Class NmrMolecule


  • public class NmrMolecule
    extends Object
    • Constructor Detail

      • NmrMolecule

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

      • addAtomstoMatrix

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