Field Detail

• viewer

  protected final NMR_Viewer viewer

• nmrPanel

  final NMR_JmolPanel nmrPanel

• bsMol

  private final javajs.util.BS bsMol

• labelArray

  private final java.lang.String[] labelArray

• distances

  protected final java.util.Vector<java.lang.Double> distances

• couples

  protected final java.util.Vector<java.lang.Double> couples

• couplesWhole

  protected final java.util.Vector<NmrMolecule.DihedralCouple> couplesWhole

• noeMatrix

  protected NMRNoeMatrix noeMatrix

• CHequation

  protected java.lang.String CHequation

• params

  NMRNoeMatrix.NOEParams params

Constructor Detail

• NmrMolecule

  public NmrMolecule​(NMR_JmolPanel nmrPanel,
                     javajs.util.BS bsMol,
                     java.lang.String[] labelArray,
                     boolean forNOE)

  Parameters:

  nmrPanel -

  bsMol -

  labelArray - optional array of atom labels, one per atom in the current frame

  forNOE -

Method Detail

• getDihedralCouple

  protected NmrMolecule.DihedralCouple getDihedralCouple​(Atom[] atoms)

• addAtomstoMatrix

  protected void addAtomstoMatrix()

  Generate noeMatrix and map fields for DistanceJMolecule.

• getDistances

  public java.util.Vector<java.lang.Double> getDistances()

• getCouples

  public java.util.Vector<java.lang.Double> getCouples()

• calcNOEs

  public void calcNOEs()

• addCouple

  public void addCouple​(Atom[] atoms)

• addJmolCouple

  public void addJmolCouple​(int a1,
                            int a2,
                            int a3,
                            int a4)

• calcCouple

  public double[] calcCouple​(Atom[] atoms)

• calcJmolCouple

  public double[] calcJmolCouple​(int a1,
                                 int a2,
                                 int a3,
                                 int a4)

• setCorrelationTimeTauPS

  public void setCorrelationTimeTauPS​(double t)

• setMixingTimeSec

  public void setMixingTimeSec​(double t)

  sets the mixing time for the NOE experiment

  Parameters:

  t - the mixing time in seconds. Typically 0.5-1.5 seconds for small molecules

• setNMRfreqMHz

  public void setNMRfreqMHz​(double f)

  set the NMR frequency for the NOE simulation

  Parameters:

  f - the frequency in MHz

• setCutoffAng

  public void setCutoffAng​(double c)

  sets the cutoff distance beyond which atom interactions are not considered

  Parameters:

  c - the cutoff distance in Angstroms

• setRhoStar

  public void setRhoStar​(double c)

• setNoesy

  public void setNoesy​(boolean b)

• setCHequation

  public void setCHequation​(java.lang.String eq)

• getJmolNoe

  public double getJmolNoe​(int a,
                           int b)

• addJmolDistance

  public void addJmolDistance​(int a,
                              int b)

  Add using Jmol atom index

  Parameters:

  a -

  b -

• getJmolDistance

  public double getJmolDistance​(int a,
                                int b)

  Calc using Jmol atom index

  Parameters:

  a -

  b -

  Returns:

  NOE-based distance, averaged for equivalent H atoms