protein-quest 0.6.0__tar.gz → 0.7.0__tar.gz

protein_quest-0.7.0/.python-version

@@ -0,0 +1 @@
+3.13

{protein_quest-0.6.0 → protein_quest-0.7.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: protein_quest
-Version: 0.6.0
+Version: 0.7.0
 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
@@ -11,7 +11,6 @@ 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: aiopath>=0.7.7
 Requires-Dist: attrs>=25.3.0
 Requires-Dist: cattrs[orjson]>=24.1.3
 Requires-Dist: dask>=2025.5.1
@@ -27,7 +26,7 @@ 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'
+Requires-Dist: pydantic>=2.12.0; extra == 'mcp'
 Description-Content-Type: text/markdown
 
 # protein-quest
@@ -62,6 +61,7 @@ graph TB;
     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]
@@ -73,6 +73,7 @@ graph TB;
     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
@@ -80,7 +81,9 @@ graph TB;
     fetchemdb:::dashedBorder
     searchintactionpartners:::dashedBorder
     searchcomplexes:::dashedBorder
+    searchuniprotdetails:::dashedBorder
     convert2cif:::dashedBorder
+    convert2uniprot_accessions:::dashedBorder
 ```
 
 (Dotted nodes and edges are side-quests.)
@@ -111,7 +114,7 @@ This behavior can be customized with the `--no-cache`, `--cache-dir`, and `--cop
 protein-quest search uniprot \
     --taxon-id 9606 \
     --reviewed \
-    --subcellular-location-uniprot nucleus \
+    --subcellular-location-uniprot "nucleus" \
     --subcellular-location-go GO:0005634 \
     --molecular-function-go GO:0003677 \
     --limit 100 \
@@ -194,7 +197,7 @@ protein-quest filter residue  \
 
 ### To filter on secondary structure
 
-To filter on structure being mostly alpha helices and have no beta sheets.
+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 \
@@ -245,12 +248,35 @@ 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 --output-dir ./filtered-cif ./filtered-ss
+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-0.6.0 → protein_quest-0.7.0}/README.md

@@ -30,6 +30,7 @@ graph TB;
     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]
@@ -41,6 +42,7 @@ graph TB;
     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
@@ -48,7 +50,9 @@ graph TB;
     fetchemdb:::dashedBorder
     searchintactionpartners:::dashedBorder
     searchcomplexes:::dashedBorder
+    searchuniprotdetails:::dashedBorder
     convert2cif:::dashedBorder
+    convert2uniprot_accessions:::dashedBorder
 ```
 
 (Dotted nodes and edges are side-quests.)
@@ -79,7 +83,7 @@ This behavior can be customized with the `--no-cache`, `--cache-dir`, and `--cop
 protein-quest search uniprot \
     --taxon-id 9606 \
     --reviewed \
-    --subcellular-location-uniprot nucleus \
+    --subcellular-location-uniprot "nucleus" \
     --subcellular-location-go GO:0005634 \
     --molecular-function-go GO:0003677 \
     --limit 100 \
@@ -162,7 +166,7 @@ protein-quest filter residue  \
 
 ### To filter on secondary structure
 
-To filter on structure being mostly alpha helices and have no beta sheets.
+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 \
@@ -213,12 +217,35 @@ 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 --output-dir ./filtered-cif ./filtered-ss
+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-0.7.0/docs/notebooks/alphafold.ipynb

@@ -0,0 +1,463 @@
+{
+ "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 and predicted Aligned error document (peaDoc) file for 3 AlphaFold entries given their uniprot accessions.\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "e32b474a",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "Fetching Alphafold summaries: 100%|██████████| 3/3 [00:00<00:00, 553.10it/s]\n",
+      "Downloading AlphaFold files: 100%|██████████| 6/6 [00:00<00:00, 38245.93it/s]"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "[AlphaFoldEntry(uniprot_accession='A1YPR0',\n",
+      "                summary=EntrySummary(allVersions=[1, 2, 3, 4, 5, 6],\n",
+      "                                     bcifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v6.bcif'),\n",
+      "                                     cifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v6.cif'),\n",
+      "                                     entityType='protein',\n",
+      "                                     fractionPlddtConfident=0.26,\n",
+      "                                     fractionPlddtLow=0.099,\n",
+      "                                     fractionPlddtVeryHigh=0.089,\n",
+      "                                     fractionPlddtVeryLow=0.553,\n",
+      "                                     globalMetricValue=56.03,\n",
+      "                                     isUniProt=True,\n",
+      "                                     latestVersion=6,\n",
+      "                                     modelCreatedDate='2025-08-01T00:00:00Z',\n",
+      "                                     modelEntityId='AF-A1YPR0-F1',\n",
+      "                                     paeDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-predicted_aligned_error_v6.json'),\n",
+      "                                     pdbUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-model_v6.pdb'),\n",
+      "                                     providerId='GDM',\n",
+      "                                     sequence='MANDIDELIGIPFPNHSSEVLCSLNEQRHDGLLCDVLLVVQEQEYRTHRSVLAACSKYFKKLFTAGTLASQPYVYEIDFVQPEALAAILEFAYTSTLTITAGNVKHILNAARMLEIQCIVNVCLEIMEPGGDGGEEDDKEDDDDDEDDDDEEDEEEEEEEEEDDDDDTEDFADQENLPDPQDISCHQSPSKTDHLTEKAYSDTPRDFPDSFQAGSPGHLGVIRDFSIESLLRENLYPKANIPDRRPSLSPFAPDFFPHLWPGDFGAFAQLPEQPMDSGPLDLVIKNRKIKEEEKEELPPPPPPPFPNDFFKDMFPDLPGGPLGPIKAENDYGAYLNFLSATHLGGLFPPWPLVEERKLKPKASQQCPICHKVIMGAGKLPRHMRTHTGEKPYMCTICEVRFTRQDKLKIHMRKHTGERPYLCIHCNAKFVHNYDLKNHMRIHTGVRPYQCEFCYKSFTRSDHLHRHIKRQSCRMARPRRGRKPAAWRAASLLFGPGGPAPDKAAFVMPPALGEVGGHLGGAAVCLPGPSPAKHFLAAPKGALSLQELERQFEETQMKLFGRAQLEAERNAGGLLAFALAENVAAARPYFPLPDPWAAGLAGLPGLAGLNHVASMSEANN',\n",
+      "                                     sequenceChecksum='73D82A34502B55BF',\n",
+      "                                     sequenceEnd=619,\n",
+      "                                     sequenceStart=1,\n",
+      "                                     sequenceVersionDate='2007-02-06T00:00:00Z',\n",
+      "                                     toolUsed='AlphaFold Monomer v2.0 pipeline',\n",
+      "                                     alternativeNames=None,\n",
+      "                                     amAnnotationsHg19Url=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg19.csv'),\n",
+      "                                     amAnnotationsHg38Url=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-hg38.csv'),\n",
+      "                                     amAnnotationsUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-aa-substitutions.csv'),\n",
+      "                                     catalyticActivities=None,\n",
+      "                                     complexName=None,\n",
+      "                                     functions=None,\n",
+      "                                     gene='ZBTB7C',\n",
+      "                                     geneSynonyms=None,\n",
+      "                                     ipSAE=None,\n",
+      "                                     ipTM=None,\n",
+      "                                     isUniProtReferenceProteome=True,\n",
+      "                                     isUniProtReviewed=True,\n",
+      "                                     keywords=None,\n",
+      "                                     msaUrl=URL('https://alphafold.ebi.ac.uk/files/msa/AF-A1YPR0-F1-msa_v6.a3m'),\n",
+      "                                     organismCommonNames=None,\n",
+      "                                     organismScientificName='Homo sapiens',\n",
+      "                                     organismSynonyms=None,\n",
+      "                                     plddtDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-A1YPR0-F1-confidence_v6.json'),\n",
+      "                                     proteinFullNames=None,\n",
+      "                                     proteinShortNames=None,\n",
+      "                                     stoichiometry=None,\n",
+      "                                     taxId=9606,\n",
+      "                                     taxonomyLineage=None,\n",
+      "                                     uniprotAccession='A1YPR0',\n",
+      "                                     uniprotDescription='Zinc finger and BTB '\n",
+      "                                                        'domain-containing '\n",
+      "                                                        'protein 7C',\n",
+      "                                     uniprotId='ZBT7C_HUMAN'),\n",
+      "                summary_file=PosixPath('alphafold_files/A1YPR0.json'),\n",
+      "                bcif_file=None,\n",
+      "                cif_file=PosixPath('alphafold_files/AF-A1YPR0-F1-model_v6.cif'),\n",
+      "                pdb_file=None,\n",
+      "                pae_doc_file=PosixPath('alphafold_files/AF-A1YPR0-F1-predicted_aligned_error_v6.json'),\n",
+      "                am_annotations_file=None,\n",
+      "                am_annotations_hg19_file=None,\n",
+      "                am_annotations_hg38_file=None,\n",
+      "                msa_file=None,\n",
+      "                plddt_doc_file=None),\n",
+      " AlphaFoldEntry(uniprot_accession='O60481',\n",
+      "                summary=EntrySummary(allVersions=[1, 2, 3, 4, 5, 6],\n",
+      "                                     bcifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v6.bcif'),\n",
+      "                                     cifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v6.cif'),\n",
+      "                                     entityType='protein',\n",
+      "                                     fractionPlddtConfident=0.289,\n",
+      "                                     fractionPlddtLow=0.107,\n",
+      "                                     fractionPlddtVeryHigh=0.0,\n",
+      "                                     fractionPlddtVeryLow=0.604,\n",
+      "                                     globalMetricValue=53.88,\n",
+      "                                     isUniProt=True,\n",
+      "                                     latestVersion=6,\n",
+      "                                     modelCreatedDate='2025-08-01T00:00:00Z',\n",
+      "                                     modelEntityId='AF-O60481-F1',\n",
+      "                                     paeDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-predicted_aligned_error_v6.json'),\n",
+      "                                     pdbUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-model_v6.pdb'),\n",
+      "                                     providerId='GDM',\n",
+      "                                     sequence='MTMLLDGGPQFPGLGVGSFGAPRHHEMPNREPAGMGLNPFGDSTHAAAAAAAAAAFKLSPAAAHDLSSGQSSAFTPQGSGYANALGHHHHHHHHHHHTSQVPSYGGAASAAFNSTREFLFRQRSSGLSEAASGGGQHGLFAGSASSLHAPAGIPEPPSYLLFPGLHEQGAGHPSPTGHVDNNQVHLGLRGELFGRADPYRPVASPRTDPYAAGAQFPNYSPMNMNMGVNVAAHHGPGAFFRYMRQPIKQELSCKWIDEAQLSRPKKSCDRTFSTMHELVTHVTMEHVGGPEQNNHVCYWEECPREGKSFKAKYKLVNHIRVHTGEKPFPCPFPGCGKIFARSENLKIHKRTHTGEKPFKCEFEGCDRRFANSSDRKKHMHVHTSDKPYICKVCDKSYTHPSSLRKHMKVHESQGSDSSPAASSGYESSTPPAIASANSKDTTKTPSAVQTSTSHNPGLPPNFNEWYV',\n",
+      "                                     sequenceChecksum='3150CF13C0679568',\n",
+      "                                     sequenceEnd=467,\n",
+      "                                     sequenceStart=1,\n",
+      "                                     sequenceVersionDate='1998-08-01T00:00:00Z',\n",
+      "                                     toolUsed='AlphaFold Monomer v2.0 pipeline',\n",
+      "                                     alternativeNames=None,\n",
+      "                                     amAnnotationsHg19Url=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg19.csv'),\n",
+      "                                     amAnnotationsHg38Url=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-hg38.csv'),\n",
+      "                                     amAnnotationsUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-aa-substitutions.csv'),\n",
+      "                                     catalyticActivities=None,\n",
+      "                                     complexName=None,\n",
+      "                                     functions=None,\n",
+      "                                     gene='ZIC3',\n",
+      "                                     geneSynonyms=None,\n",
+      "                                     ipSAE=None,\n",
+      "                                     ipTM=None,\n",
+      "                                     isUniProtReferenceProteome=True,\n",
+      "                                     isUniProtReviewed=True,\n",
+      "                                     keywords=None,\n",
+      "                                     msaUrl=URL('https://alphafold.ebi.ac.uk/files/msa/AF-O60481-F1-msa_v6.a3m'),\n",
+      "                                     organismCommonNames=None,\n",
+      "                                     organismScientificName='Homo sapiens',\n",
+      "                                     organismSynonyms=None,\n",
+      "                                     plddtDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-O60481-F1-confidence_v6.json'),\n",
+      "                                     proteinFullNames=None,\n",
+      "                                     proteinShortNames=None,\n",
+      "                                     stoichiometry=None,\n",
+      "                                     taxId=9606,\n",
+      "                                     taxonomyLineage=None,\n",
+      "                                     uniprotAccession='O60481',\n",
+      "                                     uniprotDescription='Zinc finger protein '\n",
+      "                                                        'ZIC 3',\n",
+      "                                     uniprotId='ZIC3_HUMAN'),\n",
+      "                summary_file=PosixPath('alphafold_files/O60481.json'),\n",
+      "                bcif_file=None,\n",
+      "                cif_file=PosixPath('alphafold_files/AF-O60481-F1-model_v6.cif'),\n",
+      "                pdb_file=None,\n",
+      "                pae_doc_file=PosixPath('alphafold_files/AF-O60481-F1-predicted_aligned_error_v6.json'),\n",
+      "                am_annotations_file=None,\n",
+      "                am_annotations_hg19_file=None,\n",
+      "                am_annotations_hg38_file=None,\n",
+      "                msa_file=None,\n",
+      "                plddt_doc_file=None),\n",
+      " AlphaFoldEntry(uniprot_accession='P50613',\n",
+      "                summary=EntrySummary(allVersions=[1, 2, 3, 4, 5, 6],\n",
+      "                                     bcifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v6.bcif'),\n",
+      "                                     cifUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v6.cif'),\n",
+      "                                     entityType='protein',\n",
+      "                                     fractionPlddtConfident=0.127,\n",
+      "                                     fractionPlddtLow=0.092,\n",
+      "                                     fractionPlddtVeryHigh=0.618,\n",
+      "                                     fractionPlddtVeryLow=0.162,\n",
+      "                                     globalMetricValue=82.0,\n",
+      "                                     isUniProt=True,\n",
+      "                                     latestVersion=6,\n",
+      "                                     modelCreatedDate='2025-08-01T00:00:00Z',\n",
+      "                                     modelEntityId='AF-P50613-F1',\n",
+      "                                     paeDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-predicted_aligned_error_v6.json'),\n",
+      "                                     pdbUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-model_v6.pdb'),\n",
+      "                                     providerId='GDM',\n",
+      "                                     sequence='MALDVKSRAKRYEKLDFLGEGQFATVYKARDKNTNQIVAIKKIKLGHRSEAKDGINRTALREIKLLQELSHPNIIGLLDAFGHKSNISLVFDFMETDLEVIIKDNSLVLTPSHIKAYMLMTLQGLEYLHQHWILHRDLKPNNLLLDENGVLKLADFGLAKSFGSPNRAYTHQVVTRWYRAPELLFGARMYGVGVDMWAVGCILAELLLRVPFLPGDSDLDQLTRIFETLGTPTEEQWPDMCSLPDYVTFKSFPGIPLHHIFSAAGDDLLDLIQGLFLFNPCARITATQALKMKYFSNRPGPTPGCQLPRPNCPVETLKEQSNPALAIKRKRTEALEQGGLPKKLIF',\n",
+      "                                     sequenceChecksum='0A94BFA7DD416CEB',\n",
+      "                                     sequenceEnd=346,\n",
+      "                                     sequenceStart=1,\n",
+      "                                     sequenceVersionDate='1996-10-01T00:00:00Z',\n",
+      "                                     toolUsed='AlphaFold Monomer v2.0 pipeline',\n",
+      "                                     alternativeNames=None,\n",
+      "                                     amAnnotationsHg19Url=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg19.csv'),\n",
+      "                                     amAnnotationsHg38Url=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-hg38.csv'),\n",
+      "                                     amAnnotationsUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-aa-substitutions.csv'),\n",
+      "                                     catalyticActivities=None,\n",
+      "                                     complexName=None,\n",
+      "                                     functions=None,\n",
+      "                                     gene='CDK7',\n",
+      "                                     geneSynonyms=None,\n",
+      "                                     ipSAE=None,\n",
+      "                                     ipTM=None,\n",
+      "                                     isUniProtReferenceProteome=True,\n",
+      "                                     isUniProtReviewed=True,\n",
+      "                                     keywords=None,\n",
+      "                                     msaUrl=URL('https://alphafold.ebi.ac.uk/files/msa/AF-P50613-F1-msa_v6.a3m'),\n",
+      "                                     organismCommonNames=None,\n",
+      "                                     organismScientificName='Homo sapiens',\n",
+      "                                     organismSynonyms=None,\n",
+      "                                     plddtDocUrl=URL('https://alphafold.ebi.ac.uk/files/AF-P50613-F1-confidence_v6.json'),\n",
+      "                                     proteinFullNames=None,\n",
+      "                                     proteinShortNames=None,\n",
+      "                                     stoichiometry=None,\n",
+      "                                     taxId=9606,\n",
+      "                                     taxonomyLineage=None,\n",
+      "                                     uniprotAccession='P50613',\n",
+      "                                     uniprotDescription='Cyclin-dependent '\n",
+      "                                                        'kinase 7',\n",
+      "                                     uniprotId='CDK7_HUMAN'),\n",
+      "                summary_file=PosixPath('alphafold_files/P50613.json'),\n",
+      "                bcif_file=None,\n",
+      "                cif_file=PosixPath('alphafold_files/AF-P50613-F1-model_v6.cif'),\n",
+      "                pdb_file=None,\n",
+      "                pae_doc_file=PosixPath('alphafold_files/AF-P50613-F1-predicted_aligned_error_v6.json'),\n",
+      "                am_annotations_file=None,\n",
+      "                am_annotations_hg19_file=None,\n",
+      "                am_annotations_hg38_file=None,\n",
+      "                msa_file=None,\n",
+      "                plddt_doc_file=None)]\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    }
+   ],
+   "source": [
+    "summaries = [\n",
+    "    s async for s in fetch_many_async([\"A1YPR0\", \"O60481\", \"P50613\"], save_dir, what={\"summary\", \"cif\", \"paeDoc\"})\n",
+    "]\n",
+    "pprint(summaries)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "2d3595e6",
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "total 4.3M\n",
+      "4.0K A1YPR0.json\n",
+      "556K AF-A1YPR0-F1-model_v6.cif\n",
+      "1.1M AF-A1YPR0-F1-predicted_aligned_error_v6.json\n",
+      "412K AF-O60481-2-F1-model_v6.cif\n",
+      "600K AF-O60481-2-F1-predicted_aligned_error_v6.json\n",
+      "412K AF-O60481-F1-model_v6.cif\n",
+      "628K AF-O60481-F1-predicted_aligned_error_v6.json\n",
+      "324K AF-P50613-F1-model_v6.cif\n",
+      "276K AF-P50613-F1-predicted_aligned_error_v6.json\n",
+      "8.0K 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": "3.13.5"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

{protein_quest-0.6.0 → protein_quest-0.7.0}/docs/notebooks/uniprot.ipynb

@@ -32,7 +32,7 @@
    "id": "5378e1d5",
    "metadata": {},
    "source": [
-    "## Search for uniprot acessions based on a query"
+    "## Search for uniprot accessions based on a query"
    ]
   },
   {