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

tooluniverse/molecule_3d_tool.py

@@ -0,0 +1,441 @@
+"""
+Molecule 3D Visualization Tool
+==============================
+
+Tool for visualizing 3D molecular structures using RDKit and py3Dmol.
+Supports SMILES, MOL files, SDF content, and various visualization styles.
+"""
+
+from typing import Any, Dict
+from .visualization_tool import VisualizationTool
+from .tool_registry import register_tool
+
+
+@register_tool("Molecule3DTool")
+class Molecule3DTool(VisualizationTool):
+    """Tool for visualizing 3D molecular structures using RDKit and py3Dmol."""
+
+    def run(self, arguments: Dict[str, Any]) -> Dict[str, Any]:
+        """Generate 3D molecular structure visualization."""
+        try:
+            import py3Dmol
+            from rdkit import Chem
+            from rdkit.Chem import AllChem
+
+            # Extract parameters
+            smiles = arguments.get("smiles")
+            mol_content = arguments.get("mol_content")
+            sdf_content = arguments.get("sdf_content")
+            style = arguments.get("style", "stick")
+            color_scheme = arguments.get("color_scheme", "default")
+            width = arguments.get("width", self.default_width)
+            height = arguments.get("height", self.default_height)
+            show_hydrogens = arguments.get("show_hydrogens", True)
+            show_surface = arguments.get("show_surface", False)
+            generate_conformers = arguments.get("generate_conformers", True)
+            conformer_count = arguments.get("conformer_count", 1)
+
+            # Create molecule object
+            mol = None
+            input_type = ""
+            input_data = ""
+
+            if smiles:
+                mol = Chem.MolFromSmiles(smiles)
+                input_type = "SMILES"
+                input_data = smiles
+            elif mol_content:
+                mol = Chem.MolFromMolBlock(mol_content)
+                input_type = "MOL"
+                input_data = (
+                    mol_content[:100] + "..." if len(mol_content) > 100 else mol_content
+                )
+            elif sdf_content:
+                mol = Chem.MolFromMolBlock(sdf_content)
+                input_type = "SDF"
+                input_data = (
+                    sdf_content[:100] + "..." if len(sdf_content) > 100 else sdf_content
+                )
+            else:
+                return self.create_error_response(
+                    "Either smiles, mol_content, or sdf_content must be " "provided"
+                )
+
+            if mol is None:
+                return self.create_error_response(
+                    "Failed to create molecule from input"
+                )
+
+            # Add hydrogens if requested
+            if show_hydrogens:
+                mol = Chem.AddHs(mol)
+
+            # Generate 3D coordinates
+            if generate_conformers:
+                # Generate multiple conformers
+                conformers = []
+                for _ in range(conformer_count):
+                    conf_mol = Chem.Mol(mol)
+                    try:
+                        AllChem.EmbedMolecule(conf_mol, AllChem.ETKDG())
+                        AllChem.MMFFOptimizeMolecule(conf_mol)
+                        conformers.append(conf_mol)
+                    except Exception:
+                        # Fallback to basic embedding
+                        AllChem.EmbedMolecule(conf_mol)
+                        conformers.append(conf_mol)
+                # Use the first conformer for visualization
+                mol = conformers[0] if conformers else mol
+            else:
+                # Generate single conformer
+                try:
+                    AllChem.EmbedMolecule(mol, AllChem.ETKDG())
+                    AllChem.MMFFOptimizeMolecule(mol)
+                except Exception:
+                    # Fallback to basic embedding
+                    AllChem.EmbedMolecule(mol)
+
+            # Convert to MOL block for py3Dmol
+            mol_block = Chem.MolToMolBlock(mol)
+
+            # Create py3Dmol viewer
+            viewer = py3Dmol.view(width=width, height=height)
+            viewer.addModel(mol_block, "mol")
+
+            # Apply visualization style
+            if style == "stick":
+                viewer.setStyle({"stick": {"color": color_scheme}})
+            elif style == "sphere":
+                viewer.setStyle({"sphere": {"color": color_scheme}})
+            elif style == "cartoon":
+                viewer.setStyle({"cartoon": {"color": color_scheme}})
+            elif style == "line":
+                viewer.setStyle({"line": {"color": color_scheme}})
+            elif style == "spacefill":
+                viewer.setStyle({"sphere": {"scale": 0.3, "color": color_scheme}})
+            else:
+                viewer.setStyle({"stick": {"color": color_scheme}})
+
+            # Add surface if requested
+            if show_surface:
+                viewer.addSurface(py3Dmol.VDW, {"opacity": 0.7, "color": "white"})
+
+            # Zoom to fit
+            viewer.zoomTo()
+
+            # Calculate molecular properties first
+            mol_props = self._calculate_molecular_properties(mol)
+
+            # Generate HTML with modern UI
+            viewer_html = viewer._make_html()
+
+            # Create control panel
+            control_panel = self._create_molecule_control_panel(style, color_scheme)
+
+            # Create toolbar
+            toolbar = self._create_toolbar()
+
+            # Create info cards
+            info_cards = self._create_molecule_info_cards(input_data, mol_props)
+
+            # Generate modern HTML
+            html_content = self.create_py3dmol_html(
+                viewer_html,
+                width,
+                height,
+                title=f"3D Molecular Structure: {input_data[:20]}{'...' if len(input_data) > 20 else ''}",
+                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,
+                "input_type": input_type,
+                "show_hydrogens": show_hydrogens,
+                "show_surface": show_surface,
+                "generate_conformers": generate_conformers,
+                "conformer_count": conformer_count,
+                "molecular_properties": mol_props,
+            }
+
+            return self.create_visualization_response(
+                html_content=html_content,
+                viz_type="molecule_3d",
+                data={
+                    "input_data": input_data,
+                    "molecular_properties": mol_props,
+                    "smiles": Chem.MolToSmiles(mol) if mol else None,
+                    "conformer_count": len(conformers) if generate_conformers else 1,
+                },
+                metadata=metadata,
+            )
+
+        except ImportError as e:
+            missing_package = "py3Dmol" if "py3Dmol" in str(e) else "rdkit"
+            return self.create_error_response(
+                f"{missing_package} is not installed. Please install it with: "
+                f"pip install {missing_package}",
+                "MissingDependency",
+            )
+        except Exception as e:
+            return self.create_error_response(
+                f"Failed to create molecule 3D visualization: {str(e)}"
+            )
+
+    def _calculate_molecular_properties(self, mol) -> Dict[str, Any]:
+        """Calculate basic molecular properties."""
+        try:
+            from rdkit import Chem
+            from rdkit.Chem import rdMolDescriptors
+
+            return {
+                "molecular_weight": rdMolDescriptors.CalcExactMolWt(mol),
+                "logp": rdMolDescriptors.CalcCrippenDescriptors(mol)[0],
+                "hbd": rdMolDescriptors.CalcNumHBD(mol),
+                "hba": rdMolDescriptors.CalcNumHBA(mol),
+                "tpsa": rdMolDescriptors.CalcTPSA(mol),
+                "rotatable_bonds": rdMolDescriptors.CalcNumRotatableBonds(mol),
+                "aromatic_rings": rdMolDescriptors.CalcNumAromaticRings(mol),
+                "heavy_atoms": mol.GetNumHeavyAtoms(),
+                "formal_charge": Chem.rdmolops.GetFormalCharge(mol),
+                "num_conformers": mol.GetNumConformers(),
+            }
+        except Exception:
+            return {}
+
+    def _create_molecule_html(
+        self,
+        mol,
+        input_data: str,
+        input_type: str,
+        width: int,
+        height: int,
+        mol_props: Dict[str, Any],
+        style: str,
+        color_scheme: str,
+    ) -> str:
+        """Create HTML content for molecule 3D visualization."""
+        try:
+            from rdkit import Chem
+
+            smiles = Chem.MolToSmiles(mol) if mol else "N/A"
+
+            # Create properties table
+            props_html = ""
+            if mol_props:
+                props_html = (
+                    "<table border='1' "
+                    "style='border-collapse: collapse; margin: 10px 0;'>"
+                )
+                props_html += "<tr><th>Property</th><th>Value</th></tr>"
+                for prop, value in mol_props.items():
+                    if isinstance(value, float):
+                        value = f"{value:.2f}"
+                    props_html += f"<tr><td>{prop}</td><td>{value}</td></tr>"
+                props_html += "</table>"
+
+            return f"""
+            <!DOCTYPE html>
+            <html>
+            <head>
+                <meta charset="utf-8">
+                <title>3D Molecule Visualization</title>
+                <style>
+                    body {{
+                        font-family: Arial, sans-serif;
+                        margin: 20px;
+                        max-width: 1200px;
+                    }}
+                    .molecule-container {{
+                        border: 1px solid #ccc;
+                        border-radius: 5px;
+                        padding: 20px;
+                        margin: 10px 0;
+                        text-align: center;
+                    }}
+                    .properties {{
+                        margin: 20px 0;
+                        text-align: left;
+                    }}
+                    .info {{
+                        background-color: #f5f5f5;
+                        padding: 10px;
+                        border-radius: 5px;
+                        margin: 10px 0;
+                    }}
+                    .viewer-container {{
+                        border: 1px solid #ccc;
+                        border-radius: 5px;
+                        margin: 10px 0;
+                    }}
+                </style>
+            </head>
+            <body>
+                <h2>3D Molecular Structure Visualization</h2>
+
+                <div class="info">
+                    <h3>Input Information</h3>
+                    <p><strong>Type:</strong> {input_type}</p>
+                    <p><strong>Data:</strong> {input_data}</p>
+                    <p><strong>SMILES:</strong> {smiles}</p>
+                </div>
+
+                <div class="molecule-container">
+                    <h3>3D Molecular Structure</h3>
+                    <div class="viewer-container">
+                        <!-- 3D viewer will be embedded here -->
+                    </div>
+                </div>
+
+                <div class="properties">
+                    <h3>Molecular Properties</h3>
+                    {props_html}
+                </div>
+
+                <div class="info">
+                    <h3>Visualization Details</h3>
+                    <p><strong>Dimensions:</strong> {width} × {height} "
+                    "pixels</p>
+                    <p><strong>Style:</strong> {style}</p>
+                    <p><strong>Color Scheme:</strong> {color_scheme}</p>
+                </div>
+            </body>
+            </html>
+            """
+        except Exception as e:
+            return f"<div class='error'>Error creating HTML: {str(e)}</div>"
+
+    def _create_molecule_control_panel(
+        self, current_style: str, current_color: str
+    ) -> str:
+        """Create floating control panel HTML for molecules."""
+        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="stick" {'selected' if current_style == 'stick' else ''}>Stick</option>
+                    <option value="sphere" {'selected' if current_style == 'sphere' else ''}>Sphere</option>
+                    <option value="cartoon" {'selected' if current_style == 'cartoon' else ''}>Cartoon</option>
+                    <option value="line" {'selected' if current_style == 'line' else ''}>Line</option>
+                    <option value="spacefill" {'selected' if current_style == 'spacefill' else ''}>Spacefill</option>
+                </select>
+            </div>
+            <div class="control-group">
+                <label class="control-label">Color Scheme</label>
+                <select class="control-select" id="colorSelect" onchange="changeColor()">
+                    <option value="default" {'selected' if current_color == 'default' else ''}>Default</option>
+                    <option value="spectrum" {'selected' if current_color == 'spectrum' else ''}>Spectrum</option>
+                    <option value="rainbow" {'selected' if current_color == 'rainbow' else ''}>Rainbow</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_molecule_info_cards(
+        self, input_data: str, mol_props: Dict[str, Any]
+    ) -> str:
+        """Create molecule information cards."""
+        smiles = mol_props.get("smiles", "N/A")
+        mol_weight = mol_props.get("molecular_weight", 0)
+        logp = mol_props.get("logp", 0)
+        hbd = mol_props.get("hbd", 0)
+        hba = mol_props.get("hba", 0)
+        tpsa = mol_props.get("tpsa", 0)
+        rotatable_bonds = mol_props.get("rotatable_bonds", 0)
+        aromatic_rings = mol_props.get("aromatic_rings", 0)
+        heavy_atoms = mol_props.get("heavy_atoms", 0)
+        formal_charge = mol_props.get("formal_charge", 0)
+
+        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>
+                Molecule Information
+            </h3>
+            <div class="info-grid">
+                <div class="info-item">
+                    <span class="info-label">SMILES</span>
+                    <span class="info-value">{smiles[:30]}{'...' if len(smiles) > 30 else ''}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Molecular Weight</span>
+                    <span class="info-value">{mol_weight:.2f} Da</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Heavy Atoms</span>
+                    <span class="info-value">{heavy_atoms}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Formal Charge</span>
+                    <span class="info-value">{formal_charge}</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>
+                Drug Properties
+            </h3>
+            <div class="info-grid">
+                <div class="info-item">
+                    <span class="info-label">LogP</span>
+                    <span class="info-value">{logp:.2f}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">TPSA</span>
+                    <span class="info-value">{tpsa:.2f} Ų</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">H-Bond Donors</span>
+                    <span class="info-value">{hbd}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">H-Bond Acceptors</span>
+                    <span class="info-value">{hba}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Rotatable Bonds</span>
+                    <span class="info-value">{rotatable_bonds}</span>
+                </div>
+                <div class="info-item">
+                    <span class="info-label">Aromatic Rings</span>
+                    <span class="info-value">{aromatic_rings}</span>
+                </div>
+            </div>
+        </div>
+        """

tooluniverse/odphp_tool.py

@@ -86,17 +86,27 @@ class ODPHPMyHealthfinder(ODPHPRESTTool):
         res = self._make_request(params)
 
         # Optional: attach PlainSections if requested
-        if isinstance(res, dict) and not res.get("error") and arguments.get("strip_html"):
+        if (
+            isinstance(res, dict)
+            and not res.get("error")
+            and arguments.get("strip_html")
+        ):
             data = res.get("data") or {}
-            resources = (((data.get("Resources") or {}).get("All") or {}).get("Resource")) or []
+            resources = (
+                ((data.get("Resources") or {}).get("All") or {}).get("Resource")
+            ) or []
             if isinstance(resources, list):
                 for r in resources:
                     plain = []
                     for sec in _sections_array(r):
-                        plain.append({
-                            "Title": sec.get("Title", ""),
-                            "PlainContent": _strip_html_to_text(sec.get("Content", "")),
-                        })
+                        plain.append(
+                            {
+                                "Title": sec.get("Title", ""),
+                                "PlainContent": _strip_html_to_text(
+                                    sec.get("Content", "")
+                                ),
+                            }
+                        )
                     if plain:
                         r["PlainSections"] = plain
         return res
@@ -133,17 +143,25 @@ class ODPHPTopicSearch(ODPHPRESTTool):
         res = self._make_request(params)
 
         # Optional: attach PlainSections if requested
-        if isinstance(res, dict) and not res.get("error") and arguments.get("strip_html"):
+        if (
+            isinstance(res, dict)
+            and not res.get("error")
+            and arguments.get("strip_html")
+        ):
             data = res.get("data") or {}
             resources = ((data.get("Resources") or {}).get("Resource")) or []
             if isinstance(resources, list):
                 for r in resources:
                     plain = []
                     for sec in _sections_array(r):
-                        plain.append({
-                            "Title": sec.get("Title", ""),
-                            "PlainContent": _strip_html_to_text(sec.get("Content", "")),
-                        })
+                        plain.append(
+                            {
+                                "Title": sec.get("Title", ""),
+                                "PlainContent": _strip_html_to_text(
+                                    sec.get("Content", "")
+                                ),
+                            }
+                        )
                     if plain:
                         r["PlainSections"] = plain
         return res
@@ -187,7 +205,11 @@ class ODPHPOutlinkFetch(BaseTool):
         elif soup.title and soup.title.string:
             title = soup.title.string.strip()
 
-        text = candidate.get_text("\n", strip=True) if candidate else soup.get_text("\n", strip=True)
+        text = (
+            candidate.get_text("\n", strip=True)
+            if candidate
+            else soup.get_text("\n", strip=True)
+        )
         text = re.sub(r"\n{2,}", "\n\n", text)
         return {"title": title, "text": text}
 
@@ -204,7 +226,11 @@ class ODPHPOutlinkFetch(BaseTool):
             try:
                 resp = requests.get(u, timeout=self.timeout, allow_redirects=True)
                 ct = resp.headers.get("Content-Type", "")
-                item: Dict[str, Any] = {"url": u, "status": resp.status_code, "content_type": ct}
+                item: Dict[str, Any] = {
+                    "url": u,
+                    "status": resp.status_code,
+                    "content_type": ct,
+                }
 
                 if "text/html" in ct or (not ct and resp.text.startswith("<!")):
                     ex = self._extract_text(resp.text)
@@ -221,6 +247,15 @@ class ODPHPOutlinkFetch(BaseTool):
                     item["text"] = ""
                 out.append(item)
             except requests.exceptions.RequestException as e:
-                out.append({"url": u, "status": 0, "content_type": "", "title": "", "text": "", "error": str(e)})
+                out.append(
+                    {
+                        "url": u,
+                        "status": 0,
+                        "content_type": "",
+                        "title": "",
+                        "text": "",
+                        "error": str(e),
+                    }
+                )
 
         return {"results": out, "metadata": {"source": "ODPHP OutlinkFetch"}}

tooluniverse/openaire_tool.py

@@ -30,9 +30,7 @@ class OpenAIRETool(BaseTool):
         endpoint = self._endpoint_for_type(prod_type)
         if endpoint is None:
             return {
-                "error": (
-                    "Unsupported type. Use publications/datasets/software."
-                ),
+                "error": ("Unsupported type. Use publications/datasets/software."),
             }
 
         params = {
@@ -67,25 +65,15 @@ class OpenAIRETool(BaseTool):
         results = []
         # OpenAIRE JSON has a root 'response' with 'results' → 'result' list
         try:
-            items = (
-                data.get("response", {})
-                .get("results", {})
-                .get("result", [])
-            )
+            items = data.get("response", {}).get("results", {}).get("result", [])
         except Exception:
             items = []
 
         for it in items:
             # header may contain identifiers, not used presently
-            _ = (
-                it.get("header", {})
-                if isinstance(it.get("header"), dict)
-                else {}
-            )
+            _ = it.get("header", {}) if isinstance(it.get("header"), dict) else {}
             metadata = (
-                it.get("metadata", {})
-                if isinstance(it.get("metadata"), dict)
-                else {}
+                it.get("metadata", {}) if isinstance(it.get("metadata"), dict) else {}
             )
             title = None
             authors = []
@@ -111,10 +99,7 @@ class OpenAIRETool(BaseTool):
                             authors.append(name)
 
                 # Year
-                date_obj = (
-                    result_obj.get("dateofacceptance")
-                    or result_obj.get("date")
-                )
+                date_obj = result_obj.get("dateofacceptance") or result_obj.get("date")
                 if isinstance(date_obj, dict):
                     year = date_obj.get("year") or date_obj.get("$")
 

tooluniverse/openalex_tool.py

@@ -151,6 +151,26 @@ class OpenAlexTool(BaseTool):
         open_access = work.get("open_access", {}).get("is_oa", False)
         pdf_url = work.get("open_access", {}).get("oa_url")
 
+        # Extract keywords/concepts
+        keywords = []
+        concepts = work.get("concepts", [])
+        if isinstance(concepts, list):
+            for concept in concepts:
+                if isinstance(concept, dict):
+                    concept_name = concept.get("display_name", "")
+                    if concept_name:
+                        keywords.append(concept_name)
+
+        # Extract article type
+        article_type = work.get("type", "Unknown")
+
+        # Extract publisher
+        publisher = (
+            work.get("primary_location", {})
+            .get("source", {})
+            .get("publisher", "Unknown")
+        )
+
         return {
             "title": title,
             "abstract": abstract,
@@ -162,8 +182,22 @@ class OpenAlexTool(BaseTool):
             "citation_count": citation_count,
             "open_access": open_access,
             "pdf_url": pdf_url,
+            "keywords": keywords if keywords else "Keywords not available",
+            "article_type": article_type,
+            "publisher": publisher,
             "openalex_id": work.get("id", ""),
             "url": work.get("doi") if work.get("doi") else work.get("id", ""),
+            "data_quality": {
+                "has_abstract": bool(abstract and abstract != "Abstract not available"),
+                "has_authors": bool(authors),
+                "has_venue": bool(venue and venue != "Unknown venue"),
+                "has_year": bool(
+                    publication_year and publication_year != "Year not available"
+                ),
+                "has_doi": bool(doi and doi != "No DOI"),
+                "has_citation_count": bool(citation_count and citation_count > 0),
+                "has_keywords": bool(keywords),
+            },
         }
 
     def get_paper_by_doi(self, doi):

tooluniverse/osf_preprints_tool.py

@@ -64,4 +64,4 @@ class OSFPreprintsTool(BaseTool):
                 }
             )
 
-        return results
+        return results