file with cluster assignments. [required]

Parameters:

  • --stats: Optional output CSV file with per-accession cluster summary. Only written when provided.
  • --condensed-distances: Optional output CSV file with condensed distances from all accessions. Writes a single file with uniprot_accession as first column.
  • --linkage-matrix: Optional output CSV file with linkage rows from all accessions. Writes a single file with uniprot_accession as first column.
  • --dendrogram: Optional output directory for per-accession Newick files. Writes <accession>_dendrogram.nwk files into this directory.
  • --scheduler-address: Address of the Dask scheduler to connect to. If not provided, will create a local cluster. If set to sequential will run tasks sequentially.

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]

protein-quest mcp

protein-quest mcp [OPTIONS]

Run Model Context Protocol (MCP) server

Parameters:

  • --transport: Transport protocol to use. [choices: stdio, http, sse, streamable-http] [default: stdio]
  • --host: Host to bind the server to. [default: 127.0.0.1]
  • --port: Port to bind the server to. [default: 8000]

Common:

  • --verbose, -v: Increase verbosity (use multiple times for more detail). [default: 0]
  • --quiet, -q: Decrease verbosity (use multiple times for less output). [default: 0]
  • --prov: Whether to write provenance information about the command execution to ro-crate-metadata.json file. [default: False]