├── .github └── workflows │ ├── maven.yml │ └── packaging.yml ├── .gitignore ├── .vscode └── settings.json ├── CITATION.cff ├── EditorApplet.html ├── META-INF ├── applet-core.files ├── applet-editor-opts.files ├── applet-editor.files ├── applet-resources-core.files ├── applet-viewer-opts.files └── jchempaint.datafiles ├── Native └── OSX │ ├── Makefile │ ├── SetClipboard.swift │ ├── setclipboard.c │ ├── setclipboard.h │ └── setclipboard_swift.h ├── README.md ├── ViewerApplet.html ├── ViewerAppletReaction.html ├── ViewerAppletSmall.html ├── app-jar ├── pom.xml └── src │ └── main │ └── resources │ └── org │ └── openscience │ └── jchempaint │ └── resources │ └── JCPShort_Cuts.properties ├── app-osx ├── codesign-app.sh ├── entitlements.plist ├── make-dmg.sh ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── openscience │ │ └── jchempaint │ │ └── OsxClipboard.java │ └── resources │ └── org │ └── openscience │ └── jchempaint │ ├── libSetClipboard.dylib │ └── resources │ └── JCPShort_Cuts.properties ├── app-windows ├── pom.xml └── src │ └── main │ └── resources │ └── org │ └── openscience │ └── jchempaint │ └── resources │ └── JCPShort_Cuts.properties ├── applettests ├── a_arginine.ms1.cml ├── a_asparagine.ms1.cml └── big.mol ├── appstream ├── io.github.jchempaint.JChemPaint.256.png ├── io.github.jchempaint.JChemPaint.512.png ├── io.github.jchempaint.JChemPaint.desktop └── io.github.jchempaint.JChemPaint.metainfo.xml ├── changelog.txt ├── core ├── po │ ├── ar.po │ ├── ca.po │ ├── cs.po │ ├── de.po │ ├── es.po │ ├── hu.po │ ├── keys.pot │ ├── nl.po │ ├── pl.po │ ├── pt_BR.po │ ├── ru.po │ ├── th.po │ └── zh.po ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── openscience │ │ │ └── jchempaint │ │ │ ├── AbstractJChemPaintPanel.java │ │ │ ├── AtomBondSet.java │ │ │ ├── GT.java │ │ │ ├── InsertTextPanel.java │ │ │ ├── JCPMenuTextMaker.java │ │ │ ├── JCPPropertyHandler.java │ │ │ ├── JCPToolBar.java │ │ │ ├── JCPTransferHandler.java │ │ │ ├── JChemPaintMenuBar.java │ │ │ ├── JChemPaintMenuHelper.java │ │ │ ├── JChemPaintPanel.java │ │ │ ├── JChemPaintPopupMenu.java │ │ │ ├── JChemPaintViewerPanel.java │ │ │ ├── JExternalFrame.java │ │ │ ├── RenderPanel.java │ │ │ ├── StringHelper.java │ │ │ ├── SwingPopupModule.java │ │ │ ├── action │ │ │ ├── AboutAction.java │ │ │ ├── AddHydrogenAction.java │ │ │ ├── ChangeAtomSymbolAction.java │ │ │ ├── ChangeBondAction.java │ │ │ ├── ChangeIsotopeAction.java │ │ │ ├── ChangeModeAction.java │ │ │ ├── ChangeSingleElectronAction.java │ │ │ ├── ChangeValenceAction.java │ │ │ ├── ChargeAction.java │ │ │ ├── CleanupAction.java │ │ │ ├── CloseAction.java │ │ │ ├── ConvertToPseudoAtomAction.java │ │ │ ├── CopyPasteAction.java │ │ │ ├── CreateInChIAction.java │ │ │ ├── CreateReactionAction.java │ │ │ ├── CreateSmilesAction.java │ │ │ ├── EditAtomContainerPropsAction.java │ │ │ ├── EditChemObjectPropsAction.java │ │ │ ├── ExitAction.java │ │ │ ├── ExportAction.java │ │ │ ├── FlipAction.java │ │ │ ├── HelpAction.java │ │ │ ├── InsertStructureAction.java │ │ │ ├── JCPAction.java │ │ │ ├── MenuBarAction.java │ │ │ ├── ModifySettingsAction.java │ │ │ ├── NewAction.java │ │ │ ├── OpenAction.java │ │ │ ├── PrintAction.java │ │ │ ├── RGroupAction.java │ │ │ ├── RedoAction.java │ │ │ ├── SaveAction.java │ │ │ ├── SaveAsAction.java │ │ │ ├── ToolBarAction.java │ │ │ ├── UndoAction.java │ │ │ └── ZoomAction.java │ │ │ ├── applet │ │ │ ├── JChemPaintAbstractApplet.java │ │ │ ├── JChemPaintEditorApplet.java │ │ │ └── JChemPaintViewerApplet.java │ │ │ ├── application │ │ │ └── JChemPaint.java │ │ │ ├── controller │ │ │ ├── AbstractSelectModule.java │ │ │ ├── AddAtomModule.java │ │ │ ├── AddBondDragModule.java │ │ │ ├── AddRingModule.java │ │ │ ├── AtomAtomMappingModule.java │ │ │ ├── CDKPopupMenu.java │ │ │ ├── ChainModule.java │ │ │ ├── ChangeFormalChargeModule.java │ │ │ ├── ChangeSingleElectronModule.java │ │ │ ├── ChangeValenceModule.java │ │ │ ├── Changed.java │ │ │ ├── ConjugationTools.java │ │ │ ├── ControllerHub.java │ │ │ ├── ControllerModel.java │ │ │ ├── ControllerModuleAdapter.java │ │ │ ├── ControllerParameters.java │ │ │ ├── CycleSymbolModule.java │ │ │ ├── HighlightModule.java │ │ │ ├── IAtomBondEdits.java │ │ │ ├── IChangeModeListener.java │ │ │ ├── IChemModelEventRelayHandler.java │ │ │ ├── IChemModelRelay.java │ │ │ ├── IControllerModel.java │ │ │ ├── IControllerModule.java │ │ │ ├── IMouseEventRelay.java │ │ │ ├── IViewEventRelay.java │ │ │ ├── MoveModule.java │ │ │ ├── PhantomArrowGenerator.java │ │ │ ├── PhantomAtomGenerator.java │ │ │ ├── PhantomBondGenerator.java │ │ │ ├── PhantomTextGenerator.java │ │ │ ├── ReactionArrowModule.java │ │ │ ├── ReactionHub.java │ │ │ ├── RemoveModule.java │ │ │ ├── Rotate3DModule.java │ │ │ ├── RotateModule.java │ │ │ ├── SelectLassoModule.java │ │ │ ├── SelectSquareModule.java │ │ │ ├── SwingEventRelay.java │ │ │ ├── SwingMouseEventRelay.java │ │ │ ├── UndoAdapter.java │ │ │ ├── ZoomModule.java │ │ │ └── undoredo │ │ │ │ ├── AddAtomsAndBondsEdit.java │ │ │ │ ├── AddSingleElectronEdit.java │ │ │ │ ├── AdjustBondOrdersEdit.java │ │ │ │ ├── ChangeAtomSymbolEdit.java │ │ │ │ ├── ChangeChargeEdit.java │ │ │ │ ├── ChangeCoordsEdit.java │ │ │ │ ├── ChangeHydrogenCountEdit.java │ │ │ │ ├── ChangeIsotopeEdit.java │ │ │ │ ├── ChangeValenceEdit.java │ │ │ │ ├── ClearAllEdit.java │ │ │ │ ├── CompoundEdit.java │ │ │ │ ├── IUndoListener.java │ │ │ │ ├── IUndoRedoFactory.java │ │ │ │ ├── IUndoRedoable.java │ │ │ │ ├── LoadNewModelEdit.java │ │ │ │ ├── MakeReactantOrProductInExistingReactionEdit.java │ │ │ │ ├── MakeReactantOrProductInNewReactionEdit.java │ │ │ │ ├── MergeMoleculesEdit.java │ │ │ │ ├── MoveAtomEdit.java │ │ │ │ ├── RGroupEdit.java │ │ │ │ ├── RemoveAtomsAndBondsEdit.java │ │ │ │ ├── ReplaceAtomEdit.java │ │ │ │ └── UndoRedoHandler.java │ │ │ ├── dialog │ │ │ ├── AboutDialog.java │ │ │ ├── EnterElementOrGroupDialog.java │ │ │ ├── EnterElementSwingModule.java │ │ │ ├── FieldTablePanel.java │ │ │ ├── HelpDialog.java │ │ │ ├── ModifyRenderOptionsDialog.java │ │ │ ├── PeriodicTableDialog.java │ │ │ ├── PeriodicTablePanel.java │ │ │ ├── TemplateBrowser.java │ │ │ ├── TextViewDialog.java │ │ │ ├── WaitDialog.java │ │ │ ├── editor │ │ │ │ ├── AtomContainerEditor.java │ │ │ │ ├── AtomEditor.java │ │ │ │ ├── BondEditor.java │ │ │ │ ├── ChemObjectEditor.java │ │ │ │ ├── ChemObjectPropertyDialog.java │ │ │ │ ├── PropertiesModelEditor.java │ │ │ │ ├── PseudoAtomEditor.java │ │ │ │ ├── RGroupEditor.java │ │ │ │ └── ReactionEditor.java │ │ │ └── templates │ │ │ │ └── DummyClass.java │ │ │ ├── io │ │ │ ├── ChemicalFilesFilter.java │ │ │ ├── FileHandler.java │ │ │ ├── IJCPFileFilter.java │ │ │ ├── JCPExportFileFilter.java │ │ │ ├── JCPFileFilter.java │ │ │ ├── JCPFileView.java │ │ │ └── JCPSaveFileFilter.java │ │ │ ├── renderer │ │ │ └── JCPAction2D.java │ │ │ ├── rgroups │ │ │ └── RGroupHandler.java │ │ │ └── undoredo │ │ │ ├── SwingUndoRedoFactory.java │ │ │ └── SwingUndoableEdit.java │ └── resources │ │ └── org │ │ └── openscience │ │ └── jchempaint │ │ ├── controller │ │ └── cursors │ │ │ └── rotate.png │ │ ├── dialog │ │ └── templates │ │ │ ├── Alkaloids │ │ │ ├── ChEBI_17303.mol │ │ │ ├── ChEBI_17303.png │ │ │ ├── caffeine.mol │ │ │ ├── caffeine.png │ │ │ ├── codeine.mol │ │ │ ├── codeine.png │ │ │ ├── quinine.mol │ │ │ └── quinine.png │ │ │ ├── Amino_Acids │ │ │ ├── alanine.mol │ │ │ ├── alanine.png │ │ │ ├── arginine.mol │ │ │ ├── arginine.png │ │ │ ├── asparagine.mol │ │ │ ├── asparagine.png │ │ │ ├── aspartic_acid.mol │ │ │ ├── aspartic_acid.png │ │ │ ├── citruline.mol │ │ │ ├── citruline.png │ │ │ ├── cysteine.mol │ │ │ ├── cysteine.png │ │ │ ├── glutamic_acid.mol │ │ │ ├── glutamic_acid.png │ │ │ ├── glutamine.mol │ │ │ ├── glutamine.png │ │ │ ├── glycine.mol │ │ │ ├── glycine.png │ │ │ ├── histidine.mol │ │ │ ├── histidine.png │ │ │ ├── isoleucine.mol │ │ │ ├── isoleucine.png │ │ │ ├── leucine.mol │ │ │ ├── leucine.png │ │ │ ├── lysine.mol │ │ │ ├── lysine.png │ │ │ ├── methionine.mol │ │ │ ├── methionine.png │ │ │ ├── ornithine.mol │ │ │ ├── ornithine.png │ │ │ ├── phenylalanine.mol │ │ │ ├── phenylalanine.png │ │ │ ├── proline.mol │ │ │ ├── proline.png │ │ │ ├── serine.mol │ │ │ ├── serine.png │ │ │ ├── threonine.mol │ │ │ ├── threonine.png │ │ │ ├── tryptophan.mol │ │ │ ├── tryptophan.png │ │ │ ├── tyrosine.mol │ │ │ ├── tyrosine.png │ │ │ ├── valine.mol │ │ │ └── valine.png │ │ │ ├── Beta_Lactams │ │ │ ├── ChEBI_17334.mol │ │ │ ├── ChEBI_17334.png │ │ │ ├── ChEBI_23064.mol │ │ │ └── ChEBI_23064.png │ │ │ ├── Carbohydrates │ │ │ ├── ChEBI_17012.mol │ │ │ ├── ChEBI_17012.png │ │ │ ├── ChEBI_17716.mol │ │ │ ├── ChEBI_17716.png │ │ │ ├── ChEBI_17992.mol │ │ │ ├── ChEBI_17992.png │ │ │ ├── ChEBI_4167.mol │ │ │ ├── ChEBI_4167.png │ │ │ ├── ChEBI_50254.mol │ │ │ └── ChEBI_50254.png │ │ │ ├── Inositols │ │ │ ├── nmrshiftdb_10026409.mol │ │ │ └── nmrshiftdb_10026409.png │ │ │ ├── Lipids │ │ │ ├── ChEBI_17351.mol │ │ │ ├── ChEBI_17351.png │ │ │ ├── ChEBI_17579.mol │ │ │ ├── ChEBI_17579.png │ │ │ ├── ChEBI_49183.mol │ │ │ └── ChEBI_49183.png │ │ │ ├── Miscellaneous │ │ │ ├── ChEBI_33128.mol │ │ │ └── ChEBI_33128.png │ │ │ ├── Nucleosides │ │ │ ├── ChEBI_15346.mol │ │ │ ├── ChEBI_15346.png │ │ │ ├── ChEBI_16335.mol │ │ │ ├── ChEBI_16335.png │ │ │ ├── ChEBI_16704.mol │ │ │ ├── ChEBI_16704.png │ │ │ ├── ChEBI_16750.mol │ │ │ ├── ChEBI_16750.png │ │ │ ├── ChEBI_17562.mol │ │ │ ├── ChEBI_17562.png │ │ │ ├── ChEBI_17748.mol │ │ │ ├── ChEBI_17748.png │ │ │ ├── ChEBI_44215.mol │ │ │ └── ChEBI_44215.png │ │ │ ├── PAHs │ │ │ ├── benzopyrene.mol │ │ │ ├── benzopyrene.png │ │ │ ├── chrysene.mol │ │ │ ├── chrysene.png │ │ │ ├── corannulene.mol │ │ │ ├── corannulene.png │ │ │ ├── coronene.mol │ │ │ ├── coronene.png │ │ │ ├── ovalene.mol │ │ │ ├── ovalene.png │ │ │ ├── phenanthrene.mol │ │ │ ├── phenanthrene.png │ │ │ ├── pyrene.mol │ │ │ ├── pyrene.png │ │ │ ├── triphenylene.mol │ │ │ └── triphenylene.png │ │ │ ├── Porphyrins │ │ │ ├── ChEBI_27630.mol │ │ │ ├── ChEBI_27630.png │ │ │ ├── ChEBI_8337.mol │ │ │ └── ChEBI_8337.png │ │ │ ├── Protecting_Groups │ │ │ ├── alloc.mol │ │ │ ├── alloc.png │ │ │ ├── boc.mol │ │ │ ├── boc.png │ │ │ ├── cbz.mol │ │ │ ├── cbz.png │ │ │ ├── dmt.mol │ │ │ ├── dmt.png │ │ │ ├── fmoc.mol │ │ │ ├── fmoc.png │ │ │ ├── pht.mol │ │ │ ├── pht.png │ │ │ ├── trt.mol │ │ │ └── trt.png │ │ │ └── Steroids │ │ │ ├── ChEBI_16113.mol │ │ │ ├── ChEBI_16113.png │ │ │ ├── ChEBI_17026.mol │ │ │ ├── ChEBI_17026.png │ │ │ ├── ChEBI_17263.mol │ │ │ ├── ChEBI_17263.png │ │ │ ├── ChEBI_17347.mol │ │ │ └── ChEBI_17347.png │ │ ├── fonts │ │ ├── JCPIcons.map │ │ └── JCPIcons.ttf │ │ └── resources │ │ ├── JCPGUI_applet.properties │ │ ├── JCPGUI_application.properties │ │ ├── JChemPaintResources.properties │ │ ├── apponly │ │ ├── R.png │ │ ├── cleanup.png │ │ ├── new.png │ │ ├── open.gif │ │ ├── print.png │ │ └── save.png │ │ ├── features.properties │ │ ├── funcgroups.txt │ │ ├── icons-dark │ │ ├── Br.png │ │ ├── C.png │ │ ├── Cl.png │ │ ├── F.png │ │ ├── H.png │ │ ├── I.png │ │ ├── N.png │ │ ├── O.png │ │ ├── P.png │ │ ├── S.png │ │ ├── benzene.png │ │ ├── bond.png │ │ ├── chain.png │ │ ├── cleanup.png │ │ ├── copy.png │ │ ├── cut.png │ │ ├── doubleBond.png │ │ ├── down_bond.png │ │ ├── enterR.png │ │ ├── enterelement.png │ │ ├── erase.png │ │ ├── flipHorizontal.png │ │ ├── flipVertical.png │ │ ├── hexagon.png │ │ ├── lasso.png │ │ ├── new.png │ │ ├── octagon.png │ │ ├── open.png │ │ ├── paste.png │ │ ├── pentagon.png │ │ ├── periodictable.png │ │ ├── print.png │ │ ├── reactionArrow.png │ │ ├── redo.png │ │ ├── rotate.png │ │ ├── rotate3d.png │ │ ├── save.png │ │ ├── select.png │ │ ├── square.png │ │ ├── template.png │ │ ├── triangle.png │ │ ├── tripleBond.png │ │ ├── undefined_bond.png │ │ ├── undefined_stereo_bond.png │ │ ├── undo.png │ │ ├── up_bond.png │ │ ├── zoomin.png │ │ └── zoomout.png │ │ ├── icons-light │ │ ├── Br.png │ │ ├── C.png │ │ ├── Cl.png │ │ ├── F.png │ │ ├── H.png │ │ ├── I.png │ │ ├── N.png │ │ ├── O.png │ │ ├── P.png │ │ ├── S.png │ │ ├── benzene.png │ │ ├── bond.png │ │ ├── chain.png │ │ ├── cleanup.png │ │ ├── copy.png │ │ ├── cut.png │ │ ├── doubleBond.png │ │ ├── down_bond.png │ │ ├── enterR.png │ │ ├── enterelement.png │ │ ├── erase.png │ │ ├── flipHorizontal.png │ │ ├── flipVertical.png │ │ ├── hexagon.png │ │ ├── lasso.png │ │ ├── new.png │ │ ├── octagon.png │ │ ├── open.png │ │ ├── paste.png │ │ ├── pentagon.png │ │ ├── periodictable.png │ │ ├── print.png │ │ ├── reactionArrow.png │ │ ├── redo.png │ │ ├── rotate.png │ │ ├── rotate3d.png │ │ ├── save.png │ │ ├── select.png │ │ ├── square.png │ │ ├── template.png │ │ ├── triangle.png │ │ ├── tripleBond.png │ │ ├── undefined_bond.png │ │ ├── undefined_stereo_bond.png │ │ ├── undo.png │ │ ├── up_bond.png │ │ ├── zoomin.png │ │ └── zoomout.png │ │ ├── large-bin │ │ ├── icon_16x16.gif │ │ ├── icon_32x32.gif │ │ ├── icon_large.gif │ │ ├── jcplogo.gif │ │ ├── rdemo1.png │ │ ├── reactionPositions.gif │ │ ├── rgroup-config.png │ │ └── rgroup.png │ │ ├── small-bin │ │ ├── Br.gif │ │ ├── C.gif │ │ ├── Cl.gif │ │ ├── F.gif │ │ ├── H.gif │ │ ├── I.gif │ │ ├── N.gif │ │ ├── O.gif │ │ ├── P.gif │ │ ├── S.gif │ │ ├── atomatommap.gif │ │ ├── benzene.gif │ │ ├── bond.gif │ │ ├── caffeine.gif │ │ ├── chain.gif │ │ ├── copy.gif │ │ ├── cut.gif │ │ ├── doubleBond.gif │ │ ├── down_bond.gif │ │ ├── element.gif │ │ ├── enterelement.gif │ │ ├── eraser.gif │ │ ├── flip_H.gif │ │ ├── flip_V.gif │ │ ├── hexagon.gif │ │ ├── hg_proc.gif │ │ ├── lasso.gif │ │ ├── lasso.png │ │ ├── min_one.gif │ │ ├── move.gif │ │ ├── octagon.gif │ │ ├── paste.gif │ │ ├── pentagon.gif │ │ ├── plus_one.gif │ │ ├── quadBond.gif │ │ ├── reactionArrow.gif │ │ ├── redo.gif │ │ ├── redo_disabled.gif │ │ ├── rotation.3d.gif │ │ ├── rotation.gif │ │ ├── rotation3d.gif │ │ ├── rotation3d.png │ │ ├── select.gif │ │ ├── select.png │ │ ├── selectsquare.gif │ │ ├── selectsquare.png │ │ ├── square.gif │ │ ├── templates.gif │ │ ├── triangle.gif │ │ ├── tripleBond.gif │ │ ├── undefined_bond.gif │ │ ├── undefined_stereo_bond.gif │ │ ├── undo.gif │ │ ├── undo_disabled.gif │ │ ├── up_bond.gif │ │ ├── zoomin.gif │ │ └── zoomout.gif │ │ └── userhelp_jcp │ │ ├── en_US │ │ ├── contain │ │ │ ├── aboutJCP.html │ │ │ ├── bibliography.html │ │ │ ├── bottomButtons.html │ │ │ ├── button.html │ │ │ ├── contextMenuAtom.html │ │ │ ├── contextMenuBond.html │ │ │ ├── contextMenuChemmodel.html │ │ │ ├── contextMenuPseudoatom.html │ │ │ ├── drawingButtons.html │ │ │ ├── elementButtons.html │ │ │ ├── feedback.html │ │ │ ├── feedback_frame.html │ │ │ ├── formats.html │ │ │ ├── keyboard.html │ │ │ ├── menu.html │ │ │ ├── menuEdit.html │ │ │ ├── menuFile.html │ │ │ ├── menuHelp.html │ │ │ ├── menuTools.html │ │ │ ├── menuView.html │ │ │ ├── misc.html │ │ │ ├── otherButtons.html │ │ │ ├── participate.html │ │ │ ├── reactions.html │ │ │ ├── referenceGuide.html │ │ │ ├── rgroup_tutorial.html │ │ │ ├── rgroup_tutorial_frame.html │ │ │ ├── tutorial.html │ │ │ ├── tutorial_frame.html │ │ │ └── whatIs.html │ │ ├── contents.html │ │ ├── index.html │ │ ├── jcp.css │ │ ├── jcp.html │ │ ├── jcp_frame.html │ │ ├── lgpl.license │ │ └── license.html │ │ ├── license.html │ │ └── ru │ │ ├── contain │ │ ├── aboutJCP.html │ │ ├── bibliography.html │ │ ├── bottomButtons.html │ │ ├── button.html │ │ ├── contextMenuAtom.html │ │ ├── contextMenuBond.html │ │ ├── contextMenuChemmodel.html │ │ ├── contextMenuPseudoatom.html │ │ ├── drawingButtons.html │ │ ├── elementButtons.html │ │ ├── feedback.html │ │ ├── feedback_frame.html │ │ ├── formats.html │ │ ├── keyboard.html │ │ ├── menu.html │ │ ├── menuEdit.html │ │ ├── menuFile.html │ │ ├── menuHelp.html │ │ ├── menuTools.html │ │ ├── menuView.html │ │ ├── misc.html │ │ ├── otherButtons.html │ │ ├── participate.html │ │ ├── reactions.html │ │ ├── referenceGuide.html │ │ ├── rgroup_tutorial.html │ │ ├── rgroup_tutorial_frame.html │ │ ├── tutorial.html │ │ ├── tutorial_frame.html │ │ └── whatIs.html │ │ ├── contents.html │ │ ├── index.html │ │ ├── jcp.css │ │ ├── jcp.html │ │ ├── jcp_frame.html │ │ ├── lgpl.license │ │ └── license.html │ └── test │ ├── java │ └── org │ │ └── openscience │ │ ├── cdk │ │ └── CDKTestCase.java │ │ └── jchempaint │ │ ├── AbstractAppletTest.java │ │ ├── AllJCPTests.java │ │ ├── BugSF65Test.java │ │ ├── BugSF70Test.java │ │ ├── BugSF75Test.java │ │ ├── BugSF80Test.java │ │ ├── Issue10Test.java │ │ ├── Issue116Test.java │ │ ├── Issue11Test.java │ │ ├── Issue129Test.java │ │ ├── Issue137Test.java │ │ ├── Issue139Test.java │ │ ├── Issue19Test.java │ │ ├── Issue32Test.java │ │ ├── Issue40Test.java │ │ ├── Issue4Test.java │ │ ├── Issue58Test.java │ │ ├── Issue71Test.java │ │ ├── Issue73Test.java │ │ ├── Issue76Test.java │ │ ├── Issue81Test.java │ │ ├── Issue82Test.java │ │ ├── Issue8Test.java │ │ ├── JCPEditorAppletBugsTest.java │ │ ├── JCPEditorAppletDrawingTest.java │ │ ├── JCPEditorAppletMenuTest.java │ │ ├── JCPEditorAppletUndoRedoTest.java │ │ ├── MenuCutTest.java │ │ ├── MenuIsotopeTest.java │ │ ├── SetSmilesTest.java │ │ ├── controller │ │ └── ConjugationToolsTest.java │ │ └── matchers │ │ ├── ButtonTextComponentMatcher.java │ │ ├── ComboBoxTextComponentMatcher.java │ │ └── DialogTitleComponentMatcher.java │ └── resources │ ├── data │ ├── a-pinen.cml │ ├── basic.mol │ ├── chebi │ │ ├── ChEBI_26120.mol │ │ ├── ChEBI_30735.mol │ │ ├── ChEBI_33258.mol │ │ ├── ChEBI_33806.mol │ │ ├── ChEBI_3793.mol │ │ ├── ChEBI_51719.mol │ │ ├── ChEBI_5397.mol │ │ └── ChEBI_7455.mol │ └── smiles.smi │ └── org │ └── openscience │ └── jchempaint │ └── resources │ └── JCPShort_Cuts.properties ├── hourglass.gif ├── inchi-jni ├── pom.xml └── src │ └── main │ ├── java │ └── org │ │ └── openscience │ │ └── jchempaint │ │ └── inchi │ │ └── JNIInChIHandler.java │ └── resources │ └── META-INF │ └── services │ └── org.openscience.jchempaint.inchi.InChIHandler ├── inchi-nestedvm ├── dep │ └── inchi-1.0.2.jar ├── pom.xml └── src │ ├── main │ ├── java │ │ └── org │ │ │ └── openscience │ │ │ └── jchempaint │ │ │ └── inchi │ │ │ ├── StdInChIGenerator.java │ │ │ ├── StdInChIHandler.java │ │ │ ├── StdInChIParser.java │ │ │ ├── StdInChIReader.java │ │ │ └── StdInChITool.java │ └── resources │ │ └── META-INF │ │ └── services │ │ └── org.openscience.jchempaint.inchi.InChIHandler │ └── test │ └── java │ └── org │ └── openscience │ └── jchempaint │ └── inchi │ └── StdInChIGeneratorTest.java ├── inchi ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── openscience │ └── jchempaint │ └── inchi │ ├── InChI.java │ ├── InChIHandler.java │ └── InChITool.java ├── pom.xml ├── render ├── pom.xml └── src │ └── main │ └── java │ └── org │ └── openscience │ └── jchempaint │ └── renderer │ ├── AtomContainerRenderer.java │ ├── BoundsCalculator.java │ ├── IRenderer.java │ ├── JChemPaintRendererModel.java │ ├── Renderer.java │ ├── RenderingParameters.java │ ├── elements │ ├── TextElement.java │ ├── TextGroupElement.java │ └── WigglyLineElement.java │ ├── font │ ├── FreeSansBoldGM.java │ └── GlyphMetrics.java │ ├── generators │ ├── AtomContainerBoundsGenerator.java │ ├── AtomContainerTitleGenerator.java │ ├── AtomMassGenerator.java │ ├── AtomNumberGenerator.java │ ├── BoundsGenerator.java │ ├── ControllerFeedbackGenerator.java │ ├── ExtendedAtomGenerator.java │ ├── ExternalHighlightAtomGenerator.java │ ├── ExternalHighlightBondGenerator.java │ ├── HighlightAtomGenerator.java │ ├── HighlightBondGenerator.java │ ├── IReactionGenerator.java │ ├── IReactionSetGenerator.java │ ├── LonePairGenerator.java │ ├── MappingGenerator.java │ ├── MergeAtomsGenerator.java │ ├── ProductsBoxGenerator.java │ ├── RadicalGenerator.java │ ├── ReactantsBoxGenerator.java │ ├── ReactionArrowGenerator.java │ ├── ReactionBoxGenerator.java │ ├── ReactionPlusGenerator.java │ ├── SelectAtomGenerator.java │ ├── SelectBondGenerator.java │ ├── SelectControlGenerator.java │ ├── SelectionToolGenerator.java │ └── TooltipGenerator.java │ ├── selection │ ├── AtomContainerSelection.java │ ├── IncrementalSelection.java │ ├── LassoSelection.java │ ├── LogicalSelection.java │ ├── MultiSelection.java │ ├── RectangleSelection.java │ ├── ShapeSelection.java │ └── SingleSelection.java │ └── visitor │ ├── AWTDrawVisitor.java │ ├── AbstractAWTDrawVisitor.java │ ├── DistanceSearchVisitor.java │ ├── IDrawVisitor.java │ ├── PrintVisitor.java │ └── SVGGenerator.java ├── sonar-runner.properties ├── src └── util │ ├── ExtractCoprightInfo.java │ ├── HtmlExample.java │ ├── JCPParamsTaglet.java │ ├── TemplateImagesMaker.java │ └── fontsvg │ ├── FreeSansBoldGM.java │ ├── characters.txt │ ├── compile.sh │ └── ttf2svgpath.c ├── src_icons ├── AppIcon.afdesign ├── JChemPaint.icns ├── JChemPaint.iconset │ ├── icon_128.png │ ├── icon_16.png │ ├── icon_256.png │ ├── icon_32.png │ ├── icon_512.png │ └── icon_64.png ├── affinitydesigner │ ├── icons_flat_black.afdesign │ └── icons_flat_white.afdesign ├── gif files │ ├── Br.gif │ ├── C.gif │ ├── Cl.gif │ ├── F.gif │ ├── H.gif │ ├── I.gif │ ├── N.gif │ ├── O.gif │ ├── P.gif │ ├── S.gif │ ├── background.gif │ ├── benzene.gif │ ├── bond.gif │ ├── copy.gif │ ├── cut.gif │ ├── doubleBond.gif │ ├── down_bond.gif │ ├── element.gif │ ├── enterelement.gif │ ├── eraser.gif │ ├── flip_H.gif │ ├── flip_V.gif │ ├── hexagon.gif │ ├── lasso.gif │ ├── min_one.gif │ ├── octagon.gif │ ├── paste.gif │ ├── pentagon.gif │ ├── plus_one.gif │ ├── redo.gif │ ├── rotate.gif │ ├── select.gif │ ├── selectsquare.gif │ ├── square.gif │ ├── templates.gif │ ├── triangle.gif │ ├── tripleBond.gif │ ├── undefined_bond.gif │ ├── undefined_stereo_bond.gif │ ├── undo.gif │ ├── up_bond.gif │ ├── zoomin.gif │ └── zoomout.gif ├── gimp files │ ├── Br.xcf │ ├── N.xcf │ ├── O.xcf │ ├── anyStereoBond.xcf │ ├── benzene.xcf │ ├── benzeneMine.xcf │ ├── c.xcf │ ├── copy.xcf │ ├── cut.xcf │ ├── doubleBond.xcf │ ├── down_bond.xcf │ ├── element.xcf │ ├── enterelement.xcf │ ├── eraser1.xcf │ ├── 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