tooluniverse 1.0.5__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/tools/PMC_search_papers.py

@@ -0,0 +1,67 @@
+"""
+PMC_search_papers
+
+Search for full-text biomedical literature using PMC (PubMed Central) API. PMC is the free full-t...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PMC_search_papers(
+    query: str,
+    limit: int,
+    date_from: str,
+    date_to: str,
+    article_type: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search for full-text biomedical literature using PMC (PubMed Central) API. PMC is the free full-t...
+
+    Parameters
+    ----------
+    query : str
+        Search query for PMC papers. Use keywords separated by spaces to refine your ...
+    limit : int
+        Maximum number of papers to return. This sets the maximum number of papers re...
+    date_from : str
+        Start date for publication date filter (YYYY/MM/DD format). Optional paramete...
+    date_to : str
+        End date for publication date filter (YYYY/MM/DD format). Optional parameter ...
+    article_type : str
+        Article type filter (e.g., 'research-article', 'review', 'case-report'). Opti...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PMC_search_papers",
+            "arguments": {
+                "query": query,
+                "limit": limit,
+                "date_from": date_from,
+                "date_to": date_to,
+                "article_type": article_type,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PMC_search_papers"]

tooluniverse/tools/ProtocolOptimizer.py

@@ -0,0 +1,49 @@
+"""
+ProtocolOptimizer
+
+Reviews an initial protocol and delivers targeted revisions that improve clarity, feasibility, ri...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ProtocolOptimizer(
+    initial_protocol: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Reviews an initial protocol and delivers targeted revisions that improve clarity, feasibility, ri...
+
+    Parameters
+    ----------
+    initial_protocol : str
+
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "ProtocolOptimizer",
+            "arguments": {"initial_protocol": initial_protocol},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ProtocolOptimizer"]

tooluniverse/tools/PubChem_get_CID_by_SMILES.py

@@ -0,0 +1,46 @@
+"""
+PubChem_get_CID_by_SMILES
+
+Retrieve corresponding CID list by SMILES string.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_get_CID_by_SMILES(
+    smiles: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve corresponding CID list by SMILES string.
+
+    Parameters
+    ----------
+    smiles : str
+        SMILES expression (e.g., "CC(=O)OC1=CC=CC=C1C(=O)O" corresponds to aspirin).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "PubChem_get_CID_by_SMILES", "arguments": {"smiles": smiles}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_get_CID_by_SMILES"]

tooluniverse/tools/PubChem_get_CID_by_compound_name.py

@@ -0,0 +1,46 @@
+"""
+PubChem_get_CID_by_compound_name
+
+Retrieve corresponding CID list (IdentifierList) by chemical name.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_get_CID_by_compound_name(
+    name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Retrieve corresponding CID list (IdentifierList) by chemical name.
+
+    Parameters
+    ----------
+    name : str
+        Chemical name (e.g., "Aspirin" or IUPAC name).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "PubChem_get_CID_by_compound_name", "arguments": {"name": name}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_get_CID_by_compound_name"]

tooluniverse/tools/PubChem_get_associated_patents_by_CID.py

@@ -0,0 +1,46 @@
+"""
+PubChem_get_associated_patents_by_CID
+
+Get a list of patents associated with a specific compound CID.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_get_associated_patents_by_CID(
+    cid: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get a list of patents associated with a specific compound CID.
+
+    Parameters
+    ----------
+    cid : int
+        PubChem compound ID to query, e.g., 2244 (Aspirin).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "PubChem_get_associated_patents_by_CID", "arguments": {"cid": cid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_get_associated_patents_by_CID"]

tooluniverse/tools/PubChem_get_compound_2D_image_by_CID.py

@@ -0,0 +1,52 @@
+"""
+PubChem_get_compound_2D_image_by_CID
+
+Get 2D structure image (PNG format) of compound by CID.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_get_compound_2D_image_by_CID(
+    cid: int,
+    image_size: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get 2D structure image (PNG format) of compound by CID.
+
+    Parameters
+    ----------
+    cid : int
+        Compound ID to get image for, e.g., 2244.
+    image_size : str
+        Optional parameter, image size, like "200x200" (default).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PubChem_get_compound_2D_image_by_CID",
+            "arguments": {"cid": cid, "image_size": image_size},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_get_compound_2D_image_by_CID"]

tooluniverse/tools/PubChem_get_compound_properties_by_CID.py

@@ -0,0 +1,46 @@
+"""
+PubChem_get_compound_properties_by_CID
+
+Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_get_compound_properties_by_CID(
+    cid: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, ...
+
+    Parameters
+    ----------
+    cid : int
+        PubChem compound ID to query, e.g., 2244 (Aspirin).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "PubChem_get_compound_properties_by_CID", "arguments": {"cid": cid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_get_compound_properties_by_CID"]

tooluniverse/tools/PubChem_get_compound_synonyms_by_CID.py

@@ -0,0 +1,46 @@
+"""
+PubChem_get_compound_synonyms_by_CID
+
+Get complete list of synonyms for compound by CID.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_get_compound_synonyms_by_CID(
+    cid: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get complete list of synonyms for compound by CID.
+
+    Parameters
+    ----------
+    cid : int
+        Compound ID to query synonyms for, e.g., 2244.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {"name": "PubChem_get_compound_synonyms_by_CID", "arguments": {"cid": cid}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_get_compound_synonyms_by_CID"]

tooluniverse/tools/PubChem_get_compound_xrefs_by_CID.py

@@ -0,0 +1,52 @@
+"""
+PubChem_get_compound_xrefs_by_CID
+
+Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_get_compound_xrefs_by_CID(
+    cid: int,
+    xref_types: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.
+
+    Parameters
+    ----------
+    cid : int
+        Compound ID to query external references for, e.g., 2244.
+    xref_types : list[Any]
+        List of external database types to query, e.g., ["RegistryID", "RN", "PubMedI...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PubChem_get_compound_xrefs_by_CID",
+            "arguments": {"cid": cid, "xref_types": xref_types},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_get_compound_xrefs_by_CID"]

tooluniverse/tools/PubChem_search_compounds_by_similarity.py

@@ -0,0 +1,52 @@
+"""
+PubChem_search_compounds_by_similarity
+
+Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_search_compounds_by_similarity(
+    smiles: str,
+    threshold: float,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above ...
+
+    Parameters
+    ----------
+    smiles : str
+        SMILES expression of target molecule.
+    threshold : float
+        Similarity threshold (between 0 and 1), e.g., 0.9 means 90% similarity.
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PubChem_search_compounds_by_similarity",
+            "arguments": {"smiles": smiles, "threshold": threshold},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_search_compounds_by_similarity"]

tooluniverse/tools/PubChem_search_compounds_by_substructure.py

@@ -0,0 +1,49 @@
+"""
+PubChem_search_compounds_by_substructure
+
+Search for all CIDs in PubChem that contain the given substructure (SMILES).
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubChem_search_compounds_by_substructure(
+    smiles: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Search for all CIDs in PubChem that contain the given substructure (SMILES).
+
+    Parameters
+    ----------
+    smiles : str
+        SMILES of substructure (e.g., "c1ccccc1" corresponds to benzene ring).
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    Any
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PubChem_search_compounds_by_substructure",
+            "arguments": {"smiles": smiles},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubChem_search_compounds_by_substructure"]

tooluniverse/tools/PubMed_Guidelines_Search.py

@@ -0,0 +1,55 @@
+"""
+PubMed_Guidelines_Search
+
+Search PubMed for peer-reviewed clinical practice guidelines using NCBI E-utilities. Filters resu...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubMed_Guidelines_Search(
+    query: str,
+    limit: int,
+    api_key: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> dict[str, Any]:
+    """
+    Search PubMed for peer-reviewed clinical practice guidelines using NCBI E-utilities. Filters resu...
+
+    Parameters
+    ----------
+    query : str
+        Medical condition, treatment, or clinical topic to search for (e.g., 'diabete...
+    limit : int
+        Maximum number of guidelines to return (default: 10)
+    api_key : str
+        Optional NCBI API key for higher rate limits. Get your free key at https://ww...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    dict[str, Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PubMed_Guidelines_Search",
+            "arguments": {"query": query, "limit": limit, "api_key": api_key},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubMed_Guidelines_Search"]

tooluniverse/tools/PubMed_search_articles.py

@@ -0,0 +1,55 @@
+"""
+PubMed_search_articles
+
+Search PubMed using NCBI E-utilities (esearch + esummary) and return articles. Returns articles w...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def PubMed_search_articles(
+    query: str,
+    limit: int,
+    api_key: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search PubMed using NCBI E-utilities (esearch + esummary) and return articles. Returns articles w...
+
+    Parameters
+    ----------
+    query : str
+        Search query for PubMed articles. Use keywords separated by spaces to refine ...
+    limit : int
+        Number of articles to return. This sets the maximum number of articles retrie...
+    api_key : str
+        Optional NCBI API key for higher rate limits. Get your free key at https://ww...
+    stream_callback : Callable, optional
+        Callback for streaming output
+    use_cache : bool, default False
+        Enable caching
+    validate : bool, default True
+        Validate parameters
+
+    Returns
+    -------
+    list[Any]
+    """
+    # Handle mutable defaults to avoid B006 linting error
+
+    return get_shared_client().run_one_function(
+        {
+            "name": "PubMed_search_articles",
+            "arguments": {"query": query, "limit": limit, "api_key": api_key},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["PubMed_search_articles"]