chemaxon.calculations.nmr

Class NMRCalculator

java.lang.Object

chemaxon.calculator.ProgressableCalculator<Molecule,NMRSpectrum>

chemaxon.calculations.nmr.NMRCalculator

All Implemented Interfaces:

chemaxon.calculator.Calculator<Molecule,NMRSpectrum>, chemaxon.license.Licensable

public class NMRCalculator
extends chemaxon.calculator.ProgressableCalculator<Molecule,NMRSpectrum>

Class for NMR spectrum calculation. API example for 1H NMR:

        // input molecule for 1H NMR prediction
        Molecule mol = MolImporter.importMol("c1c(Cl)cccc1C=O");
        // instantiate builder
        NMRCalculator.Builder builder = new NMRCalculator.Builder();
        // settings
        builder.setFrequency(400.0);
        builder.setUnit(NMRSpectrum.Unit.Hz);
        builder.setNucleus(NMRSpectrum.Nucleus.H1);
        builder.setCoupled(true);
        // instantiate calculator
        NMRCalculator nmrCalc = builder.build();
        // spectrum calculation
        NMRSpectrum spectrum = nmrCalc.calculate(mol);
        // explicit hydrogen mode
        spectrum.setImplicitHydrogenMode(false);
        // multiplets of the NMR spectrum
        Multiplet[] multiplets = spectrum.getMultiplets();
        for (Multiplet m: multiplets) {
            System.out.println(m.getShift()+"\t"+m.getNetIntensity());
                for (int i=0; i < m.getNumberOfLines(); i++) {
                    System.out.println(m.getPosition(i)+"\t"+m.getIntensity(i));
                }
            }
        // exporting the NMR spectrum into JCAMP-DX format
        String jcamp = NMRExporter.exportToJcampDX(spectrum);
        // exporting the NMR spectrum into Molecule with an NMR property
        String propertyName = "1H NMR shifts";
        Molecule molWithNMR = NMRExporter.exportToMol(spectrum, propertyName);

 

API example for 1H NMR:

        // input molecule for 13C NMR prediction
        Molecule mol = MolImporter.importMol("c1c(Cl)cccc1C=O");
        // instantiate NMRCalculator, the default settings are used
        NMRCalculator nmrCalc = new NMRCalculator.Builder().build();
        // spectrum calculation
        NMRSpectrum spectrum = nmrCalc.calculate(mol);
        // chemical shifts with atom indexes
        Shift[] shifts = spectrum.getShifts();
        for (Shift s: shifts) {
            System.out.println(s.getAtomIndex()+"\t"+s.getShift());
        }
        // sampling the NMR spectrum and integrated NMR spectrum functions 
        double domainMin = spectrum.getDomainMin();
        double domainMax = spectrum.getDomainMax();
        double resolution = 0.1;
        for (double x = domainMin; x <= domainMax; x += resolution) {
            System.out.println(x+"\t"+spectrum.getValueAt(x)+"\t"+spectrum.getIntegralValueAt(x));
        }
        // or exporting the x and y values of the NMR spectrum function directly
        double[][] xy = NMRExporter.export(spectrum, domainMin, domainMax, resolution);
 

Since:

5.8

Author:

Rita Veréb, Csaba Fábri

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	NMRCalculator.Builder Builder class for NMRCalculator.

Nested classes/interfaces inherited from class chemaxon.calculator.ProgressableCalculator

chemaxon.calculator.ProgressableCalculator.CalculatorMProgressMonitor

Field Summary

Fields

Modifier and Type	Field and Description
static String	C_SHIFT_PROP_NAME Name of the 13C chemical shift atom property.
static String	H_SHIFT_PROP_NAME Name of the 1H chemical shift atom property.

Fields inherited from class chemaxon.calculator.ProgressableCalculator

cancelled, licenseEnvironment, PROGRESS, running, RUNNING

Method Summary

Methods

Modifier and Type	Method and Description
NMRSpectrum	calculate(Molecule data) Calculates NMR spectrum for the given input molecule.
List<chemaxon.calculator.CalculatorInputValidator.CalculatorError>	check(Molecule data)
chemaxon.calculator.CalculatorFormatter	getFormatter()
double	getFrequency() Returns NMR measurement frequency.
NMRSpectrum.Nucleus	getNucleus() Returns the NMR active nucleus.
String	getProductName()
NMRSpectrum.Unit	getUnit() Returns NMR spectrum unit.
boolean	isCoupled() Coupled/decoupled spectrum.

Methods inherited from class chemaxon.calculator.ProgressableCalculator

addPropertyChangeListener, addPropertyChangeListener, cancel, cancelCalculation, checkData, checkLicense, finishCalculation, getErrorMessage, isCancelled, isLicensed, isRunning, removePropertyChangeListener, removePropertyChangeListener, sendProgress, setLicenseEnvironment, startCalculation

Methods inherited from class java.lang.Object

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

Field Detail

C_SHIFT_PROP_NAME

public static final String C_SHIFT_PROP_NAME

Name of the 13C chemical shift atom property.

See Also:

Constant Field Values

H_SHIFT_PROP_NAME

public static final String H_SHIFT_PROP_NAME

Name of the 1H chemical shift atom property.

See Also:

Constant Field Values

Method Detail

getNucleus

public NMRSpectrum.Nucleus getNucleus()

Returns the NMR active nucleus. NMRSpectrum.Nucleus.C13.

Returns:

NMRSpectrum.Nucleus.C13 or NMRSpectrum.Nucleus.H1

getUnit

public NMRSpectrum.Unit getUnit()

Returns NMR spectrum unit. Default value is NMRSpectrum.Unit.ppm

Returns:

NMRSpectrum.Unit.ppm or NMRSpectrum.Unit.Hz

isCoupled

public boolean isCoupled()

Coupled/decoupled spectrum. Default value is true.

Returns:

True if spectrum is coupled, false otherwise.

getFrequency

public double getFrequency()

Returns NMR measurement frequency. Default value is 500 MHz.

Returns:

NMR frequency in MHz.

calculate

public NMRSpectrum calculate(Molecule data)
                      throws chemaxon.license.LicenseException

Calculates NMR spectrum for the given input molecule.

Returns:

Calculated NMR spectrum.

Throws:

chemaxon.license.LicenseException

getFormatter

public chemaxon.calculator.CalculatorFormatter getFormatter()

check

public List<chemaxon.calculator.CalculatorInputValidator.CalculatorError> check(Molecule data)

getProductName

public String getProductName()

Specified by:

getProductName in class chemaxon.calculator.ProgressableCalculator<Molecule,NMRSpectrum>