org.helm.notation2.calculation

Class MoleculePropertyCalculator

java.lang.Object

org.helm.notation2.calculation.MoleculePropertyCalculator

public final class MoleculePropertyCalculator
extends Object

MoleculeInformation, class to

Author:

hecht

Method Summary

Methods

Modifier and Type	Method and Description
static double	getExactMass(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to get the ExactMass for the whole HELM
static String	getMolecularFormular(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to get the MolecularFormular for the whole HELM
static double	getMolecularWeight(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to get the molecular weight for the whole HELM
static MoleculeProperty	getMoleculeProperties(org.helm.notation2.parser.notation.HELM2Notation helm2notation) method to get all molecule properties for one HELM2Notation

Methods inherited from class java.lang.Object

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

Method Detail

getMolecularWeight

public static double getMolecularWeight(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                                 throws BuilderMoleculeException,
                                        org.helm.chemtoolkit.CTKException,
                                        ChemistryException

method to get the molecular weight for the whole HELM

Parameters:

helm2notation - input HELM2Notation

Returns:

MolecularWeight of the whole HELM

Throws:

BuilderMoleculeException - if the whole molecule can not be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the Chemistry Engine can not be initialized

getExactMass

public static double getExactMass(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                           throws BuilderMoleculeException,
                                  org.helm.chemtoolkit.CTKException,
                                  ChemistryException

method to get the ExactMass for the whole HELM

Parameters:

helm2notation - input HELM2Notation

Returns:

ExactMass of the whole HELM

Throws:

BuilderMoleculeException - if the whole molecule can not be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the Chemistry Engine can not be initialized

getMolecularFormular

public static String getMolecularFormular(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                                   throws BuilderMoleculeException,
                                          org.helm.chemtoolkit.CTKException,
                                          ChemistryException

method to get the MolecularFormular for the whole HELM

Parameters:

helm2notation - input HELM2Notation

Returns:

MolecularFormular of the whole HELM

Throws:

BuilderMoleculeException - if the whole molecule can not be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ChemistryException - if the Chemistry Engine can not be initialized

getMoleculeProperties

public static MoleculeProperty getMoleculeProperties(org.helm.notation2.parser.notation.HELM2Notation helm2notation)
                                              throws BuilderMoleculeException,
                                                     org.helm.chemtoolkit.CTKException,
                                                     ExtinctionCoefficientException,
                                                     ChemistryException

method to get all molecule properties for one HELM2Notation

Parameters:

helm2notation - given HELM2 object

Returns:

List of molecule properties: molecular formula, molecular weight, exact mass, extinction coefficient

Throws:

BuilderMoleculeException - if helm molecule can not be built

org.helm.chemtoolkit.CTKException - general ChemToolKit exception passed to HELMToolKit

ExtinctionCoefficientException - if the extinction coefficient can not be calculated

ChemistryException - if the Chemistry Engine can not be initialized