Class RDBERule

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

public class RDBERule extends Object implements IRule

Ring Double Bond Equivalents (RDBE) or Double Bond Equivalents (DBE) are calculated from valence values of elements contained in a formula and should tell the number of bonds - or rings. Since this formula will fail for MFs with higher valence states such as N(V), P(V), S(IV) or S(VI), this method will focus on the lowest valence state for these elements.

The equation used is: D = 1 + [0.5 SUM_i(N_i(V_I-2))]

where D is the unsaturation, i is the total number of different elements in the composition, N_i the number of atoms of element i, and Vi is the common valence of the atom i.

Table 1: Parameters set by this rule.
Name Default Description
charge 0.0 The RDBE rule of MolecularFormula
Author:
miguelrojasch
Source code:
main
Belongs to CDK module:
formula
Created on:
2008-06-11
  • Constructor Details

    • RDBERule

      public RDBERule()
      Constructor for the RDBE object.
  • Method Details

    • setParameters

      public void setParameters(Object[] params) throws CDKException
      Sets the parameters attribute of the RDBE 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 RDBRule object.
      Specified by:
      getParameters in interface IRule
      Returns:
      The parameters value
      See Also:
    • validate

      public double validate(IMolecularFormula formula) throws CDKException
      Validate the RDBRule of this IMolecularFormula.
      Specified by:
      validate in interface IRule
      Parameters:
      formula - Parameter is the IMolecularFormula
      Returns:
      A double value meaning 1.0 True, 0.0 False
      Throws:
      CDKException - if an error occurs during the validation. See documentation for individual rules
    • validate

      public boolean validate(IMolecularFormula formula, double value) throws CDKException
      Validate the ion state. It takes into account that neutral, nonradical compounds always have an even-numbered pair-wiser arrangement of binding electrons signilizaded by an integer DBE value. Charged compounds due to soft ionzation techniques will give an odd number of binding electrons and a fractional DBE (X.05).
      Parameters:
      formula - Parameter is the IMolecularFormula
      value - The RDBE value
      Returns:
      True, if corresponds with
      Throws:
      CDKException
    • getRDBEValue

      public List<Double> getRDBEValue(IMolecularFormula formula)
      Method to extract the Ring Double Bond Equivalents (RDB) value. It test all possible oxidation states.
      Parameters:
      formula - The IMolecularFormula object
      Returns:
      The RDBE value
      See Also:
      • createTable()