A comprehensive Ruby library for interacting with the PubChem PUG REST API. This library provides a user-friendly interface to access PubChem data and services, mapping API responses onto Ruby classes for seamless integration into your applications.

Warning: This implementation is unfinished and has known issues. Basic usage is functional, no guarantees beyond that.

• Features
• Installation
• Getting Started
  • Initialization
  • Usage Examples
    • Retrieve Compound Data by CID
    • Retrieve Compound Data by Name
    • Perform a Similarity Search
    • Retrieve Taxonomy Summary by TaxID
• Available Methods
• Error Handling
• License

• Comprehensive Endpoint Coverage: Access various PubChem resources such as compounds, substances, assays, genes, proteins, and more.
• Object Mapping: API responses are mapped to Ruby classes, allowing easy access to data without handling raw JSON or XML.
• Error Handling: Custom APIError class provides detailed error messages and codes.
• Parameter Validation: Ensures that only valid parameters are sent to the API.
• Extensible Design: The code structure should make it easy to extend the library with additional endpoints or complex data mapping, in case something is missing.

Add this line to your application's Gemfile:

gem 'pubchem_api'

Or install it yourself as:

$ gem install pubchem_api

Note: This gem depends on httparty and nokogiri

$ gem install httparty nokogiri

Require the library in your Ruby script:

require 'pubchem_api'

Initialize the client:

client = PubChemAPI::Client.new

begin compound = client.get_compound_by_cid(2244, 'record') puts "CID: #{compound.cid}" puts "Molecular Formula: #{compound.molecular_formula}" puts "Molecular Weight: #{compound.molecular_weight}" puts "Canonical SMILES: #{compound.canonical_smiles}" puts "InChIKey: #{compound.inchi_key}" rescue PubChemAPI::APIError => e puts "API Error (#{e.code}): #{e.message}" end

begin compound = client.get_compound_by_name('aspirin', 'record') puts "CID: #{compound.cid}" puts "Molecular Formula: #{compound.molecular_formula}" puts "Molecular Weight: #{compound.molecular_weight}" rescue PubChemAPI::APIError => e puts "API Error (#{e.code}): #{e.message}" end

begin options = {} options['Threshold'] = 90 results = client.compound_structure_search( 'fastsimilarity_2d', 'smiles', 'CC(=O)OC1=CC=CC=C1C(=O)O', 'JSON', options ) cids = results['IdentifierList']['CID'] puts "Found CIDs: #{cids.join(', ')}" rescue PubChemAPI::APIError => e puts "API Error (#{e.code}): #{e.message}" end

begin taxonomy = client.get_taxonomy_summary_by_taxid(9606) puts "Scientific Name: #{taxonomy.scientific_name}" puts "Common Name: #{taxonomy.common_name}" puts "Rank: #{taxonomy.rank}" rescue PubChemAPI::APIError => e puts "API Error (#{e.code}): #{e.message}" end

• get_compound_by_cid(cid, operation, output = DEFAULT_OUTPUT, options = {})
• get_compound_by_name(name, operation, output = DEFAULT_OUTPUT, options = {})
• get_compound_conformers(cid, output = DEFAULT_OUTPUT, options = {})
• compound_structure_search(search_type, namespace, identifier, output = DEFAULT_OUTPUT, options = {})

• get_substance_by_sid(sid, operation, output = DEFAULT_OUTPUT, options = {})

• get_assay_by_aid(aid, operation, output = DEFAULT_OUTPUT, options = {})
• get_assay_doseresponse(aid, output = DEFAULT_OUTPUT, options = {})
• get_assay_targets(aid, target_type, output = DEFAULT_OUTPUT, options = {})

• get_gene_summary_by_geneid(geneid, output = DEFAULT_OUTPUT, options = {})
• get_gene_summary_by_synonym(synonym, output = DEFAULT_OUTPUT, options = {})

• get_protein_summary_by_synonym(synonym, output = DEFAULT_OUTPUT, options = {})

• get_taxonomy_summary_by_taxid(taxid, output = DEFAULT_OUTPUT, options = {})

• get_pathway_summary_by_pwacc(pwacc, output = DEFAULT_OUTPUT, options = {})

• get_classification_nodes(hnid, idtype, output = DEFAULT_OUTPUT, list_return, options = {})

• get_compounds_by_listkey(listkey, output = DEFAULT_OUTPUT, options = {})

The library raises a PubChemAPI::APIError exception for API errors:

begin # API call rescue PubChemAPI::APIError => e puts "API Error (#{e.code}): #{e.message}" end

APIError definition:

• APIError.code: HTTP status code
• APIError.message: Error message from the API

This project is licensed under the MIT License.

Disclaimer: This library is not affiliated with or endorsed by PubChem. Use responsibly.