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Augmented-Nature

PubChem MCP Server

assess_drug_likeness

Evaluate drug-likeness of chemical compounds using Lipinski's Rule of Five, Veber rules, and PAINS filters by inputting PubChem CID or SMILES string.

Instructions

Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters

Input Schema

TableJSON Schema
NameRequiredDescriptionDefault
cidNoPubChem Compound ID (CID)
smilesNoSMILES string (alternative to CID)

Implementation Reference

  • Handler function that executes the assess_drug_likeness tool logic. Currently returns a placeholder message indicating implementation is pending.
    private async handleAssessDrugLikeness(args: any) {
      return { content: [{ type: 'text', text: JSON.stringify({ message: 'Drug-likeness assessment not yet implemented', args }, null, 2) }] };
    }
  • Tool registration entry including name, description, and input schema definition for assess_drug_likeness.
    {
      name: 'assess_drug_likeness',
      description: 'Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          smiles: { type: 'string', description: 'SMILES string (alternative to CID)' },
        },
        required: [],
      },
    },
  • src/index.ts:772-773 (registration)
    Dispatch case in the tool handler switch statement that routes calls to the assess_drug_likeness handler.
    case 'assess_drug_likeness':
      return await this.handleAssessDrugLikeness(args);
Behavior2/5

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

No annotations are provided, so the description carries the full burden of behavioral disclosure. It mentions the assessment methods (Lipinski, Veber, PAINS) but doesn't describe what the tool returns (e.g., pass/fail results, scores, or detailed outputs), whether it's read-only or has side effects, or any limitations like rate limits or input constraints. This leaves significant gaps for a tool with no annotation coverage.

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 a single, efficient sentence that front-loads the core purpose without unnecessary words. Every part ('Assess drug-likeness' and the methods list) earns its place by conveying essential information concisely.

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

Completeness2/5

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

Given no annotations and no output schema, the description is incomplete for a tool that assesses compound properties. It lacks details on return values (e.g., what the assessment outputs), behavioral traits (e.g., if it's a read operation), and usage context. For a tool with 2 parameters and complex functionality (drug-likeness assessment), this leaves too many gaps.

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%, with both parameters ('cid' and 'smiles') well-documented in the schema. The description doesn't add any parameter-specific information beyond what's in the schema (e.g., it doesn't clarify if both parameters are required together or alternatives, or provide examples). Baseline 3 is appropriate since the schema does the heavy lifting.

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

Purpose4/5

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

The description clearly states the tool's purpose: 'Assess drug-likeness using Lipinski Rule of Five, Veber rules, and PAINS filters'. It specifies the action ('assess') and the resource ('drug-likeness'), and mentions the specific methods used. However, it doesn't explicitly differentiate from siblings like 'predict_admet_properties' or 'calculate_descriptors', which might also evaluate compound properties.

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

Usage Guidelines2/5

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

The description provides no guidance on when to use this tool versus alternatives. It doesn't mention prerequisites (e.g., needing a CID or SMILES), exclusions, or compare it to sibling tools like 'predict_admet_properties' or 'calculate_descriptors' that might overlap in assessing compound characteristics. Usage is implied but not explicitly stated.

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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