protein-quest 0.9.0__py3-none-any.whl

protein_quest-0.9.0.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: protein_quest
+Version: 0.9.0
+Summary: Search/retrieve/filter proteins and protein structures
+Project-URL: Homepage, https://github.com/haddocking/protein-quest
+Project-URL: Issues, https://github.com/haddocking/protein-quest/issues
+Project-URL: Documentation, https://www.bonvinlab.org/protein-quest/
+Project-URL: Source, https://github.com/haddocking/protein-quest
+License-File: LICENSE
+Requires-Python: >=3.13
+Requires-Dist: aiofiles>=24.1.0
+Requires-Dist: aiohttp-retry>=2.9.1
+Requires-Dist: aiohttp[speedups]>=3.11.18
+Requires-Dist: attrs>=25.3.0
+Requires-Dist: cattrs[orjson]>=24.1.3
+Requires-Dist: dask>=2025.5.1
+Requires-Dist: distributed>=2025.5.1
+Requires-Dist: gemmi>=0.7.3
+Requires-Dist: mmcif>=0.92.0
+Requires-Dist: platformdirs>=4.3.8
+Requires-Dist: psutil>=7.0.0
+Requires-Dist: rich-argparse>=1.7.1
+Requires-Dist: rich>=14.0.0
+Requires-Dist: shtab>=1.7.2
+Requires-Dist: sparqlwrapper>=2.0.0
+Requires-Dist: tqdm>=4.67.1
+Requires-Dist: yarl>=1.20.1
+Provides-Extra: mcp
+Requires-Dist: fastmcp>=2.11.3; extra == 'mcp'
+Requires-Dist: pydantic>=2.12.0; extra == 'mcp'
+Description-Content-Type: text/markdown
+
+# protein-quest
+
+[![Documentation](https://img.shields.io/badge/Documentation-bonvinlab.org-blue?style=flat-square&logo=gitbook)](https://www.bonvinlab.org/protein-quest/)
+[![CI](https://github.com/haddocking/protein-quest/actions/workflows/ci.yml/badge.svg)](https://github.com/haddocking/protein-quest/actions/workflows/ci.yml)
+[![Research Software Directory Badge](https://img.shields.io/badge/rsd-00a3e3.svg)](https://www.research-software.nl/software/protein-quest)
+[![PyPI](https://img.shields.io/pypi/v/protein-quest)](https://pypi.org/project/protein-quest/)
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.16941288.svg)](https://doi.org/10.5281/zenodo.16941288)
+[![Codacy Badge](https://app.codacy.com/project/badge/Coverage/7a3f3f1fe64640d583a5e50fe7ba828e)](https://app.codacy.com/gh/haddocking/protein-quest/coverage?utm_source=gh&utm_medium=referral&utm_content=&utm_campaign=Badge_coverage)
+
+Python package to search/retrieve/filter proteins and protein structures.
+
+It uses
+
+- [Uniprot Sparql endpoint](https://sparql.uniprot.org/) to search for proteins and their measured or predicted 3D structures.
+- [Uniprot taxonomy](https://www.uniprot.org/taxonomy?query=*) to search for taxonomy.
+- [QuickGO](https://www.ebi.ac.uk/QuickGO/api/index.html) to search for Gene Ontology terms.
+- [gemmi](https://project-gemmi.github.io/) to work with macromolecular models.
+- [dask-distributed](https://docs.dask.org/en/latest/) to compute in parallel.
+
+The package is used by
+
+- [protein-detective](https://github.com/haddocking/protein-detective)
+
+An example workflow:
+
+```mermaid
+graph TB;
+    taxonomy[/Search taxon/] -. taxon_ids .-> searchuniprot[/Search UniprotKB/]
+    goterm[/Search GO term/] -. go_ids .-> searchuniprot[/Search UniprotKB/]
+    searchuniprot --> |uniprot_accessions|searchpdbe[/Search PDBe/]
+    searchuniprot --> |uniprot_accessions|searchaf[/Search Alphafold/]
+    searchuniprot -. uniprot_accessions .-> searchemdb[/Search EMDB/]
+    searchuniprot -. uniprot_accessions .-> searchuniprotdetails[/Search UniProt details/]
+    searchintactionpartners[/Search interaction partners/] -.-x |uniprot_accessions|searchuniprot
+    searchcomplexes[/Search complexes/]
+    searchpdbe -->|pdb_ids|fetchpdbe[Retrieve PDBe]
+    searchaf --> |uniprot_accessions|fetchad(Retrieve AlphaFold)
+    searchemdb -. emdb_ids .->fetchemdb[Retrieve EMDB]
+    fetchpdbe -->|mmcif_files| chainfilter{{Filter on chain of uniprot}}
+    chainfilter --> |mmcif_files| residuefilter{{Filter on chain length}}
+    fetchad -->|mmcif_files| confidencefilter{{Filter out low confidence}}
+    confidencefilter --> |mmcif_files| ssfilter{{Filter on secondary structure}}
+    residuefilter --> |mmcif_files| ssfilter
+    ssfilter -. mmcif_files .-> convert2cif([Convert to cif])
+    ssfilter -. mmcif_files .-> convert2uniprot_accessions([Convert to UniProt accessions])
+    classDef dashedBorder stroke-dasharray: 5 5;
+    goterm:::dashedBorder
+    taxonomy:::dashedBorder
+    searchemdb:::dashedBorder
+    fetchemdb:::dashedBorder
+    searchintactionpartners:::dashedBorder
+    searchcomplexes:::dashedBorder
+    searchuniprotdetails:::dashedBorder
+    convert2cif:::dashedBorder
+    convert2uniprot_accessions:::dashedBorder
+```
+
+(Dotted nodes and edges are side-quests.)
+
+## Install
+
+```shell
+pip install protein-quest
+```
+
+Or to use the latest development version:
+```
+pip install git+https://github.com/haddocking/protein-quest.git
+```
+
+## Usage
+
+The main entry point is the `protein-quest` command line tool which has multiple subcommands to perform actions.
+
+To use programmaticly, see the [Jupyter notebooks](https://www.bonvinlab.org/protein-quest/notebooks) and [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/summary/).
+
+While downloading or copying files it uses a global cache (located at `~/.cache/protein-quest`) and hardlinks to save disk space and improve speed.
+This behavior can be customized with the `--no-cache`, `--cache-dir`, and `--copy-method` command line arguments.
+
+### Search Uniprot accessions
+
+```shell
+protein-quest search uniprot \
+    --taxon-id 9606 \
+    --reviewed \
+    --subcellular-location-uniprot "nucleus" \
+    --subcellular-location-go GO:0005634 \
+    --molecular-function-go GO:0003677 \
+    --limit 100 \
+    uniprot_accs.txt
+```
+([GO:0005634](https://www.ebi.ac.uk/QuickGO/term/GO:0005634) is "Nucleus" and [GO:0003677](https://www.ebi.ac.uk/QuickGO/term/GO:0003677) is  "DNA binding")
+
+### Search for PDBe structures of uniprot accessions
+
+```shell
+protein-quest search pdbe uniprot_accs.txt pdbe.csv
+```
+
+`pdbe.csv` file is written containing the the PDB id and chain of each uniprot accession.
+
+### Search for Alphafold structures of uniprot accessions
+
+```shell
+protein-quest search alphafold uniprot_accs.txt alphafold.csv
+```
+
+### Search for EMDB structures of uniprot accessions
+
+```shell
+protein-quest search emdb uniprot_accs.txt emdbs.csv
+```
+
+### To retrieve PDB structure files
+
+```shell
+protein-quest retrieve pdbe pdbe.csv downloads-pdbe/
+```
+
+### To retrieve AlphaFold structure files
+
+```shell
+protein-quest retrieve alphafold alphafold.csv downloads-af/
+```
+
+For each entry downloads the cif file.
+
+### To retrieve EMDB volume files
+
+```shell
+protein-quest retrieve emdb emdbs.csv downloads-emdb/
+```
+
+### To filter AlphaFold structures on confidence
+
+Filter AlphaFoldDB structures based on confidence (pLDDT).
+Keeps entries with requested number of residues which have a confidence score above the threshold.
+Also writes pdb files with only those residues.
+
+```shell
+protein-quest filter confidence \
+    --confidence-threshold 50 \
+    --min-residues 100 \
+    --max-residues 1000 \
+    ./downloads-af ./filtered
+```
+
+### To filter PDBe files on chain of uniprot accession
+
+Make PDBe files smaller by only keeping first chain of found uniprot entry and renaming to chain A.
+
+```shell
+protein-quest filter chain \
+    pdbe.csv \
+    ./downloads-pdbe ./filtered-chains
+```
+
+### To filter PDBe files on nr of residues
+
+```shell
+protein-quest filter residue  \
+    --min-residues 100 \
+    --max-residues 1000 \
+    ./filtered-chains ./filtered
+```
+
+### To filter on secondary structure
+
+To filter on structure being mostly alpha helices and have no beta sheets. See the following [notebook](https://www.bonvinlab.org/protein-detective/SSE_elements.html) to determine the ratio of secondary structure elements.
+
+```shell
+protein-quest filter secondary-structure \
+    --ratio-min-helix-residues 0.5 \
+    --ratio-max-sheet-residues 0.0 \
+    --write-stats filtered-ss/stats.csv \
+    ./filtered-chains ./filtered-ss
+```
+
+### Search Taxonomy
+
+```shell
+protein-quest search taxonomy "Homo sapiens" -
+```
+
+### Search Gene Ontology (GO)
+
+You might not know what the identifier of a [Gene Ontology](https://geneontology.org/) term is at `protein-quest search uniprot`.
+You can use following command to search for a Gene Ontology (GO) term.
+
+```shell
+protein-quest search go --limit 5 --aspect cellular_component apoptosome -
+```
+
+### Search for interaction partners
+
+Use https://www.ebi.ac.uk/complexportal to find interaction partners of given UniProt accession.
+
+```shell
+protein-quest search interaction-partners Q05471 interaction-partners-of-Q05471.txt
+```
+
+The `interaction-partners-of-Q05471.txt` file contains uniprot accessions (one per line).
+
+### Search for complexes
+
+Given Uniprot accessions search for macromolecular complexes at https://www.ebi.ac.uk/complexportal
+and return the complex entries and their members.
+
+```shell
+echo Q05471 | protein-quest search complexes - complexes.csv
+```
+
+The `complexes.csv` looks like
+
+```csv
+query_protein,complex_id,complex_url,complex_title,members
+Q05471,CPX-2122,https://www.ebi.ac.uk/complexportal/complex/CPX-2122,Swr1 chromatin remodelling complex,P31376;P35817;P38326;P53201;P53930;P60010;P80428;Q03388;Q03433;Q03940;Q05471;Q06707;Q12464;Q12509
+```
+
+### Search for UniProt details
+
+To get details (like protein name, sequence length, organism) for a list of UniProt accessions.
+
+```shell
+protein-quest search uniprot-details uniprot_accs.txt uniprot_details.csv
+```
+
+The `uniprot_details.csv` looks like:
+
+```csv
+uniprot_accession,uniprot_id,sequence_length,reviewed,protein_name,taxon_id,taxon_name
+A0A087WUV0,ZN892_HUMAN,522,True,Zinc finger protein 892,9606,Homo sapiens
+```
+
+### Convert structure files to .cif format
+
+Some tools (for example [powerfit](https://github.com/haddocking/powerfit)) only work with `.cif` files and not `*.cif.gz` or `*.bcif` files.
+
+```shell
+protein-quest convert structures --format cif --output-dir ./filtered-cif ./filtered-ss
+```
+
+### Convert structure files to UniProt accessions
+
+After running some filters you might want to know which UniProt accessions are still present in the filtered structures.
+
+```shell
+protein-quest convert uniprot ./filtered-ss uniprot_accs.filtered.txt
+```
+
+##  Model Context Protocol (MCP) server
+
+Protein quest can also help LLMs like Claude Sonnet 4 by providing a [set of tools](https://modelcontextprotocol.io/docs/learn/server-concepts#tools-ai-actions) for protein structures.
+
+![Protein Quest MCP workflow](https://github.com/haddocking/protein-quest/raw/main/docs/protein-quest-mcp.png)
+
+To run mcp server you have to install the `mcp` extra with:
+
+```shell
+pip install protein-quest[mcp]
+```
+
+The server can be started with:
+
+```shell
+protein-quest mcp
+```
+
+The mcp server contains an prompt template to search/retrieve/filter candidate structures.
+
+## Shell autocompletion
+
+The `protein-quest` command line tool supports shell autocompletion using [shtab](https://shtab.readthedocs.io/).
+
+Initialize for bash shell with:
+
+```shell
+mkdir -p ~/.local/share/bash-completion/completions
+protein-quest --print-completion bash > ~/.local/share/bash-completion/completions/protein-quest
+```
+
+Initialize for zsh shell with:
+
+```shell
+mkdir -p ~/.local/share/zsh/site-functions
+protein-quest --print-completion zsh > ~/.local/share/zsh/site-functions/_protein-quest
+fpath=("$HOME/.local/share/zsh/site-functions" $fpath)
+autoload -Uz compinit && compinit
+```
+
+## Contributing
+
+For development information and contribution guidelines, please see [CONTRIBUTING.md](CONTRIBUTING.md).

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protein_quest-0.9.0.dist-info/WHEEL

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+Generator: hatchling 1.27.0
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protein_quest-0.9.0.dist-info/entry_points.txt

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+[console_scripts]
+protein-quest = protein_quest.cli:main

protein_quest-0.9.0.dist-info/licenses/LICENSE

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