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reinvent_validate_input

Validate SMILES/CSV files for REINVENT4 by checking line counts, duplicates, and RDKit validity, with optional cleaning of valid, deduplicated SMILES.

Instructions

Validate SMILES/CSV input file before passing to REINVENT4.

Checks line counts, detects duplicates, validates each SMILES with RDKit, and applies generator-specific constraints (attachment points, fragments, etc.).

Args: smiles_file: Path to CSV or SMILES file generator: One of 'reinvent', 'libinvent', 'linkinvent', 'mol2mol' clean: If True, write _cleaned.smi with valid, deduplicated SMILES

Returns: { "valid": bool, "total_lines": int, "valid_smiles": int, "invalid_smiles": int, "duplicates": int, "cleaned_file": str (if clean=True), "errors": [{index, smiles, reason}, ...] (first 10) }

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cleanNo
generatorNoreinvent
smiles_fileYes
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 and does well: it lists specific checks (line counts, duplicates, RDKit validation, generator constraints) and discloses the side effect of writing a cleaned file when clean=True. It also describes the return object, including error details, without leaving major behavioral gaps.

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

Conciseness5/5

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

The description is well-structured with Args and Returns sections, the purpose is front-loaded in the first sentence, and every sentence provides useful information without waste. It is appropriately concise for the complexity.

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

Completeness4/5

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

Despite the lack of annotations and output schema, the description provides a thorough overview of validation checks, side effects, and a detailed return object. It is sufficient for an agent to select and invoke the tool. Minor gaps in generator-specific constraints prevent a perfect score.

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?

The schema has 0% description coverage, so the description must compensate. It defines smiles_file as a path, explains clean's behavior, but generator's description only restates the enum values without explaining what each generator does or what constraints apply. This partial compensation earns a 3.

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 a specific verb ('Validate') and resource ('SMILES/CSV input file') with a contextual purpose ('before passing to REINVENT4'). This distinguishes it from sibling tools like reinvent_validate_toml, which validates config files.

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?

It provides context for when to use the tool ('before passing to REINVENT4') but does not explicitly list alternatives or exclusion criteria. The focus on SMILES/CSV implicitly differentiates it from the TOML validator, but a direct comparison would strengthen the guidance.

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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