search_similar_structures

Find chemically similar compounds in patent databases by comparing molecular structures to a reference chemical, enabling discovery of related substances and prior art.

Instructions

Find structurally similar chemicals using similarity search

Input Schema

TableJSON Schema

Name	Required	Description
`reference_id`	Yes	Reference chemical ID for similarity search
`threshold`	No	Similarity threshold (0.0-1.0, default: 0.7)
`limit`	No	Number of results to return (1-100, default: 25)

Implementation Reference

src/index.ts:1063-1118 (handler)

The handler function executing the tool logic. It fetches the reference chemical and returns a mock similarity search result with suggestions since direct similarity search is not supported.

private async handleSearchSimilarStructures(args: any) {
  if (!args || typeof args.reference_id !== 'string') {
    throw new McpError(ErrorCode.InvalidParams, 'Invalid reference chemical ID');
  }

  try {
    // Get the reference chemical first
    const refResponse = await this.apiClient.get(`/chemical/id/${args.reference_id}`);
    const refChemical = refResponse.data.data?.[0];

    if (!refChemical) {
      throw new Error('Reference chemical not found');
    }

    // Since SureChEMBL doesn't have direct similarity search, we'll provide a mock implementation
    // that explains the limitation and suggests alternatives
    const similarityResult = {
      reference_chemical: {
        id: args.reference_id,
        name: refChemical.name,
        smiles: refChemical.smiles,
        molecular_weight: refChemical.mol_weight
      },
      search_parameters: {
        threshold: args.threshold || 0.7,
        limit: args.limit || 25
      },
      message: 'Direct similarity search not available in SureChEMBL API',
      suggestions: [
        'Use chemical name variations to find related compounds',
        'Search by molecular weight ranges',
        'Use external cheminformatics tools for similarity search',
        'Try searching by chemical class or functional groups'
      ],
      alternative_searches: {
        by_name_fragments: `Try searching for fragments of "${refChemical.name}"`,
        by_molecular_weight: `Search for compounds with molecular weight around ${refChemical.mol_weight}`,
        by_chemical_class: 'Search for compounds in the same chemical class'
      }
    };

    return {
      content: [
        {
          type: 'text',
          text: JSON.stringify(similarityResult, null, 2),
        },
      ],
    };
  } catch (error) {
    throw new McpError(
      ErrorCode.InternalError,
      `Failed to search similar structures: ${error instanceof Error ? error.message : 'Unknown error'}`
    );
  }
}

src/index.ts:513-521 (schema)

Input schema defining parameters for the search_similar_structures tool.

inputSchema: {
  type: 'object',
  properties: {
    reference_id: { type: 'string', description: 'Reference chemical ID for similarity search' },
    threshold: { type: 'number', description: 'Similarity threshold (0.0-1.0, default: 0.7)', minimum: 0.0, maximum: 1.0 },
    limit: { type: 'number', description: 'Number of results to return (1-100, default: 25)', minimum: 1, maximum: 100 },
  },
  required: ['reference_id'],
},

src/index.ts:510-522 (registration)

Tool registration object including name, description, and schema in the tools array.

{
  name: 'search_similar_structures',
  description: 'Find structurally similar chemicals using similarity search',
  inputSchema: {
    type: 'object',
    properties: {
      reference_id: { type: 'string', description: 'Reference chemical ID for similarity search' },
      threshold: { type: 'number', description: 'Similarity threshold (0.0-1.0, default: 0.7)', minimum: 0.0, maximum: 1.0 },
      limit: { type: 'number', description: 'Number of results to return (1-100, default: 25)', minimum: 1, maximum: 100 },
    },
    required: ['reference_id'],
  },
},

src/index.ts:574-575 (registration)
Switch case in the request handler dispatching to the tool handler.
```
case 'search_similar_structures':
  return await this.handleSearchSimilarStructures(args);
```

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