tooluniverse 1.0.6__py3-none-any.whl → 1.0.8__py3-none-any.whl

tooluniverse/tools/ADMETAI_predict_physicochemical_properties.py

@@ -0,0 +1,49 @@
+"""
+ADMETAI_predict_physicochemical_properties
+
+Predicts physicochemical properties (molecular weight, logP, hydrogen bond acceptors/donors, Lipi...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ADMETAI_predict_physicochemical_properties(
+    smiles: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Predicts physicochemical properties (molecular weight, logP, hydrogen bond acceptors/donors, Lipi...
+
+    Parameters
+    ----------
+    smiles : list[Any]
+        The list of SMILES strings.
+    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": "ADMETAI_predict_physicochemical_properties",
+            "arguments": {"smiles": smiles},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ADMETAI_predict_physicochemical_properties"]

tooluniverse/tools/ADMETAI_predict_solubility_lipophilicity_hydration.py

@@ -0,0 +1,49 @@
+"""
+ADMETAI_predict_solubility_lipophilicity_hydration
+
+Predicts solubility, lipophilicity, and hydration endpoints (Solubility_AqSolDB, Lipophilicity_As...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ADMETAI_predict_solubility_lipophilicity_hydration(
+    smiles: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Predicts solubility, lipophilicity, and hydration endpoints (Solubility_AqSolDB, Lipophilicity_As...
+
+    Parameters
+    ----------
+    smiles : list[Any]
+        The list of SMILES strings.
+    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": "ADMETAI_predict_solubility_lipophilicity_hydration",
+            "arguments": {"smiles": smiles},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ADMETAI_predict_solubility_lipophilicity_hydration"]

tooluniverse/tools/ADMETAI_predict_stress_response.py

@@ -0,0 +1,46 @@
+"""
+ADMETAI_predict_stress_response
+
+Predicts stress response endpoints (SR-ARE, SR-ATAD5, SR-HSE, SR-MMP, SR-p53) for a given list of...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ADMETAI_predict_stress_response(
+    smiles: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Predicts stress response endpoints (SR-ARE, SR-ATAD5, SR-HSE, SR-MMP, SR-p53) for a given list of...
+
+    Parameters
+    ----------
+    smiles : list[Any]
+        The list of SMILES strings.
+    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": "ADMETAI_predict_stress_response", "arguments": {"smiles": smiles}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ADMETAI_predict_stress_response"]

tooluniverse/tools/ADMETAI_predict_toxicity.py

@@ -0,0 +1,46 @@
+"""
+ADMETAI_predict_toxicity
+
+Predicts toxicity endpoints (AMES, Carcinogens_Lagunin, ClinTox, DILI, LD50_Zhu, Skin_Reaction, h...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ADMETAI_predict_toxicity(
+    smiles: list[Any],
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Predicts toxicity endpoints (AMES, Carcinogens_Lagunin, ClinTox, DILI, LD50_Zhu, Skin_Reaction, h...
+
+    Parameters
+    ----------
+    smiles : list[Any]
+        The list of SMILES strings.
+    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": "ADMETAI_predict_toxicity", "arguments": {"smiles": smiles}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ADMETAI_predict_toxicity"]

tooluniverse/tools/ADMETAnalyzerAgent.py

@@ -0,0 +1,59 @@
+"""
+ADMETAnalyzerAgent
+
+AI agent that analyzes ADMET data and provides insights on drug-likeness and safety profiles
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ADMETAnalyzerAgent(
+    compounds: str,
+    admet_data: str,
+    disease_context: Optional[str] = "",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    AI agent that analyzes ADMET data and provides insights on drug-likeness and safety profiles
+
+    Parameters
+    ----------
+    compounds : str
+        List of compounds to analyze (comma-separated)
+    admet_data : str
+        ADMET data from computational tools to analyze
+    disease_context : str
+        Disease context for ADMET evaluation
+    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": "ADMETAnalyzerAgent",
+            "arguments": {
+                "compounds": compounds,
+                "admet_data": admet_data,
+                "disease_context": disease_context,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ADMETAnalyzerAgent"]

tooluniverse/tools/AdvancedCodeQualityAnalyzer.py

@@ -0,0 +1,63 @@
+"""
+AdvancedCodeQualityAnalyzer
+
+Performs deep analysis of code quality including complexity, security, performance, and maintaina...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdvancedCodeQualityAnalyzer(
+    source_code: str,
+    language: Optional[str] = "python",
+    analysis_depth: Optional[str] = "comprehensive",
+    domain_context: Optional[str] = None,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Performs deep analysis of code quality including complexity, security, performance, and maintaina...
+
+    Parameters
+    ----------
+    source_code : str
+        The source code to analyze for quality assessment
+    language : str
+        Programming language (python, javascript, etc.)
+    analysis_depth : str
+        Level of analysis depth to perform
+    domain_context : str
+        Domain context for specialized analysis (e.g., bioinformatics, web development)
+    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": "AdvancedCodeQualityAnalyzer",
+            "arguments": {
+                "source_code": source_code,
+                "language": language,
+                "analysis_depth": analysis_depth,
+                "domain_context": domain_context,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdvancedCodeQualityAnalyzer"]

tooluniverse/tools/AdverseEventICDMapper.py

@@ -0,0 +1,46 @@
+"""
+AdverseEventICDMapper
+
+Extracts adverse events from narrative clinical or pharmacovigilance text and maps each event to ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdverseEventICDMapper(
+    source_text: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Extracts adverse events from narrative clinical or pharmacovigilance text and maps each event to ...
+
+    Parameters
+    ----------
+    source_text : str
+        Unstructured narrative text that may mention adverse events.
+    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": "AdverseEventICDMapper", "arguments": {"source_text": source_text}},
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdverseEventICDMapper"]

tooluniverse/tools/AdverseEventPredictionQuestionGenerator.py

@@ -0,0 +1,52 @@
+"""
+AdverseEventPredictionQuestionGenerator
+
+Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdverseEventPredictionQuestionGenerator(
+    disease_name: str,
+    drug_name: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+
+    Parameters
+    ----------
+    disease_name : str
+        The name of the disease or condition
+    drug_name : str
+        The name of the drug
+    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": "AdverseEventPredictionQuestionGenerator",
+            "arguments": {"disease_name": disease_name, "drug_name": drug_name},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdverseEventPredictionQuestionGenerator"]

tooluniverse/tools/AdverseEventPredictionQuestionGeneratorWithContext.py

@@ -0,0 +1,59 @@
+"""
+AdverseEventPredictionQuestionGeneratorWithContext
+
+Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def AdverseEventPredictionQuestionGeneratorWithContext(
+    disease_name: str,
+    drug_name: str,
+    context_information: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Generates a set of personalized adverse‐event prediction questions for a given disease and drug, ...
+
+    Parameters
+    ----------
+    disease_name : str
+        The name of the disease or condition
+    drug_name : str
+        The name of the drug
+    context_information : str
+        Additional context information such as patient medical history, clinical find...
+    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": "AdverseEventPredictionQuestionGeneratorWithContext",
+            "arguments": {
+                "disease_name": disease_name,
+                "drug_name": drug_name,
+                "context_information": context_information,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["AdverseEventPredictionQuestionGeneratorWithContext"]

tooluniverse/tools/ArXiv_search_papers.py

@@ -0,0 +1,63 @@
+"""
+ArXiv_search_papers
+
+Search arXiv for papers by keyword using the public arXiv API. Returns papers with title, abstrac...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ArXiv_search_papers(
+    query: str,
+    limit: Optional[int] = 10,
+    sort_by: Optional[str] = "relevance",
+    sort_order: Optional[str] = "descending",
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search arXiv for papers by keyword using the public arXiv API. Returns papers with title, abstrac...
+
+    Parameters
+    ----------
+    query : str
+        Search query for arXiv papers. Use keywords separated by spaces to refine you...
+    limit : int
+        Number of papers to return. This sets the maximum number of papers retrieved ...
+    sort_by : str
+        Sort order for results. Options: 'relevance', 'lastUpdatedDate', 'submittedDate'
+    sort_order : str
+        Sort direction. Options: 'ascending', 'descending'
+    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": "ArXiv_search_papers",
+            "arguments": {
+                "query": query,
+                "limit": limit,
+                "sort_by": sort_by,
+                "sort_order": sort_order,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ArXiv_search_papers"]

tooluniverse/tools/ArgumentDescriptionOptimizer.py

@@ -0,0 +1,55 @@
+"""
+ArgumentDescriptionOptimizer
+
+Optimizes the descriptions of tool arguments/parameters based on test case results and actual usa...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def ArgumentDescriptionOptimizer(
+    parameter_schema: str,
+    test_results: str,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> Any:
+    """
+    Optimizes the descriptions of tool arguments/parameters based on test case results and actual usa...
+
+    Parameters
+    ----------
+    parameter_schema : str
+        JSON string of the original parameter schema with properties and descriptions.
+    test_results : str
+        A JSON string containing test case input/output pairs showing parameter usage.
+    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": "ArgumentDescriptionOptimizer",
+            "arguments": {
+                "parameter_schema": parameter_schema,
+                "test_results": test_results,
+            },
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["ArgumentDescriptionOptimizer"]

tooluniverse/tools/BioRxiv_search_preprints.py

@@ -0,0 +1,52 @@
+"""
+BioRxiv_search_preprints
+
+Search bioRxiv preprints using the public bioRxiv API. Returns preprints with title, authors, yea...
+"""
+
+from typing import Any, Optional, Callable
+from ._shared_client import get_shared_client
+
+
+def BioRxiv_search_preprints(
+    query: str,
+    max_results: int,
+    *,
+    stream_callback: Optional[Callable[[str], None]] = None,
+    use_cache: bool = False,
+    validate: bool = True,
+) -> list[Any]:
+    """
+    Search bioRxiv preprints using the public bioRxiv API. Returns preprints with title, authors, yea...
+
+    Parameters
+    ----------
+    query : str
+        Search query for bioRxiv preprints. Use keywords separated by spaces to refin...
+    max_results : int
+        Maximum number of preprints to return. Default is 10, maximum is 200.
+    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": "BioRxiv_search_preprints",
+            "arguments": {"query": query, "max_results": max_results},
+        },
+        stream_callback=stream_callback,
+        use_cache=use_cache,
+        validate=validate,
+    )
+
+
+__all__ = ["BioRxiv_search_preprints"]