Package org.jmol.quantum

Class NMRCalculation

java.lang.Object
org.jmol.quantum.NMRCalculation
All Implemented Interfaces:
JmolNMRInterface
public class NMRCalculation extends Object implements JmolNMRInterface

  • Field Details

  • Constructor Details

    • NMRCalculation

      public NMRCalculation()

  • Method Details

    • setViewer

      public JmolNMRInterface setViewer(Viewer vwr)
      Specified by:
      setViewer in interface JmolNMRInterface

    • getQuadrupolarConstant

      public float getQuadrupolarConstant(Tensor efg)
      Description copied from interface: JmolNMRInterface
      Quadrupolar constant, directly proportional to Vzz and dependent on the quadrupolar moment of the isotope considered
      Specified by:
      getQuadrupolarConstant in interface JmolNMRInterface
      Parameters:
      efg -
      Returns:
      float value

    • getUniqueTensorSet

      public BS getUniqueTensorSet(BS bsAtoms)
      Description copied from interface: JmolNMRInterface
      An attempt to find unique atoms using tensors.
      Specified by:
      getUniqueTensorSet in interface JmolNMRInterface
      Parameters:
      bsAtoms -
      Returns:
      bitset of atoms

    • getJCouplingHz

      public float getJCouplingHz(Atom a1, Atom a2, String type, Tensor isc)

    • getIsoOrAnisoHz

      public float getIsoOrAnisoHz(boolean isIso, Atom a1, Atom a2, String units, Tensor isc)
      Description copied from interface: JmolNMRInterface
      If t is null, then a1, a2, and type are used to find the appropriate tensor.
      Specified by:
      getIsoOrAnisoHz in interface JmolNMRInterface
      Parameters:
      isIso -
      a1 -
      a2 -
      units -
      isc -
      Returns:
      0 if not found

    • getDipolarConstantHz

      public float getDipolarConstantHz(Atom a1, Atom a2)
      Specified by:
      getDipolarConstantHz in interface JmolNMRInterface
      Parameters:
      a1 -
      a2 -
      Returns:
      desired constant

    • getDipolarCouplingHz

      public float getDipolarCouplingHz(Atom a1, Atom a2, V3 vField)
      Specified by:
      getDipolarCouplingHz in interface JmolNMRInterface
      Parameters:
      a1 -
      a2 -
      vField -
      Returns:
      projected value

    • getInfo

      public Object getInfo(String what)
      Specified by:
      getInfo in interface JmolNMRInterface
      Parameters:
      what - "C" or "14C" or "all"
      Returns:
      list of double[isotopeNumber,g,Q] if no isotope number is given, or a single double[] if it does.

    • getChemicalShift

      public float getChemicalShift(Atom atom)
      Description copied from interface: JmolNMRInterface
      If shift reference has not been set, it defaults to 0 and just displays the negative of magnetic shielding
      Specified by:
      getChemicalShift in interface JmolNMRInterface
      Parameters:
      atom -
      Returns:
      value

    • getMagneticShielding

      public float getMagneticShielding(Atom atom)
      Specified by:
      getMagneticShielding in interface JmolNMRInterface

    • getState

      public boolean getState(SB sb)
      Specified by:
      getState in interface JmolNMRInterface

    • setChemicalShiftReference

      public boolean setChemicalShiftReference(String element, float value)
      Specified by:
      setChemicalShiftReference in interface JmolNMRInterface

    • getTensorInfo

      public Lst<Object> getTensorInfo(String tensorType, String infoType, BS bs)
      Specified by:
      getTensorInfo in interface JmolNMRInterface

    • getMinDistances

      public Map<String,Integer> getMinDistances(MeasurementData md)
      Specified by:
      getMinDistances in interface JmolNMRInterface

    • calcJKarplus

      public static double calcJKarplus(double theta)

    • calc3JCH

      public static double calc3JCH(String CHequation, double theta, boolean is23Double)
      Parameters:
      CHequation - 'was' Simple equation for 3JCH, from Wasylishen and Schaefer Can J Chem (1973) 51 961 used in Kozerski et al. J Chem Soc Perkin 2, (1997) 1811 'tva' Tvaroska and Taravel Adv. Carbohydrate Chem. Biochem. (1995) 51, 15-61 'ayd' Aydin and Guether Mag. Res. Chem. (1990) 28, 448-457
      theta - dihedral
      is23Double -
      Returns:
      3JCH prediction

    • calcNOE

      public static double[] calcNOE(Viewer viewer, Atom atom1, Atom atom2)

    • calc2or3JorNOE

      public static double[] calc2or3JorNOE(Viewer viewer, Atom[] atoms, String CHEquation, int mode)
      Calculate a 2-bond (geminal) or 3-bond (vicinal) coupling constant or an NOE;
      Parameters:
      viewer -
      atoms - required Atom[4]; can be just two atoms, then in atom[0] and atom[4]
      CHEquation - 'none' or 'was' or 'tva' or 'ayd'
      mode -
      Returns:
      [theta, jvalue, atom2.i, atom3.i] for 3JHH; [theta, jvalue, center.i] for 2JHH; [distance, noe] for NOE

    • getCalcType

      public static int getCalcType(Atom[] atoms, String[] elementsToFill, int mode)

    • getNOEorJHH

      public double[] getNOEorJHH(Atom[] atoms, int mode)
      Specified by:
      getNOEorJHH in interface JmolNMRInterface