Package org.openscience.jmol.app.janocchio

Class NoeTable

java.lang.Object
java.awt.Component
java.awt.Container
javax.swing.JComponent
javax.swing.JTabbedPane
org.openscience.jmol.app.janocchio.NoeTable
All Implemented Interfaces:
ImageObserver, MenuContainer, Serializable, Accessible, SwingConstants
public class NoeTable extends JTabbedPane
See Also:

  • Field Details

    • nmrPanel

      NMR_JmolPanel nmrPanel

    • viewer

      NMR_Viewer viewer

    • labelArray

      String[] labelArray

    • molCDKuptodate

      boolean molCDKuptodate

    • natomsPerModel

      int natomsPerModel

    • expNoes

      String[][] expNoes

    • expDists

      String[][] expDists

    • lexpNoes

      boolean lexpNoes

    • calcProps

      NmrMolecule calcProps

    • freq

      double freq

    • tau

      double tau

    • tMix

      double tMix

    • cutoff

      double cutoff

    • rhoStar

      double rhoStar

    • noesy

      boolean noesy

    • yellowValue

      double yellowValue

    • redValue

      double redValue

    • frameDeltaDisplay

      FrameDeltaDisplay frameDeltaDisplay

    • colorCellRenderer

      NMRTableCellRenderer colorCellRenderer

    • noeTable

      JTable noeTable

    • noeTableModel

      private NoeTable.NoeTableModel noeTableModel

    • noeSelection

      private ListSelectionModel noeSelection

    • selectedNoeRow

      int[] selectedNoeRow

    • noedeleteButton

      JButton noedeleteButton

    • noedeleteAllButton

      private JButton noedeleteAllButton

    • noesetRefButton

      JButton noesetRefButton

    • expOrDistButton

      JComboBox<String> expOrDistButton

    • noeNPrefValue

      double noeNPrefValue

    • noeNPrefIndices

      int[] noeNPrefIndices

    • noeExprefValue

      double noeExprefValue

    • lrefSingle

      boolean lrefSingle

    • noeParameterSelectionPanel

      public NoeParameterSelectionPanel noeParameterSelectionPanel

    • noeColourSelectionPanel

      public NoeColourSelectionPanel noeColourSelectionPanel

  • Constructor Details

    • 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 Details

    • 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()