Package org.biopax.paxtools.model.level3

Interface ChemicalStructure

All Superinterfaces:
BioPAXElement, Cloneable, Level3Element, Serializable, UtilityClass
All Known Implementing Classes:
ChemicalStructureImpl
public interface ChemicalStructure extends UtilityClass
Definition: The chemical structure of a small molecule. Usage: Structure information is stored in the property structureData, in one of the three formats: CML, SMILES or InChI.The structureFormat property specifies which format is used. Examples: The following SMILES string describes the structure of glucose-6-phosphate: 'C(OP(=O)(O)O)[CH]1([CH](O) [CH](O)[CH](O)[CH](O)O1)'.

  • Method Details

    • getStructureData

      String getStructureData()
      This property holds a string defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.
      Returns:
      a string defining chemical structure

    • setStructureData

      void setStructureData(String structureData)
      This property holds a string of data defining chemical structure,in one of the three formats: CML, SMILES or InChI. If, for example,the CML format is used, then the value of this property is a string containing the XML encoding of the CML data.
      Parameters:
      structureData - a string defining chemical structure

    • getStructureFormat

      StructureFormatType getStructureFormat()
      This property specifies which format is used to define chemical structure.
      Returns:
      format used to define chemical structure

    • setStructureFormat

      void setStructureFormat(StructureFormatType structureFormat)
      This property specifies which format is used to define chemical structure.
      Parameters:
      structureFormat - format used to define chemical structure