Class NoeTable

    • Constructor Detail

      • NoeTable

        public NoeTable​(NMR_JmolPanel nmrPanel,
                        JFrame parentFrame)
        Constructor
        Parameters:
        parentFrame - the parent frame
        nmrPanel - the NMRViewer in which the animation will take place (?)
    • Method Detail

      • constructNoeTable

        JComponent constructNoeTable()
      • constructNoeButtonPanel

        JComponent constructNoeButtonPanel()
      • constructDismissButtonPanel

        JComponent constructDismissButtonPanel()
      • centerDialog

        protected void centerDialog()
      • close

        public void close()
      • activate

        public void activate()
      • updateNoeTableData

        void updateNoeTableData()
      • updateNoeTableStructure

        void updateNoeTableStructure()
      • getRowCount

        public int getRowCount()
      • getMeasurementCountPlusIndices

        public int[] getMeasurementCountPlusIndices​(int row)
      • calcFrameDelta

        private void calcFrameDelta()
      • updateTables

        public void updateTables()
      • getViewerRow

        protected int getViewerRow​(int i)
      • checkNoe

        boolean checkNoe​(int i)
      • calcNatomsPerModel

        int calcNatomsPerModel()
        TODO This assumes we have the same structure in each model.
        Returns:
        average number of atoms per model ??
      • addMol

        public void addMol()
      • setmolCDKuptodate

        public void setmolCDKuptodate​(boolean value)
      • allocateLabelArray

        public void allocateLabelArray​(int numAtoms)
      • allocateExpNoes

        public void allocateExpNoes​(int numAtoms)
      • getExpNoe

        public String getExpNoe​(int i,
                                int j)
      • getExpDist

        public String getExpDist​(int i,
                                 int j)
      • setExpNoe

        public void setExpNoe​(String value,
                              int i,
                              int j)
      • setExpDist

        public void setExpDist​(String value,
                               int i,
                               int j)
      • setLabelArray

        public void setLabelArray​(String[] labelArray)
      • setCorrelationTime

        public void setCorrelationTime​(double t)
        set the correlation time to be used in the NOE calculation
        Parameters:
        t - the correlation time in seconds. Typical value would be 80E-12.
      • setMixingTime

        public void setMixingTime​(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
      • setNMRfreq

        public void setNMRfreq​(double f)
        set the NMR frequency for the NOE simulation
        Parameters:
        f - the frequency in MHz
      • setCutoff

        public void setCutoff​(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)
      • setlrefSingle

        public void setlrefSingle​(boolean l)
      • getCorrelationTime

        public double getCorrelationTime()
        get the correlation time in seconds
        Returns:
        the correlation time in seconds
      • getMixingTime

        public double getMixingTime()
        get the mixing time
        Returns:
        the mixing time in seconds
      • getNMRfreq

        public double getNMRfreq()
        gets the NMR frequency
        Returns:
        the NMR frequency in MHz
      • getCutoff

        public double getCutoff()
        get the cutoff distance
        Returns:
        the cutoff in Angstroms
      • getRhoStar

        public double getRhoStar()
      • getNoesy

        public boolean getNoesy()
      • setRedValue

        public void setRedValue​(double value)
      • setYellowValue

        public void setYellowValue​(double value)
      • getRedValue

        public double getRedValue()
      • getYellowValue

        public double getYellowValue()
      • getnoeNPrefIndices

        public int[] getnoeNPrefIndices()
      • setNoeNPrefIndices

        public void setNoeNPrefIndices​(int[] noeNPrefIndices)
      • getNoeExprefValue

        public double getNoeExprefValue()
      • setNoeExprefValue

        public void setNoeExprefValue​(double value)
      • setFrameDeltaDisplay

        public void setFrameDeltaDisplay​(FrameDeltaDisplay frameDeltaDisplay)
      • getlexpNoes

        public boolean getlexpNoes()