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molecule_lookup

Convert chemical names and identifiers to SMILES strings for molecular workflows using the Chemical Identifier Resolver.

Instructions

Convert molecule names to SMILES using Chemical Identifier Resolver (CIR).

Args: molecule_name: Common name, IUPAC name, or CAS number of molecule (e.g., 'aspirin', 'caffeine', '50-78-2') fallback_to_input: If lookup fails, return the input string assuming it might be SMILES

This tool enables natural language input for molecules by converting common names, IUPAC names, CAS numbers, and other identifiers to SMILES strings that can be used with Rowan workflows.

Supported Input Types:

  • Common names: 'aspirin', 'caffeine', 'benzene', 'glucose'

  • IUPAC names: '2-acetoxybenzoic acid', '1,3,7-trimethylpurine-2,6-dione'

  • CAS numbers: '50-78-2' (aspirin), '58-08-2' (caffeine)

  • InChI strings

  • Already valid SMILES (will be validated)

Returns: SMILES string if successful, error message if not found

Examples: # Common drug name result = molecule_lookup("aspirin") # Returns: "CC(=O)Oc1ccccc1C(=O)O"

# IUPAC name
result = molecule_lookup("2-acetoxybenzoic acid")
# Returns: "CC(=O)Oc1ccccc1C(=O)O"

# CAS number
result = molecule_lookup("50-78-2")
# Returns: "CC(=O)Oc1ccccc1C(=O)O"

# Complex molecule
result = molecule_lookup("paracetamol")
# Returns: "CC(=O)Nc1ccc(O)cc1"

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
molecule_nameYesCommon name, IUPAC name, or CAS number of molecule (e.g., 'aspirin', 'caffeine', '50-78-2')
fallback_to_inputNoIf lookup fails, return the input string assuming it might be SMILES

Output Schema

TableJSON Schema
NameRequiredDescriptionDefault
resultYes
Behavior4/5

Does the description disclose side effects, auth requirements, rate limits, or destructive behavior?

With no annotations provided, the description carries the full burden of behavioral disclosure. It effectively describes the tool's behavior: it converts identifiers to SMILES, handles various input types, includes a fallback mechanism, returns SMILES or error messages, and provides examples of successful conversions. It lacks details on rate limits, authentication needs, or error handling specifics, but covers core functionality well.

Agents need to know what a tool does to the world before calling it. Descriptions should go beyond structured annotations to explain consequences.

Conciseness4/5

Is the description appropriately sized, front-loaded, and free of redundancy?

The description is well-structured with clear sections (purpose, args, context, returns, examples) and uses bullet points for readability. It is appropriately sized but includes some redundancy (e.g., repeating parameter info from the schema). Most sentences add value, such as explaining the tool's role in workflows and listing input types.

Shorter descriptions cost fewer tokens and are easier for agents to parse. Every sentence should earn its place.

Completeness5/5

Given the tool's complexity, does the description cover enough for an agent to succeed on first attempt?

Given the tool's moderate complexity, no annotations, and an output schema (implied by 'Returns' section), the description is complete. It covers purpose, parameters, usage context, return values, and examples. The output schema handles return format details, so the description need not elaborate further, making it sufficient for effective use.

Complex tools with many parameters or behaviors need more documentation. Simple tools need less. This dimension scales expectations accordingly.

Parameters3/5

Does the description clarify parameter syntax, constraints, interactions, or defaults beyond what the schema provides?

Schema description coverage is 100%, so the schema already documents both parameters thoroughly. The description adds minimal value beyond the schema: it repeats the parameter descriptions in the 'Args' section and provides examples of 'molecule_name' inputs. No additional syntax, format, or constraints are explained, meeting the baseline for high schema coverage.

Input schemas describe structure but not intent. Descriptions should explain non-obvious parameter relationships and valid value ranges.

Purpose5/5

Does the description clearly state what the tool does and how it differs from similar tools?

The description clearly states the tool's purpose: 'Convert molecule names to SMILES using Chemical Identifier Resolver (CIR).' It specifies the verb ('convert'), resource ('molecule names'), and output format ('SMILES'), and distinguishes it from siblings like 'validate_smiles' (which validates rather than converts) and 'batch_molecule_lookup' (which handles multiple inputs).

Agents choose between tools based on descriptions. A clear purpose with a specific verb and resource helps agents select the right tool.

Usage Guidelines4/5

Does the description explain when to use this tool, when not to, or what alternatives exist?

The description provides clear context for when to use this tool: 'enables natural language input for molecules by converting common names, IUPAC names, CAS numbers, and other identifiers to SMILES strings that can be used with Rowan workflows.' It lists supported input types and includes examples. However, it does not explicitly state when not to use it or name alternatives like 'validate_smiles' for already-known SMILES strings.

Agents often have multiple tools that could apply. Explicit usage guidance like "use X instead of Y when Z" prevents misuse.

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