Class MMElementRule

java.lang.Object
org.openscience.cdk.formula.rules.MMElementRule
All Implemented Interfaces:
IRule

public class MMElementRule extends Object implements IRule
This class validate if the occurrence of the IElements in the IMolecularFormula, for metabolites, are into a maximal limit according paper: . The study is from 2 different mass spectral databases and according different mass of the metabolites. The analysis don't take account if the IElement is not contained in the matrix. It will be jumped.

The rules is based from Tobias Kind paper with the title "Seven Golden Rules for heuristic filtering of molecular formula" [Kind, Tobias and Fiehn, Oliver. BMC Bioinformatics. 2007. 8].

Table 1: Parameters set by this rule.
Name Default Description
database willey Mass spectral databases extraction
massRange < 500 Mass to take account
Author:
miguelrojasch
Source code:
main
Belongs to CDK module:
formula
Created on:
2007-11-20
  • Constructor Details

    • MMElementRule

      public MMElementRule()
      Constructor for the MMElementRule object.
  • Method Details

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the MMElementRule object.
      Specified by:
      setParameters in interface IRule
      Parameters:
      params - The new parameters value
      Throws:
      CDKException - Description of the Exception
      See Also:
    • getParameters

      public Object[] getParameters()
      Gets the parameters attribute of the MMElementRule object.
      Specified by:
      getParameters in interface IRule
      Returns:
      The parameters value
      See Also:
    • validate

      public double validate(IMolecularFormula formula) throws CDKException
      Validate the occurrence of this IMolecularFormula.
      Specified by:
      validate in interface IRule
      Parameters:
      formula - Parameter is the IMolecularFormula
      Returns:
      An ArrayList containing 9 elements in the order described above
      Throws:
      CDKException - if an error occurs during the validation. See documentation for individual rules