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

tooluniverse/data/packages/structural_biology_tools.json

@@ -11,7 +11,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "biopandas",
     "local_info": {
@@ -55,7 +58,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "openmm",
     "local_info": {
@@ -151,7 +157,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "ase",
     "local_info": {
@@ -195,7 +204,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "pyscf",
     "local_info": {

tooluniverse/data/packages/visualization_tools.json

@@ -11,7 +11,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "matplotlib",
     "local_info": {
@@ -55,7 +58,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "seaborn",
     "local_info": {
@@ -99,7 +105,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "opencv-python",
     "local_info": {
@@ -195,7 +204,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "cellpose",
     "local_info": {
@@ -239,7 +251,10 @@
           "description": "Whether to include usage examples and quick start guide",
           "default": true
         }
-      }
+      },
+      "required": [
+        "include_examples"
+      ]
     },
     "package_name": "igraph",
     "local_info": {

tooluniverse/data/pmc_tools.json

@@ -1,109 +1,117 @@
 [
-    {
-        "type": "PMCTool",
-        "name": "PMC_search_papers",
-        "description": "Search for full-text biomedical literature using PMC (PubMed Central) API. PMC is the free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine.",
-        "parameter": {
-            "type": "object",
-            "properties": {
-                "query": {
-                    "type": "string",
-                    "description": "Search query for PMC papers. Use keywords separated by spaces to refine your search."
-                },
-                "limit": {
-                    "type": "integer",
-                    "description": "Maximum number of papers to return. This sets the maximum number of papers retrieved from PMC.",
-                    "default": 10,
-                    "minimum": 1,
-                    "maximum": 100
-                },
-                "date_from": {
-                    "type": "string",
-                    "description": "Start date for publication date filter (YYYY/MM/DD format). Optional parameter to limit search to papers published from this date onwards."
-                },
-                "date_to": {
-                    "type": "string",
-                    "description": "End date for publication date filter (YYYY/MM/DD format). Optional parameter to limit search to papers published up to this date."
-                },
-                "article_type": {
-                    "type": "string",
-                    "description": "Article type filter (e.g., 'research-article', 'review', 'case-report'). Optional parameter to limit search to specific article types."
-                }
-            },
-            "required": ["query"]
+  {
+    "type": "PMCTool",
+    "name": "PMC_search_papers",
+    "description": "Search for full-text biomedical literature using PMC (PubMed Central) API. PMC is the free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine.",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "query": {
+          "type": "string",
+          "description": "Search query for PMC papers. Use keywords separated by spaces to refine your search."
+        },
+        "limit": {
+          "type": "integer",
+          "description": "Maximum number of papers to return. This sets the maximum number of papers retrieved from PMC.",
+          "default": 10,
+          "minimum": 1,
+          "maximum": 100
+        },
+        "date_from": {
+          "type": "string",
+          "description": "Start date for publication date filter (YYYY/MM/DD format). Optional parameter to limit search to papers published from this date onwards."
         },
-        "return_schema": {
+        "date_to": {
+          "type": "string",
+          "description": "End date for publication date filter (YYYY/MM/DD format). Optional parameter to limit search to papers published up to this date."
+        },
+        "article_type": {
+          "type": "string",
+          "description": "Article type filter (e.g., 'research-article', 'review', 'case-report'). Optional parameter to limit search to specific article types."
+        }
+      },
+      "required": [
+        "query",
+        "limit",
+        "date_from",
+        "date_to",
+        "article_type"
+      ]
+    },
+    "return_schema": {
+      "type": "array",
+      "description": "List of full-text biomedical papers from PMC matching the search query",
+      "items": {
+        "type": "object",
+        "properties": {
+          "title": {
+            "type": "string",
+            "description": "Title of the paper"
+          },
+          "abstract": {
+            "type": "string",
+            "description": "Abstract of the paper"
+          },
+          "authors": {
             "type": "array",
-            "description": "List of full-text biomedical papers from PMC matching the search query",
             "items": {
-                "type": "object",
-                "properties": {
-                    "title": {
-                        "type": "string",
-                        "description": "Title of the paper"
-                    },
-                    "abstract": {
-                        "type": "string",
-                        "description": "Abstract of the paper"
-                    },
-                    "authors": {
-                        "type": "array",
-                        "items": {"type": "string"},
-                        "description": "List of author names"
-                    },
-                    "year": {
-                        "type": "string",
-                        "description": "Publication year"
-                    },
-                    "pmc_id": {
-                        "type": "string",
-                        "description": "PMC identifier"
-                    },
-                    "pmid": {
-                        "type": "string",
-                        "description": "PubMed identifier"
-                    },
-                    "doi": {
-                        "type": "string",
-                        "description": "Digital Object Identifier (DOI) of the paper"
-                    },
-                    "url": {
-                        "type": "string",
-                        "description": "URL to access the paper on PMC"
-                    },
-                    "venue": {
-                        "type": "string",
-                        "description": "Journal or venue name"
-                    },
-                    "open_access": {
-                        "type": "boolean",
-                        "description": "Open access status (always true for PMC)"
-                    },
-                    "source": {
-                        "type": "string",
-                        "description": "Source identifier (always 'PMC')"
-                    },
-                    "article_type": {
-                        "type": "string",
-                        "description": "Type of article (e.g., research-article, review)"
-                    },
-                    "citations": {
-                        "type": "integer",
-                        "description": "Number of citations"
-                    }
-                }
-            }
-        },
-        "test_examples": [
-            {
-                "query": "cancer research",
-                "limit": 2
+              "type": "string"
             },
-            {
-                "query": "COVID-19",
-                "limit": 1,
-                "date_from": "2020/01/01"
-            }
-        ]
-    }
+            "description": "List of author names"
+          },
+          "year": {
+            "type": "string",
+            "description": "Publication year"
+          },
+          "pmc_id": {
+            "type": "string",
+            "description": "PMC identifier"
+          },
+          "pmid": {
+            "type": "string",
+            "description": "PubMed identifier"
+          },
+          "doi": {
+            "type": "string",
+            "description": "Digital Object Identifier (DOI) of the paper"
+          },
+          "url": {
+            "type": "string",
+            "description": "URL to access the paper on PMC"
+          },
+          "venue": {
+            "type": "string",
+            "description": "Journal or venue name"
+          },
+          "open_access": {
+            "type": "boolean",
+            "description": "Open access status (always true for PMC)"
+          },
+          "source": {
+            "type": "string",
+            "description": "Source identifier (always 'PMC')"
+          },
+          "article_type": {
+            "type": "string",
+            "description": "Type of article (e.g., research-article, review)"
+          },
+          "citations": {
+            "type": "integer",
+            "description": "Number of citations"
+          }
+        }
+      }
+    },
+    "test_examples": [
+      {
+        "query": "cancer research",
+        "limit": 2
+      },
+      {
+        "query": "COVID-19",
+        "limit": 1,
+        "date_from": "2020/01/01"
+      }
+    ]
+  }
 ]

tooluniverse/data/protein_structure_3d_tools.json

@@ -0,0 +1,138 @@
+[
+  {
+    "name": "visualize_protein_structure_3d",
+    "description": "Visualize 3D protein structures using py3Dmol. Supports PDB IDs, PDB file content, and various visualization styles including cartoon, surface, and stick representations.",
+    "type": "ProteinStructure3DTool",
+    "parameter": {
+      "type": "object",
+      "properties": {
+        "pdb_id": {
+          "type": "string",
+          "description": "PDB identifier (e.g., '1CRN', '7CGO'). Either pdb_id or pdb_content must be provided."
+        },
+        "pdb_content": {
+          "type": "string",
+          "description": "Raw PDB file content as string. Either pdb_id or pdb_content must be provided."
+        },
+        "style": {
+          "type": "string",
+          "enum": [
+            "cartoon",
+            "stick",
+            "sphere",
+            "line"
+          ],
+          "default": "cartoon",
+          "description": "Visualization style"
+        },
+        "color_scheme": {
+          "type": "string",
+          "enum": [
+            "spectrum",
+            "rainbow",
+            "ssPyMOL",
+            "ssJmol",
+            "Jmol",
+            "amino",
+            "shapely",
+            "nucleic",
+            "chain",
+            "default"
+          ],
+          "default": "spectrum",
+          "description": "Color scheme for the structure"
+        },
+        "width": {
+          "type": "integer",
+          "default": 800,
+          "description": "Width of the visualization in pixels"
+        },
+        "height": {
+          "type": "integer",
+          "default": 600,
+          "description": "Height of the visualization in pixels"
+        },
+        "show_sidechains": {
+          "type": "boolean",
+          "default": false,
+          "description": "Whether to show sidechain atoms"
+        },
+        "show_surface": {
+          "type": "boolean",
+          "default": false,
+          "description": "Whether to show molecular surface"
+        }
+      },
+      "required": [
+        "pdb_id",
+        "pdb_content"
+      ]
+    },
+    "default_width": 800,
+    "default_height": 600,
+    "default_style": {
+      "style": "cartoon",
+      "color_scheme": "spectrum"
+    },
+    "return_schema": {
+      "type": "object",
+      "properties": {
+        "success": {
+          "type": "boolean",
+          "description": "Whether the visualization was created successfully"
+        },
+        "visualization": {
+          "type": "object",
+          "properties": {
+            "html": {
+              "type": "string",
+              "description": "Complete HTML content for the 3D protein visualization"
+            },
+            "type": {
+              "type": "string",
+              "description": "Type of visualization (protein_structure_3d)"
+            },
+            "data": {
+              "type": "object",
+              "description": "Raw PDB data used for visualization"
+            },
+            "metadata": {
+              "type": "object",
+              "properties": {
+                "width": {
+                  "type": "integer"
+                },
+                "height": {
+                  "type": "integer"
+                },
+                "style": {
+                  "type": "string"
+                },
+                "color_scheme": {
+                  "type": "string"
+                },
+                "pdb_id": {
+                  "type": "string"
+                },
+                "show_sidechains": {
+                  "type": "boolean"
+                },
+                "show_surface": {
+                  "type": "boolean"
+                }
+              }
+            }
+          }
+        },
+        "error": {
+          "type": "string",
+          "description": "Error message if visualization failed"
+        },
+        "error_type": {
+          "type": "string",
+          "description": "Type of error if visualization failed"
+        }
+      }
+    }
+  }
+]

tooluniverse/data/pubchem_tools.json

@@ -10,7 +10,9 @@
           "description": "PubChem compound ID to query, e.g., 2244 (Aspirin)."
         }
       },
-      "required": ["cid"]
+      "required": [
+        "cid"
+      ]
     },
     "fields": {
       "endpoint": "/data/compound/{cid}/JSON?heading=Patents",
@@ -33,14 +35,20 @@
           "description": "PubChem compound ID to query, e.g., 2244 (Aspirin)."
         }
       },
-      "required": ["cid"]
+      "required": [
+        "cid"
+      ]
     },
     "fields": {
       "endpoint": "/compound/cid/{cid}/property/{property_list}/JSON",
       "use_pugview": false,
       "input_description": "Input is a PubChem compound ID (integer).",
       "output_description": "Returns a JSON object with structure example:\n{\n  \"PropertyTable\": {\n    \"Properties\": [\n      {\n        \"CID\": 2244,\n        \"MolecularWeight\": 180.157,\n        \"IUPACName\": \"2-acetyloxybenzoic acid\",\n        \"CanonicalSMILES\": \"CC(=O)OC1=CC=CC=C1C(=O)O\",\n        ...\n      }\n    ]\n  }\n}\n\nWhere:\n- PropertyTable.Properties list: each element contains properties for that CID;\n- Property names determined by {property_list}, example here is [\"MolecularWeight\",\"IUPACName\",\"CanonicalSMILES\"].\nAfter calling, LLM can directly access these important molecular properties for subsequent chemical/pharmacological reasoning.",
-      "property_list": ["MolecularWeight", "IUPACName", "CanonicalSMILES"]
+      "property_list": [
+        "MolecularWeight",
+        "IUPACName",
+        "CanonicalSMILES"
+      ]
     },
     "type": "PubChemRESTTool"
   },
@@ -55,7 +63,9 @@
           "description": "Chemical name (e.g., \"Aspirin\" or IUPAC name)."
         }
       },
-      "required": ["name"]
+      "required": [
+        "name"
+      ]
     },
     "fields": {
       "endpoint": "/compound/name/{name}/cids/JSON",
@@ -77,7 +87,9 @@
           "description": "SMILES expression (e.g., \"CC(=O)OC1=CC=CC=C1C(=O)O\" corresponds to aspirin)."
         }
       },
-      "required": ["smiles"]
+      "required": [
+        "smiles"
+      ]
     },
     "fields": {
       "endpoint": "/compound/smiles/{smiles}/cids/JSON",
@@ -99,7 +111,9 @@
           "description": "SMILES of substructure (e.g., \"c1ccccc1\" corresponds to benzene ring)."
         }
       },
-      "required": ["smiles"]
+      "required": [
+        "smiles"
+      ]
     },
     "fields": {
       "endpoint": "/compound/fastsubstructure/smiles/{smiles}/cids/JSON",
@@ -126,7 +140,10 @@
           "default": 0.9
         }
       },
-      "required": ["smiles"]
+      "required": [
+        "smiles",
+        "threshold"
+      ]
     },
     "fields": {
       "endpoint": "/compound/fastsimilarity_2d/smiles/{smiles}/cids/JSON",
@@ -144,8 +161,8 @@
       "type": "object",
       "properties": {
         "cid": {
-            "type": "integer",
-            "description": "Compound ID to get image for, e.g., 2244."
+          "type": "integer",
+          "description": "Compound ID to get image for, e.g., 2244."
         },
         "image_size": {
           "type": "string",
@@ -153,7 +170,10 @@
           "default": "200x200"
         }
       },
-      "required": ["cid"]
+      "required": [
+        "cid",
+        "image_size"
+      ]
     },
     "fields": {
       "endpoint": "/compound/cid/{cid}/PNG?image_size={image_size}",
@@ -174,7 +194,9 @@
           "description": "Compound ID to query synonyms for, e.g., 2244."
         }
       },
-      "required": ["cid"]
+      "required": [
+        "cid"
+      ]
     },
     "fields": {
       "endpoint": "/compound/cid/{cid}/synonyms/JSON",
@@ -202,7 +224,10 @@
           }
         }
       },
-      "required": ["cid", "xref_types"]
+      "required": [
+        "cid",
+        "xref_types"
+      ]
     },
     "fields": {
       "endpoint": "/compound/cid/{cid}/xrefs/{xref_types}/JSON",