Package 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

    Modifier and Type Method 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 Details

    • 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