PubChem MCP Server

assess_environmental_fate

Analyze chemical biodegradation and bioaccumulation potential using PubChem data to evaluate environmental persistence and ecological impact.

Instructions

Assess environmental fate including biodegradation and bioaccumulation

Input Schema

TableJSON Schema

Name	Required	Description	Default
`cid`	Yes	PubChem Compound ID (CID)

Implementation Reference

src/index.ts:1187-1189 (handler)

The main handler function for the 'assess_environmental_fate' tool. It currently returns a placeholder message indicating that the feature is not yet implemented.

private async handleAssessEnvironmentalFate(args: any) {
  return { content: [{ type: 'text', text: JSON.stringify({ message: 'Environmental fate assessment not yet implemented', args }, null, 2) }] };
}

src/index.ts:661-671 (schema)

The tool schema definition including name, description, and input schema (requires 'cid' as number or string). Part of the tools list returned by ListToolsRequest.

{
  name: 'assess_environmental_fate',
  description: 'Assess environmental fate including biodegradation and bioaccumulation',
  inputSchema: {
    type: 'object',
    properties: {
      cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
    },
    required: ['cid'],
  },
},

src/index.ts:796-797 (registration)
The dispatch case in the CallToolRequestSchema handler that routes calls to the tool's handler function.
```
case 'assess_environmental_fate':
  return await this.handleAssessEnvironmentalFate(args);
```

src/index.ts:368-732 (registration)

The tool is registered in the comprehensive list of 30+ tools provided to ListToolsRequestHandler. This is the primary registration point.

  tools: [
    // Chemical Search & Retrieval (6 tools)
    {
      name: 'search_compounds',
      description: 'Search PubChem database for compounds by name, CAS number, formula, or identifier',
      inputSchema: {
        type: 'object',
        properties: {
          query: { type: 'string', description: 'Search query (compound name, CAS, formula, or identifier)' },
          search_type: { type: 'string', enum: ['name', 'smiles', 'inchi', 'sdf', 'cid', 'formula'], description: 'Type of search to perform (default: name)' },
          max_records: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 },
        },
        required: ['query'],
      },
    },
    {
      name: 'get_compound_info',
      description: 'Get detailed information for a specific compound by PubChem CID',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          format: { type: 'string', enum: ['json', 'sdf', 'xml', 'asnt', 'asnb'], description: 'Output format (default: json)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'search_by_smiles',
      description: 'Search for compounds by SMILES string (exact match)',
      inputSchema: {
        type: 'object',
        properties: {
          smiles: { type: 'string', description: 'SMILES string of the query molecule' },
        },
        required: ['smiles'],
      },
    },
    {
      name: 'search_by_inchi',
      description: 'Search for compounds by InChI or InChI key',
      inputSchema: {
        type: 'object',
        properties: {
          inchi: { type: 'string', description: 'InChI string or InChI key' },
        },
        required: ['inchi'],
      },
    },
    {
      name: 'search_by_cas_number',
      description: 'Search for compounds by CAS Registry Number',
      inputSchema: {
        type: 'object',
        properties: {
          cas_number: { type: 'string', description: 'CAS Registry Number (e.g., 50-78-2)' },
        },
        required: ['cas_number'],
      },
    },
    {
      name: 'get_compound_synonyms',
      description: 'Get all names and synonyms for a compound',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },

    // Structure Analysis & Similarity (5 tools)
    {
      name: 'search_similar_compounds',
      description: 'Find chemically similar compounds using Tanimoto similarity',
      inputSchema: {
        type: 'object',
        properties: {
          smiles: { type: 'string', description: 'SMILES string of the query molecule' },
          threshold: { type: 'number', description: 'Similarity threshold (0-100, default: 90)', minimum: 0, maximum: 100 },
          max_records: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 },
        },
        required: ['smiles'],
      },
    },
    {
      name: 'substructure_search',
      description: 'Find compounds containing a specific substructure',
      inputSchema: {
        type: 'object',
        properties: {
          smiles: { type: 'string', description: 'SMILES string of the substructure query' },
          max_records: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 },
        },
        required: ['smiles'],
      },
    },
    {
      name: 'superstructure_search',
      description: 'Find larger compounds that contain the query structure',
      inputSchema: {
        type: 'object',
        properties: {
          smiles: { type: 'string', description: 'SMILES string of the query structure' },
          max_records: { type: 'number', description: 'Maximum number of results (1-10000, default: 100)', minimum: 1, maximum: 10000 },
        },
        required: ['smiles'],
      },
    },
    {
      name: 'get_3d_conformers',
      description: 'Get 3D conformer data and structural information',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          conformer_type: { type: 'string', enum: ['3d', '2d'], description: 'Type of conformer data (default: 3d)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'analyze_stereochemistry',
      description: 'Analyze stereochemistry, chirality, and isomer information',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },

    // Chemical Properties & Descriptors (6 tools)
    {
      name: 'get_compound_properties',
      description: 'Get molecular properties (MW, logP, TPSA, etc.)',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          properties: { type: 'array', items: { type: 'string' }, description: 'Specific properties to retrieve (optional)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'calculate_descriptors',
      description: 'Calculate comprehensive molecular descriptors and fingerprints',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          descriptor_type: { type: 'string', enum: ['all', 'basic', 'topological', '3d'], description: 'Type of descriptors (default: all)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'predict_admet_properties',
      description: 'Predict ADMET properties (Absorption, Distribution, Metabolism, Excretion, Toxicity)',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          smiles: { type: 'string', description: 'SMILES string (alternative to CID)' },
        },
        required: [],
      },
    },
    {
      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: [],
      },
    },
    {
      name: 'analyze_molecular_complexity',
      description: 'Analyze molecular complexity and synthetic accessibility',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'get_pharmacophore_features',
      description: 'Get pharmacophore features and binding site information',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },

    // Bioassay & Activity Data (5 tools)
    {
      name: 'search_bioassays',
      description: 'Search for biological assays by target, description, or source',
      inputSchema: {
        type: 'object',
        properties: {
          query: { type: 'string', description: 'General search query' },
          target: { type: 'string', description: 'Target protein or gene name' },
          source: { type: 'string', description: 'Data source (e.g., ChEMBL, NCGC)' },
          max_records: { type: 'number', description: 'Maximum number of results (1-1000, default: 100)', minimum: 1, maximum: 1000 },
        },
        required: [],
      },
    },
    {
      name: 'get_assay_info',
      description: 'Get detailed information for a specific bioassay by AID',
      inputSchema: {
        type: 'object',
        properties: {
          aid: { type: 'number', description: 'PubChem Assay ID (AID)' },
        },
        required: ['aid'],
      },
    },
    {
      name: 'get_compound_bioactivities',
      description: 'Get all bioassay results and activities for a compound',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          activity_outcome: { type: 'string', enum: ['active', 'inactive', 'inconclusive', 'all'], description: 'Filter by activity outcome (default: all)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'search_by_target',
      description: 'Find compounds tested against a specific biological target',
      inputSchema: {
        type: 'object',
        properties: {
          target: { type: 'string', description: 'Target name (gene, protein, or pathway)' },
          activity_type: { type: 'string', description: 'Type of activity (e.g., IC50, EC50, Ki)' },
          max_records: { type: 'number', description: 'Maximum number of results (1-1000, default: 100)', minimum: 1, maximum: 1000 },
        },
        required: ['target'],
      },
    },
    {
      name: 'compare_activity_profiles',
      description: 'Compare bioactivity profiles across multiple compounds',
      inputSchema: {
        type: 'object',
        properties: {
          cids: { type: 'array', items: { type: 'number' }, description: 'Array of PubChem CIDs (2-50)', minItems: 2, maxItems: 50 },
          activity_type: { type: 'string', description: 'Specific activity type for comparison (optional)' },
        },
        required: ['cids'],
      },
    },

    // Safety & Toxicity (4 tools)
    {
      name: 'get_safety_data',
      description: 'Get GHS hazard classifications and safety information',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'get_toxicity_info',
      description: 'Get toxicity data including LD50, carcinogenicity, and mutagenicity',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'assess_environmental_fate',
      description: 'Assess environmental fate including biodegradation and bioaccumulation',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'get_regulatory_info',
      description: 'Get regulatory information from FDA, EPA, and international agencies',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },

    // Cross-References & Integration (4 tools)
    {
      name: 'get_external_references',
      description: 'Get links to external databases (ChEMBL, DrugBank, KEGG, etc.)',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'search_patents',
      description: 'Search for chemical patents and intellectual property information',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
          query: { type: 'string', description: 'Patent search query (alternative to CID)' },
        },
        required: [],
      },
    },
    {
      name: 'get_literature_references',
      description: 'Get PubMed citations and scientific literature references',
      inputSchema: {
        type: 'object',
        properties: {
          cid: { type: ['number', 'string'], description: 'PubChem Compound ID (CID)' },
        },
        required: ['cid'],
      },
    },
    {
      name: 'batch_compound_lookup',
      description: 'Process multiple compound IDs efficiently',
      inputSchema: {
        type: 'object',
        properties: {
          cids: { type: 'array', items: { type: 'number' }, description: 'Array of PubChem CIDs (1-200)', minItems: 1, maxItems: 200 },
          operation: { type: 'string', enum: ['property', 'synonyms', 'classification', 'description'], description: 'Operation to perform (default: property)' },
        },
        required: ['cids'],
      },
    },
  ],
}));

Schema Changelog

Changes observed during successful MCP inspections.

First observedSep 29, 2025

TDQS

C2.9/5.0

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 states the tool assesses environmental fate but doesn't describe what the assessment entails (e.g., returns predictions, scores, or detailed reports), whether it's a read-only operation, potential limitations, or error conditions. For a tool with no annotation coverage, this leaves significant gaps in understanding its behavior.

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 extremely concise—a single sentence that directly states the tool's purpose without unnecessary words. It's front-loaded with the core action and resource, making it easy to parse. Every word earns its place by specifying the assessment focus ('environmental fate') and key components ('biodegradation and bioaccumulation').

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 the complexity of environmental fate assessment and the lack of annotations and output schema, the description is incomplete. It doesn't explain what the tool returns (e.g., scores, predictions, or detailed analyses), potential dependencies, or how it differs from related tools. For a tool with no structured output information, the description should provide more context to guide 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?

The input schema has 100% description coverage, with the 'cid' parameter clearly documented as 'PubChem Compound ID (CID).' The description doesn't add any parameter-specific information beyond what the schema provides, such as format examples or constraints. However, with high schema coverage, the baseline score of 3 is appropriate, as the schema adequately handles parameter documentation.

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 environmental fate including biodegradation and bioaccumulation.' It specifies the action ('assess') and the resource ('environmental fate'), and distinguishes it from siblings by focusing on environmental properties rather than molecular complexity, stereochemistry, drug-likeness, or other chemical analyses. However, it doesn't explicitly name the resource being assessed (e.g., 'compound' or 'chemical'), which prevents a perfect score.

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, context for environmental fate assessment, or differentiate from similar tools like 'get_safety_data' or 'get_toxicity_info' that might overlap with environmental concerns. Without any usage context, the agent must infer when this tool is appropriate.

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