Field Detail

• MAGNETOGYRIC_RATIO

  private static final int MAGNETOGYRIC_RATIO

  See Also:

  Constant Field Values

• QUADRUPOLE_MOMENT

  private static final int QUADRUPOLE_MOMENT

  See Also:

  Constant Field Values

• e_charge

  private static final double e_charge

  See Also:

  Constant Field Values

• h_planck

  private static final double h_planck

  See Also:

  Constant Field Values

• h_bar_planck

  private static final double h_bar_planck

  See Also:

  Constant Field Values

• DIPOLAR_FACTOR

  private static final double DIPOLAR_FACTOR

  See Also:

  Constant Field Values

• J_FACTOR

  private static final double J_FACTOR

  See Also:

  Constant Field Values

• Q_FACTOR

  private static final double Q_FACTOR

  See Also:

  Constant Field Values

• MODE_CALC_INVALID

  public static final int MODE_CALC_INVALID

  See Also:

  Constant Field Values

• MODE_CALC_2JHH

  public static final int MODE_CALC_2JHH

  See Also:

  Constant Field Values

• MODE_CALC_3JHH

  public static final int MODE_CALC_3JHH

  See Also:

  Constant Field Values

• MODE_CALC_JHH

  public static final int MODE_CALC_JHH

  See Also:

  Constant Field Values

• MODE_CALC_3JCH

  public static final int MODE_CALC_3JCH

  See Also:

  Constant Field Values

• MODE_CALC_J

  public static final int MODE_CALC_J

  See Also:

  Constant Field Values

• MODE_CALC_NOE

  public static final int MODE_CALC_NOE

  See Also:

  Constant Field Values

• MODE_CALC_ALL

  public static final int MODE_CALC_ALL

  See Also:

  Constant Field Values

• vwr

  private Viewer vwr

• isotopeData

  private java.util.Map<java.lang.String,​double[]> isotopeData

  isotopeData keyed by nnnSym, for example: 1H, 19F, etc.; and also by element name itself: H, F, etc., for default

• resource

  private static final java.lang.String resource

  NOTE! Do not change this txt file! Instead, edit trunk/Jmol/_documents/nmr_data.xls and then clip its contents to org/jmol/quantum/nmr_data.txt.

  See Also:

  Constant Field Values

• shiftRefsPPM

  private java.util.Map<java.lang.String,​java.lang.Float> shiftRefsPPM

• deltaElectro

  static java.util.Hashtable<java.lang.String,​java.lang.Double> deltaElectro

  Calculate an H-X-X-H or C-X-X-H coupling constant. Use Altoona equation (Tetrahedron 36, 2783-2792) If there are fewer than three substituents on each central atom, or if either central atom is not carbon, defaults to general Karplus equation.

• pAltona

  static double[][] pAltona

• JCH3_NONE

  public static final java.lang.String JCH3_NONE

  See Also:

  Constant Field Values

• JCH3_WASYLISHEN_SCHAEFER

  public static final java.lang.String JCH3_WASYLISHEN_SCHAEFER

  See Also:

  Constant Field Values

• JCH3_TVAROSKA_TARAVEL

  public static final java.lang.String JCH3_TVAROSKA_TARAVEL

  See Also:

  Constant Field Values

• JCH3_AYDIN_GUETHER

  public static final java.lang.String JCH3_AYDIN_GUETHER

  See Also:

  Constant Field Values

Constructor Detail

• NMRCalculation

  public NMRCalculation()

Method Detail

• 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

  Returns:

  float value

• getInteractionTensorList

  private javajs.util.Lst<Tensor> getInteractionTensorList​(java.lang.String type,
                                                           javajs.util.BS bsA)

  Returns a list of tensors that are of the specified type and have both atomIndex1 and atomIndex2 in bsA. If there is just one atom specified, then the list is "all tensors involving this atom". We have to use atom sites, because interaction tensors are not duplicated.

  Parameters:

  type -

  bsA -

  Returns:

  list of Tensors

• getAtomSiteBS

  private javajs.util.BS getAtomSiteBS​(javajs.util.BS bsA)

  Interaction tensors are not repeated for every possible combination. They are just for the base atom set. These are identified as a.atomIndex == models[b.modelIndex].firstAtomIndex + b.atomSite - 1

  Parameters:

  bsA -

  Returns:

  new bs in terms of atom sites

• getUniqueTensorSet

  public javajs.util.BS getUniqueTensorSet​(javajs.util.BS bsAtoms)

  Description copied from interface: JmolNMRInterface
  An attempt to find unique atoms using tensors.

  Specified by:

  getUniqueTensorSet in interface JmolNMRInterface

  Returns:

  bitset of atoms

• getJCouplingHz

  public float getJCouplingHz​(Atom a1,
                              Atom a2,
                              java.lang.String type,
                              Tensor isc)

• getIsoOrAnisoHz

  public float getIsoOrAnisoHz​(boolean isIso,
                               Atom a1,
                               Atom a2,
                               java.lang.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

  Returns:

  0 if not found

• getISCtype

  private java.lang.String getISCtype​(Atom a1,
                                      java.lang.String type)

• getDipolarConstantHz

  public float getDipolarConstantHz​(Atom a1,
                                    Atom a2)

  Specified by:

  getDipolarConstantHz in interface JmolNMRInterface

  Returns:

  desired constant

• getDipolarCouplingHz

  public float getDipolarCouplingHz​(Atom a1,
                                    Atom a2,
                                    javajs.util.V3 vField)

  Specified by:

  getDipolarCouplingHz in interface JmolNMRInterface

  Returns:

  projected value

• getIsotopeData

  private double getIsotopeData​(Atom a,
                                int iType)

  Get magnetogyricRatio (gamma/10^7 rad s^-1 T^-1) and quadrupoleMoment (Q/10^-2 fm^2) for a given isotope or for the default isotope of an element.

  Parameters:

  a -

  iType -

  Returns:

  g or Q

• getData

  private void getData()

  Creates the data set necessary for doing NMR calculations. Values are retrievable using getProperty "nmrInfo" "Xx"; each entry is float[+/-isotopeNumber, g, Q], where [0] < 0 for the default value.

• getInfo

  public java.lang.Object getInfo​(java.lang.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

  Returns:

  value

• getMagneticShielding

  public float getMagneticShielding​(Atom atom)

  Specified by:

  getMagneticShielding in interface JmolNMRInterface

• getState

  public boolean getState​(javajs.util.SB sb)

  Specified by:

  getState in interface JmolNMRInterface

• setChemicalShiftReference

  public boolean setChemicalShiftReference​(java.lang.String element,
                                           float value)

  Specified by:

  setChemicalShiftReference in interface JmolNMRInterface

• getTensorInfo

  public javajs.util.Lst<java.lang.Object> getTensorInfo​(java.lang.String tensorType,
                                                         java.lang.String infoType,
                                                         javajs.util.BS bs)

  Specified by:

  getTensorInfo in interface JmolNMRInterface

• getMinDistances

  public java.util.Map<java.lang.String,​java.lang.Integer> getMinDistances​(MeasurementData md)

  Specified by:

  getMinDistances in interface JmolNMRInterface

• calcJKarplus

  public static double calcJKarplus​(double theta)

• getInitialJValue

  private static double getInitialJValue​(int nNonH,
                                         double theta)

• getIncrementalJValue

  private static double getIncrementalJValue​(int nNonH,
                                             java.lang.String element,
                                             javajs.util.V3 sA_cA,
                                             javajs.util.V3 v21,
                                             javajs.util.V3 v23,
                                             double theta,
                                             int f)

• getSubSign

  private static int getSubSign​(javajs.util.V3 sA_cA,
                                javajs.util.V3 v21,
                                javajs.util.V3 v23,
                                int f)

  Look for sign of (v23 x v21).dot.(sA_cA). But note that for the second carbon, we must reverse this.

  Parameters:

  sA_cA - C to sub

  v21 - C to H

  v23 - C to other C

  f - 1 for carbon A; -1 for carbon B

  Returns:

  f or -f (+1 or -1)

• calc3JHHOnly

  private static double calc3JHHOnly​(java.lang.String[][] subElements,
                                     javajs.util.V3[][] subVectors,
                                     javajs.util.V3 v21,
                                     javajs.util.V3 v34,
                                     javajs.util.V3 v23,
                                     double theta,
                                     boolean is23Double)

  Parameters:

  subElements - int[2][3] with element names

  subVectors - V3[2][4] with vectors TO these substituents from their respective centers

  v21 - vector from cA to hA

  v34 - vector from cB to hB

  v23 - vector from cA to cB

  theta - dihedral angle hA-cA-cB-hB

  is23Double -

  Returns:

  estimated coupling constant

• calc3JCH

  public static double calc3JCH​(java.lang.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,
                                        java.lang.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,
                                java.lang.String[] elementsToFill,
                                int mode)

• calc2JHH

  private static double[] calc2JHH​(Atom h1,
                                   Atom c,
                                   Atom h2)

• calcNOEImpl

  private static double[] calcNOEImpl​(Viewer viewer,
                                      Atom atom1,
                                      Atom atom2)

• getNOEorJHH

  public double[] getNOEorJHH​(Atom[] atoms,
                              int mode)

  Specified by:

  getNOEorJHH in interface JmolNMRInterface