Package org.openscience.cdk.formula.rules

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

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
class	RDBERule.Combinations

Constructor Summary

Constructors

Constructor	Description
RDBERule()	Constructor for the RDBE object.

Method Summary

Modifier and Type	Method	Description
Object[]	getParameters()	Gets the parameters attribute of the RDBRule object.
List<Double>	getRDBEValue(IMolecularFormula formula)	Method to extract the Ring Double Bond Equivalents (RDB) value.
void	setParameters(Object[] params)	Sets the parameters attribute of the RDBE object.
double	validate(IMolecularFormula formula)	Validate the RDBRule of this IMolecularFormula.
boolean	validate(IMolecularFormula formula, double value)	Validate the ion state.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

RDBERule

public RDBERule()

Constructor for the RDBE object.

Method Detail

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()

getParameters

public Object[] getParameters()

Gets the parameters attribute of the RDBRule object.

Specified by:

getParameters in interface IRule

Returns:

The parameters value

See Also:

setParameters(java.lang.Object[])

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()