Package org.biopax.paxtools.pattern.util

Class ChemicalNameNormalizer

java.lang.Object
org.biopax.paxtools.pattern.util.ChemicalNameNormalizer
public class ChemicalNameNormalizer extends Object
This class is used for finding a standard name for a small molecule. During detection of ubiquitous small molecules, we map the duplicated small molecules to one standard name, otherwise their degree would be divided and this would spoil the detection method.
Author:
Ozgun Babur

  • Constructor Details

    • ChemicalNameNormalizer

      public ChemicalNameNormalizer(Model model)
      Constructor that also infers all the mapping.
      Parameters:
      model - the big picture

  • Method Details

    • getName

      public String getName(SmallMoleculeReference smr)
      Gets the standard name of the small molecule.
      Parameters:
      smr - the molecule to check standard name
      Returns:
      standard name