Class NmrMolecule

java.lang.Object
org.openscience.jmol.app.janocchio.NmrMolecule
public class NmrMolecule extends Object

  • Field Details

    • viewer

      protected final NMR_Viewer viewer

    • distances

      protected final Vector<Double> distances

    • couples

      protected final Vector<Double> couples

    • couplesWhole

      protected final Vector<org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCouple> couplesWhole

    • noeMatrix

      protected NMRNoeMatrix noeMatrix

    • CHequation

      protected String CHequation

  • Constructor Details

    • NmrMolecule

      public NmrMolecule(NMR_JmolPanel nmrPanel, BS bsMol, String[] labelArray, boolean forNOE)
      Parameters:
      nmrPanel -
      bsMol -
      labelArray - optional array of atom labels, one per atom in the current frame
      forNOE -

  • Method Details

    • getDihedralCouple

      protected org.openscience.jmol.app.janocchio.NmrMolecule.DihedralCouple getDihedralCouple(Atom[] atoms)

    • addAtomstoMatrix

      protected void addAtomstoMatrix()
      Generate noeMatrix and map fields for DistanceJMolecule.

    • getDistances

      public Vector<Double> getDistances()

    • getCouples

      public Vector<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(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