Package chemaxon.calculations.nmr

Class NMRSpectrum

java.lang.Object
chemaxon.calculations.nmr.NMRSpectrum
All Implemented Interfaces:
chemaxon.calculations.nmr.Spectrum
@PublicApi public class NMRSpectrum extends Object implements chemaxon.calculations.nmr.Spectrum
Class for the representation of NMR spectra.
Since:
5.7

  • Field Details

    • functionScale

      protected double functionScale
      Scale factor for NMR spectrum function scaling.

  • Constructor Details

    • NMRSpectrum

      public NMRSpectrum(Molecule mol)
      Constructor. Default nucleus setting is 13C NMR.
      Parameters:
      mol - Input molecule, needs to be explicitly hydrogenized in case of 1H NMR.

    • NMRSpectrum

      public NMRSpectrum(Molecule mol, NMRSpectrum.Nucleus nucleusType)
      Constructor.
      Parameters:
      mol - Input molecule, needs to be explicitly hydrogenized in case of 1H NMR.
      nucleusType - NMRSpectrum.Nucleus

  • Method Details

    • getMolecule

      public Molecule getMolecule()
      Returns the molecule under examination.
      Returns:
      Molecule under examination.

    • getStrictMolecule

      protected Molecule getStrictMolecule()

    • getNumberOfNMRActiveNuclei

      public int getNumberOfNMRActiveNuclei()
      Returns number of the NMR active nuclei.
      Returns:
      Number of NMR active nuclei.

    • setNumberOfNMRActiveNuclei

      public void setNumberOfNMRActiveNuclei(int numberOfNMRActiveNuclei)
      Sets number of the NMR active nuclei.
      Parameters:
      numberOfNMRActiveNuclei - Number of NMR active nuclei.

    • getShifts

      public Shift[] getShifts()
      Returns chemical shifts.
      Returns:
      Array of chemical shifts.

    • setShifts

      public void setShifts(Shift[] shifts)
      Sets chemical shifts.
      Parameters:
      shifts - Array of chemical shifts.

    • getAtomIndexes

      public List<Integer> getAtomIndexes()
      Returns the atom indices of the NMR active nuclei.
      Returns:
      Atom indices.

    • getCouplingConstants

      public double[][] getCouplingConstants()
      Returns coupling constants.
      Returns:
      Array of coupling constants.

    • getCouplingConstants

      public double[][] getCouplingConstants(NMRSpectrum.Unit unit)
      Returns coupling constants in the given unit.
      Parameters:
      unit - Unit requested.
      Returns:
      Coupling constant array in the requested unit.

    • setCouplingConstants

      public void setCouplingConstants(double[][] couplingConstants)
      Sets coupling constants.
      Parameters:
      couplingConstants - Array of coupling constants.

    • getNucleusType

      public NMRSpectrum.Nucleus getNucleusType()
      Returns the type of the nucleus under examination.
      Returns:
      NMRSpectrum.Nucleus.

    • getNucleusString

      public String getNucleusString()
      Returns the nucleus type string.
      Returns:
      Nucleus type string.

    • isImplicitHydrogenMode

      public boolean isImplicitHydrogenMode()
      Returns implicit hydrogen mode.
      Returns:
      Returns true if implicit hydrogen mode is used.

    • setImplicitHydrogenMode

      public void setImplicitHydrogenMode(boolean implicitHydrogenMode)
      Sets implicit hydrogen mode.
      Parameters:
      implicitHydrogenMode - True if implicit hydrogen mode is needed.

    • getFrequency

      public double getFrequency()
      Returns the NMR measurement frequency in MHz unit.
      Returns:
      NMR frequency.

    • setFrequency

      public void setFrequency(double frequency)
      Sets the NMR measurement frequency. Frequency should be given in MHz unit.
      Parameters:
      frequency - NMR frequency.

    • getHalfWidth

      public double getHalfWidth()
      Returns NMR half-width.
      Returns:
      NMR half-width.

    • setHalfWidth

      public void setHalfWidth(double halfWidth)
      Sets NMR half-width.
      Parameters:
      halfWidth - NMR half-width.

    • getUnit

      public NMRSpectrum.Unit getUnit()
      Returns the unit type.
      Returns:
      NMRSpectrum.Unit

    • setUnit

      public void setUnit(NMRSpectrum.Unit unit)
      Sets the unit type.
      Parameters:
      unit - NMRSpectrum.Unit

    • isCouplingNeeded

      public boolean isCouplingNeeded()
      Returns whether spin-spin couplings are taken into account.
      Returns:
      True if spin-spin couplings are taken into account.

    • setCouplingNeeded

      public void setCouplingNeeded(boolean couplingNeeded)
      Sets whether spin-spin couplings are taken into account.
      Parameters:
      couplingNeeded - True if spin-spin couplings are taken into account.

    • getMeaningfulFrequencies

      public static double[] getMeaningfulFrequencies()
      Returns the array of meaningful NMR measurement frequencies in MHz.
      Returns:
      NMR measurement frequency array.

    • getLocalMaximumPlaces

      public double[] getLocalMaximumPlaces()
      Specified by:
      getLocalMaximumPlaces in interface chemaxon.calculations.nmr.Spectrum

    • getDomainMin

      public double getDomainMin()
      Returns the lower end of the spectrum.
      Returns:
      Lower end of the spectrum.

    • setDomainMin

      public void setDomainMin(double domainMin)
      Sets the lower end of the spectrum.
      Parameters:
      domainMin - Lower end of the spectrum.

    • getDomainMax

      public double getDomainMax()
      Returns the upper end of the spectrum.
      Returns:
      Upper end of the spectrum.

    • setDomainMax

      public void setDomainMax(double domainMax)
      Sets the upper end of the spectrum.
      Parameters:
      domainMax - Upper end of the spectrum.

    • getName

      public String getName()
      Returns the name of the NMR spectrum.
      Returns:
      spectrum name

    • setName

      public void setName(String name)
      Sets the name of the NMR spectrum

    • getValueAt

      public double getValueAt(double location)
      Returns the value of the NMR spectrum function at a given x point.
      Parameters:
      location - x value where the function is evaluated.
      Returns:
      Value of the NMR spectrum function at a given point.

    • getRawValueAt

      public double getRawValueAt(double location)
      Returns the value of the unscaled NMR spectrum function at a given x point.
      Parameters:
      location - x value where the function is evaluated.
      Returns:
      Value of the unscaled NMR spectrum function at a given point.

    • getIntegralValueAt

      public double getIntegralValueAt(double location)
      Returns the value of the NMR integral function at a given x point.
      Parameters:
      location - x value where the function is evaluated.
      Returns:
      Value of the NMR integral function at a given point.

    • getMultiplets

      public Multiplet[] getMultiplets()
      Specified by:
      getMultiplets in interface chemaxon.calculations.nmr.Spectrum

    • setMultiplets

      public void setMultiplets(Multiplet[] multiplets)
      Sets Multiplet array of the spectrum.
      Parameters:
      multiplets - New Multiplet array.

    • getDefaultValue

      public double getDefaultValue()
      Specified by:
      getDefaultValue in interface chemaxon.calculations.nmr.Spectrum

    • getRangeMax

      public double getRangeMax()
      Maximal y value of the NMR spectrum function.
      Returns:
      Maximal y value.

    • getRangeMin

      public double getRangeMin()
      Minimal y value of the NMR spectrum function.
      Returns:
      Minimal y value.

    • computeFunctionScale

      public void computeFunctionScale()
      Computes the scaling factor for the unscaled NMR spectrum function. As a result the maxima of the spectrum and integral functions are the same and correspond to the number of NMR active nuclei.

    • computeFunctionScale

      protected void computeFunctionScale(double aimedMaxValue, double[] places)

    • getFunctionScale

      protected double getFunctionScale()