protein-quest 0.3.0__tar.gz → 0.3.2__tar.gz

{protein_quest-0.3.0 → protein_quest-0.3.2}/.github/workflows/ci.yml

@@ -3,7 +3,7 @@ name: CI
 on:
   push:
     branches:
-    - main
+      - main
   pull_request:
 
 concurrency:
@@ -70,3 +70,18 @@ jobs:
         run: uv sync --locked --dev --extra mcp
       - name: Run type checkers
         run: uv run pyrefly check src tests
+  typing-docs:
+    name: typing-docs
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - name: Install uv
+        uses: astral-sh/setup-uv@v6
+      - name: Install the project
+        run: uv sync --group docs-type
+      - name: Convert notebooks to Python scripts
+        run: |
+          find docs/ -name "*.ipynb" -exec uv run --group docs-type marimo convert {} -o {}.py \;
+      - name: Run type checkers on docs
+        run: uv run --group docs-type pyrefly check docs/notebooks/*.ipynb.py
+

{protein_quest-0.3.0 → protein_quest-0.3.2}/CITATION.cff

@@ -23,5 +23,4 @@ repository-code: https://github.com/haddocking/protein-quest
 identifiers:
   - description: Latest version of software
     type: doi
-    # TODO update once release has been made
-    value: 10.5281/zenodo.15632658
+    value: 10.5281/zenodo.16941288

{protein_quest-0.3.0 → protein_quest-0.3.2}/CONTRIBUTING.md

@@ -82,9 +82,23 @@ uv run mkdocs build
 python3 -m http.server -d site
 ```
 
+<details>
+<summary>Type checking notebooks</summary>
+
+[Pyrefly](https://pyrefly.org/) does not support notebooks yet, so we need to convert them to python scripts and then run pyrefly on them.
+
+```shell
+find docs/ -name "*.ipynb" -exec uv run --group docs-type marimo convert {} -o {}.py \;
+uv run --group docs-type pyrefly check docs/notebooks/*.ipynb.py
+rm docs/notebooks/*.ipynb.py
+```
+
+</details>
+
+
 ## Contributing to tests
 
-The code coverage are stored at https://app.codacy.com/gh/haddocking/protein-quest/coverage .
+The code coverage is stored at [https://app.codacy.com/gh/haddocking/protein-quest/coverage](https://app.codacy.com/gh/haddocking/protein-quest/coverage) .
 
 The search functions of the protein-quest package talk to web services on the Internet.
 To have fast tests we use [pytest-recording](https://github.com/kiwicom/pytest-recording) to record and replay HTTP interactions.

{protein_quest-0.3.0 → protein_quest-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: protein_quest
-Version: 0.3.0
+Version: 0.3.2
 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
@@ -13,19 +13,16 @@ Requires-Dist: aiohttp-retry>=2.9.1
 Requires-Dist: aiohttp[speedups]>=3.11.18
 Requires-Dist: aiopath>=0.7.7
 Requires-Dist: attrs>=25.3.0
-Requires-Dist: bokeh>=3.7.3
 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: molviewspec>=1.6.0
-Requires-Dist: pandas>=2.3.0
-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: 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>=2.11.7; extra == 'mcp'
@@ -37,8 +34,7 @@ Description-Content-Type: text/markdown
 [![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/)
-<!-- TODO replace with correct zenodo id -->
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15632658.svg)](https://doi.org/10.5281/zenodo.15632658)
+[![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.
@@ -63,9 +59,11 @@ graph TB;
     searchpdbe -->|pdb_ids|fetchpdbe[Retrieve PDBe]
     searchaf --> |uniprot_accessions|fetchad(Retrieve AlphaFold)
     searchemdb -. emdb_ids .->fetchemdb[Retrieve EMDB]
-    fetchpdbe -->|mmcif_files_with_uniprot_acc| chainfilter{Filter on chain of uniprot}
-    chainfilter --> |mmcif_files| residuefilter{Filter on chain length}
-    fetchad -->|pdb_files| confidencefilter{Filter out low confidence}
+    fetchpdbe -->|mmcif_files_with_uniprot_acc| chainfilter{{Filter on chain of uniprot}}
+    chainfilter --> |mmcif_files| residuefilter{{Filter on chain length}}
+    fetchad -->|pdb_files| confidencefilter{{Filter out low confidence}}
+    confidencefilter --> |mmcif_files| ssfilter{{Filter on secondary structure}}
+    residuefilter --> |mmcif_files| ssfilter
     classDef dashedBorder stroke-dasharray: 5 5;
     goterm:::dashedBorder
     taxonomy:::dashedBorder
@@ -90,7 +88,7 @@ pip install git+https://github.com/haddocking/protein-quest.git
 
 The main entry point is the `protein-quest` command line tool which has multiple subcommands to perform actions.
 
-To use programmaticly, see [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/summary/).
+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/).
 
 ### Search Uniprot accessions
 
@@ -179,6 +177,18 @@ protein-quest filter residue  \
     ./filtered-chains ./filtered
 ```
 
+### To filter on secondary structure
+
+To filter on structure being mostly alpha helices and have no beta sheets.
+
+```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-0.3.0 → protein_quest-0.3.2}/README.md

@@ -4,8 +4,7 @@
 [![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/)
-<!-- TODO replace with correct zenodo id -->
-[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.15632658.svg)](https://doi.org/10.5281/zenodo.15632658)
+[![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.
@@ -30,9 +29,11 @@ graph TB;
     searchpdbe -->|pdb_ids|fetchpdbe[Retrieve PDBe]
     searchaf --> |uniprot_accessions|fetchad(Retrieve AlphaFold)
     searchemdb -. emdb_ids .->fetchemdb[Retrieve EMDB]
-    fetchpdbe -->|mmcif_files_with_uniprot_acc| chainfilter{Filter on chain of uniprot}
-    chainfilter --> |mmcif_files| residuefilter{Filter on chain length}
-    fetchad -->|pdb_files| confidencefilter{Filter out low confidence}
+    fetchpdbe -->|mmcif_files_with_uniprot_acc| chainfilter{{Filter on chain of uniprot}}
+    chainfilter --> |mmcif_files| residuefilter{{Filter on chain length}}
+    fetchad -->|pdb_files| confidencefilter{{Filter out low confidence}}
+    confidencefilter --> |mmcif_files| ssfilter{{Filter on secondary structure}}
+    residuefilter --> |mmcif_files| ssfilter
     classDef dashedBorder stroke-dasharray: 5 5;
     goterm:::dashedBorder
     taxonomy:::dashedBorder
@@ -57,7 +58,7 @@ pip install git+https://github.com/haddocking/protein-quest.git
 
 The main entry point is the `protein-quest` command line tool which has multiple subcommands to perform actions.
 
-To use programmaticly, see [API documentation](https://www.bonvinlab.org/protein-quest/autoapi/summary/).
+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/).
 
 ### Search Uniprot accessions
 
@@ -146,6 +147,18 @@ protein-quest filter residue  \
     ./filtered-chains ./filtered
 ```
 
+### To filter on secondary structure
+
+To filter on structure being mostly alpha helices and have no beta sheets.
+
+```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-0.3.2/docs/notebooks/.gitignore

@@ -0,0 +1,4 @@
+pdb_files/
+alphafold_files/
+filtered/
+session/

protein_quest-0.3.2/docs/notebooks/alphafold.ipynb

@@ -0,0 +1,384 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "24b1926c",
+   "metadata": {},
+   "source": [
+    "# AlphaFold\n",
+    "\n",
+    "You can download and filter AlphaFold files on confidence."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "681ba946",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# Generic imports\n",
+    "import logging\n",
+    "from pathlib import Path\n",
+    "from pprint import pprint\n",
+    "\n",
+    "logging.basicConfig(level=logging.WARNING)\n",
+    "# Set to WARNING to see only warnings\n",
+    "# Set to INFO to see sparql queries\n",
+    "# Set to DEBUG to see raw results"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "4959258c",
+   "metadata": {},
+   "source": [
+    "\n",
+    "## Download Alphafold files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "81e449db",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from protein_quest.alphafold.fetch import fetch_many_async"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "5c2e6ee3",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "save_dir = Path(\"alphafold_files\")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "f38991cf",
+   "metadata": {},
+   "source": [
+    "To download the summary, the cif, predicted Aligned error document (peaDoc) and the pdb file for 3 AlphaFold entries given their uniprot accessions.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 8,
+   "id": "e32b474a",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Fetching Alphafold summaries: 100%|██████████| 3/3 [00:00<00:00,  8.07it/s]\n",
+      "Downloading AlphaFold files: 100%|██████████| 9/9 [00:00<00:00, 55.82it/s]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[AlphaFoldEntry(uniprot_acc='A1YPR0',\n",
+      "                summary=EntrySummary(entryId='AF-A1YPR0-F1',\n",
+      "                                     uniprotAccession='A1YPR0',\n",
+      "                                     uniprotId='ZBT7C_HUMAN',\n",
+      "                                     uniprotDescription='Zinc finger and BTB '\n",
+      "                                                        'domain-containing '\n",
+      "                                                        'protein 7C',\n",
+      "                                     taxId=9606,\n",
+      "                                     organismScientificName='Homo sapiens',\n",
+      "                                     uniprotStart=1,\n",
+      "                                     uniprotEnd=619,\n",
+      "                                     uniprotSequence='MANDIDELIGIPFPNHSSEVLCSLNEQRHDGLLCDVLLVVQEQEYRTHRSVLAACSKYFKKLFTAGTLASQPYVYEIDFVQPEALAAILEFAYTSTLTITAGNVKHILNAARMLEIQCIVNVCLEIMEPGGDGGEEDDKEDDDDDEDDDDEEDEEEEEEEEEDDDDDTEDFADQENLPDPQDISCHQSPSKTDHLTEKAYSDTPRDFPDSFQAGSPGHLGVIRDFSIESLLRENLYPKANIPDRRPSLSPFAPDFFPHLWPGDFGAFAQLPEQPMDSGPLDLVIKNRKIKEEEKEELPPPPPPPFPNDFFKDMFPDLPGGPLGPIKAENDYGAYLNFLSATHLGGLFPPWPLVEERKLKPKASQQCPICHKVIMGAGKLPRHMRTHTGEKPYMCTICEVRFTRQDKLKIHMRKHTGERPYLCIHCNAKFVHNYDLKNHMRIHTGVRPYQCEFCYKSFTRSDHLHRHIKRQSCRMARPRRGRKPAAWRAASLLFGPGGPAPDKAAFVMPPALGEVGGHLGGAAVCLPGPSPAKHFLAAPKGALSLQELERQFEETQMKLFGRAQLEAERNAGGLLAFALAENVAAARPYFPLPDPWAAGLAGLPGLAGLNHVASMSEANN',\n",
+      "                                     modelCreatedDate='2022-06-01T00:00:00Z',\n",
+      "                                     latestVersion=4,\n",
+      "                                     allVersions=[1, 2, 3, 4],\n",
+      "                                     bcifUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v4.bcif',\n",
+      "                                     cifUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v4.cif',\n",
+      "                                     pdbUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v4.pdb',\n",
+      "                                     paeImageUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-predicted_aligned_error_v4.png',\n",
+      "                                     paeDocUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-predicted_aligned_error_v4.json',\n",
+      "                                     gene='ZBTB7C',\n",
+      "                                     sequenceChecksum='73D82A34502B55BF',\n",
+      "                                     sequenceVersionDate='2007-02-06T00:00:00Z',\n",
+      "                                     amAnnotationsUrl='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-aa-substitutions.csv',\n",
+      "                                     amAnnotationsHg19Url='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg19.csv',\n",
+      "                                     amAnnotationsHg38Url='https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg38.csv',\n",
+      "                                     isReviewed=True,\n",
+      "                                     isReferenceProteome=True),\n",
+      "                bcif_file=None,\n",
+      "                cif_file=PosixPath('alphafold_files/AF-A1YPR0-F1-model_v4.cif'),\n",
+      "                pdb_file=PosixPath('alphafold_files/AF-A1YPR0-F1-model_v4.pdb'),\n",
+      "                pae_image_file=None,\n",
+      "                pae_doc_file=PosixPath('alphafold_files/AF-A1YPR0-F1-predicted_aligned_error_v4.json'),\n",
+      "                am_annotations_file=None,\n",
+      "                am_annotations_hg19_file=None,\n",
+      "                am_annotations_hg38_file=None),\n",
+      " AlphaFoldEntry(uniprot_acc='O60481',\n",
+      "                summary=EntrySummary(entryId='AF-O60481-F1',\n",
+      "                                     uniprotAccession='O60481',\n",
+      "                                     uniprotId='ZIC3_HUMAN',\n",
+      "                                     uniprotDescription='Zinc finger protein '\n",
+      "                                                        'ZIC 3',\n",
+      "                                     taxId=9606,\n",
+      "                                     organismScientificName='Homo sapiens',\n",
+      "                                     uniprotStart=1,\n",
+      "                                     uniprotEnd=467,\n",
+      "                                     uniprotSequence='MTMLLDGGPQFPGLGVGSFGAPRHHEMPNREPAGMGLNPFGDSTHAAAAAAAAAAFKLSPAAAHDLSSGQSSAFTPQGSGYANALGHHHHHHHHHHHTSQVPSYGGAASAAFNSTREFLFRQRSSGLSEAASGGGQHGLFAGSASSLHAPAGIPEPPSYLLFPGLHEQGAGHPSPTGHVDNNQVHLGLRGELFGRADPYRPVASPRTDPYAAGAQFPNYSPMNMNMGVNVAAHHGPGAFFRYMRQPIKQELSCKWIDEAQLSRPKKSCDRTFSTMHELVTHVTMEHVGGPEQNNHVCYWEECPREGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGKIFARSENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHMHVHTSDKPYICKVCDKSYTHPSSLRKHMKVHESQGSDSSPAASSGYESSTPPAIASANSKDTTKTPSAVQTSTSHNPGLPPNFNEWYV',\n",
+      "                                     modelCreatedDate='2022-06-01T00:00:00Z',\n",
+      "                                     latestVersion=4,\n",
+      "                                     allVersions=[1, 2, 3, 4],\n",
+      "                                     bcifUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v4.bcif',\n",
+      "                                     cifUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v4.cif',\n",
+      "                                     pdbUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v4.pdb',\n",
+      "                                     paeImageUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-predicted_aligned_error_v4.png',\n",
+      "                                     paeDocUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-predicted_aligned_error_v4.json',\n",
+      "                                     gene='ZIC3',\n",
+      "                                     sequenceChecksum='3150CF13C0679568',\n",
+      "                                     sequenceVersionDate='1998-08-01T00:00:00Z',\n",
+      "                                     amAnnotationsUrl='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-aa-substitutions.csv',\n",
+      "                                     amAnnotationsHg19Url='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg19.csv',\n",
+      "                                     amAnnotationsHg38Url='https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg38.csv',\n",
+      "                                     isReviewed=True,\n",
+      "                                     isReferenceProteome=True),\n",
+      "                bcif_file=None,\n",
+      "                cif_file=PosixPath('alphafold_files/AF-O60481-F1-model_v4.cif'),\n",
+      "                pdb_file=PosixPath('alphafold_files/AF-O60481-F1-model_v4.pdb'),\n",
+      "                pae_image_file=None,\n",
+      "                pae_doc_file=PosixPath('alphafold_files/AF-O60481-F1-predicted_aligned_error_v4.json'),\n",
+      "                am_annotations_file=None,\n",
+      "                am_annotations_hg19_file=None,\n",
+      "                am_annotations_hg38_file=None),\n",
+      " AlphaFoldEntry(uniprot_acc='P50613',\n",
+      "                summary=EntrySummary(entryId='AF-P50613-F1',\n",
+      "                                     uniprotAccession='P50613',\n",
+      "                                     uniprotId='CDK7_HUMAN',\n",
+      "                                     uniprotDescription='Cyclin-dependent '\n",
+      "                                                        'kinase 7',\n",
+      "                                     taxId=9606,\n",
+      "                                     organismScientificName='Homo sapiens',\n",
+      "                                     uniprotStart=1,\n",
+      "                                     uniprotEnd=346,\n",
+      "                                     uniprotSequence='MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF',\n",
+      "                                     modelCreatedDate='2022-06-01T00:00:00Z',\n",
+      "                                     latestVersion=4,\n",
+      "                                     allVersions=[1, 2, 3, 4],\n",
+      "                                     bcifUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v4.bcif',\n",
+      "                                     cifUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v4.cif',\n",
+      "                                     pdbUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v4.pdb',\n",
+      "                                     paeImageUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-predicted_aligned_error_v4.png',\n",
+      "                                     paeDocUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-predicted_aligned_error_v4.json',\n",
+      "                                     gene='CDK7',\n",
+      "                                     sequenceChecksum='0A94BFA7DD416CEB',\n",
+      "                                     sequenceVersionDate='1996-10-01T00:00:00Z',\n",
+      "                                     amAnnotationsUrl='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-aa-substitutions.csv',\n",
+      "                                     amAnnotationsHg19Url='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg19.csv',\n",
+      "                                     amAnnotationsHg38Url='https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg38.csv',\n",
+      "                                     isReviewed=True,\n",
+      "                                     isReferenceProteome=True),\n",
+      "                bcif_file=None,\n",
+      "                cif_file=PosixPath('alphafold_files/AF-P50613-F1-model_v4.cif'),\n",
+      "                pdb_file=PosixPath('alphafold_files/AF-P50613-F1-model_v4.pdb'),\n",
+      "                pae_image_file=None,\n",
+      "                pae_doc_file=PosixPath('alphafold_files/AF-P50613-F1-predicted_aligned_error_v4.json'),\n",
+      "                am_annotations_file=None,\n",
+      "                am_annotations_hg19_file=None,\n",
+      "                am_annotations_hg38_file=None)]\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "summaries = [s async for s in fetch_many_async([\"A1YPR0\", \"O60481\", \"P50613\"], save_dir, what={\"pdb\", \"cif\", \"paeDoc\"})]\n",
+    "pprint(summaries)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 9,
+   "id": "2d3595e6",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "total 4.2M\n",
+      "4.0K A1YPR0.json\n",
+      "548K AF-A1YPR0-F1-model_v4.cif\n",
+      "392K AF-A1YPR0-F1-model_v4.pdb\n",
+      "1.1M AF-A1YPR0-F1-predicted_aligned_error_v4.json\n",
+      "408K AF-O60481-F1-model_v4.cif\n",
+      "292K AF-O60481-F1-model_v4.pdb\n",
+      "632K AF-O60481-F1-predicted_aligned_error_v4.json\n",
+      "320K AF-P50613-F1-model_v4.cif\n",
+      "224K AF-P50613-F1-model_v4.pdb\n",
+      "280K AF-P50613-F1-predicted_aligned_error_v4.json\n",
+      "4.0K O60481.json\n",
+      "4.0K P50613.json\n"
+     ]
+    }
+   ],
+   "source": [
+    "!ls -sh {save_dir}"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "a43edd87",
+   "metadata": {},
+   "source": [
+    "## Filter AlphFold structure files on confidence\n",
+    "\n",
+    "Filter AlphaFold mmcif/PDB files by confidence (plDDT). Passed files are written with residues below threshold removed."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 10,
+   "id": "cc96c63a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "from protein_quest.alphafold.confidence import ConfidenceFilterQuery, filter_files_on_confidence"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "724141d4",
+   "metadata": {},
+   "source": [
+    "Take one of the downloaded files"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 12,
+   "id": "73a61cf6",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[PosixPath('alphafold_files/AF-A1YPR0-F1-model_v4.cif'),\n",
+       " PosixPath('alphafold_files/AF-O60481-F1-model_v4.cif'),\n",
+       " PosixPath('alphafold_files/AF-P50613-F1-model_v4.cif')]"
+      ]
+     },
+     "execution_count": 12,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "input_files = [entry.cif_file for entry in summaries if entry.cif_file is not None]\n",
+    "input_files"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "da8f2f67",
+   "metadata": {},
+   "source": [
+    "We only write a filtered cif file when in the input file there are between 100 and 1000 residues that have a pLDDT score above 50."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fbfdf472",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "query = ConfidenceFilterQuery(confidence=80, min_residues=100, max_residues=1000)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 14,
+   "id": "152aec9a",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "output_dir = Path(\"./filtered\")\n",
+    "output_dir.mkdir(exist_ok=True)\n",
+    "result = filter_files_on_confidence(input_files, query, output_dir)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "6a6f8e3f",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "text/plain": [
+       "[ConfidenceFilterResult(input_file='AF-A1YPR0-F1-model_v4.cif', count=175, filtered_file=PosixPath('filtered/AF-A1YPR0-F1-model_v4.cif')),\n",
+       " ConfidenceFilterResult(input_file='AF-O60481-F1-model_v4.cif', count=76, filtered_file=None),\n",
+       " ConfidenceFilterResult(input_file='AF-P50613-F1-model_v4.cif', count=244, filtered_file=PosixPath('filtered/AF-P50613-F1-model_v4.cif'))]"
+      ]
+     },
+     "execution_count": 17,
+     "metadata": {},
+     "output_type": "execute_result"
+    }
+   ],
+   "source": [
+    "list(\n",
+    "    filter_files_on_confidence(\n",
+    "        input_files, ConfidenceFilterQuery(confidence=80, min_residues=100, max_residues=1000), output_dir\n",
+    "    )\n",
+    ")"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "0fe1e388",
+   "metadata": {},
+   "source": [
+    "2 files have passed, but 1 file only has 75 high confidence residues so it is discarded."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "83ffc09b",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "protein-quest",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.13.2"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

protein_quest-0.3.2/docs/notebooks/index.md

@@ -0,0 +1,3 @@
+# Example notebooks
+
+The Jupyter notebooks show how to use the protein-quest package via its API.