Package org.openscience.cdk.formula

Class IsotopePatternGenerator

java.lang.Object

org.openscience.cdk.formula.IsotopePatternGenerator

public class IsotopePatternGenerator
extends Object

Generates all Combinatorial chemical isotopes given a structure.

Author:

Miguel Rojas Cherto

Source code:

main

Belongs to CDK module:

formula

Keywords:

isotope pattern

Created on:

2007-11-20

Constructor Summary

Constructors

Constructor	Description
IsotopePatternGenerator()	Constructor for the IsotopeGenerator.
IsotopePatternGenerator(double minIntensity)	Constructor for the IsotopeGenerator.

Method Summary

Modifier and Type	Method	Description
IsotopePattern	getIsotopes(IMolecularFormula molFor)	Get all combinatorial chemical isotopes given a structure.
IsotopePatternGenerator	setMinIntensity(double minIntensity)	Set the minimum (normalised) intensity to generate.
IsotopePatternGenerator	setMinResolution(double resolution)	Set the minimum resolution at which peaks within this mass difference should be considered equivalent.
IsotopePatternGenerator	setStoreFormulas(boolean storeFormula)	When generating the isotope containers store the MF for each IsotopeContainer.

Methods inherited from class java.lang.Object

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

Constructor Detail

IsotopePatternGenerator

public IsotopePatternGenerator()

Constructor for the IsotopeGenerator. The minimum abundance is set to 0.1 (10% abundance) by default.

IsotopePatternGenerator

public IsotopePatternGenerator(double minIntensity)

Constructor for the IsotopeGenerator.

Parameters:

minIntensity - Minimal intensity of the isotopes to be added in the combinatorial search (scale 0.0 to 1.0)

Method Detail

setMinIntensity

public IsotopePatternGenerator setMinIntensity(double minIntensity)

Set the minimum (normalised) intensity to generate.

Parameters:

minIntensity - the minimum intensity

Returns:

self for method chaining

setMinResolution

public IsotopePatternGenerator setMinResolution(double resolution)

Set the minimum resolution at which peaks within this mass difference should be considered equivalent.

Parameters:

resolution - the minimum resolution

Returns:

self for method chaining

setStoreFormulas

public IsotopePatternGenerator setStoreFormulas(boolean storeFormula)

When generating the isotope containers store the MF for each IsotopeContainer.

Parameters:

storeFormula - formulas should be stored

Returns:

self for method chaining

getIsotopes

public IsotopePattern getIsotopes(IMolecularFormula molFor)

Get all combinatorial chemical isotopes given a structure.

Parameters:

molFor - The IMolecularFormula to start

Returns:

A IsotopePattern object containing the different combinations