A panel with a molecular viewer and attachment point table. More...

Inheritance diagram for denoptim.gui.FragmentViewPanel:

Collaboration diagram for denoptim.gui.FragmentViewPanel:

Classes
class	PausableTableModelListener

Public Member Functions
	FragmentViewPanel (boolean editableTable)
	Constructor that allows to specify whether the AP table is editable or not. More...

	FragmentViewPanel (JComponent parent, boolean editableTable)
	Constructor that allows to specify whether the AP table is editable or not. More...

	FragmentViewPanel (JComponent parent, boolean editableTable, int dividerPosition)
	Constructor that allows to specify whether the AP table is editable or not. More...

boolean	hasUnsavedAPEdits ()
	Check for unsaved edits to the AP data. More...

void	deprotectEdits ()
	Overrides the flag signaling unsaved edits to saying that there are no altered data. More...

String	getDataFromJmol ()

boolean	loadSMILES (String smiles)
	Loads a molecule build from a smiles string. More...

Fragment	getLoadedStructure ()
	Returns the chemical representation of the currently loaded chemical object. More...

void	loadPlainStructure (IAtomContainer mol)
	Loads a structure in the Jmol viewer. More...

void	loadFragmentToViewer (Fragment frag)
	Loads the given fragments to this viewer. More...

void	clearAll (boolean dataIsComing)
	Removes the currently visualized molecule and AP table. More...

void	clearAPTable ()
	Clears the table of attachment points. More...

void	clearMolecularViewer (boolean dataIsComing)
	Clears the molecular viewer. More...

ArrayList< AttachmentPoint >	getSelectedAPs ()
	Identifies which attachment points are selected in the visualized table. More...

ArrayList< Integer >	getSelectedAPIDs ()
	Identifies which attachment points are selected in the visualized table. More...

ArrayList< IAtom >	getAtomsSelectedFromJMol ()
	Identifies the atoms that are selected in the Jmol viewer. More...

void	activateTabEditsListener (boolean var)
	Allows to activate and deactivate the listener. More...

void	dispose ()

Map< Integer, AttachmentPoint >	getMapOfAPsInTable ()

DefaultTableModel	getAPTableModel ()

ArrayList< Integer >	getSelectedAPIDs ()

Map< Integer, AttachmentPoint >	getMapOfAPsInTable ()

DefaultTableModel	getAPTableModel ()

Public Attributes
boolean	alteredAPData = false
	Flag signalling that data about APs has been changed in the GUI. More...

Public Attributes inherited from denoptim.gui.IVertexAPSelection
final String	APDATACHANGEEVENT = "APDATA"

Protected Attributes
Map< Integer, AttachmentPoint >	mapAPs = null
	Temporary list of attachment points of the current fragment. More...

DefaultTableModel	apTabModel

JTable	apTable

Private Member Functions
void	initialize (int dividerPosition)

void	waitForJmolViewer (int milliSecFirst, String cause)
	Waits until Jmol is finished. More...

void	make3DusingCDKgenerator (String smiles) throws CDKException, CloneNotSupportedException, IOException

IAtomContainer	getStructureFromJmolViewer () throws DENOPTIMException

void	putAPsFromTableIntoIAtomContainer (Fragment mol) throws DENOPTIMException

void	loadStructure ()
	Loads the structure of the currently loaded 'fragment' (i.e., our member) into the Jmol viewer. More...

void	updateAPsMapAndTable ()
	Uses the AP of the `Fragment` to create a new map and table of APs. More...

void	preSelectAPs ()

void	updateAPsInJmolViewer ()

String	getJmolPositionStr (double[] position)

void	setJmolViewer ()

Private Attributes
Fragment	fragment
	The currently loaded fragment. More...

JmolPanel	jmolPanel

JScrollPane	tabPanel

boolean	editableAPTable = false

final String	NL = System.getProperty("line.separator")

String	tmpSDFFile

JComponent	parent

Static Private Attributes
static final long	serialVersionUID = 912850110991449553L
	Version UID. More...

Detailed Description

A panel with a molecular viewer and attachment point table.

Author: Marco Foscato

Definition at line 78 of file FragmentViewPanel.java.

Constructor & Destructor Documentation

◆ FragmentViewPanel() [1/3]

denoptim.gui.FragmentViewPanel.FragmentViewPanel ( boolean editableTable )

Constructor that allows to specify whether the AP table is editable or not.

Parameters

editableTable use true to make the AP table editable

Definition at line 121 of file FragmentViewPanel.java.

◆ FragmentViewPanel() [2/3]

denoptim.gui.FragmentViewPanel.FragmentViewPanel	(	JComponent	parent,
		boolean	editableTable
	)

Constructor that allows to specify whether the AP table is editable or not.

Parameters

parent	the parent component
editableTable	use `true` to make the AP table editable

Definition at line 134 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.parent.

◆ FragmentViewPanel() [3/3]

denoptim.gui.FragmentViewPanel.FragmentViewPanel	(	JComponent	parent,
		boolean	editableTable,
		int	dividerPosition
	)

Constructor that allows to specify whether the AP table is editable or not.

Parameters

parent	the parent component
editableTable	use `true` to make the AP table editable
dividerPosition	allows to set the initial position of the divide

Definition at line 148 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.editableAPTable, denoptim.gui.FragmentViewPanel.initialize(), and denoptim.gui.FragmentViewPanel.parent.

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Member Function Documentation

◆ activateTabEditsListener()

void denoptim.gui.FragmentViewPanel.activateTabEditsListener ( boolean var )

Allows to activate and deactivate the listener.

Parameters

var	use `true` to activate the listener

Definition at line 1043 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.apTabModel, and denoptim.gui.FragmentViewPanel.PausableTableModelListener.setActive().

Referenced by denoptim.gui.VertexViewPanel.activateTabEditsListener(), denoptim.gui.FragmentViewPanel.clearAPTable(), denoptim.gui.FragmentViewPanel.preSelectAPs(), and denoptim.gui.FragmentViewPanel.updateAPsMapAndTable().

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◆ clearAll()

void denoptim.gui.FragmentViewPanel.clearAll ( boolean dataIsComing )

Removes the currently visualized molecule and AP table.

Parameters

dataIsComing set true when there is incoming molecular data to visualize. In such case we do not run the very slow zap script in JMol because the molecular data will be overwritten anyway.

Definition at line 841 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.clearAPTable(), and denoptim.gui.FragmentViewPanel.clearMolecularViewer().

Referenced by denoptim.gui.GraphVertexMolViewerPanel.clearVertexViewer(), denoptim.gui.VertexViewPanel.loadTemplateToViewer(), denoptim.gui.GraphVertexMolViewerPanel.resetFragViewerCardDeck(), and denoptim.gui.GraphVertexMolViewerPanel.visualizeVertexInNestedViewer().

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◆ clearAPTable()

void denoptim.gui.FragmentViewPanel.clearAPTable ( )

Clears the table of attachment points.

Definition at line 852 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.activateTabEditsListener(), and denoptim.gui.FragmentViewPanel.apTabModel.

Referenced by denoptim.gui.FragmentViewPanel.clearAll(), denoptim.gui.VertexViewPanel.clearCurrentSystem(), denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), and denoptim.gui.FragmentViewPanel.updateAPsMapAndTable().

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◆ clearMolecularViewer()

void denoptim.gui.FragmentViewPanel.clearMolecularViewer ( boolean dataIsComing )

Clears the molecular viewer.

WARNING: this is VERY SLOW: do not do it unless you are sure you really need to clear the data. Typically, if there is incoming data, you do not need to run this, as the old data will be overwritten anyway.

Parameters

dataIsComing set true when there is incoming molecular data to visualize.

Definition at line 874 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.jmolPanel, and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.FragmentViewPanel.clearAll(), denoptim.gui.VertexViewPanel.clearMolecularViewer(), denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), denoptim.gui.FragmentViewPanel.make3DusingCDKgenerator(), and denoptim.gui.FragmentViewPanel.waitForJmolViewer().

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◆ deprotectEdits()

void denoptim.gui.FragmentViewPanel.deprotectEdits ( )

Overrides the flag signaling unsaved edits to saying that there are no altered data.

Use this after processing/saving the changes.

Definition at line 219 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.alteredAPData.

Referenced by denoptim.gui.VertexViewPanel.deprotectEdits().

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◆ dispose()

void denoptim.gui.FragmentViewPanel.dispose ( )

Definition at line 1063 of file FragmentViewPanel.java.

References denoptim.gui.JmolPanel.dispose(), and denoptim.gui.FragmentViewPanel.jmolPanel.

Referenced by denoptim.gui.GraphVertexMolViewerPanel.dispose(), and denoptim.gui.VertexViewPanel.dispose().

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◆ getAPTableModel()

DefaultTableModel denoptim.gui.FragmentViewPanel.getAPTableModel ( )

Implements denoptim.gui.IVertexAPSelection.

Definition at line 1079 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.apTabModel.

◆ getAtomsSelectedFromJMol()

ArrayList< IAtom > denoptim.gui.FragmentViewPanel.getAtomsSelectedFromJMol ( )

Identifies the atoms that are selected in the Jmol viewer.

Returns: the list of selected atoms

Definition at line 990 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.fragment, denoptim.graph.Fragment.getAtom(), denoptim.graph.Fragment.getAtomCount(), denoptim.gui.FragmentViewPanel.jmolPanel, and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.VertexViewPanel.getAtomsSelectedFromJMol().

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◆ getDataFromJmol()

String denoptim.gui.FragmentViewPanel.getDataFromJmol ( )

Definition at line 371 of file FragmentViewPanel.java.

References denoptim.constants.DENOPTIMConstants.DUMMYATMSYMBOL, denoptim.gui.FragmentViewPanel.jmolPanel, and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), and denoptim.gui.FragmentViewPanel.loadSMILES().

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◆ getJmolPositionStr()

String denoptim.gui.FragmentViewPanel.getJmolPositionStr ( double[] position )

private

Definition at line 929 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer().

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◆ getLoadedStructure()

Fragment denoptim.gui.FragmentViewPanel.getLoadedStructure ( )

Returns the chemical representation of the currently loaded chemical object.

In case of mismatch between the system loaded into the Jmol viewer and the one in the local memory, we take that from Jmol and made it be The 'current fragment'. Previously set references to the previous 'current fragment' will make no sense anymore.

Returns: the chemical representation of what is currently visualised. Can be empty and null.

Definition at line 607 of file FragmentViewPanel.java.

References denoptim.graph.Vertex.BBType.FRAGMENT, denoptim.gui.FragmentViewPanel.fragment, denoptim.graph.Fragment.getAtom(), denoptim.graph.Fragment.getAtomCount(), denoptim.graph.Fragment.getIAtomContainer(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.utils.MoleculeUtils.getSMILESForMolecule(), denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), denoptim.gui.GUI.GUILOGGER, denoptim.gui.FragmentViewPanel.putAPsFromTableIntoIAtomContainer(), and denoptim.gui.FragmentViewPanel.setJmolViewer().

Referenced by denoptim.gui.VertexViewPanel.getLoadedStructure().

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◆ getMapOfAPsInTable()

Map< Integer, AttachmentPoint > denoptim.gui.FragmentViewPanel.getMapOfAPsInTable ( )

Implements denoptim.gui.IVertexAPSelection.

Definition at line 1071 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.mapAPs.

◆ getSelectedAPIDs()

ArrayList< Integer > denoptim.gui.FragmentViewPanel.getSelectedAPIDs ( )

Identifies which attachment points are selected in the visualized table.

Returns: the list of attachment points indexes

Implements denoptim.gui.IVertexAPSelection.

Definition at line 974 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.apTable.

◆ getSelectedAPs()

ArrayList< AttachmentPoint > denoptim.gui.FragmentViewPanel.getSelectedAPs ( )

Identifies which attachment points are selected in the visualized table.

Returns: the list of attachment points

Definition at line 956 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.apTable, and denoptim.gui.FragmentViewPanel.mapAPs.

◆ getStructureFromJmolViewer()

IAtomContainer denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer ( ) throws DENOPTIMException

private

Definition at line 537 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.clearAPTable(), denoptim.gui.FragmentViewPanel.clearMolecularViewer(), denoptim.gui.FragmentViewPanel.getDataFromJmol(), denoptim.gui.FragmentViewPanel.NL, denoptim.io.DenoptimIO.readAllAtomContainers(), denoptim.gui.FragmentViewPanel.tmpSDFFile, and denoptim.io.DenoptimIO.writeData().

Referenced by denoptim.gui.FragmentViewPanel.getLoadedStructure(), denoptim.gui.FragmentViewPanel.loadSMILES(), and denoptim.gui.FragmentViewPanel.make3DusingCDKgenerator().

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◆ hasUnsavedAPEdits()

boolean denoptim.gui.FragmentViewPanel.hasUnsavedAPEdits ( )

Check for unsaved edits to the AP data.

Returns: true if there are unsaved edits

Definition at line 208 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.alteredAPData.

◆ initialize()

void denoptim.gui.FragmentViewPanel.initialize ( int dividerPosition )

private

Definition at line 159 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.apTable, denoptim.gui.FragmentViewPanel.apTabModel, denoptim.gui.FragmentViewPanel.editableAPTable, denoptim.gui.Utils.getTempFile(), denoptim.gui.FragmentViewPanel.jmolPanel, denoptim.gui.FragmentViewPanel.tabPanel, and denoptim.gui.FragmentViewPanel.tmpSDFFile.

Referenced by denoptim.gui.FragmentViewPanel.FragmentViewPanel().

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◆ loadFragmentToViewer()

void denoptim.gui.FragmentViewPanel.loadFragmentToViewer ( Fragment frag )

Loads the given fragments to this viewer.

The molecular data is loaded in the Jmol viewer, and the attachment point (AP) information in the the list of APs. Jmol is not aware of AP-related information, so this also launches the generation of the graphical objects representing the APs.

Parameters

frag	the fragment to visualize

Definition at line 771 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.loadStructure(), denoptim.gui.FragmentViewPanel.preSelectAPs(), denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer(), and denoptim.gui.FragmentViewPanel.updateAPsMapAndTable().

Referenced by denoptim.gui.VertexViewPanel.loadFragmentToViewer(), and denoptim.gui.GraphVertexMolViewerPanel.visualizeVertexInNestedViewer().

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◆ loadPlainStructure()

void denoptim.gui.FragmentViewPanel.loadPlainStructure ( IAtomContainer mol )

Loads a structure in the Jmol viewer.

Parameters

mol	the structure to load

Returns: the atom container created to visualize the molecular content. This is needed for operations involving the identification by means of reference to the atoms selected/present in the viewer.

Definition at line 710 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.fragment, denoptim.gui.FragmentViewPanel.loadStructure(), and denoptim.graph.Vertex.BBType.UNDEFINED.

Referenced by denoptim.gui.VertexViewPanel.loadPlainStructure(), and denoptim.gui.FragmentViewPanel.make3DusingCDKgenerator().

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◆ loadSMILES()

boolean denoptim.gui.FragmentViewPanel.loadSMILES ( String smiles )

Loads a molecule build from a smiles string.

The 3D geometry is either taken from remote CACTUS service (requires connection to the Internet) or built with CDK tools, as a fall-back. The CDK builder, however will produce a somewhat lower quality conformation than that obtained from on online generator.

Parameters

smiles the SMILES of the molecule to load

Returns: true if the SMILES could be converted into a 3D structure

Exceptions

DENOPTIMException

Definition at line 392 of file FragmentViewPanel.java.

Referenced by denoptim.gui.VertexViewPanel.loadSMILES().

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◆ loadStructure()

void denoptim.gui.FragmentViewPanel.loadStructure ( )

private

Loads the structure of the currently loaded 'fragment' (i.e., our member) into the Jmol viewer.

Definition at line 727 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.fragment, denoptim.graph.Fragment.getIAtomContainer(), denoptim.gui.FragmentViewPanel.jmolPanel, denoptim.gui.FragmentViewPanel.setJmolViewer(), denoptim.gui.FragmentViewPanel.tmpSDFFile, denoptim.gui.JmolPanel.viewer, and denoptim.io.DenoptimIO.writeSDFFile().

Referenced by denoptim.gui.FragmentViewPanel.loadFragmentToViewer(), and denoptim.gui.FragmentViewPanel.loadPlainStructure().

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◆ make3DusingCDKgenerator()

void denoptim.gui.FragmentViewPanel.make3DusingCDKgenerator ( String smiles ) throws CDKException, CloneNotSupportedException, IOException

private

Definition at line 315 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.clearMolecularViewer(), denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), denoptim.gui.FragmentViewPanel.jmolPanel, denoptim.gui.FragmentViewPanel.loadPlainStructure(), denoptim.gui.JmolPanel.viewer, and denoptim.gui.FragmentViewPanel.waitForJmolViewer().

Referenced by denoptim.gui.FragmentViewPanel.loadSMILES().

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◆ preSelectAPs()

void denoptim.gui.FragmentViewPanel.preSelectAPs ( )

private

Definition at line 810 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.activateTabEditsListener(), denoptim.gui.FragmentViewPanel.apTable, denoptim.gui.FragmentViewPanel.fragment, denoptim.graph.Vertex.getProperty(), denoptim.gui.GUIVertexSelector.PRESELECTEDAPSFIELD, and denoptim.gui.GUIVertexSelector.PRESELECTEDAPSFIELDSEP.

Referenced by denoptim.gui.FragmentViewPanel.loadFragmentToViewer().

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◆ putAPsFromTableIntoIAtomContainer()

void denoptim.gui.FragmentViewPanel.putAPsFromTableIntoIAtomContainer ( Fragment mol ) throws DENOPTIMException

private

Definition at line 665 of file FragmentViewPanel.java.

References denoptim.graph.AttachmentPoint.getAPClass(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.AttachmentPoint.getDirectionVector(), and denoptim.gui.FragmentViewPanel.mapAPs.

Referenced by denoptim.gui.FragmentViewPanel.getLoadedStructure().

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◆ setJmolViewer()

void denoptim.gui.FragmentViewPanel.setJmolViewer ( )

private

Definition at line 941 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.jmolPanel, denoptim.gui.FragmentViewPanel.NL, and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.FragmentViewPanel.getLoadedStructure(), denoptim.gui.FragmentViewPanel.loadSMILES(), and denoptim.gui.FragmentViewPanel.loadStructure().

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◆ updateAPsInJmolViewer()

void denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer ( )

private

Definition at line 882 of file FragmentViewPanel.java.

References denoptim.utils.MathUtils.add(), denoptim.gui.FragmentViewPanel.fragment, denoptim.graph.Fragment.getAtom(), denoptim.graph.AttachmentPoint.getAtomPositionNumber(), denoptim.graph.AttachmentPoint.getDirectionVector(), denoptim.gui.FragmentViewPanel.getJmolPositionStr(), denoptim.utils.MoleculeUtils.getPoint3d(), denoptim.gui.FragmentViewPanel.jmolPanel, denoptim.gui.FragmentViewPanel.mapAPs, denoptim.gui.FragmentViewPanel.NL, denoptim.utils.MathUtils.scale(), denoptim.utils.MathUtils.subtract(), and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.FragmentViewPanel.loadFragmentToViewer().

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◆ updateAPsMapAndTable()

void denoptim.gui.FragmentViewPanel.updateAPsMapAndTable ( )

private

Uses the AP of the Fragment to create a new map and table of APs.

Definition at line 786 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.activateTabEditsListener(), denoptim.gui.FragmentViewPanel.apTabModel, denoptim.gui.FragmentViewPanel.clearAPTable(), denoptim.gui.FragmentViewPanel.fragment, denoptim.graph.Fragment.getCurrentAPs(), and denoptim.gui.FragmentViewPanel.mapAPs.

Referenced by denoptim.gui.FragmentViewPanel.loadFragmentToViewer().

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◆ waitForJmolViewer()

void denoptim.gui.FragmentViewPanel.waitForJmolViewer	(	int	milliSecFirst,
		String	cause
	)

private

Waits until Jmol is finished.

Parameters

milliSecFirst

Definition at line 230 of file FragmentViewPanel.java.

References denoptim.gui.FragmentViewPanel.clearMolecularViewer(), denoptim.gui.FragmentViewPanel.jmolPanel, denoptim.gui.FragmentViewPanel.parent, and denoptim.gui.JmolPanel.viewer.

Referenced by denoptim.gui.FragmentViewPanel.loadSMILES(), and denoptim.gui.FragmentViewPanel.make3DusingCDKgenerator().

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Member Data Documentation

◆ alteredAPData

boolean denoptim.gui.FragmentViewPanel.alteredAPData = false

Flag signalling that data about APs has been changed in the GUI.

Definition at line 98 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.deprotectEdits(), denoptim.gui.FragmentViewPanel.hasUnsavedAPEdits(), and denoptim.gui.FragmentViewPanel.PausableTableModelListener.tableChanged().

◆ apTable

JTable denoptim.gui.FragmentViewPanel.apTable

protected

Definition at line 103 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.getSelectedAPIDs(), denoptim.gui.FragmentViewPanel.getSelectedAPs(), denoptim.gui.FragmentViewPanel.initialize(), and denoptim.gui.FragmentViewPanel.preSelectAPs().

◆ apTabModel

DefaultTableModel denoptim.gui.FragmentViewPanel.apTabModel

protected

Definition at line 102 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.activateTabEditsListener(), denoptim.gui.FragmentViewPanel.clearAPTable(), denoptim.gui.FragmentViewPanel.getAPTableModel(), denoptim.gui.FragmentViewPanel.initialize(), and denoptim.gui.FragmentViewPanel.updateAPsMapAndTable().

◆ editableAPTable

boolean denoptim.gui.FragmentViewPanel.editableAPTable = false

private

Definition at line 105 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.FragmentViewPanel(), and denoptim.gui.FragmentViewPanel.initialize().

◆ fragment

Fragment denoptim.gui.FragmentViewPanel.fragment

private

The currently loaded fragment.

Definition at line 88 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.getAtomsSelectedFromJMol(), denoptim.gui.FragmentViewPanel.getLoadedStructure(), denoptim.gui.FragmentViewPanel.loadPlainStructure(), denoptim.gui.FragmentViewPanel.loadSMILES(), denoptim.gui.FragmentViewPanel.loadStructure(), denoptim.gui.FragmentViewPanel.preSelectAPs(), denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer(), and denoptim.gui.FragmentViewPanel.updateAPsMapAndTable().

◆ jmolPanel

JmolPanel denoptim.gui.FragmentViewPanel.jmolPanel

private

Definition at line 100 of file FragmentViewPanel.java.

◆ mapAPs

Map<Integer,AttachmentPoint> denoptim.gui.FragmentViewPanel.mapAPs = null

protected

Temporary list of attachment points of the current fragment.

Definition at line 93 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.getMapOfAPsInTable(), denoptim.gui.FragmentViewPanel.getSelectedAPs(), denoptim.gui.FragmentViewPanel.putAPsFromTableIntoIAtomContainer(), denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer(), and denoptim.gui.FragmentViewPanel.updateAPsMapAndTable().

◆ NL

final String denoptim.gui.FragmentViewPanel.NL = System.getProperty("line.separator")

private

Definition at line 107 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), denoptim.gui.FragmentViewPanel.setJmolViewer(), and denoptim.gui.FragmentViewPanel.updateAPsInJmolViewer().

◆ parent

JComponent denoptim.gui.FragmentViewPanel.parent

private

Definition at line 111 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.FragmentViewPanel(), denoptim.gui.FragmentViewPanel.loadSMILES(), and denoptim.gui.FragmentViewPanel.waitForJmolViewer().

◆ serialVersionUID

final long denoptim.gui.FragmentViewPanel.serialVersionUID = 912850110991449553L

staticprivate

Version UID.

Definition at line 83 of file FragmentViewPanel.java.

◆ tabPanel

JScrollPane denoptim.gui.FragmentViewPanel.tabPanel

private

Definition at line 101 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.initialize().

◆ tmpSDFFile

String denoptim.gui.FragmentViewPanel.tmpSDFFile

private

Definition at line 109 of file FragmentViewPanel.java.

Referenced by denoptim.gui.FragmentViewPanel.getStructureFromJmolViewer(), denoptim.gui.FragmentViewPanel.initialize(), and denoptim.gui.FragmentViewPanel.loadStructure().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/gui/FragmentViewPanel.java

Classes

Public Member Functions

Public Attributes

Protected Attributes

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ FragmentViewPanel() [1/3]

◆ FragmentViewPanel() [2/3]

◆ FragmentViewPanel() [3/3]

Member Function Documentation

◆ activateTabEditsListener()

◆ clearAll()

◆ clearAPTable()

◆ clearMolecularViewer()

◆ deprotectEdits()

◆ dispose()

◆ getAPTableModel()

◆ getAtomsSelectedFromJMol()

◆ getDataFromJmol()

◆ getJmolPositionStr()

◆ getLoadedStructure()

◆ getMapOfAPsInTable()

◆ getSelectedAPIDs()

◆ getSelectedAPs()

◆ getStructureFromJmolViewer()

◆ hasUnsavedAPEdits()

◆ initialize()

◆ loadFragmentToViewer()

◆ loadPlainStructure()

◆ loadSMILES()

◆ loadStructure()

◆ make3DusingCDKgenerator()

◆ preSelectAPs()

◆ putAPsFromTableIntoIAtomContainer()

◆ setJmolViewer()

◆ updateAPsInJmolViewer()

◆ updateAPsMapAndTable()

◆ waitForJmolViewer()

Member Data Documentation

◆ alteredAPData

◆ apTable

◆ apTabModel

◆ editableAPTable

◆ fragment

◆ jmolPanel

◆ mapAPs

◆ NL

◆ parent

◆ serialVersionUID

◆ tabPanel

◆ tmpSDFFile