Class NoeTable
- java.lang.Object
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- java.awt.Component
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- java.awt.Container
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- javax.swing.JComponent
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- javax.swing.JTabbedPane
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- org.openscience.jmol.app.janocchio.NoeTable
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- All Implemented Interfaces:
ImageObserver
,MenuContainer
,Serializable
,Accessible
,SwingConstants
public class NoeTable extends JTabbedPane
- See Also:
- Serialized Form
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Nested Class Summary
Nested Classes Modifier and Type Class Description (package private) class
NoeTable.NoeListWindowListener
(package private) class
NoeTable.NoeTableModel
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Nested classes/interfaces inherited from class javax.swing.JTabbedPane
JTabbedPane.AccessibleJTabbedPane, JTabbedPane.ModelListener
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Nested classes/interfaces inherited from class javax.swing.JComponent
JComponent.AccessibleJComponent
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Nested classes/interfaces inherited from class java.awt.Container
Container.AccessibleAWTContainer
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Nested classes/interfaces inherited from class java.awt.Component
Component.AccessibleAWTComponent, Component.BaselineResizeBehavior, Component.BltBufferStrategy, Component.FlipBufferStrategy
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Field Summary
Fields Modifier and Type Field Description (package private) NmrMolecule
calcProps
(package private) NMRTableCellRenderer
colorCellRenderer
(package private) double
cutoff
(package private) String[][]
expDists
(package private) String[][]
expNoes
(package private) JComboBox<String>
expOrDistButton
(package private) FrameDeltaDisplay
frameDeltaDisplay
(package private) double
freq
(package private) String[]
labelArray
(package private) boolean
lexpNoes
(package private) boolean
lrefSingle
(package private) boolean
molCDKuptodate
(package private) int
natomsPerModel
(package private) NMR_JmolPanel
nmrPanel
NoeColourSelectionPanel
noeColourSelectionPanel
private JButton
noedeleteAllButton
(package private) JButton
noedeleteButton
(package private) double
noeExprefValue
(package private) int[]
noeNPrefIndices
(package private) double
noeNPrefValue
NoeParameterSelectionPanel
noeParameterSelectionPanel
private ListSelectionModel
noeSelection
(package private) JButton
noesetRefButton
(package private) boolean
noesy
(package private) JTable
noeTable
private NoeTable.NoeTableModel
noeTableModel
(package private) double
redValue
(package private) double
rhoStar
(package private) int[]
selectedNoeRow
(package private) double
tau
(package private) double
tMix
(package private) NMR_Viewer
viewer
(package private) double
yellowValue
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Fields inherited from class javax.swing.JTabbedPane
changeEvent, changeListener, model, SCROLL_TAB_LAYOUT, tabPlacement, WRAP_TAB_LAYOUT
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Fields inherited from class javax.swing.JComponent
listenerList, TOOL_TIP_TEXT_KEY, ui, UNDEFINED_CONDITION, WHEN_ANCESTOR_OF_FOCUSED_COMPONENT, WHEN_FOCUSED, WHEN_IN_FOCUSED_WINDOW
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Fields inherited from class java.awt.Component
accessibleContext, BOTTOM_ALIGNMENT, CENTER_ALIGNMENT, LEFT_ALIGNMENT, RIGHT_ALIGNMENT, TOP_ALIGNMENT
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Fields inherited from interface java.awt.image.ImageObserver
ABORT, ALLBITS, ERROR, FRAMEBITS, HEIGHT, PROPERTIES, SOMEBITS, WIDTH
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Fields inherited from interface javax.swing.SwingConstants
BOTTOM, CENTER, EAST, HORIZONTAL, LEADING, LEFT, NEXT, NORTH, NORTH_EAST, NORTH_WEST, PREVIOUS, RIGHT, SOUTH, SOUTH_EAST, SOUTH_WEST, TOP, TRAILING, VERTICAL, WEST
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Constructor Summary
Constructors Constructor Description NoeTable(NMR_JmolPanel nmrPanel, JFrame parentFrame)
Constructor
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
activate()
void
addMol()
void
allocateExpNoes(int numAtoms)
void
allocateLabelArray(int numAtoms)
private void
calcFrameDelta()
(package private) int
calcNatomsPerModel()
TODO This assumes we have the same structure in each model.protected void
centerDialog()
(package private) boolean
checkNoe(int i)
void
close()
(package private) JComponent
constructDismissButtonPanel()
(package private) JComponent
constructNoeButtonPanel()
(package private) JComponent
constructNoeTable()
double
getCorrelationTime()
get the correlation time in secondsdouble
getCutoff()
get the cutoff distanceString
getExpDist(int i, int j)
String
getExpNoe(int i, int j)
boolean
getlexpNoes()
int[]
getMeasurementCountPlusIndices(int row)
double
getMixingTime()
get the mixing timedouble
getNMRfreq()
gets the NMR frequencydouble
getNoeExprefValue()
int[]
getnoeNPrefIndices()
boolean
getNoesy()
double
getRedValue()
double
getRhoStar()
int
getRowCount()
protected int
getViewerRow(int i)
double
getYellowValue()
void
setCorrelationTime(double t)
set the correlation time to be used in the NOE calculationvoid
setCutoff(double c)
sets the cutoff distance beyond which atom interactions are not consideredvoid
setExpDist(String value, int i, int j)
void
setExpNoe(String value, int i, int j)
void
setFrameDeltaDisplay(FrameDeltaDisplay frameDeltaDisplay)
void
setLabelArray(String[] labelArray)
void
setlrefSingle(boolean l)
void
setMixingTime(double t)
sets the mixing time for the NOE experimentvoid
setmolCDKuptodate(boolean value)
void
setNMRfreq(double f)
set the NMR frequency for the NOE simulationvoid
setNoeExprefValue(double value)
void
setNoeNPrefIndices(int[] noeNPrefIndices)
void
setNoesy(boolean b)
void
setRedValue(double value)
void
setRhoStar(double c)
void
setYellowValue(double value)
(package private) void
updateNoeTableData()
(package private) void
updateNoeTableStructure()
void
updateTables()
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Methods inherited from class javax.swing.JTabbedPane
add, add, add, add, add, addChangeListener, addTab, addTab, addTab, createChangeListener, fireStateChanged, getAccessibleContext, getBackgroundAt, getBoundsAt, getChangeListeners, getComponentAt, getDisabledIconAt, getDisplayedMnemonicIndexAt, getForegroundAt, getIconAt, getMnemonicAt, getModel, getSelectedComponent, getSelectedIndex, getTabComponentAt, getTabCount, getTabLayoutPolicy, getTabPlacement, getTabRunCount, getTitleAt, getToolTipText, getToolTipTextAt, getUI, getUIClassID, indexAtLocation, indexOfComponent, indexOfTab, indexOfTab, indexOfTabComponent, insertTab, isEnabledAt, paramString, remove, remove, removeAll, removeChangeListener, removeTabAt, setBackgroundAt, setComponentAt, setDisabledIconAt, setDisplayedMnemonicIndexAt, setEnabledAt, setForegroundAt, setIconAt, setMnemonicAt, setModel, setSelectedComponent, setSelectedIndex, setTabComponentAt, setTabLayoutPolicy, setTabPlacement, setTitleAt, setToolTipTextAt, setUI, updateUI
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Methods inherited from class javax.swing.JComponent
addAncestorListener, addNotify, addVetoableChangeListener, computeVisibleRect, contains, createToolTip, disable, enable, firePropertyChange, firePropertyChange, firePropertyChange, fireVetoableChange, getActionForKeyStroke, getActionMap, getAlignmentX, getAlignmentY, getAncestorListeners, getAutoscrolls, getBaseline, getBaselineResizeBehavior, getBorder, getBounds, getClientProperty, getComponentGraphics, getComponentPopupMenu, getConditionForKeyStroke, getDebugGraphicsOptions, getDefaultLocale, getFontMetrics, getGraphics, getHeight, getInheritsPopupMenu, getInputMap, getInputMap, getInputVerifier, getInsets, getInsets, getListeners, getLocation, getMaximumSize, getMinimumSize, getNextFocusableComponent, getPopupLocation, getPreferredSize, getRegisteredKeyStrokes, getRootPane, getSize, getToolTipLocation, getToolTipText, getTopLevelAncestor, getTransferHandler, getVerifyInputWhenFocusTarget, getVetoableChangeListeners, getVisibleRect, getWidth, getX, getY, grabFocus, hide, isDoubleBuffered, isLightweightComponent, isManagingFocus, isOpaque, isOptimizedDrawingEnabled, isPaintingForPrint, isPaintingOrigin, isPaintingTile, isRequestFocusEnabled, isValidateRoot, paint, paintBorder, paintChildren, paintComponent, paintImmediately, paintImmediately, print, printAll, printBorder, printChildren, printComponent, processComponentKeyEvent, processKeyBinding, processKeyEvent, processMouseEvent, processMouseMotionEvent, putClientProperty, registerKeyboardAction, registerKeyboardAction, removeAncestorListener, removeNotify, removeVetoableChangeListener, repaint, repaint, requestDefaultFocus, requestFocus, requestFocus, requestFocusInWindow, requestFocusInWindow, resetKeyboardActions, reshape, revalidate, scrollRectToVisible, setActionMap, setAlignmentX, setAlignmentY, setAutoscrolls, setBackground, setBorder, setComponentPopupMenu, setDebugGraphicsOptions, setDefaultLocale, setDoubleBuffered, setEnabled, setFocusTraversalKeys, setFont, setForeground, setInheritsPopupMenu, setInputMap, setInputVerifier, setMaximumSize, setMinimumSize, setNextFocusableComponent, setOpaque, setPreferredSize, setRequestFocusEnabled, setToolTipText, setTransferHandler, setUI, setVerifyInputWhenFocusTarget, setVisible, unregisterKeyboardAction, update
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Methods inherited from class java.awt.Container
addContainerListener, addImpl, addPropertyChangeListener, addPropertyChangeListener, applyComponentOrientation, areFocusTraversalKeysSet, countComponents, deliverEvent, doLayout, findComponentAt, findComponentAt, getComponent, getComponentAt, getComponentAt, getComponentCount, getComponents, getComponentZOrder, getContainerListeners, getFocusTraversalKeys, getFocusTraversalPolicy, getLayout, getMousePosition, insets, invalidate, isAncestorOf, isFocusCycleRoot, isFocusCycleRoot, isFocusTraversalPolicyProvider, isFocusTraversalPolicySet, layout, list, list, locate, minimumSize, paintComponents, preferredSize, printComponents, processContainerEvent, processEvent, removeContainerListener, setComponentZOrder, setFocusCycleRoot, setFocusTraversalPolicy, setFocusTraversalPolicyProvider, setLayout, transferFocusDownCycle, validate, validateTree
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Methods inherited from class java.awt.Component
action, add, addComponentListener, addFocusListener, addHierarchyBoundsListener, addHierarchyListener, addInputMethodListener, addKeyListener, addMouseListener, addMouseMotionListener, addMouseWheelListener, bounds, checkImage, checkImage, coalesceEvents, contains, createImage, createImage, createVolatileImage, createVolatileImage, disableEvents, dispatchEvent, enable, enableEvents, enableInputMethods, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, firePropertyChange, getBackground, getBounds, getColorModel, getComponentListeners, getComponentOrientation, getCursor, getDropTarget, getFocusCycleRootAncestor, getFocusListeners, getFocusTraversalKeysEnabled, getFont, getForeground, getGraphicsConfiguration, getHierarchyBoundsListeners, getHierarchyListeners, getIgnoreRepaint, getInputContext, getInputMethodListeners, getInputMethodRequests, getKeyListeners, getLocale, getLocation, getLocationOnScreen, getMouseListeners, getMouseMotionListeners, getMousePosition, getMouseWheelListeners, getName, getParent, getPropertyChangeListeners, getPropertyChangeListeners, getSize, getToolkit, getTreeLock, gotFocus, handleEvent, hasFocus, imageUpdate, inside, isBackgroundSet, isCursorSet, isDisplayable, isEnabled, isFocusable, isFocusOwner, isFocusTraversable, isFontSet, isForegroundSet, isLightweight, isMaximumSizeSet, isMinimumSizeSet, isPreferredSizeSet, isShowing, isValid, isVisible, keyDown, keyUp, list, list, list, location, lostFocus, mouseDown, mouseDrag, mouseEnter, mouseExit, mouseMove, mouseUp, move, nextFocus, paintAll, postEvent, prepareImage, prepareImage, processComponentEvent, processFocusEvent, processHierarchyBoundsEvent, processHierarchyEvent, processInputMethodEvent, processMouseWheelEvent, remove, removeComponentListener, removeFocusListener, removeHierarchyBoundsListener, removeHierarchyListener, removeInputMethodListener, removeKeyListener, removeMouseListener, removeMouseMotionListener, removeMouseWheelListener, removePropertyChangeListener, removePropertyChangeListener, repaint, repaint, repaint, requestFocus, requestFocus, requestFocusInWindow, resize, resize, setBounds, setBounds, setComponentOrientation, setCursor, setDropTarget, setFocusable, setFocusTraversalKeysEnabled, setIgnoreRepaint, setLocale, setLocation, setLocation, setMixingCutoutShape, setName, setSize, setSize, show, show, size, toString, transferFocus, transferFocusBackward, transferFocusUpCycle
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Field Detail
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nmrPanel
NMR_JmolPanel nmrPanel
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viewer
NMR_Viewer viewer
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labelArray
String[] labelArray
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molCDKuptodate
boolean molCDKuptodate
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natomsPerModel
int natomsPerModel
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expNoes
String[][] expNoes
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expDists
String[][] expDists
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lexpNoes
boolean lexpNoes
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calcProps
NmrMolecule calcProps
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freq
double freq
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tau
double tau
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tMix
double tMix
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cutoff
double cutoff
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rhoStar
double rhoStar
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noesy
boolean noesy
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yellowValue
double yellowValue
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redValue
double redValue
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frameDeltaDisplay
FrameDeltaDisplay frameDeltaDisplay
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colorCellRenderer
NMRTableCellRenderer colorCellRenderer
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noeTable
JTable noeTable
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noeTableModel
private NoeTable.NoeTableModel noeTableModel
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noeSelection
private ListSelectionModel noeSelection
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selectedNoeRow
int[] selectedNoeRow
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noedeleteButton
JButton noedeleteButton
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noedeleteAllButton
private JButton noedeleteAllButton
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noesetRefButton
JButton noesetRefButton
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noeNPrefValue
double noeNPrefValue
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noeNPrefIndices
int[] noeNPrefIndices
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noeExprefValue
double noeExprefValue
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lrefSingle
boolean lrefSingle
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noeParameterSelectionPanel
public NoeParameterSelectionPanel noeParameterSelectionPanel
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noeColourSelectionPanel
public NoeColourSelectionPanel noeColourSelectionPanel
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Constructor Detail
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NoeTable
public NoeTable(NMR_JmolPanel nmrPanel, JFrame parentFrame)
Constructor- Parameters:
parentFrame
- the parent framenmrPanel
- the NMRViewer in which the animation will take place (?)
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Method Detail
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constructNoeTable
JComponent constructNoeTable()
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constructNoeButtonPanel
JComponent constructNoeButtonPanel()
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constructDismissButtonPanel
JComponent constructDismissButtonPanel()
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centerDialog
protected void centerDialog()
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close
public void close()
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activate
public void activate()
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updateNoeTableData
void updateNoeTableData()
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updateNoeTableStructure
void updateNoeTableStructure()
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getRowCount
public int getRowCount()
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getMeasurementCountPlusIndices
public int[] getMeasurementCountPlusIndices(int row)
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calcFrameDelta
private void calcFrameDelta()
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updateTables
public void updateTables()
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getViewerRow
protected int getViewerRow(int i)
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checkNoe
boolean checkNoe(int i)
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calcNatomsPerModel
int calcNatomsPerModel()
TODO This assumes we have the same structure in each model.- Returns:
- average number of atoms per model ??
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addMol
public void addMol()
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setmolCDKuptodate
public void setmolCDKuptodate(boolean value)
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allocateLabelArray
public void allocateLabelArray(int numAtoms)
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allocateExpNoes
public void allocateExpNoes(int numAtoms)
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getExpNoe
public String getExpNoe(int i, int j)
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getExpDist
public String getExpDist(int i, int j)
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setExpNoe
public void setExpNoe(String value, int i, int j)
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setExpDist
public void setExpDist(String value, int i, int j)
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setLabelArray
public void setLabelArray(String[] labelArray)
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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.
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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
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setNMRfreq
public void setNMRfreq(double f)
set the NMR frequency for the NOE simulation- Parameters:
f
- the frequency in MHz
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setCutoff
public void setCutoff(double c)
sets the cutoff distance beyond which atom interactions are not considered- Parameters:
c
- the cutoff distance in Angstroms
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setRhoStar
public void setRhoStar(double c)
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setNoesy
public void setNoesy(boolean b)
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setlrefSingle
public void setlrefSingle(boolean l)
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getCorrelationTime
public double getCorrelationTime()
get the correlation time in seconds- Returns:
- the correlation time in seconds
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getMixingTime
public double getMixingTime()
get the mixing time- Returns:
- the mixing time in seconds
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getNMRfreq
public double getNMRfreq()
gets the NMR frequency- Returns:
- the NMR frequency in MHz
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getCutoff
public double getCutoff()
get the cutoff distance- Returns:
- the cutoff in Angstroms
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getRhoStar
public double getRhoStar()
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getNoesy
public boolean getNoesy()
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setRedValue
public void setRedValue(double value)
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setYellowValue
public void setYellowValue(double value)
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getRedValue
public double getRedValue()
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getYellowValue
public double getYellowValue()
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getnoeNPrefIndices
public int[] getnoeNPrefIndices()
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setNoeNPrefIndices
public void setNoeNPrefIndices(int[] noeNPrefIndices)
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getNoeExprefValue
public double getNoeExprefValue()
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setNoeExprefValue
public void setNoeExprefValue(double value)
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setFrameDeltaDisplay
public void setFrameDeltaDisplay(FrameDeltaDisplay frameDeltaDisplay)
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getlexpNoes
public boolean getlexpNoes()
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