Package net.bioclipse.managers

Class ChemspiderManager

java.lang.Object
net.bioclipse.managers.ChemspiderManager
All Implemented Interfaces:
IBactingManager, net.bioclipse.managers.business.IBioclipseManager
public class ChemspiderManager extends Object implements IBactingManager
Bioclipse manager that provides functionality to interact with the ChemSpider database.

  • Constructor Details

    • ChemspiderManager

      public ChemspiderManager(String workspaceRoot)
      Creates a new ChemspiderManager.
      Parameters:
      workspaceRoot - location of the workspace, e.g. "."

  • Method Details

    • resolve

      public List<Integer> resolve(String inchiKey) throws IOException, net.bioclipse.core.business.BioclipseException, org.eclipse.core.runtime.CoreException
      Looks up ChemSpider identifiers for the given InChIKey.
      Parameters:
      inchiKey - InChIKey to resolve
      Returns:
      a Java List with ChemSpider identifiers
      Throws:
      IOException
      net.bioclipse.core.business.BioclipseException
      org.eclipse.core.runtime.CoreException

    • downloadAsString

      public String downloadAsString(Integer csid) throws IOException, net.bioclipse.core.business.BioclipseException, org.eclipse.core.runtime.CoreException
      Downloads the molecular for the given ChemSpider identifier as an SD file.
      Parameters:
      csid - the ChemSpider identifiers
      Returns:
      the molecule as String
      Throws:
      IOException
      net.bioclipse.core.business.BioclipseException
      org.eclipse.core.runtime.CoreException

    • download

      public net.bioclipse.core.domain.IMolecule download(Integer csid) throws IOException, net.bioclipse.core.business.BioclipseException, org.eclipse.core.runtime.CoreException
      Downloads the molecular for the given ChemSpider identifier as a IMolecule object.
      Parameters:
      csid - the ChemSpider identifiers
      Returns:
      the molecule as IMolecule
      Throws:
      IOException
      net.bioclipse.core.business.BioclipseException
      org.eclipse.core.runtime.CoreException

    • getManagerName

      public String getManagerName()
      Specified by:
      getManagerName in interface net.bioclipse.managers.business.IBioclipseManager

    • doi

      public List<String> doi()
      Description copied from interface: IBactingManager
      Lists the DOIs of the articles associated to this manager.
      Specified by:
      doi in interface IBactingManager
      Returns:
      a List of String with DOIs