tooluniverse 1.0.6__py3-none-any.whl → 1.0.7__py3-none-any.whl

tooluniverse/pmc_tool.py

@@ -21,15 +21,18 @@ class PMCTool(BaseTool):
         super().__init__(tool_config)
         self.base_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils"
         self.session = requests.Session()
-        self.session.headers.update({
-            'User-Agent': 'ToolUniverse/1.0',
-            'Accept': 'application/json'
-        })
-
-    def _search(self, query: str, limit: int = 10,
-                date_from: Optional[str] = None,
-                date_to: Optional[str] = None,
-                article_type: Optional[str] = None) -> List[Dict[str, Any]]:
+        self.session.headers.update(
+            {"User-Agent": "ToolUniverse/1.0", "Accept": "application/json"}
+        )
+
+    def _search(
+        self,
+        query: str,
+        limit: int = 10,
+        date_from: Optional[str] = None,
+        date_to: Optional[str] = None,
+        article_type: Optional[str] = None,
+    ) -> List[Dict[str, Any]]:
         """
         Search for papers using PMC API.
 
@@ -46,11 +49,11 @@ class PMCTool(BaseTool):
         try:
             # Step 1: Search PMC for article IDs
             search_params = {
-                'db': 'pmc',
-                'term': query,
-                'retmax': min(limit, 100),  # NCBI API max limit
-                'retmode': 'json',
-                'sort': 'relevance'
+                "db": "pmc",
+                "term": query,
+                "retmax": min(limit, 100),  # NCBI API max limit
+                "retmode": "json",
+                "sort": "relevance",
             }
 
             # Add date filters if provided
@@ -62,37 +65,29 @@ class PMCTool(BaseTool):
                     )
                 else:
                     date_filter.append(f"(:{date_to}[PDAT])")
-                search_params['term'] += f" AND {' '.join(date_filter)}"
+                search_params["term"] += f" AND {' '.join(date_filter)}"
 
             # Add article type filter if provided
             if article_type:
-                search_params['term'] += f" AND {article_type}[PT]"
+                search_params["term"] += f" AND {article_type}[PT]"
 
             # Make search request
             search_response = self.session.get(
-                f"{self.base_url}/esearch.fcgi",
-                params=search_params,
-                timeout=30
+                f"{self.base_url}/esearch.fcgi", params=search_params, timeout=30
             )
             search_response.raise_for_status()
 
             search_data = search_response.json()
-            pmc_ids = search_data.get('esearchresult', {}).get('idlist', [])
+            pmc_ids = search_data.get("esearchresult", {}).get("idlist", [])
 
             if not pmc_ids:
                 return []
 
             # Step 2: Get detailed information for each article
-            summary_params = {
-                'db': 'pmc',
-                'id': ','.join(pmc_ids),
-                'retmode': 'json'
-            }
+            summary_params = {"db": "pmc", "id": ",".join(pmc_ids), "retmode": "json"}
 
             summary_response = self.session.get(
-                f"{self.base_url}/esummary.fcgi",
-                params=summary_params,
-                timeout=30
+                f"{self.base_url}/esummary.fcgi", params=summary_params, timeout=30
             )
             summary_response.raise_for_status()
 
@@ -101,32 +96,35 @@ class PMCTool(BaseTool):
 
             # Parse results
             for pmc_id in pmc_ids:
-                article_data = summary_data.get('result', {}).get(pmc_id, {})
+                article_data = summary_data.get("result", {}).get(pmc_id, {})
 
                 paper = {
-                    'title': article_data.get('title', 'No title'),
-                    'abstract': article_data.get('abstract', 'No abstract available'),
-                    'authors': self._extract_authors(article_data.get('authors', [])),
-                    'year': self._extract_year(article_data.get('pubdate')),
-                    'pmc_id': pmc_id,
-                    'pmid': article_data.get('pmid'),
-                    'doi': article_data.get('elocationid'),
-                    'url': f"https://www.ncbi.nlm.nih.gov/pmc/articles/{pmc_id}/",
-                    'venue': article_data.get('source'),
-                    'open_access': True,  # PMC only contains open access articles
-                    'source': 'PMC',
-                    'article_type': (article_data.get('pubtype', ['Unknown'])[0]
-                                     if article_data.get('pubtype') else 'Unknown'),
-                    'citations': article_data.get('pmcrefcount', 0)
+                    "title": article_data.get("title", "No title"),
+                    "abstract": article_data.get("abstract", "No abstract available"),
+                    "authors": self._extract_authors(article_data.get("authors", [])),
+                    "year": self._extract_year(article_data.get("pubdate")),
+                    "pmc_id": pmc_id,
+                    "pmid": article_data.get("pmid"),
+                    "doi": article_data.get("elocationid"),
+                    "url": f"https://www.ncbi.nlm.nih.gov/pmc/articles/{pmc_id}/",
+                    "venue": article_data.get("source"),
+                    "open_access": True,  # PMC only contains open access articles
+                    "source": "PMC",
+                    "article_type": (
+                        article_data.get("pubtype", ["Unknown"])[0]
+                        if article_data.get("pubtype")
+                        else "Unknown"
+                    ),
+                    "citations": article_data.get("pmcrefcount", 0),
                 }
                 results.append(paper)
 
             return results
 
         except requests.exceptions.RequestException as e:
-            return [{'error': f'PMC API request failed: {str(e)}'}]
+            return [{"error": f"PMC API request failed: {str(e)}"}]
         except Exception as e:
-            return [{'error': f'PMC API error: {str(e)}'}]
+            return [{"error": f"PMC API error: {str(e)}"}]
 
     def _extract_authors(self, authors: List[Dict]) -> List[str]:
         """Extract author names from PMC API response."""
@@ -135,7 +133,7 @@ class PMCTool(BaseTool):
 
         author_names = []
         for author in authors:
-            name = author.get('name', '')
+            name = author.get("name", "")
             if name:
                 author_names.append(name)
 
@@ -144,14 +142,14 @@ class PMCTool(BaseTool):
     def _extract_year(self, pubdate: str) -> str:
         """Extract year from publication date."""
         if not pubdate:
-            return 'Unknown'
+            return "Unknown"
 
         try:
             # PMC API returns dates in various formats
             # Extract year from the beginning of the string
             return pubdate[:4]
         except Exception:
-            return 'Unknown'
+            return "Unknown"
 
     def run(self, tool_arguments) -> List[Dict[str, Any]]:
         """
@@ -163,19 +161,19 @@ class PMCTool(BaseTool):
         Returns:
             List of paper dictionaries
         """
-        query = tool_arguments.get('query', '')
+        query = tool_arguments.get("query", "")
         if not query:
-            return [{'error': 'Query parameter is required'}]
+            return [{"error": "Query parameter is required"}]
 
-        limit = tool_arguments.get('limit', 10)
-        date_from = tool_arguments.get('date_from')
-        date_to = tool_arguments.get('date_to')
-        article_type = tool_arguments.get('article_type')
+        limit = tool_arguments.get("limit", 10)
+        date_from = tool_arguments.get("date_from")
+        date_to = tool_arguments.get("date_to")
+        article_type = tool_arguments.get("article_type")
 
         return self._search(
             query=query,
             limit=limit,
             date_from=date_from,
             date_to=date_to,
-            article_type=article_type
-        )
+            article_type=article_type,
+        )

tooluniverse/protein_structure_3d_tool.py

@@ -0,0 +1,295 @@
+"""
+Protein Structure 3D Visualization Tool
+=======================================
+
+Tool for visualizing 3D protein structures using py3Dmol.
+Supports PDB IDs, PDB file content, and various visualization styles.
+"""
+
+import requests
+from typing import Any, Dict
+from .visualization_tool import VisualizationTool
+from .tool_registry import register_tool
+
+
+@register_tool("ProteinStructure3DTool")
+class ProteinStructure3DTool(VisualizationTool):
+    """Tool for visualizing 3D protein structures using py3Dmol."""
+
+    def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+        """Generate 3D protein structure visualization."""
+        try:
+            import py3Dmol
+
+            # Extract parameters
+            pdb_id = arguments.get("pdb_id")
+            pdb_content = arguments.get("pdb_content")
+            style = arguments.get("style", "cartoon")
+            color_scheme = arguments.get("color_scheme", "spectrum")
+            width = arguments.get("width", self.default_width)
+            height = arguments.get("height", self.default_height)
+            show_sidechains = arguments.get("show_sidechains", False)
+            show_surface = arguments.get("show_surface", False)
+
+            # Get PDB content
+            if pdb_content:
+                pdb_data = pdb_content
+            elif pdb_id:
+                pdb_data = self._fetch_pdb_content(pdb_id)
+            else:
+                return self.create_error_response(
+                    "Either pdb_id or pdb_content must be provided"
+                )
+
+            # Create py3Dmol viewer
+            viewer = py3Dmol.view(width=width, height=height)
+            viewer.addModel(pdb_data, "pdb")
+
+            # Apply visualization style
+            if style == "cartoon":
+                viewer.setStyle({"cartoon": {"color": color_scheme}})
+            elif style == "stick":
+                viewer.setStyle({"stick": {"color": color_scheme}})
+            elif style == "sphere":
+                viewer.setStyle({"sphere": {"color": color_scheme}})
+            elif style == "line":
+                viewer.setStyle({"line": {"color": color_scheme}})
+            else:
+                viewer.setStyle({"cartoon": {"color": color_scheme}})
+
+            # Add sidechains if requested
+            if show_sidechains:
+                resn_list = [
+                    "ALA",
+                    "ARG",
+                    "ASN",
+                    "ASP",
+                    "CYS",
+                    "GLN",
+                    "GLU",
+                    "GLY",
+                    "HIS",
+                    "ILE",
+                    "LEU",
+                    "LYS",
+                    "MET",
+                    "PHE",
+                    "PRO",
+                    "SER",
+                    "THR",
+                    "TRP",
+                    "TYR",
+                    "VAL",
+                ]
+                viewer.addStyle(
+                    {"stick": {"radius": 0.1}}, {"and": [{"resn": resn_list}]}
+                )
+
+            # Add surface if requested
+            if show_surface:
+                viewer.addSurface(py3Dmol.VDW, {"opacity": 0.7, "color": "white"})
+
+            # Zoom to fit
+            viewer.zoomTo()
+
+            # Generate HTML with modern UI
+            viewer_html = viewer._make_html()
+
+            # Create control panel
+            control_panel = self._create_control_panel(style, color_scheme)
+
+            # Create toolbar
+            toolbar = self._create_toolbar()
+
+            # Create info cards
+            info_cards = self._create_protein_info_cards(pdb_id, pdb_data)
+
+            # Generate modern HTML
+            html_content = self.create_py3dmol_html(
+                viewer_html,
+                width,
+                height,
+                title=f"Protein Structure: {pdb_id or 'Custom PDB'}",
+                control_panel=control_panel,
+                toolbar=toolbar,
+                info_cards=info_cards,
+            )
+
+            # Add JavaScript controls
+            html_content = html_content.replace(
+                "</body>", f"{self.add_3d_controls_script()}</body>"
+            )
+
+            # Prepare metadata
+            metadata = {
+                "width": width,
+                "height": height,
+                "style": style,
+                "color_scheme": color_scheme,
+                "pdb_id": pdb_id,
+                "show_sidechains": show_sidechains,
+                "show_surface": show_surface,
+            }
+
+            return self.create_visualization_response(
+                html_content=html_content,
+                viz_type="protein_structure_3d",
+                data={
+                    "pdb_content": (
+                        pdb_data[:500] + "..." if len(pdb_data) > 500 else pdb_data
+                    )
+                },
+                metadata=metadata,
+            )
+
+        except ImportError:
+            return self.create_error_response(
+                "py3Dmol is not installed. Please install it with: "
+                "pip install py3Dmol",
+                "MissingDependency",
+            )
+        except Exception as e:
+            return self.create_error_response(
+                f"Failed to create protein visualization: {str(e)}"
+            )
+
+    def _fetch_pdb_content(self, pdb_id: str) -> str:
+        """Fetch PDB content from RCSB PDB database."""
+        try:
+            url = f"https://files.rcsb.org/view/{pdb_id.upper()}.pdb"
+            response = requests.get(url, timeout=30)
+            response.raise_for_status()
+            return response.text
+        except requests.RequestException as e:
+            raise ValueError(f"Failed to fetch PDB file for {pdb_id}: {str(e)}")
+
+    def _create_control_panel(self, current_style: str, current_color: str) -> str:
+        """Create floating control panel HTML."""
+        return f"""
+        <div class="control-panel">
+            <div class="control-group">
+                <label class="control-label">Style</label>
+                <select class="control-select" id="styleSelect" onchange="changeStyle()">
+                    <option value="cartoon" {'selected' if current_style == 'cartoon' else ''}>Cartoon</option>
+                    <option value="stick" {'selected' if current_style == 'stick' else ''}>Stick</option>
+                    <option value="sphere" {'selected' if current_style == 'sphere' else ''}>Sphere</option>
+                    <option value="line" {'selected' if current_style == 'line' else ''}>Line</option>
+                    <option value="surface" {'selected' if current_style == 'surface' else ''}>Surface</option>
+                </select>
+            </div>
+            <div class="control-group">
+                <label class="control-label">Color Scheme</label>
+                <select class="control-select" id="colorSelect" onchange="changeColor()">
+                    <option value="spectrum" {'selected' if current_color == 'spectrum' else ''}>Spectrum</option>
+                    <option value="rainbow" {'selected' if current_color == 'rainbow' else ''}>Rainbow</option>
+                    <option value="ss" {'selected' if current_color == 'ss' else ''}>Secondary Structure</option>
+                    <option value="chain" {'selected' if current_color == 'chain' else ''}>Chain</option>
+                    <option value="elem" {'selected' if current_color == 'elem' else ''}>Element</option>
+                </select>
+            </div>
+            <div class="control-group">
+                <label class="control-label">Background</label>
+                <select class="control-select" id="bgSelect" onchange="changeBackground()">
+                    <option value="white" selected>White</option>
+                    <option value="black">Black</option>
+                    <option value="gray">Gray</option>
+                </select>
+            </div>
+        </div>
+        """
+
+    def _create_toolbar(self) -> str:
+        """Create bottom toolbar HTML."""
+        return """
+        <div class="toolbar">
+            <button class="btn" onclick="resetView()">Reset View</button>
+            <button class="btn btn-secondary" onclick="downloadScreenshot()">Screenshot</button>
+            <button class="btn btn-outline" onclick="toggleFullscreen()">Fullscreen</button>
+        </div>
+        """
+
+    def _create_protein_info_cards(self, pdb_id: str, pdb_data: str) -> str:
+        """Create protein information cards."""
+        # Parse basic PDB info
+        lines = pdb_data.split("\n")
+        title = "Unknown Protein"
+        organism = "Unknown"
+        resolution = "N/A"
+        method = "Unknown"
+        residue_count = 0
+        atom_count = 0
+
+        for line in lines:
+            if line.startswith("TITLE"):
+                title = line[10:].strip()
+            elif line.startswith("SOURCE"):
+                if "ORGANISM_SCIENTIFIC" in line:
+                    organism = (
+                        line.split("ORGANISM_SCIENTIFIC:")[1].split(";")[0].strip()
+                    )
+            elif line.startswith("REMARK   2 RESOLUTION"):
+                resolution = line.split("RESOLUTION.")[1].split("ANGSTROMS")[0].strip()
+            elif line.startswith("EXPDTA"):
+                method = line[10:].strip()
+            elif line.startswith("ATOM"):
+                atom_count += 1
+                if atom_count == 1:
+                    residue_count = 1
+                elif line[22:26].strip() != lines[atom_count - 2][22:26].strip():
+                    residue_count += 1
+
+        return f"""
+        <div class="card">
+            <h3 class="card-title">
+                <svg class="card-icon" viewBox="0 0 24 24">
+                    <path d="M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M12,4A8,8 0 0,1 20,12A8,8 0 0,1 12,20A8,8 0 0,1 4,12A8,8 0 0,1 12,4M12,6A6,6 0 0,0 6,12A6,6 0 0,0 12,18A6,6 0 0,0 18,12A6,6 0 0,0 12,6M12,8A4,4 0 0,1 16,12A4,4 0 0,1 12,16A4,4 0 0,1 8,12A4,4 0 0,1 12,8Z"/>
+                </svg>
+                Protein Information
+            </h3>
+            <div class="info-grid">
+                <div class="info-item">
+                    <span class="info-label">PDB ID</span>
+                    <span class="info-value">{pdb_id or 'Custom'}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Title</span>
+                    <span class="info-value">{title[:30]}{'...' if len(title) > 30 else ''}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Organism</span>
+                    <span class="info-value">{organism[:20]}{'...' if len(organism) > 20 else ''}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Method</span>
+                    <span class="info-value">{method}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Resolution</span>
+                    <span class="info-value">{resolution}</span>
+                </div>
+            </div>
+        </div>
+
+        <div class="card">
+            <h3 class="card-title">
+                <svg class="card-icon" viewBox="0 0 24 24">
+                    <path d="M12,2A10,10 0 0,0 2,12A10,10 0 0,0 12,22A10,10 0 0,0 22,12A10,10 0 0,0 12,2M12,4A8,8 0 0,1 20,12A8,8 0 0,1 12,20A8,8 0 0,1 4,12A8,8 0 0,1 12,4M12,6A6,6 0 0,0 6,12A6,6 0 0,0 12,18A6,6 0 0,0 18,12A6,6 0 0,0 12,6M12,8A4,4 0 0,1 16,12A4,4 0 0,1 12,16A4,4 0 0,1 8,12A4,4 0 0,1 12,8Z"/>
+                </svg>
+                Structure Statistics
+            </h3>
+            <div class="info-grid">
+                <div class="info-item">
+                    <span class="info-label">Residues</span>
+                    <span class="info-value">{residue_count}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Atoms</span>
+                    <span class="info-value">{atom_count}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Chains</span>
+                    <span class="info-value">1</span>
+                </div>
+            </div>
+        </div>
+        """

tooluniverse/pubmed_tool.py

@@ -12,9 +12,7 @@ class PubMedTool(BaseTool):
 
     def __init__(self, tool_config):
         super().__init__(tool_config)
-        self.esearch_url = (
-            "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
-        )
+        self.esearch_url = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi"
         self.esummary_url = (
             "https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi"
         )
@@ -87,23 +85,88 @@ class PubMedTool(BaseTool):
             rec = result.get(uid, {})
             title = rec.get("title")
             journal = rec.get("fulljournalname") or rec.get("source")
+
+            # Extract author information
+            authors = []
+            author_list = rec.get("authors", [])
+            if isinstance(author_list, list):
+                for author in author_list:
+                    if isinstance(author, dict):
+                        name = author.get("name", "")
+                        if name:
+                            authors.append(name)
+
+            # Extract year
             year = None
             pubdate = rec.get("pubdate")
             if pubdate and len(pubdate) >= 4 and pubdate[:4].isdigit():
                 year = int(pubdate[:4])
+
+            # Extract DOI
             doi = None
             for id_obj in rec.get("articleids", []):
                 if id_obj.get("idtype") == "doi":
                     doi = id_obj.get("value")
                     break
+
+            # Extract citation count (PubMed doesn't provide this directly)
+            citations = 0
+            # PubMed API itself doesn't provide citation count, keeping it as 0
+
+            # Extract open access status
+            open_access = False
+            # PubMed API itself doesn't directly provide open access status
+
+            # Extract keywords
+            keywords = []
+            mesh_terms = rec.get("meshterms", [])
+            if isinstance(mesh_terms, list):
+                for term in mesh_terms:
+                    if isinstance(term, dict):
+                        keyword = term.get("term", "")
+                        if keyword:
+                            keywords.append(keyword)
+
+            # Extract article type
+            article_type = rec.get("pubtype", [])
+            if isinstance(article_type, list) and article_type:
+                article_type = (
+                    article_type[0]
+                    if isinstance(article_type[0], str)
+                    else str(article_type[0])
+                )
+            else:
+                article_type = "Unknown"
+
+            # Build URL
             url = f"https://pubmed.ncbi.nlm.nih.gov/{uid}/"
+
             articles.append(
                 {
-                    "title": title,
-                    "journal": journal,
+                    "title": title or "Title not available",
+                    "abstract": "Abstract not available",  # PubMed API itself doesn't provide abstracts
+                    "authors": (
+                        authors if authors else "Author information not available"
+                    ),
+                    "journal": journal or "Journal information not available",
                     "year": year,
-                    "doi": doi,
+                    "doi": doi or "DOI not available",
                     "url": url,
+                    "citations": citations,
+                    "open_access": open_access,
+                    "keywords": keywords if keywords else "Keywords not available",
+                    "article_type": article_type,
+                    "source": "PubMed",
+                    "data_quality": {
+                        "has_abstract": False,  # PubMed API itself doesn't provide abstracts
+                        "has_authors": bool(authors),
+                        "has_journal": bool(journal),
+                        "has_year": bool(year),
+                        "has_doi": bool(doi),
+                        "has_citations": False,  # PubMed API itself doesn't provide citation count
+                        "has_keywords": bool(keywords),
+                        "has_url": bool(url),
+                    },
                 }
             )
 

tooluniverse/remote/boltz/boltz_mcp_server.py

@@ -47,4 +47,6 @@ def run_boltz2(query: dict):
 
 
 if __name__ == "__main__":
-    server.run(transport="streamable-http", host="0.0.0.0", port=8080, stateless_http=True)
+    server.run(
+        transport="streamable-http", host="0.0.0.0", port=8080, stateless_http=True
+    )

tooluniverse/remote/uspto_downloader/uspto_downloader_mcp_server.py

@@ -58,4 +58,6 @@ def download_full_text(query: dict):
 
 
 if __name__ == "__main__":
-    server.run(transport="streamable-http", host="0.0.0.0", port=8081, stateless_http=True)
+    server.run(
+        transport="streamable-http", host="0.0.0.0", port=8081, stateless_http=True
+    )