Package net.bioclipse.managers

Class OpsinManager

java.lang.Object
net.bioclipse.managers.OpsinManager
All Implemented Interfaces:
IBactingManager, net.bioclipse.managers.business.IBioclipseManager
public class OpsinManager extends Object implements IBactingManager
Bioclipse manager that wraps OPSIN functionality for processing IUPAC names.

  • Constructor Details

    • OpsinManager

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

  • Method Details

    • parseIUPACName

      public net.bioclipse.cdk.domain.ICDKMolecule parseIUPACName(String iupacName) throws net.bioclipse.core.business.BioclipseException
      Parses a IUPAC name into a molecule.
      Parameters:
      iupacName - the IUPAC name
      Returns:
      the molecule as ICDKMolecule
      Throws:
      net.bioclipse.core.business.BioclipseException

    • parseIUPACNameAsCML

      public String parseIUPACNameAsCML(String iupacName) throws net.bioclipse.core.business.BioclipseException
      Parses a IUPAC name into a molecule.
      Parameters:
      iupacName - the IUPAC name
      Returns:
      the molecule as CML string
      Throws:
      net.bioclipse.core.business.BioclipseException

    • parseIUPACNameAsSMILES

      public String parseIUPACNameAsSMILES(String iupacName) throws net.bioclipse.core.business.BioclipseException
      Parses a IUPAC name into a molecule.
      Parameters:
      iupacName - the IUPAC name
      Returns:
      the molecule as SMILES string
      Throws:
      net.bioclipse.core.business.BioclipseException

    • 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