valence-lime.vercel.app

{
  "name": "select_elements",
  "kind": "act",
  "impl": "imperative",
  "description": "Set the periodic-table selection and arm the assembly stage. Symbols are case-sensitive element symbols like H, Na, Cl.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "symbols": {
        "type": "array",
        "items": {
          "type": "string"
        },
        "description": "Element symbols to select"
      }
    },
    "required": [
      "symbols"
    ],
    "additionalProperties": false
  }
}

{
  "name": "predict_bond",
  "kind": "act",
  "impl": "imperative",
  "description": "Offline chemistry: given element symbols, say whether they bond and why, using electronegativity and valence. Returns verdict (bond / no-bond / alloy), bond type, likely formula, and a plain-language explanation. No network.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "symbols": {
        "type": "array",
        "items": {
          "type": "string"
        },
        "description": "Element symbols; defaults to the current selection"
      }
    },
    "required": [],
    "additionalProperties": false
  }
}

{
  "name": "combine_selection",
  "kind": "act",
  "impl": "imperative",
  "description": "Resolve the current element selection to a real compound via PubChem and render it on the stage. Optionally pass stoichiometry to fix the ratio.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "stoichiometry": {
        "type": "object",
        "additionalProperties": {
          "type": "integer",
          "minimum": 1
        },
        "description": "Symbol to count, e.g. { \"H\": 2, \"O\": 1 }"
      }
    },
    "required": [],
    "additionalProperties": false
  }
}

{
  "name": "search_pubchem",
  "kind": "answer",
  "impl": "imperative",
  "description": "Resolve a name, formula, SMILES, or InChIKey to PubChem compound IDs and load the top hit onto the stage.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "query": {
        "type": "string"
      },
      "by": {
        "type": "string",
        "enum": [
          "name",
          "formula",
          "smiles",
          "inchikey"
        ]
      }
    },
    "required": [
      "query",
      "by"
    ],
    "additionalProperties": false
  }
}

{
  "name": "fetch_properties",
  "kind": "answer",
  "impl": "imperative",
  "description": "Fetch molecular properties for a PubChem CID: weight, TPSA, logP, H-bond donors/acceptors, rotatable bonds.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid": {
        "type": "integer",
        "minimum": 1
      }
    },
    "required": [
      "cid"
    ],
    "additionalProperties": false
  }
}

{
  "name": "fetch_3d_conformer",
  "kind": "act",
  "impl": "imperative",
  "description": "Fetch a 3D conformer (SDF) for a CID from PubChem and render a rotatable, labelled ball-and-stick model on the stage.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid": {
        "type": "integer",
        "minimum": 1
      }
    },
    "required": [
      "cid"
    ],
    "additionalProperties": false
  }
}

{
  "name": "assess_hazard_profile",
  "kind": "act",
  "impl": "imperative",
  "description": "Read the GHS hazard classification for a CID and render a hazard badge: signal word, pictograms, hazard statements.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid": {
        "type": "integer",
        "minimum": 1
      }
    },
    "required": [
      "cid"
    ],
    "additionalProperties": false
  }
}

{
  "name": "find_similar_compounds",
  "kind": "answer",
  "impl": "imperative",
  "description": "Run a 2D similarity search against PubChem for a SMILES and show the top matches with a green-chemistry score.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "smiles": {
        "type": "string"
      },
      "threshold": {
        "type": "integer",
        "minimum": 50,
        "maximum": 100,
        "default": 90
      },
      "limit": {
        "type": "integer",
        "minimum": 1,
        "maximum": 8,
        "default": 3
      }
    },
    "required": [
      "smiles"
    ],
    "additionalProperties": false
  }
}

{
  "name": "industrial_viability",
  "kind": "act",
  "impl": "imperative",
  "description": "Estimate how sourceable a compound is: vendor count and linked patent count from PubChem, with a plain-language verdict.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid": {
        "type": "integer",
        "minimum": 1
      }
    },
    "required": [
      "cid"
    ],
    "additionalProperties": false
  }
}

{
  "name": "industrial_uses",
  "kind": "act",
  "impl": "imperative",
  "description": "List what a compound is actually used for in industry and consumer products, from PubChem's Uses annotations.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid": {
        "type": "integer",
        "minimum": 1
      }
    },
    "required": [
      "cid"
    ],
    "additionalProperties": false
  }
}

{
  "name": "describe_compound",
  "kind": "answer",
  "impl": "imperative",
  "description": "A plain-language description of a compound from PubChem, plus common names. Good for a beginner asking 'what is this?'.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid": {
        "type": "integer",
        "minimum": 1
      }
    },
    "required": [
      "cid"
    ],
    "additionalProperties": false
  }
}

{
  "name": "bioactivity_bridge",
  "kind": "answer",
  "impl": "imperative",
  "description": "Summarise a compound's bioassay history from PubChem: active assay count, tested targets, pharmacology notes.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid": {
        "type": "integer",
        "minimum": 1
      }
    },
    "required": [
      "cid"
    ],
    "additionalProperties": false
  }
}

{
  "name": "substitute_and_compare",
  "kind": "act",
  "impl": "imperative",
  "description": "Apply a substituent change to a SMILES (-OH, -CH3, -F, -NH2, -COOH, or a full target SMILES) and report how the properties move.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "base_smiles": {
        "type": "string"
      },
      "change": {
        "type": "string"
      }
    },
    "required": [
      "base_smiles",
      "change"
    ],
    "additionalProperties": false
  }
}

{
  "name": "compare_compounds",
  "kind": "act",
  "impl": "imperative",
  "description": "Put two compounds side by side on the stage: A vs B, each identified by name, formula, SMILES, or CID. Renders both structures, a property delta table, and short descriptions.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "a": {
        "type": "string"
      },
      "b": {
        "type": "string"
      }
    },
    "required": [
      "a",
      "b"
    ],
    "additionalProperties": false
  }
}

{
  "name": "close_comparison",
  "kind": "act",
  "impl": "imperative",
  "description": "Leave side-by-side comparison mode and return to the single-compound view.",
  "inputSchema": {
    "type": "object",
    "properties": {},
    "required": [],
    "additionalProperties": false
  }
}

{
  "name": "build_to_constraints",
  "kind": "act",
  "impl": "imperative",
  "description": "The headline flow, asynchronous. Given a goal (e.g. 'non-toxic polymer precursor') and constraints (allowed elements or a period number, weight/logP caps, non-toxic), it starts a job and returns a jobId immediately. The job resolves candidates, dedupes them, hazard-checks every one, scores transparently, and commits the ranked result to the stage in a single step. Poll get_build_status; stop early with cancel_build.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "goal": {
        "type": "string"
      },
      "constraints": {
        "type": "object",
        "properties": {
          "elements": {
            "type": "array",
            "items": {
              "type": "string"
            }
          },
          "period": {
            "type": "integer",
            "minimum": 1,
            "maximum": 7
          },
          "nonToxic": {
            "type": "boolean"
          },
          "maxWeight": {
            "type": "number"
          },
          "maxLogP": {
            "type": "number"
          }
        },
        "required": [],
        "additionalProperties": false
      }
    },
    "required": [
      "goal"
    ],
    "additionalProperties": false
  }
}

{
  "name": "get_build_status",
  "kind": "answer",
  "impl": "imperative",
  "description": "Poll a build_to_constraints job: current phase, progress counter, elapsed time, whether a time budget cut it short, and the ranked candidates with each one's score breakdown and rejection reason. Omit jobId for the most recent job.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "jobId": {
        "type": "string"
      }
    },
    "required": [],
    "additionalProperties": false
  }
}

{
  "name": "cancel_build",
  "kind": "transact",
  "impl": "imperative",
  "description": "Request that a running build_to_constraints job stop. It halts at the next checkpoint and commits whatever it has already fully ranked, never a half-scored state. Omit jobId for the most recent job.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "jobId": {
        "type": "string"
      }
    },
    "required": [],
    "additionalProperties": false
  }
}

{
  "name": "propose_greener_alternatives",
  "kind": "act",
  "impl": "imperative",
  "description": "Given a CID or SMILES, find structurally similar compounds and rank them by a transparent green-chemistry score.",
  "inputSchema": {
    "type": "object",
    "properties": {
      "cid_or_smiles": {
        "type": "string"
      }
    },
    "required": [
      "cid_or_smiles"
    ],
    "additionalProperties": false
  }
}

{
  "name": "render_recipe_card",
  "kind": "act",
  "impl": "imperative",
  "description": "Export the current stage build as a downloadable recipe card: structure, properties, hazard summary, source.",
  "inputSchema": {
    "type": "object",
    "properties": {},
    "required": [],
    "additionalProperties": false
  }
}

{
  "name": "explain",
  "kind": "act",
  "impl": "imperative",
  "description": "Teach mode. Explain a chemistry concept the bench uses (SMILES, TPSA, logP, GHS, Tanimoto, polymer precursor, conformer, and more).",
  "inputSchema": {
    "type": "object",
    "properties": {
      "topic": {
        "type": "string"
      }
    },
    "required": [
      "topic"
    ],
    "additionalProperties": false
  }
}

{
  "name": "get_canvas_state",
  "kind": "answer",
  "impl": "imperative",
  "description": "Return the full bench state as JSON: selection, stage compound, properties, hazard, similars, candidates, recent notebook entries.",
  "inputSchema": {
    "type": "object",
    "properties": {},
    "required": [],
    "additionalProperties": false
  }
}

{
  "name": "reset_canvas",
  "kind": "act",
  "impl": "imperative",
  "description": "Clear the selection and the stage.",
  "inputSchema": {
    "type": "object",
    "properties": {},
    "required": [],
    "additionalProperties": false
  }
}