protein-quest 0.3.2__py3-none-any.whl → 0.4.0__py3-none-any.whl

protein_quest/__version__.py

@@ -1,2 +1,2 @@
-__version__ = "0.3.2"
+__version__ = "0.4.0"
 """The version of the package."""

protein_quest/cli.py

@@ -15,6 +15,7 @@ from textwrap import dedent
 from cattrs import structure
 from rich import print as rprint
 from rich.logging import RichHandler
+from rich.markdown import Markdown
 from rich.panel import Panel
 from rich_argparse import ArgumentDefaultsRichHelpFormatter
 from tqdm.rich import tqdm
@@ -31,7 +32,17 @@ from protein_quest.pdbe import fetch as pdbe_fetch
 from protein_quest.pdbe.io import glob_structure_files, locate_structure_file
 from protein_quest.ss import SecondaryStructureFilterQuery, filter_files_on_secondary_structure
 from protein_quest.taxonomy import SearchField, _write_taxonomy_csv, search_fields, search_taxon
-from protein_quest.uniprot import PdbResult, Query, search4af, search4emdb, search4pdb, search4uniprot
+from protein_quest.uniprot import (
+    ComplexPortalEntry,
+    PdbResult,
+    Query,
+    search4af,
+    search4emdb,
+    search4interaction_partners,
+    search4macromolecular_complexes,
+    search4pdb,
+    search4uniprot,
+)
 from protein_quest.utils import CopyMethod, copy_methods, copyfile
 
 logger = logging.getLogger(__name__)
@@ -211,6 +222,73 @@ def _add_search_taxonomy_parser(subparser: argparse._SubParsersAction):
     parser.add_argument("--limit", type=int, default=100, help="Maximum number of results to return")
 
 
+def _add_search_interaction_partners_parser(subparsers: argparse._SubParsersAction):
+    """Add search interaction partners subcommand parser."""
+    parser = subparsers.add_parser(
+        "interaction-partners",
+        help="Search for interaction partners of given UniProt accession",
+        description=dedent("""\
+            Search for interaction partners of given UniProt accession
+            in the Uniprot SPARQL endpoint and Complex Portal.
+        """),
+        formatter_class=ArgumentDefaultsRichHelpFormatter,
+    )
+    parser.add_argument(
+        "uniprot_acc",
+        type=str,
+        help="UniProt accession (for example P12345).",
+    )
+    parser.add_argument(
+        "--exclude",
+        type=str,
+        action="append",
+        help="UniProt accessions to exclude from the results. For example already known interaction partners.",
+    )
+    parser.add_argument(
+        "output_csv",
+        type=argparse.FileType("w", encoding="UTF-8"),
+        help="Output CSV with interaction partners per UniProt accession. Use `-` for stdout.",
+    )
+    parser.add_argument(
+        "--limit", type=int, default=10_000, help="Maximum number of interaction partner uniprot accessions to return"
+    )
+    parser.add_argument("--timeout", type=int, default=1_800, help="Maximum seconds to wait for query to complete")
+
+
+def _add_search_complexes_parser(subparsers: argparse._SubParsersAction):
+    """Add search complexes subcommand parser."""
+    description = dedent("""\
+        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
+    """)
+    parser = subparsers.add_parser(
+        "complexes",
+        help="Search for complexes in the Complex Portal",
+        description=Markdown(description, style="argparse.text"),  # type: ignore using rich formatter makes this OK
+        formatter_class=ArgumentDefaultsRichHelpFormatter,
+    )
+    parser.add_argument(
+        "uniprot_accs",
+        type=argparse.FileType("r", encoding="UTF-8"),
+        help="Text file with UniProt accessions (one per line) as query for searching complexes. Use `-` for stdin.",
+    )
+    parser.add_argument(
+        "output_csv",
+        type=argparse.FileType("w", encoding="UTF-8"),
+        help="Output CSV file with complex results. Use `-` for stdout.",
+    )
+    parser.add_argument("--limit", type=int, default=100, help="Maximum number of complex results to return")
+    parser.add_argument("--timeout", type=int, default=1_800, help="Maximum seconds to wait for query to complete")
+
+
 def _add_retrieve_pdbe_parser(subparsers: argparse._SubParsersAction):
     """Add retrieve pdbe subcommand parser."""
     parser = subparsers.add_parser(
@@ -458,6 +536,8 @@ def _add_search_subcommands(subparsers: argparse._SubParsersAction):
     _add_search_emdb_parser(subsubparsers)
     _add_search_go_parser(subsubparsers)
     _add_search_taxonomy_parser(subsubparsers)
+    _add_search_interaction_partners_parser(subsubparsers)
+    _add_search_complexes_parser(subsubparsers)
 
 
 def _add_retrieve_subcommands(subparsers: argparse._SubParsersAction):
@@ -636,6 +716,32 @@ def _handle_search_taxonomy(args):
     _write_taxonomy_csv(results, output_csv)
 
 
+def _handle_search_interaction_partners(args: argparse.Namespace):
+    uniprot_acc: str = args.uniprot_acc
+    excludes: set[str] = set(args.exclude) if args.exclude else set()
+    limit: int = args.limit
+    timeout: int = args.timeout
+    output_csv: TextIOWrapper = args.output_csv
+
+    rprint(f"Searching for interaction partners of '{uniprot_acc}'")
+    results = search4interaction_partners(uniprot_acc, excludes=excludes, limit=limit, timeout=timeout)
+    rprint(f"Found {len(results)} interaction partners, written to {output_csv.name}")
+    _write_lines(output_csv, results.keys())
+
+
+def _handle_search_complexes(args: argparse.Namespace):
+    uniprot_accs = args.uniprot_accs
+    limit = args.limit
+    timeout = args.timeout
+    output_csv = args.output_csv
+
+    accs = _read_lines(uniprot_accs)
+    rprint(f"Finding complexes for {len(accs)} uniprot accessions")
+    results = search4macromolecular_complexes(accs, limit=limit, timeout=timeout)
+    rprint(f"Found {len(results)} complexes, written to {output_csv.name}")
+    _write_complexes_csv(results, output_csv)
+
+
 def _handle_retrieve_pdbe(args):
     pdbe_csv = args.pdbe_csv
     output_dir = args.output_dir
@@ -875,6 +981,8 @@ HANDLERS: dict[tuple[str, str | None], Callable] = {
     ("search", "emdb"): _handle_search_emdb,
     ("search", "go"): _handle_search_go,
     ("search", "taxonomy"): _handle_search_taxonomy,
+    ("search", "interaction-partners"): _handle_search_interaction_partners,
+    ("search", "complexes"): _handle_search_complexes,
     ("retrieve", "pdbe"): _handle_retrieve_pdbe,
     ("retrieve", "alphafold"): _handle_retrieve_alphafold,
     ("retrieve", "emdb"): _handle_retrieve_emdb,
@@ -937,3 +1045,33 @@ def _iter_csv_rows(file: TextIOWrapper) -> Generator[dict[str, str]]:
 
 def _read_column_from_csv(file: TextIOWrapper, column: str) -> set[str]:
     return {row[column] for row in _iter_csv_rows(file)}
+
+
+def _write_complexes_csv(complexes: list[ComplexPortalEntry], output_csv: TextIOWrapper) -> None:
+    """Write ComplexPortal information to a CSV file.
+
+    Args:
+        complexes: List of ComplexPortalEntry objects.
+        output_csv: TextIOWrapper to write the CSV data to.
+    """
+    writer = csv.writer(output_csv)
+    writer.writerow(
+        [
+            "query_protein",
+            "complex_id",
+            "complex_url",
+            "complex_title",
+            "members",
+        ]
+    )
+    for entry in complexes:
+        members_str = ";".join(sorted(entry.members))
+        writer.writerow(
+            [
+                entry.query_protein,
+                entry.complex_id,
+                entry.complex_url,
+                entry.complex_title,
+                members_str,
+            ]
+        )

protein_quest/converter.py

@@ -13,6 +13,7 @@ type PositiveInt = int
 converter = make_converter()
 """cattrs converter to read JSON document or dict to Python objects."""
 converter.register_structure_hook(URL, lambda v, _: URL(v))
+converter.register_unstructure_hook(URL, lambda u: str(u))
 
 
 @converter.register_structure_hook

protein_quest/mcp_server.py

@@ -48,7 +48,15 @@ from protein_quest.pdbe.fetch import fetch as pdbe_fetch
 from protein_quest.pdbe.io import glob_structure_files, nr_residues_in_chain, write_single_chain_pdb_file
 from protein_quest.ss import filter_file_on_secondary_structure
 from protein_quest.taxonomy import search_taxon
-from protein_quest.uniprot import PdbResult, Query, search4af, search4emdb, search4pdb, search4uniprot
+from protein_quest.uniprot import (
+    PdbResult,
+    Query,
+    search4af,
+    search4emdb,
+    search4macromolecular_complexes,
+    search4pdb,
+    search4uniprot,
+)
 
 mcp = FastMCP("protein-quest")
 
@@ -137,6 +145,7 @@ def search_alphafolds(
 
 
 mcp.tool(search4emdb, name="search_emdb")
+mcp.tool(search4macromolecular_complexes, name="search_macromolecular_complexes")
 
 
 @mcp.tool

protein_quest/ss.py

@@ -111,6 +111,26 @@ class SecondaryStructureFilterQuery:
     ratio_min_sheet_residues: Ratio | None = None
     ratio_max_sheet_residues: Ratio | None = None
 
+    def is_actionable(self) -> bool:
+        """Check if the secondary structure query has any actionable filters.
+
+        Returns:
+            True if any of the filters are set, False otherwise.
+        """
+        return any(
+            field is not None
+            for field in [
+                self.abs_min_helix_residues,
+                self.abs_max_helix_residues,
+                self.abs_min_sheet_residues,
+                self.abs_max_sheet_residues,
+                self.ratio_min_helix_residues,
+                self.ratio_max_helix_residues,
+                self.ratio_min_sheet_residues,
+                self.ratio_max_sheet_residues,
+            ]
+        )
+
 
 def _check_range(min_val, max_val, label):
     if min_val is not None and max_val is not None and min_val >= max_val:

protein_quest/uniprot.py

@@ -201,7 +201,7 @@ def _build_sparql_generic_query(select_clause: str, where_clause: str, limit: in
     """)
 
 
-def _build_sparql_generic_by_uniprot_accesions_query(
+def _build_sparql_generic_by_uniprot_accessions_query(
     uniprot_accs: Iterable[str], select_clause: str, where_clause: str, limit: int = 10_000, groupby_clause=""
 ) -> str:
     values = " ".join(f'("{ac}")' for ac in uniprot_accs)
@@ -269,7 +269,7 @@ def _build_sparql_query_pdb(uniprot_accs: Iterable[str], limit=10_000) -> str:
     """)
 
     groupby_clause = "?protein ?pdb_db ?pdb_method ?pdb_resolution"
-    return _build_sparql_generic_by_uniprot_accesions_query(
+    return _build_sparql_generic_by_uniprot_accessions_query(
         uniprot_accs, select_clause, where_clause, limit, groupby_clause
     )
 
@@ -284,7 +284,7 @@ def _build_sparql_query_af(uniprot_accs: Iterable[str], limit=10_000) -> str:
         ?protein rdfs:seeAlso ?af_db .
         ?af_db up:database <http://purl.uniprot.org/database/AlphaFoldDB> .
     """)
-    return _build_sparql_generic_by_uniprot_accesions_query(uniprot_accs, select_clause, dedent(where_clause), limit)
+    return _build_sparql_generic_by_uniprot_accessions_query(uniprot_accs, select_clause, dedent(where_clause), limit)
 
 
 def _build_sparql_query_emdb(uniprot_accs: Iterable[str], limit=10_000) -> str:
@@ -297,7 +297,7 @@ def _build_sparql_query_emdb(uniprot_accs: Iterable[str], limit=10_000) -> str:
         ?protein rdfs:seeAlso ?emdb_db .
         ?emdb_db up:database <http://purl.uniprot.org/database/EMDB> .
     """)
-    return _build_sparql_generic_by_uniprot_accesions_query(uniprot_accs, select_clause, dedent(where_clause), limit)
+    return _build_sparql_generic_by_uniprot_accessions_query(uniprot_accs, select_clause, dedent(where_clause), limit)
 
 
 def _execute_sparql_search(
@@ -509,3 +509,156 @@ def search4emdb(uniprot_accs: Iterable[str], limit: int = 10_000, timeout: int =
     )
     limit_check("Search for EMDB entries on uniprot", limit, len(raw_results))
     return _flatten_results_emdb(raw_results)
+
+
+def _build_complex_sparql_query(uniprot_accs: Iterable[str], limit: int) -> str:
+    """Builds a SPARQL query to retrieve ComplexPortal information for given UniProt accessions.
+
+    Example:
+
+    ```sparql
+    PREFIX up:   <http://purl.uniprot.org/core/>
+    PREFIX rdf:  <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+    PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
+
+    SELECT
+    ?protein
+    ?cp_db
+    ?cp_comment
+    (GROUP_CONCAT(DISTINCT ?member; separator=",") AS ?complex_members)
+    (COUNT(DISTINCT ?member) AS ?member_count)
+    WHERE {
+    # Input UniProt accessions
+    VALUES (?ac) { ("P05067") ("P60709") ("Q05471")}
+    BIND (IRI(CONCAT("http://purl.uniprot.org/uniprot/", ?ac)) AS ?protein)
+
+    # ComplexPortal cross-reference for each input protein
+    ?protein a up:Protein ;
+            rdfs:seeAlso ?cp_db .
+    ?cp_db up:database <http://purl.uniprot.org/database/ComplexPortal> .
+    OPTIONAL { ?cp_db rdfs:comment ?cp_comment . }
+
+    # All member proteins of the same ComplexPortal complex
+    ?member a up:Protein ;
+            rdfs:seeAlso ?cp_db .
+    }
+    GROUP BY ?protein ?cp_db ?cp_comment
+    ORDER BY ?protein ?cp_db
+    LIMIT 500
+    ```
+
+    """
+    select_clause = dedent("""\
+        ?protein ?cp_db ?cp_comment
+        (GROUP_CONCAT(DISTINCT ?member; separator=",") AS ?complex_members)
+    """)
+    where_clause = dedent("""
+        # --- Complex Info ---
+        ?protein a up:Protein ;
+                rdfs:seeAlso ?cp_db .
+        ?cp_db up:database <http://purl.uniprot.org/database/ComplexPortal> .
+        OPTIONAL { ?cp_db rdfs:comment ?cp_comment . }
+        # All member proteins of the same ComplexPortal complex
+        ?member a up:Protein ;
+        rdfs:seeAlso ?cp_db .
+    """)
+    group_by = dedent("""
+       ?protein ?cp_db ?cp_comment
+    """)
+    return _build_sparql_generic_by_uniprot_accessions_query(
+        uniprot_accs, select_clause, where_clause, limit, groupby_clause=group_by
+    )
+
+
+@dataclass(frozen=True)
+class ComplexPortalEntry:
+    """A ComplexPortal entry.
+
+    Parameters:
+        query_protein: The UniProt accession used to find entry.
+        complex_id: The ComplexPortal identifier (for example "CPX-1234").
+        complex_url: The URL to the ComplexPortal entry.
+        complex_title: The title of the complex.
+        members: UniProt accessions which are members of the complex.
+    """
+
+    query_protein: str
+    complex_id: str
+    complex_url: str
+    complex_title: str
+    members: set[str]
+
+
+def _flatten_results_complex(raw_results) -> list[ComplexPortalEntry]:
+    results = []
+    for raw_result in raw_results:
+        query_protein = raw_result["protein"]["value"].split("/")[-1]
+        complex_id = raw_result["cp_db"]["value"].split("/")[-1]
+        complex_url = f"https://www.ebi.ac.uk/complexportal/complex/{complex_id}"
+        complex_title = raw_result.get("cp_comment", {}).get("value", "")
+        members = {m.split("/")[-1] for m in raw_result["complex_members"]["value"].split(",")}
+        results.append(
+            ComplexPortalEntry(
+                query_protein=query_protein,
+                complex_id=complex_id,
+                complex_url=complex_url,
+                complex_title=complex_title,
+                members=members,
+            )
+        )
+    return results
+
+
+def search4macromolecular_complexes(
+    uniprot_accs: Iterable[str], limit: int = 10_000, timeout: int = 1_800
+) -> list[ComplexPortalEntry]:
+    """Search for macromolecular complexes by UniProtKB accessions.
+
+    Queries for references to/from https://www.ebi.ac.uk/complexportal/ database in the Uniprot SPARQL endpoint.
+
+    Args:
+        uniprot_accs: UniProt accessions.
+        limit: Maximum number of results to return.
+        timeout: Timeout for the SPARQL query in seconds.
+
+    Returns:
+        List of ComplexPortalEntry objects.
+    """
+    sparql_query = _build_complex_sparql_query(uniprot_accs, limit)
+    logger.info("Executing SPARQL query for macromolecular complexes: %s", sparql_query)
+    raw_results = _execute_sparql_search(
+        sparql_query=sparql_query,
+        timeout=timeout,
+    )
+    limit_check("Search for complexes", limit, len(raw_results))
+    return _flatten_results_complex(raw_results)
+
+
+def search4interaction_partners(
+    uniprot_acc: str, excludes: set[str] | None = None, limit: int = 10_000, timeout: int = 1_800
+) -> dict[str, set[str]]:
+    """Search for interaction partners of a given UniProt accession using ComplexPortal database references.
+
+    Args:
+        uniprot_acc: UniProt accession to search interaction partners for.
+        excludes: Set of UniProt accessions to exclude from the results.
+            For example already known interaction partners.
+            If None then no complex members are excluded.
+        limit: Maximum number of results to return.
+        timeout: Timeout for the SPARQL query in seconds.
+
+    Returns:
+        Dictionary with UniProt accessions of interaction partners as keys and sets of ComplexPortal entry IDs
+        in which the interaction occurs as values.
+    """
+    ucomplexes = search4macromolecular_complexes([uniprot_acc], limit=limit, timeout=timeout)
+    hits: dict[str, set[str]] = {}
+    if excludes is None:
+        excludes = set()
+    for ucomplex in ucomplexes:
+        for member in ucomplex.members:
+            if member != uniprot_acc and member not in excludes:
+                if member not in hits:
+                    hits[member] = set()
+                hits[member].add(ucomplex.complex_id)
+    return hits

{protein_quest-0.3.2.dist-info → protein_quest-0.4.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: protein_quest
-Version: 0.3.2
+Version: 0.4.0
 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
@@ -56,12 +56,14 @@ 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 +71,8 @@ graph TB;
     taxonomy:::dashedBorder
     searchemdb:::dashedBorder
     fetchemdb:::dashedBorder
+    searchintactionpartners:::dashedBorder
+    searchcomplexes:::dashedBorder
 ```
 
 (Dotted nodes and edges are side-quests.)
@@ -204,6 +208,32 @@ 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-0.3.2.dist-info → protein_quest-0.4.0.dist-info}/RECORD

@@ -1,16 +1,16 @@
 protein_quest/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-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/__version__.py,sha256=je7v2gXyxr6yRVCFAS0wS-iABSLJOuCb-IPR-x90UAU,56
+protein_quest/cli.py,sha256=9Cgvn5BXbrAloIU2KCiFxLxJSyAoa2RLdmuB0HGsUJM,43078
+protein_quest/converter.py,sha256=Y-Oxf7lDNbEicL6GS-IpNWDwaAiHgIgs5bFAcEHCKdQ,1441
 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/mcp_server.py,sha256=CXw5rTStunXdAVQ3BWPXy19zmgQGwV5uPcWlN1HF9do,7389
 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/ss.py,sha256=qOr0aMycNAtZmXXvhCN-KZH3Qp4EejnBcE6fsFgCrmY,10343
 protein_quest/taxonomy.py,sha256=4mKv8zll4mX02Ow8CTvyqMJE2KJZvcq3QlTjjjLOJJk,5072
-protein_quest/uniprot.py,sha256=8qWV4GWqHTRfed0bE_TdgsLYcnDT_vzKu-6JxIgapJQ,18680
+protein_quest/uniprot.py,sha256=DIwQYzWZREZ7SGhkJT4Ozgl36pdz47FNfZ1QoEgEaXE,24239
 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
@@ -19,8 +19,8 @@ protein_quest/alphafold/fetch.py,sha256=iFHORaO-2NvPwmpm33tfOFUcSJx8mBGwMXxwc4bR
 protein_quest/pdbe/__init__.py,sha256=eNNHtN60NAGea7gvRkIzkoTXsYPK99s-ldIcKWYO6So,61
 protein_quest/pdbe/fetch.py,sha256=tlCrWoaOrwxnQFrf-PnimUUa6lmtHwwysS51efYsBcA,2379
 protein_quest/pdbe/io.py,sha256=iGLvmsD-eEYnrgZDYfkGWIDCzwDRRD5dwqB480talCs,10037
-protein_quest-0.3.2.dist-info/METADATA,sha256=wcURSjBlmkCt-ddhZX7xRYrL-7tT1VuBpJ36_mP0Iuk,7760
-protein_quest-0.3.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-protein_quest-0.3.2.dist-info/entry_points.txt,sha256=f1RtOxv9TFBO3w01EMEuFXBTMsqKsQcKlkxmj9zE-0g,57
-protein_quest-0.3.2.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
-protein_quest-0.3.2.dist-info/RECORD,,
+protein_quest-0.4.0.dist-info/METADATA,sha256=y5DAnM4mhSincjslsvQZ4zk1QcMysGmnsBltK_Vz4MQ,8842
+protein_quest-0.4.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+protein_quest-0.4.0.dist-info/entry_points.txt,sha256=f1RtOxv9TFBO3w01EMEuFXBTMsqKsQcKlkxmj9zE-0g,57
+protein_quest-0.4.0.dist-info/licenses/LICENSE,sha256=xx0jnfkXJvxRnG63LTGOxlggYnIysveWIZ6H3PNdCrQ,11357
+protein_quest-0.4.0.dist-info/RECORD,,