Package org.openscience.cdk.formula

Class MassToFormulaTool

java.lang.Object

org.openscience.cdk.formula.MassToFormulaTool

@Deprecated
public class MassToFormulaTool
extends Object

Deprecated.

Please use MolecularFormulaGenerator

Tool to determine molecular formula consistent with a given accurate mass. The molecular formulas are not validate. It only consist in generate combination according object (see MolecularFormulaChecker). The algorithm is published in Rojas-Cherto M. et.al. [Rojas-Cherto, Miguel et. al.. Bioinformatics. 2011. ].

   MassToFormulaTool mf = new MassToFormulaTool();
   double myMass = 133.004242;
   IMolecularFormulaSet mfSet = mf.generate(myMass);
 

The elements are listed according on difference with the proposed mass.

Author:

miguelrojasch

Source code:

main

Belongs to CDK module:

formula

Created on:

2007-03-01

Constructor Summary

Constructors

Constructor	Description
MassToFormulaTool(IChemObjectBuilder builder)	Deprecated. Construct an instance of MassToFormulaTool.

Method Summary

Modifier and Type	Method	Description
IMolecularFormulaSet	generate(double mass)	Deprecated. Method that actually does the work of extracting the molecular formula.
List<IRule>	getRestrictions()	Deprecated. Get the restrictions that must be presents in the molecular formula.
void	setDefaultRestrictions()	Deprecated. Set the default restrictions that must be presents in the molecular formula.
void	setRestrictions(List<IRule> rulesNew)	Deprecated. Set the restrictions that must be presents in the molecular formula.

Methods inherited from class java.lang.Object

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

Constructor Detail

MassToFormulaTool

public MassToFormulaTool(IChemObjectBuilder builder)

Deprecated.

Construct an instance of MassToFormulaTool. It is necessary because different matrix have to build. Furthermore the default restrictions are initiated.

See Also:

setDefaultRestrictions()

Method Detail

setRestrictions

public void setRestrictions(List<IRule> rulesNew)
                     throws CDKException

Deprecated.

Set the restrictions that must be presents in the molecular formula.

Parameters:

rulesNew - The restrictions to impose

Throws:

CDKException

See Also:

getRestrictions(), setDefaultRestrictions(), IRule

getRestrictions

public List<IRule> getRestrictions()

Deprecated.

Get the restrictions that must be presents in the molecular formula.

Returns:

The restrictions to be imposed

See Also:

setDefaultRestrictions()

setDefaultRestrictions

public void setDefaultRestrictions()

Deprecated.

Set the default restrictions that must be presents in the molecular formula.

See Also:

getRestrictions()

generate

public IMolecularFormulaSet generate(double mass)

Deprecated.

Method that actually does the work of extracting the molecular formula.

Parameters:

mass - molecular formula to create from the mass

Returns:

the filled molecular formulas as IMolecularFormulaSet