Class PubChemReader

java.lang.Object
org.episteme.core.io.AbstractResourceReader<Compound>
org.episteme.natural.chemistry.loaders.PubChemReader
All Implemented Interfaces:
ResourceIO<Compound>, ResourceReader<Compound>
public class PubChemReader extends AbstractResourceReader<Compound>
Modernized loader for the PubChem chemical compound database.

Fetches compound information from the NCBI PubChem PUG REST API. Uses the Episteme ResourceReader framework for consistent data access.

Since:
1.0
Author:
Silvere Martin-Michiellot, Gemini AI (Google DeepMind)

  • Constructor Details

    • PubChemReader

      public PubChemReader()

    • PubChemReader

      public PubChemReader(String baseUrl)

  • Method Details

    • getCategory

      public String getCategory()
      Description copied from interface: ResourceIO
      Returns the category for grouping. MUST be implemented with I18N support.
      Returns:
      the category name

    • getName

      public String getName()
      Description copied from interface: ResourceIO
      Returns the display name of this resource handler. MUST be implemented with I18N support.
      Returns:
      the display name

    • getDescription

      public String getDescription()
      Description copied from interface: ResourceIO
      Returns a short description of this resource handler. MUST be implemented with I18N support.
      Returns:
      the description

    • getLongDescription

      public String getLongDescription()
      Description copied from interface: ResourceIO
      Returns a long description of this resource handler. MUST be implemented with I18N support.
      Returns:
      the long description

    • getResourcePath

      public String getResourcePath()
      Description copied from interface: ResourceIO
      Returns the base path where this resource is located.

    • getResourceType

      public Class<Compound> getResourceType()
      Description copied from interface: ResourceIO
      Returns the type of resource.

    • getSupportedVersions

      public String[] getSupportedVersions()
      Description copied from interface: ResourceIO
      Returns the supported versions of the format this reader/writer handles.

      Each implementation MUST override this method to declare which versions of the underlying format are supported. The returned array should contain version strings in the format's standard notation (e.g., "3.0", "2.1", "Level 3 Version 2").

      Examples:

      • MathML: {"3.0", "2.0"}
      • SBML: {"Level 3 Version 2", "Level 3 Version 1", "Level 2 Version 5"}
      • PhyloXML: {"1.10", "1.00"}

      Returns:
      array of supported version strings, never null (empty array if version-agnostic)

    • loadFromSource

      protected Compound loadFromSource(String resourceId) throws Exception
      Specified by:
      loadFromSource in class AbstractResourceReader<Compound>
      Throws:
      Exception

    • fetchByCid

      public CompletableFuture<Compound> fetchByCid(long cid)
      Fetches compound by PubChem CID.

    • searchByName

      public CompletableFuture<List<Long>> searchByName(String name)
      Searches compounds by name, returning a list of CIDs.

    • fetchBySmiles

      public CompletableFuture<Compound> fetchBySmiles(String smiles)
      Fetches compound by SMILES string.

    • getStructureImageUrl

      public String getStructureImageUrl(long cid)
      Gets 2D structure image URL for a compound.