protein-quest 0.3.2__py3-none-any.whl → 0.5.0__py3-none-any.whl

{protein_quest-0.3.2.dist-info → protein_quest-0.5.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: protein_quest
-Version: 0.3.2
+Version: 0.5.0
 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
@@ -17,6 +17,7 @@ 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: platformdirs>=4.3.8
 Requires-Dist: psutil>=7.0.0
 Requires-Dist: rich-argparse>=1.7.1
 Requires-Dist: rich>=14.0.0
@@ -47,6 +48,10 @@ It uses
 - [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
@@ -56,12 +61,14 @@ graph TB;
     searchuniprot --> |uniprot_accessions|searchpdbe[/Search PDBe/]
     searchuniprot --> |uniprot_accessions|searchaf[/Search Alphafold/]
     searchuniprot -. uniprot_accessions .-> searchemdb[/Search EMDB/]
+    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_with_uniprot_acc| chainfilter{{Filter on chain of uniprot}}
+    fetchpdbe -->|mmcif_files| chainfilter{{Filter on chain of uniprot}}
     chainfilter --> |mmcif_files| residuefilter{{Filter on chain length}}
-    fetchad -->|pdb_files| confidencefilter{{Filter out low confidence}}
+    fetchad -->|mmcif_files| confidencefilter{{Filter out low confidence}}
     confidencefilter --> |mmcif_files| ssfilter{{Filter on secondary structure}}
     residuefilter --> |mmcif_files| ssfilter
     classDef dashedBorder stroke-dasharray: 5 5;
@@ -69,6 +76,8 @@ graph TB;
     taxonomy:::dashedBorder
     searchemdb:::dashedBorder
     fetchemdb:::dashedBorder
+    searchintactionpartners:::dashedBorder
+    searchcomplexes:::dashedBorder
 ```
 
 (Dotted nodes and edges are side-quests.)
@@ -90,6 +99,9 @@ The main entry point is the `protein-quest` command line tool which has multiple
 
 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
@@ -204,6 +216,32 @@ You can use following command to search for a Gene Ontology (GO) term.
 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
+```
+
 ##  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-0.5.0.dist-info/RECORD

@@ -0,0 +1,26 @@
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+protein_quest/__version__.py,sha256=AyGZhrskazcQPC8spzJ45d4XNxgla5DnO1bmKuzRj_Q,56
+protein_quest/cli.py,sha256=xiXt_2l3MxbTbmxm2sz0w8_OdJr8gz_B68GBVv5wHjE,44182
+protein_quest/converter.py,sha256=Y-Oxf7lDNbEicL6GS-IpNWDwaAiHgIgs5bFAcEHCKdQ,1441
+protein_quest/emdb.py,sha256=641c6RwNYnu-0GBFyCFBiI58fNc0jMkd0ZZ9MW9-Jmc,1501
+protein_quest/filters.py,sha256=-gasSXR4g5SzYSYbkfcDwR-tm2KCAhCMdpIVJrUPR1w,5224
+protein_quest/go.py,sha256=lZNEcw8nTc9wpV3cl4y2FG9Lsj8wsXQ6zemmAQs_DWE,5650
+protein_quest/mcp_server.py,sha256=PCXxcU3GElKg2sjMlxbsM63OiFxg9AtmfKwBJ1_0AQE,8130
+protein_quest/parallel.py,sha256=ZJrLO1t2HXs4EeNctytvBTyROPBq-4-gLf35PiolHf0,3468
+protein_quest/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+protein_quest/ss.py,sha256=qOr0aMycNAtZmXXvhCN-KZH3Qp4EejnBcE6fsFgCrmY,10343
+protein_quest/taxonomy.py,sha256=4mKv8zll4mX02Ow8CTvyqMJE2KJZvcq3QlTjjjLOJJk,5072
+protein_quest/uniprot.py,sha256=DIwQYzWZREZ7SGhkJT4Ozgl36pdz47FNfZ1QoEgEaXE,24239
+protein_quest/utils.py,sha256=2lQ7jPHWtDySBTYnoL9VTKl5XUgQVYgp9Prb7qEnjtQ,17982
+protein_quest/alphafold/__init__.py,sha256=Ktasi5BRp71wO7-PpOGDpIRRtBEefs8knIdlKQeLQpk,51
+protein_quest/alphafold/confidence.py,sha256=pYIuwYdkuPuHLagcX1dSvSyZ_84xboRLfHUxkEoc4MY,6766
+protein_quest/alphafold/entry_summary.py,sha256=GtE3rT7wH3vIOOeiXY2s80Fo6EzdoqlcvakW8K591Yk,1257
+protein_quest/alphafold/fetch.py,sha256=wIsgPZmtnE5EoAL9G22Y6Ehx9d0md53Mw88-6LLGp0Q,12298
+protein_quest/pdbe/__init__.py,sha256=eNNHtN60NAGea7gvRkIzkoTXsYPK99s-ldIcKWYO6So,61
+protein_quest/pdbe/fetch.py,sha256=e8CHWDX2QzWnVLmYXCfNrscw1UcN1lI9Uz6Z5HmEOEQ,2510
+protein_quest/pdbe/io.py,sha256=iGLvmsD-eEYnrgZDYfkGWIDCzwDRRD5dwqB480talCs,10037
+protein_quest-0.5.0.dist-info/METADATA,sha256=atoElM2xwPd9ubxXSQsFQYz2hjALJi-AegCRkrynEYc,9236
+protein_quest-0.5.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+protein_quest-0.5.0.dist-info/entry_points.txt,sha256=f1RtOxv9TFBO3w01EMEuFXBTMsqKsQcKlkxmj9zE-0g,57
+protein_quest-0.5.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+protein_quest-0.5.0.dist-info/RECORD,,

protein_quest-0.3.2.dist-info/RECORD

@@ -1,26 +0,0 @@
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-protein_quest/__version__.py,sha256=tDIN8WjNdFKRoXsf6tArV0_n6nbcPEBWNv1zuhaRbKo,56
-protein_quest/cli.py,sha256=k4HC282QkbAAIk614vIJgaKfkS3XD9hYj7E5hEuiDxA,37893
-protein_quest/converter.py,sha256=tSDw7HOlC7UoWryr_G-sHGzGq8nwflzSq8o7Gv1hWuQ,1382
-protein_quest/emdb.py,sha256=QEeU0VJQ4lLM-o5yAU3QZlrtzDZNgnC5fCjlqPtTyAY,1370
-protein_quest/filters.py,sha256=-gasSXR4g5SzYSYbkfcDwR-tm2KCAhCMdpIVJrUPR1w,5224
-protein_quest/go.py,sha256=lZNEcw8nTc9wpV3cl4y2FG9Lsj8wsXQ6zemmAQs_DWE,5650
-protein_quest/mcp_server.py,sha256=auftrx4aBZp1P-pBcunkPiSmXLtOIZ6MTuhUuW7yrGY,7241
-protein_quest/parallel.py,sha256=ZJrLO1t2HXs4EeNctytvBTyROPBq-4-gLf35PiolHf0,3468
-protein_quest/py.typed,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-protein_quest/ss.py,sha256=MMHgqKPxjYpjyExiqslWjmyG7aeForeAeJorCYdh75g,9663
-protein_quest/taxonomy.py,sha256=4mKv8zll4mX02Ow8CTvyqMJE2KJZvcq3QlTjjjLOJJk,5072
-protein_quest/uniprot.py,sha256=8qWV4GWqHTRfed0bE_TdgsLYcnDT_vzKu-6JxIgapJQ,18680
-protein_quest/utils.py,sha256=z4PPPcog6nvPhA93DWVf7stv5uJ4h_2BP5owdhoO5mo,5626
-protein_quest/alphafold/__init__.py,sha256=Ktasi5BRp71wO7-PpOGDpIRRtBEefs8knIdlKQeLQpk,51
-protein_quest/alphafold/confidence.py,sha256=pYIuwYdkuPuHLagcX1dSvSyZ_84xboRLfHUxkEoc4MY,6766
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-protein_quest/pdbe/io.py,sha256=iGLvmsD-eEYnrgZDYfkGWIDCzwDRRD5dwqB480talCs,10037
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-protein_quest-0.3.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-protein_quest-0.3.2.dist-info/RECORD,,