From: <sh...@us...> - 2009-12-01 13:23:31
|
Revision: 15141 http://cdk.svn.sourceforge.net/cdk/?rev=15141&view=rev Author: shk3 Date: 2009-12-01 13:23:19 +0000 (Tue, 01 Dec 2009) Log Message: ----------- removed the reactions Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPFileFilter.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPSaveFileFilter.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2009-12-01 12:27:29 UTC (rev 15140) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2009-12-01 13:23:19 UTC (rev 15141) @@ -193,10 +193,10 @@ inputAdapter.setPopupMenu(ChemModel.class, new JChemPaintPopupMenu( this, "chemmodel", this.guistring)); } - if (inputAdapter.getPopupMenu(Reaction.class) == null) { + /*if (inputAdapter.getPopupMenu(Reaction.class) == null) { inputAdapter.setPopupMenu(Reaction.class, new JChemPaintPopupMenu( this, "reaction", this.guistring)); - } + }*/ } /** Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPFileFilter.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPFileFilter.java 2009-12-01 12:27:29 UTC (rev 15140) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPFileFilter.java 2009-12-01 13:23:19 UTC (rev 15141) @@ -117,7 +117,6 @@ chooser.addChoosableFileFilter(new JCPFileFilter(JCPFileFilter.smi)); chooser.addChoosableFileFilter(new JCPFileFilter(JCPFileFilter.inchi)); chooser.addChoosableFileFilter(new JCPFileFilter(JCPFileFilter.sdf)); - chooser.addChoosableFileFilter(new JCPFileFilter(JCPFileFilter.rxn)); JCPFileFilter molFilter = new JCPFileFilter(JCPFileFilter.mol); //molFilter.addType(JCPFileFilter.mol); chooser.addChoosableFileFilter(molFilter); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPSaveFileFilter.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPSaveFileFilter.java 2009-12-01 12:27:29 UTC (rev 15140) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/io/JCPSaveFileFilter.java 2009-12-01 13:23:19 UTC (rev 15141) @@ -55,7 +55,6 @@ chooser.addChoosableFileFilter(new JCPSaveFileFilter(JCPSaveFileFilter.smiles)); chooser.addChoosableFileFilter(new JCPSaveFileFilter(JCPSaveFileFilter.cdk)); chooser.addChoosableFileFilter(new JCPFileFilter(JCPFileFilter.cml)); - chooser.addChoosableFileFilter(new JCPFileFilter(JCPFileFilter.rxn)); chooser.addChoosableFileFilter(new JCPFileFilter(JCPFileFilter.mol)); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2009-12-01 12:27:29 UTC (rev 15140) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2009-12-01 13:23:19 UTC (rev 15141) @@ -76,11 +76,9 @@ atompopup=@formalCharge @hydrogen @isotopeChange @radical \ @pseudoSymbols pseudoStar @valence - @symbolChange - cut copy eraser selectFromChemObject \ - selectAll - @reaction - showChemObjectProperties showACProperties -reaction=addReactantToNewReaction addReactantToExistingReaction \ - addProductToNewReaction addProductToExistingReaction + selectAll - showChemObjectProperties showACProperties pseudopopup=makeNormal - cut copy eraser selectFromChemObject \ - selectAll - @reaction - showChemObjectProperties showACProperties + selectAll - showChemObjectProperties showACProperties symbolChange=periodictable enterelement - @commonSymbols @alkaliMetals \ @alkaliEarthMetals @transitionMetals @metals @metalloids @halogenSymbols \ @nobelSymbols @@ -103,11 +101,9 @@ pseudoSymbols=pseudoR pseudoR1 pseudoR2 pseudoR3 pseudoR4 pseudoRX bondpopup=bond up_bond down_bond undefined_bond \ undefined_stereo_bond - cut copy eraser selectFromChemObject selectAll - \ - @reaction - showChemObjectProperties showACProperties + showChemObjectProperties showACProperties chemmodelpopup= @hydrogen cleanup - cut copy eraser selectFromChemObject \ selectAll -reactionpopup=selectFromChemObject selectReactants selectProducts \ - showChemObjectProperties ####################################################### # toolbar definition # Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-12-01 12:27:29 UTC (rev 15140) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-12-01 13:23:19 UTC (rev 15141) @@ -76,11 +76,9 @@ atompopup=@formalCharge @hydrogen @isotopeChange @radical \ @pseudoSymbols pseudoStar @valence - @symbolChange - cut copy eraser selectFromChemObject \ - selectAll - @reaction - showChemObjectProperties showACProperties -reaction=addReactantToNewReaction addReactantToExistingReaction \ - addProductToNewReaction addProductToExistingReaction + selectAll - showChemObjectProperties showACProperties pseudopopup=makeNormal - cut copy eraser selectFromChemObject \ - selectAll - @reaction - showChemObjectProperties showACProperties + selectAll - showChemObjectProperties showACProperties symbolChange=periodictable enterelement - @commonSymbols @alkaliMetals \ @alkaliEarthMetals @transitionMetals @metals @metalloids @halogenSymbols \ @nobelSymbols @@ -103,11 +101,9 @@ pseudoSymbols=pseudoR pseudoR1 pseudoR2 pseudoR3 pseudoR4 pseudoRX bondpopup=bond up_bond down_bond undefined_bond \ undefined_stereo_bond - cut copy eraser selectFromChemObject selectAll - \ - @reaction - showChemObjectProperties showACProperties + showChemObjectProperties showACProperties chemmodelpopup= @hydrogen cleanup - cut copy eraser selectFromChemObject \ selectAll - toolbar++ statusbar++ menubar++ insertstructure++ -reactionpopup=selectFromChemObject selectReactants selectProducts \ - showChemObjectProperties ####################################################### # toolbar definition # This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2009-12-07 11:43:21
|
Revision: 15163 http://cdk.svn.sourceforge.net/cdk/?rev=15163&view=rev Author: shk3 Date: 2009-12-07 11:43:14 +0000 (Mon, 07 Dec 2009) Log Message: ----------- updated commentary Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java 2009-12-07 10:27:40 UTC (rev 15162) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java 2009-12-07 11:43:14 UTC (rev 15163) @@ -147,15 +147,11 @@ formatter.printHelp("JChemPaint", options); // now report on the -D options - // TODO which of these are still used? System.out.println(); System.out .println("The -D options are as follows (defaults in parathesis):"); System.out.println(" cdk.debugging [true|false] (false)"); System.out.println(" cdk.debug.stdout [true|false] (false)"); - System.out.println(" devel.gui [true|false] (false)"); - System.out - .println(" gui [stable|experimental] (stable)"); System.out.println(" user.language [DE|EN|NL|PL] (EN)"); System.exit(0); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2009-12-07 10:27:40 UTC (rev 15162) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2009-12-07 11:43:14 UTC (rev 15163) @@ -30,18 +30,8 @@ # # -# This file is the place where all the parameters determining -# the GUI of JChemPaint are stored. It only contains the menu -# ordering,*not* the actions. Those are in JChemPaint.properties. +# See JCPGUI_stable.properties for an explanation of this file. -# Textual parameters (menu titles, button titles etc) are -# stored in JCPBundle.properties. Localization are stored -# in JCPBundle_xx.properties. - -# @ before an entry means it's a submenu (so if there is @x in some menu, an x menu definition must exist -# + after an entry means it will become a check box menu item not checked at startup -# ++ after an entry means it will become a check box menu item checked at startup - ####################################################### # title of this GUI # ####################################################### Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-12-07 10:27:40 UTC (rev 15162) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-12-07 11:43:14 UTC (rev 15163) @@ -35,8 +35,9 @@ # ordering,*not* the actions. Those are in JChemPaint.properties. # Textual parameters (menu titles, button titles etc) are -# stored in JCPBundle.properties. Localization are stored -# in JCPBundle_xx.properties. +# stored in JCPBundle.properties. Note that for every menu you +# need an entry in JCPMenuTextMaker.init() for it's text. This entry +# is then picked up by the GnuText system. # @ before an entry means it's a submenu (so if there is @x in some menu, an x menu definition must exist # + after an entry means it will become a check box menu item not checked at startup This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-01-07 10:45:47
|
Revision: 15275 http://cdk.svn.sourceforge.net/cdk/?rev=15275&view=rev Author: shk3 Date: 2010-01-07 10:45:40 +0000 (Thu, 07 Jan 2010) Log Message: ----------- renamed "stable" gui to "application" Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuBar.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java Added Paths: ----------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties Removed Paths: ------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuBar.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuBar.java 2010-01-07 10:21:52 UTC (rev 15274) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuBar.java 2010-01-07 10:45:40 UTC (rev 15275) @@ -41,7 +41,7 @@ private static final long serialVersionUID = -8358165408129203644L; - private String guiString = "stable"; + private String guiString; private JChemPaintMenuHelper menuHelper=new JChemPaintMenuHelper(); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java 2010-01-07 10:21:52 UTC (rev 15274) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java 2010-01-07 10:45:40 UTC (rev 15275) @@ -96,6 +96,7 @@ public class JChemPaint { public static int instancecounter = 1; + public final static String GUI_APPLICATION="application"; @SuppressWarnings("static-access") public static void main(String[] args) { @@ -621,7 +622,7 @@ chemModel.setID(title); f.addWindowListener(new JChemPaintPanel.AppCloser()); f.setDefaultCloseOperation(JFrame.DO_NOTHING_ON_CLOSE); - JChemPaintPanel p = new JChemPaintPanel(chemModel, "stable", debug, null); + JChemPaintPanel p = new JChemPaintPanel(chemModel, GUI_APPLICATION, debug, null); f.setPreferredSize(new Dimension(1000, 500)); f.add(p); f.pack(); Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties 2010-01-07 10:45:40 UTC (rev 15275) @@ -0,0 +1,117 @@ +# $RCSfile$ +# $Author: egonw $ +# $Date: 2007-01-04 18:26:00 +0100 (Thu, 04 Jan 2007) $ +# $Revision: 7634 $ +# $Author: egonw $ +# $Date: 2007-01-04 18:26:00 +0100 (Thu, 04 Jan 2007) $ +# $Revision: 7634 $ +# +# Copyright (C) 2004-2009 Egon Willighagen, Christoph Steinbeck, Stefan Kuhn +# +# Contact: jch...@li... +# +# This program is free software; you can redistribute it and/or +# modify it under the terms of the GNU Lesser General Public License +# as published by the Free Software Foundation; either version 2.1 +# of the License, or (at your option) any later version. +# All we ask is that proper credit is given for our work, which includes +# - but is not limited to - adding the above copyright notice to the beginning +# of your source code files, and to any copyright notice that you may distribute +# with programs based on this work. +# +# This program is distributed in the hope that it will be useful, +# but WITHOUT ANY WARRANTY; without even the implied warranty of +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the +# GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public License +# along with this program; if not, write to the Free Software +# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. +# +# + +# This file is the place where all the parameters determining +# the GUI of JChemPaint are stored. It only contains the menu +# ordering,*not* the actions. Those are in JChemPaint.properties. + +# Textual parameters (menu titles, button titles etc) are +# stored in JCPBundle.properties. Note that for every menu you +# need an entry in JCPMenuTextMaker.init() for it's text. This entry +# is then picked up by the GnuText system. + +# @ before an entry means it's a submenu (so if there is @x in some menu, an x menu definition must exist +# + after an entry means it will become a check box menu item not checked at startup +# ++ after an entry means it will become a check box menu item checked at startup + +####################################################### +# title of this GUI # +####################################################### + +Title=JChemPaint + +####################################################### +# menubar definition # +####################################################### +menubar=file edit view atomMenu bondMenu tools templates + +file=new open save saveAs - export print - close - exit +edit=undo redo - cut copy copyAsSmiles paste - eraser selectAll - options +view=toolbar++ statusbar++ menubar++ insertstructure++ - zoomin zoomout zoomoriginal - cleanup @flip @hydrogen - @language +atomMenu=@formalCharge @hydrogen @isotopeChange @radical @pseudoSymbols pseudoStar @valence - @symbolChange +bondMenu=bond up_bond down_bond undefined_bond undefined_stereo_bond +tools=cleanup - createSMILES createInChI +help=help tutorial - feedback about license +templates=pasteTemplate - alkaloids beta_lactams carbohydrates inositols \ + lipids nucleosides porphyrins steroids miscellaneous + +hydrogen=hydroon hydrooff +language= +flip=flipHorizontal flipVertical +formalCharge=plus minus +valence= valenceOff valence1 valence2 valence3 valence4 valence5 valence6 valence7 valence8 +radical=convertToRadical convertFromRadical + +####################################################### +# popup menu definitions # +####################################################### + +atompopup=@formalCharge @hydrogen @isotopeChange @radical \ + @pseudoSymbols pseudoStar @valence - @symbolChange - cut copy eraser selectFromChemObject \ + selectAll - showChemObjectProperties showACProperties +pseudopopup=makeNormal - cut copy eraser selectFromChemObject \ + selectAll - showChemObjectProperties showACProperties +symbolChange=periodictable enterelement - @commonSymbols @alkaliMetals \ + @alkaliEarthMetals @transitionMetals @metals @metalloids @halogenSymbols \ + @nobelSymbols +isotopeChange=majorPlusThree majorPlusTwo majorPlusOne \ + major majorMinusOne majorMinusTwo majorMinusThree +commonSymbols=symbolH symbolC symbolN symbolO symbolS symbolF \ + symbolP symbolCl symbolBr symbolI +alkaliMetals=symbolLi symbolNa symbolK symbolRb symbolCs symbolFr +alkaliEarthMetals=symbolBe symbolMg symbolCa symbolSr symbolBa symbolRa +transitionMetals=symbolSc symbolTi symbolV symbolCr symbolMn symbolFe \ + symbolCo symbolNi symbolCu symbolZn symbolY symbolZr symbolNb symbolMo \ + symbolTc symbolRu symbolRh symbolPd symbolAg symbolCd symbolHf symbolTa \ + symbolW symbolRe symbolOs symbolIr symbolPt symbolAu symbolHg symbolRf \ + symbolDb symbolSg symbolBh symbolHs symbolMt symbolDs symbolRg +metals=symbolAl symbolGa symbolIn symbolSn symbolTl symbolPb symbolBi +metalloids=symbolB symbolSi symbolGe symbolAs symbolSb symbolTe symbolPo +nonmetalls=symbolC symbolN symbolO symbolP symbolS symbolSe +halogenSymbols=symbolF symbolCl symbolBr symbolI +nobelSymbols=symbolHe symbolNe symbolAr +pseudoSymbols=pseudoR pseudoR1 pseudoR2 pseudoR3 pseudoR4 pseudoRX +bondpopup=bond up_bond down_bond undefined_bond \ + undefined_stereo_bond - cut copy eraser selectFromChemObject selectAll - \ + showChemObjectProperties showACProperties +chemmodelpopup= @hydrogen cleanup - cut copy eraser selectFromChemObject \ + selectAll - toolbar++ statusbar++ menubar++ insertstructure++ + +####################################################### +# toolbar definition # +####################################################### + +uppertoolbar=new open save print select lasso eraser zoomin zoomout undo redo \ + cut copy paste flipHorizontal flipVertical rotate +lowertoolbar=C H O N P S F Cl Br I plus minus enterelement periodictable +righttoolbar=triangle square pentagon hexagon benzene octagon pasteTemplate +lefttoolbar=bond up_bond down_bond undefined_bond undefined_stereo_bond Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties ___________________________________________________________________ Added: svn:executable + * Deleted: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2010-01-07 10:21:52 UTC (rev 15274) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2010-01-07 10:45:40 UTC (rev 15275) @@ -1,117 +0,0 @@ -# $RCSfile$ -# $Author: egonw $ -# $Date: 2007-01-04 18:26:00 +0100 (Thu, 04 Jan 2007) $ -# $Revision: 7634 $ -# $Author: egonw $ -# $Date: 2007-01-04 18:26:00 +0100 (Thu, 04 Jan 2007) $ -# $Revision: 7634 $ -# -# Copyright (C) 2004-2009 Egon Willighagen, Christoph Steinbeck, Stefan Kuhn -# -# Contact: jch...@li... -# -# This program is free software; you can redistribute it and/or -# modify it under the terms of the GNU Lesser General Public License -# as published by the Free Software Foundation; either version 2.1 -# of the License, or (at your option) any later version. -# All we ask is that proper credit is given for our work, which includes -# - but is not limited to - adding the above copyright notice to the beginning -# of your source code files, and to any copyright notice that you may distribute -# with programs based on this work. -# -# This program is distributed in the hope that it will be useful, -# but WITHOUT ANY WARRANTY; without even the implied warranty of -# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the -# GNU Lesser General Public License for more details. -# -# You should have received a copy of the GNU Lesser General Public License -# along with this program; if not, write to the Free Software -# Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. -# -# - -# This file is the place where all the parameters determining -# the GUI of JChemPaint are stored. It only contains the menu -# ordering,*not* the actions. Those are in JChemPaint.properties. - -# Textual parameters (menu titles, button titles etc) are -# stored in JCPBundle.properties. Note that for every menu you -# need an entry in JCPMenuTextMaker.init() for it's text. This entry -# is then picked up by the GnuText system. - -# @ before an entry means it's a submenu (so if there is @x in some menu, an x menu definition must exist -# + after an entry means it will become a check box menu item not checked at startup -# ++ after an entry means it will become a check box menu item checked at startup - -####################################################### -# title of this GUI # -####################################################### - -Title=JChemPaint - -####################################################### -# menubar definition # -####################################################### -menubar=file edit view atomMenu bondMenu tools templates - -file=new open save saveAs - export print - close - exit -edit=undo redo - cut copy copyAsSmiles paste - eraser selectAll - options -view=toolbar++ statusbar++ menubar++ insertstructure++ - zoomin zoomout zoomoriginal - cleanup @flip @hydrogen - @language -atomMenu=@formalCharge @hydrogen @isotopeChange @radical @pseudoSymbols pseudoStar @valence - @symbolChange -bondMenu=bond up_bond down_bond undefined_bond undefined_stereo_bond -tools=cleanup - createSMILES createInChI -help=help tutorial - feedback about license -templates=pasteTemplate - alkaloids beta_lactams carbohydrates inositols \ - lipids nucleosides porphyrins steroids miscellaneous - -hydrogen=hydroon hydrooff -language= -flip=flipHorizontal flipVertical -formalCharge=plus minus -valence= valenceOff valence1 valence2 valence3 valence4 valence5 valence6 valence7 valence8 -radical=convertToRadical convertFromRadical - -####################################################### -# popup menu definitions # -####################################################### - -atompopup=@formalCharge @hydrogen @isotopeChange @radical \ - @pseudoSymbols pseudoStar @valence - @symbolChange - cut copy eraser selectFromChemObject \ - selectAll - showChemObjectProperties showACProperties -pseudopopup=makeNormal - cut copy eraser selectFromChemObject \ - selectAll - showChemObjectProperties showACProperties -symbolChange=periodictable enterelement - @commonSymbols @alkaliMetals \ - @alkaliEarthMetals @transitionMetals @metals @metalloids @halogenSymbols \ - @nobelSymbols -isotopeChange=majorPlusThree majorPlusTwo majorPlusOne \ - major majorMinusOne majorMinusTwo majorMinusThree -commonSymbols=symbolH symbolC symbolN symbolO symbolS symbolF \ - symbolP symbolCl symbolBr symbolI -alkaliMetals=symbolLi symbolNa symbolK symbolRb symbolCs symbolFr -alkaliEarthMetals=symbolBe symbolMg symbolCa symbolSr symbolBa symbolRa -transitionMetals=symbolSc symbolTi symbolV symbolCr symbolMn symbolFe \ - symbolCo symbolNi symbolCu symbolZn symbolY symbolZr symbolNb symbolMo \ - symbolTc symbolRu symbolRh symbolPd symbolAg symbolCd symbolHf symbolTa \ - symbolW symbolRe symbolOs symbolIr symbolPt symbolAu symbolHg symbolRf \ - symbolDb symbolSg symbolBh symbolHs symbolMt symbolDs symbolRg -metals=symbolAl symbolGa symbolIn symbolSn symbolTl symbolPb symbolBi -metalloids=symbolB symbolSi symbolGe symbolAs symbolSb symbolTe symbolPo -nonmetalls=symbolC symbolN symbolO symbolP symbolS symbolSe -halogenSymbols=symbolF symbolCl symbolBr symbolI -nobelSymbols=symbolHe symbolNe symbolAr -pseudoSymbols=pseudoR pseudoR1 pseudoR2 pseudoR3 pseudoR4 pseudoRX -bondpopup=bond up_bond down_bond undefined_bond \ - undefined_stereo_bond - cut copy eraser selectFromChemObject selectAll - \ - showChemObjectProperties showACProperties -chemmodelpopup= @hydrogen cleanup - cut copy eraser selectFromChemObject \ - selectAll - toolbar++ statusbar++ menubar++ insertstructure++ - -####################################################### -# toolbar definition # -####################################################### - -uppertoolbar=new open save print select lasso eraser zoomin zoomout undo redo \ - cut copy paste flipHorizontal flipVertical rotate -lowertoolbar=C H O N P S F Cl Br I plus minus enterelement periodictable -righttoolbar=triangle square pentagon hexagon benzene octagon pasteTemplate -lefttoolbar=bond up_bond down_bond undefined_bond undefined_stereo_bond This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-01-07 12:04:54
|
Revision: 15276 http://cdk.svn.sourceforge.net/cdk/?rev=15276&view=rev Author: shk3 Date: 2010-01-07 12:04:48 +0000 (Thu, 07 Jan 2010) Log Message: ----------- the change language is now in preferences (#61) Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/GT.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/ModifySettingsAction.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/GT.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/GT.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/GT.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -120,17 +120,18 @@ boolean wasTranslating = doTranslate; doTranslate = false; languageList = new Language[] { - new Language("nl", GT._("Dutch"), true), new Language("en_US", GT._("American English"), true), // global default for "en" will be "en_US" - new Language("de", GT._("German"), true), + new Language("ar", GT._("Arabic"), true), new Language("pt_BR", GT._("Brazilian Portuguese"), true), - new Language("es", GT._("Spanish"), true), - new Language("ar", GT._("Arabic"), true), - new Language("nb", GT._("Norwegian Bokmal"), true), new Language("cs", GT._("Czech"), true), + new Language("nl", GT._("Dutch"), true), + new Language("de", GT._("German"), true), new Language("hu", GT._("Hungarian"), true), + new Language("nb", GT._("Norwegian Bokmal"), true), + new Language("pl", GT._("Polish"), true), + new Language("ru", GT._("Russian"), true), + new Language("es", GT._("Spanish"), true), new Language("th", GT._("Thai"), true), - new Language("ru", GT._("Russian"), true), }; doTranslate = wasTranslating; return languageList; Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -321,7 +321,6 @@ entries.put("nucleosides", GT._("Nucleosides")); entries.put("porphyrins", GT._("Porphyrins")); entries.put("steroids", GT._("Steroids")); - entries.put("language", GT._("Language")); } /** Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -178,22 +178,6 @@ } }); } - if(key.equals("language")){ - final GT.Language[] languages = GT.getLanguageList(); - for(int i=0;i<languages.length;i++){ - final int counter=i; - JMenuItem jmi = new JChemPaintMenuHelper().createMenuItem(jcpPanel, languages[i].language, false); - jmi.addActionListener(new ActionListener(){ - - public void actionPerformed(ActionEvent e) { - GT.setLanguage(languages[counter].code); - jcpPanel.updateMenusWithLanguage(); - } - - }); - menu.add(jmi); - } - } if(menu instanceof JMenu) jcpPanel.menus.put(key, (JMenu)menu); else if(menu instanceof JChemPaintPopupMenu) Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -123,6 +123,7 @@ * The gui string */ public JChemPaintPanel(IChemModel chemModel, String gui, boolean debug, JChemPaintAbstractApplet applet) { + GT.setLanguage(JCPPropertyHandler.getInstance().getJCPProperties().getProperty("General.language")); this.guistring = gui; this.debug = debug; this.setLayout(new BorderLayout()); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/ModifySettingsAction.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/ModifySettingsAction.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/ModifySettingsAction.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -49,7 +49,7 @@ RendererModel renderModel = jcpPanel.get2DHub().getRenderer().getRenderer2DModel(); ModifyRenderOptionsDialog frame = - new ModifyRenderOptionsDialog(jcpPanel,renderModel); + new ModifyRenderOptionsDialog(jcpPanel,renderModel,0); frame.setVisible(true); } } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -51,7 +51,7 @@ protected int rows; - private JTabbedPane tabbedPane; + protected JTabbedPane tabbedPane; /** * Constructor for field table panel. Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -55,15 +55,18 @@ private PropertiesModelEditor editor; private RendererModel model; private JChemPaintPanel jcpPanel; + private int tabtoshow; /** * Displays the Info Dialog for JChemPaint. + * @param tabtoshow Which tab is to be displayed? */ - public ModifyRenderOptionsDialog(JChemPaintPanel jcpPanel, RendererModel model) { + public ModifyRenderOptionsDialog(JChemPaintPanel jcpPanel, RendererModel model, int tabtoshow) { super(); this.model = model; this.jcpPanel=jcpPanel; - editor = new PropertiesModelEditor(this); + this.tabtoshow = tabtoshow; + editor = new PropertiesModelEditor(this, jcpPanel, tabtoshow); createDialog(); pack(); setVisible(true); @@ -89,7 +92,7 @@ JButton apply = new JButton(GT._("Apply")); apply.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { - ApplyPressed(); + ApplyPressed(false); }} ); buttonPanel.add( apply ); @@ -106,13 +109,13 @@ validate(); } - private void ApplyPressed() { + private void ApplyPressed(boolean close) { // apply new settings - editor.applyChanges(); + editor.applyChanges(close); jcpPanel.get2DHub().updateView(); } private void OKPressed() { - ApplyPressed(); + ApplyPressed(true); closeFrame(); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java 2010-01-07 12:04:48 UTC (rev 15276) @@ -37,8 +37,10 @@ import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JColorChooser; +import javax.swing.JComboBox; import javax.swing.JFrame; import javax.swing.JLabel; +import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButton; @@ -49,7 +51,12 @@ import org.openscience.jchempaint.GT; import org.openscience.jchempaint.JCPPropertyHandler; +import org.openscience.jchempaint.JChemPaintMenuHelper; +import org.openscience.jchempaint.JChemPaintPanel; +import org.openscience.jchempaint.action.ModifySettingsAction; +import org.openscience.jchempaint.applet.JChemPaintEditorApplet; import org.openscience.jchempaint.dialog.FieldTablePanel; +import org.openscience.jchempaint.dialog.ModifyRenderOptionsDialog; import org.openscience.jchempaint.renderer.RendererModel; import org.openscience.jchempaint.renderer.RenderingParameters; @@ -82,7 +89,7 @@ //private JCheckBox showReactionBoxes; - private JCheckBox useAntiAliasing; + //private JCheckBox useAntiAliasing; private JCheckBox isFitToScreen; @@ -117,16 +124,26 @@ private Color currentColor; private JFrame frame; + + private JChemPaintPanel jcpPanel; private RendererModel model; private JCheckBox askForIOSettings; private JTextField undoStackSize; + + private JComboBox language; - public PropertiesModelEditor(JFrame frame) { + private GT.Language[] gtlanguages = GT.getLanguageList(); + + private int tabtoshow; + + public PropertiesModelEditor(JFrame frame, JChemPaintPanel jcpPanel, int tabtoshow) { super(true); this.frame = frame; + this.jcpPanel = jcpPanel; + this.tabtoshow = tabtoshow; constructPanel(); } @@ -289,7 +306,7 @@ options1.add(chooseColorButton); addField("", new JLabel(" "), options1); //addField("", chooseColorButton, options2); - + JPanel otherOptionsPanel = this.addTab(GT._("Other Preferences")); undoStackSize = new JTextField(); @@ -297,6 +314,19 @@ askForIOSettings = new JCheckBox(); addField(GT._("Ask for CML settings when saving"), askForIOSettings, otherOptionsPanel); + + String[] languagesstrings = new String[gtlanguages.length]; + for(int i=0;i<gtlanguages.length;i++){ + languagesstrings[i] = gtlanguages[i].language; + } + language = new JComboBox(languagesstrings); + for(int i=0;i<languagesstrings.length;i++){ + if(gtlanguages[i].code.equals(GT.getLanguage())) + language.setSelectedIndex(i); + } + addField(GT._("User Interface Language"), language, otherOptionsPanel); + + this.tabbedPane.setSelectedIndex(tabtoshow); } public void setModel(RendererModel model) { @@ -343,10 +373,11 @@ Properties props = JCPPropertyHandler.getInstance().getJCPProperties(); askForIOSettings.setSelected(props.getProperty("askForIOSettings", "false").equals("true")); undoStackSize.setText(props.getProperty("General.UndoStackSize")); + language.setSelectedItem(props.getProperty("General.language")); validate(); } - public void applyChanges() { + public void applyChanges(boolean close) { Properties props = JCPPropertyHandler.getInstance().getJCPProperties(); model.setDrawNumbers(drawNumbers.isSelected()); @@ -378,7 +409,11 @@ //model.setFontName(currentFontName); model.setBackColor(currentColor); + GT.setLanguage(gtlanguages[language.getSelectedIndex()].code); + jcpPanel.updateMenusWithLanguage(); + updateLanguge(); + props.setProperty("DrawNumbers",String.valueOf(drawNumbers.isSelected())); //props.setProperty("ShowAtomAtomMapping",String.valueOf(showAtomAtomMapping.isSelected())); props.setProperty("KekuleStructure",String.valueOf(useKekuleStructure.isSelected())); @@ -420,13 +455,35 @@ throw new Exception("wrong number"); props.setProperty("General.UndoStackSize", undoStackSize.getText()); - JCPPropertyHandler.getInstance().saveProperties(); - } - catch(Exception ex){ + //TODO here apply to current app + }catch(Exception ex){ JOptionPane.showMessageDialog(this, GT._("Number of undoable operations")+" "+GT._("must be a number from 1 to 100"), GT._("Number of undoable operations"), JOptionPane.WARNING_MESSAGE); } + boolean languagechanged = false; + for(int i=0;i<gtlanguages.length;i++){ + if(gtlanguages[i].language.equals((String)language.getSelectedItem())){ + if(!props.getProperty("General.language").equals(gtlanguages[i].code)){ + props.setProperty("General.language", gtlanguages[i].code); + languagechanged = true; + } + } + } + JCPPropertyHandler.getInstance().saveProperties(); + if(languagechanged && !close){ + //we need to rediplay the dialog to change its language + this.getParent().getParent().getParent().getParent().setVisible(false); + RendererModel renderModel = + jcpPanel.get2DHub().getRenderer().getRenderer2DModel(); + ModifyRenderOptionsDialog frame = + new ModifyRenderOptionsDialog(jcpPanel,renderModel, 1); + frame.setVisible(true); + } } + private void updateLanguge() { + // TODO here the language of the editor window needs to be updated + } + /** * Required by the ActionListener interface. */ Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2010-01-07 12:04:48 UTC (rev 15276) @@ -45,7 +45,7 @@ file=new open save saveAs - export print edit=undo redo - cut copy copyAsSmiles paste - eraser selectAll - options -view=zoomin zoomout zoomoriginal - cleanup @flip @hydrogen - @language +view=zoomin zoomout zoomoriginal - cleanup @flip @hydrogen atomMenu=@formalCharge @hydrogen @isotopeChange @radical @pseudoSymbols pseudoStar @valence - @symbolChange bondMenu=bond up_bond down_bond undefined_bond undefined_stereo_bond tools=cleanup - createSMILES @@ -54,7 +54,6 @@ lipids nucleosides porphyrins steroids miscellaneous hydrogen=hydroon hydrooff -language= flip=flipHorizontal flipVertical formalCharge=plus minus valence= valenceOff valence1 valence2 valence3 valence4 valence5 valence6 valence7 valence8 Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties 2010-01-07 10:45:40 UTC (rev 15275) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties 2010-01-07 12:04:48 UTC (rev 15276) @@ -56,7 +56,7 @@ file=new open save saveAs - export print - close - exit edit=undo redo - cut copy copyAsSmiles paste - eraser selectAll - options -view=toolbar++ statusbar++ menubar++ insertstructure++ - zoomin zoomout zoomoriginal - cleanup @flip @hydrogen - @language +view=toolbar++ statusbar++ menubar++ insertstructure++ - zoomin zoomout zoomoriginal - cleanup @flip @hydrogen atomMenu=@formalCharge @hydrogen @isotopeChange @radical @pseudoSymbols pseudoStar @valence - @symbolChange bondMenu=bond up_bond down_bond undefined_bond undefined_stereo_bond tools=cleanup - createSMILES createInChI @@ -65,7 +65,6 @@ lipids nucleosides porphyrins steroids miscellaneous hydrogen=hydroon hydrooff -language= flip=flipHorizontal flipVertical formalCharge=plus minus valence= valenceOff valence1 valence2 valence3 valence4 valence5 valence6 valence7 valence8 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-01-07 13:20:30
|
Revision: 15277 http://cdk.svn.sourceforge.net/cdk/?rev=15277&view=rev Author: shk3 Date: 2010-01-07 13:20:21 +0000 (Thu, 07 Jan 2010) Log Message: ----------- updated javadox Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java 2010-01-07 12:04:48 UTC (rev 15276) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java 2010-01-07 13:20:21 UTC (rev 15277) @@ -53,6 +53,7 @@ */ public abstract class AbstractJChemPaintPanel extends JPanel{ + private static final long serialVersionUID = -2229181291989083517L; // buttons/menus are remembered in here using the string from config files as key Map<String, JButton> buttons=new HashMap<String, JButton>(); Map<String, JMenuItem> menus=new HashMap<String, JMenuItem>(); @@ -66,9 +67,9 @@ LoggingToolFactory.createLoggingTool(AbstractJChemPaintPanel.class); /** + * Gets the RenderPanel in this panel. * - * - * @return + * @return The RenderPanel. */ public RenderPanel getRenderPanel() { return renderPanel; @@ -84,18 +85,18 @@ } /** - * Return the chemmodel of this JCPPanel + * Returns the chemmodel used in this panel. * - * @return + * @return The chemmodel usedin this panel. */ public IChemModel getChemModel(){ return renderPanel.getChemModel(); } /** - * Return the chemmodel of this JCPPanel + * Sets the chemmodel used in this panel. * - * @return + * @param model The chemmodel to use. */ public void setChemModel(IChemModel model){ renderPanel.setChemModel(model); @@ -103,6 +104,15 @@ renderPanel.getRenderer().getRenderer2DModel().setSelection(new LogicalSelection(LogicalSelection.Type.NONE)); } + /** + * Gives the smiles for the current chemmodel in this panel. + * + * @return The smiles for the current chemmodel in this panel. + * @throws CDKException + * @throws ClassNotFoundException + * @throws IOException + * @throws CloneNotSupportedException + */ public String getSmiles() throws CDKException, ClassNotFoundException, IOException, CloneNotSupportedException{ return CreateSmilesAction.getSmiles(getChemModel()); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2010-01-07 12:04:48 UTC (rev 15276) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintPanel.java 2010-01-07 13:20:21 UTC (rev 15277) @@ -88,6 +88,7 @@ public class JChemPaintPanel extends AbstractJChemPaintPanel implements IChemModelEventRelayHandler, ICDKChangeListener, KeyListener, IChangeModeListener { + private static final long serialVersionUID = -8932765332441119177L; private JComponent lastActionButton; private JComponent lastSecondaryButton; private File currentWorkDirectory; @@ -117,10 +118,10 @@ /** * Builds a JCPPanel with a certain model and a certain gui * - * @param chemModel - * The model - * @param gui - * The gui string + * @param chemModel The model + * @param gui The gui configuration string + * @param debug Should we be in debug mode? + * @param applet If this panel is to be in an applet, pass the applet here, else null. */ public JChemPaintPanel(IChemModel chemModel, String gui, boolean debug, JChemPaintAbstractApplet applet) { GT.setLanguage(JCPPropertyHandler.getInstance().getJCPProperties().getProperty("General.language")); @@ -164,10 +165,20 @@ }); } + /** + * Gets the top level container (JFrame, Applet) of this panel. + * + * @return The top level container. + */ public Container getTopLevelContainer() { return this.getParent().getParent().getParent().getParent(); } + /** + * If this panel is in a JFrame, sets the title of the JFrame. + * + * @param title The title to set. + */ public void setTitle(String title) { Container topLevelContainer = this.getTopLevelContainer(); if (topLevelContainer instanceof JFrame) { @@ -175,6 +186,11 @@ } } + /** + * Installs popup menus for this panel. + * + * @param inputAdapter The SwingPopupModule to use for the popup menus. + */ public void setupPopupMenus(SwingPopupModule inputAdapter) { if (inputAdapter.getPopupMenu(PseudoAtom.class) == null) { inputAdapter.setPopupMenu(PseudoAtom.class, @@ -341,6 +357,9 @@ customizeView(); } + /** + * Shows and hides menus, statusbar, toolbars according to settings. + */ public void customizeView() { if (showMenuBar) { if (menu == null) { @@ -451,6 +470,11 @@ return isAlreadyAFile; } + /** + * Gets the current gui configuration string of this panel. + * + * @return The current gui configuration string of this panel. + */ public String getGuistring() { return guistring; } @@ -475,10 +499,20 @@ return showInsertTextField; } + /** + * Gets the SVG of the chemical entities in this panel. + * + * @return The SVG of the chemical entities in this panel. + */ public String getSVGString() { return this.renderPanel.toSVG(); } + /** + * Takes an image snapshot of this panel. + * + * @return The snapshot. + */ public Image takeSnapshot() { return this.renderPanel.takeSnapshot(); } @@ -491,10 +525,7 @@ * OptionPane.YES_OPTION/OptionPane.NO_OPTION/OptionPane.CANCEL_OPTION */ public int showWarning() { - if (isModified && !guistring.equals(JChemPaintEditorApplet.GUI_APPLET)) { // TODO - // && - // !getIsOpenedByViewer()) - // { + if (isModified && !guistring.equals(JChemPaintEditorApplet.GUI_APPLET)) { int answer = JOptionPane.showConfirmDialog(this, renderPanel .getChemModel().getID() + " " + GT._("has unsaved data. Do you want to save it?"), @@ -509,12 +540,6 @@ } return answer; } else if (guistring.equals(JChemPaintEditorApplet.GUI_APPLET)) { - // In case of the applet we do not ask for save but put the clear - // into the undo stack - // ClearAllEdit coa = null; - // TODO undo redo missing coa = new - // ClearAllEdit(this.getChemModel(),(IMoleculeSet)this.getChemModel().getMoleculeSet().clone(),this.getChemModel().getReactionSet()); - // this.jchemPaintModel.getControllerModel().getUndoSupport().postEdit(coa); return JOptionPane.YES_OPTION; } else { return JOptionPane.YES_OPTION; @@ -537,14 +562,6 @@ * Description of the Parameter */ public void windowClosing(WindowEvent e) { - // JFrame rootFrame = (JFrame) e.getSource(); - /* - * TODO if (rootFrame.getContentPane().getComponent(0) instanceof - * JChemPaintEditorPanel) { JChemPaintEditorPanel panel = - * (JChemPaintEditorPanel) - * rootFrame.getContentPane().getComponent(0); - * panel.fireChange(JChemPaintEditorPanel.JCP_CLOSING); } - */ int clear = ((JChemPaintPanel) ((JFrame) e.getSource()) .getContentPane().getComponents()[0]).showWarning(); if (JOptionPane.CANCEL_OPTION != clear) { @@ -580,11 +597,17 @@ } } + /* (non-Javadoc) + * @see org.openscience.jchempaint.controller.IChemModelEventRelayHandler#coordinatesChanged() + */ public void coordinatesChanged() { setModified(true); updateStatusBar(); } + /* (non-Javadoc) + * @see org.openscience.jchempaint.controller.IChemModelEventRelayHandler#selectionChanged() + */ public void selectionChanged() { updateStatusBar(); if(this.getRenderPanel().getRenderer().getRenderer2DModel().getSelection()!=null @@ -617,6 +640,9 @@ } } + /* (non-Javadoc) + * @see org.openscience.jchempaint.controller.IChemModelEventRelayHandler#structureChanged() + */ public void structureChanged() { setModified(true); updateStatusBar(); @@ -626,6 +652,9 @@ this.get2DHub().updateView(); } + /* (non-Javadoc) + * @see org.openscience.jchempaint.controller.IChemModelEventRelayHandler#structurePropertiesChanged() + */ public void structurePropertiesChanged() { setModified(true); updateStatusBar(); @@ -634,6 +663,9 @@ this.getRenderPanel().getRenderer().getRenderer2DModel().setSelection(AbstractSelection.EMPTY_SELECTION); } + /** + * Enables/disables the undo/redo button depending on if something can be undone/redone. + */ public void updateUndoRedoControls() { UndoManager undoManager = renderPanel.getUndoManager(); JButton redoButton=buttons.get("redo"); @@ -659,16 +691,22 @@ } } + /* (non-Javadoc) + * @see org.openscience.cdk.event.ICDKChangeListener#stateChanged(java.util.EventObject) + */ public void stateChanged(EventObject event) { updateUndoRedoControls(); } - public void zoomFactorChanged(EventObject event) { - } - + /* (non-Javadoc) + * @see java.awt.event.KeyListener#keyPressed(java.awt.event.KeyEvent) + */ public void keyPressed(KeyEvent arg0) { } + /* (non-Javadoc) + * @see java.awt.event.KeyListener#keyReleased(java.awt.event.KeyEvent) + */ public void keyReleased(KeyEvent arg0) { RendererModel model = renderPanel.getRenderer().getRenderer2DModel(); ControllerHub relay = renderPanel.getHub(); @@ -691,9 +729,15 @@ } } + /* (non-Javadoc) + * @see java.awt.event.KeyListener#keyTyped(java.awt.event.KeyEvent) + */ public void keyTyped(KeyEvent arg0) { } + /* (non-Javadoc) + * @see org.openscience.jchempaint.controller.IChemModelEventRelayHandler#zoomChanged() + */ public void zoomChanged() { this.updateStatusBar(); } @@ -769,6 +813,12 @@ this.updateStatusBar(); } + /** + * Gets all atomcontainers of a chemodel in one AtomContainer. + * + * @param chemModel The chemodel + * @return The result. + */ public static IAtomContainer getAllAtomContainersInOne(IChemModel chemModel){ List<IAtomContainer> acs=ChemModelManipulator.getAllAtomContainers(chemModel); IAtomContainer allinone=chemModel.getBuilder().newAtomContainer(); @@ -778,6 +828,11 @@ return allinone; } + /** + * Sets the lastSecondaryButton attribute. Only to be used once from JCPToolBar. + * + * @param lastSecondaryButton The lastSecondaryButton. + */ public void setLastSecondaryButton(JComponent lastSecondaryButton) { this.lastSecondaryButton = lastSecondaryButton; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-01-08 14:17:48
|
Revision: 15284 http://cdk.svn.sourceforge.net/cdk/?rev=15284&view=rev Author: shk3 Date: 2010-01-08 14:17:28 +0000 (Fri, 08 Jan 2010) Log Message: ----------- When changing language, not all menus were changed Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java 2010-01-08 13:49:47 UTC (rev 15283) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/AbstractJChemPaintPanel.java 2010-01-08 14:17:28 UTC (rev 15284) @@ -29,8 +29,10 @@ package org.openscience.jchempaint; import java.io.IOException; +import java.util.ArrayList; import java.util.HashMap; import java.util.Iterator; +import java.util.List; import java.util.Map; import javax.swing.JButton; @@ -56,7 +58,7 @@ private static final long serialVersionUID = -2229181291989083517L; // buttons/menus are remembered in here using the string from config files as key Map<String, JButton> buttons=new HashMap<String, JButton>(); - Map<String, JMenuItem> menus=new HashMap<String, JMenuItem>(); + List<JMenuItem> menus=new ArrayList<JMenuItem>(); Map<String, JChemPaintPopupMenu> popupmenuitems=new HashMap<String, JChemPaintPopupMenu>(); protected InsertTextPanel insertTextPanel = null; protected JCPStatusBar statusBar; @@ -146,11 +148,10 @@ JButton button = buttons.get(key); button.setToolTipText(JCPMenuTextMaker.getInstance(guistring).getText(key + JCPAction.TIPSUFFIX)); } - it = menus.keySet().iterator(); - while(it.hasNext()){ - String key = it.next(); - JMenuItem button = menus.get(key); - button.setText(JCPMenuTextMaker.getInstance(guistring).getText(key)); + Iterator<JMenuItem> it2 = menus.iterator(); + while(it2.hasNext()){ + JMenuItem button = it2.next(); + button.setText(JCPMenuTextMaker.getInstance(guistring).getText(button.getName().charAt(button.getName().length()-1)=='2' ? button.getName().substring(0,button.getName().length()-1) : button.getName())); } it = popupmenuitems.keySet().iterator(); while(it.hasNext()){ Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java 2010-01-08 13:49:47 UTC (rev 15283) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java 2010-01-08 14:17:28 UTC (rev 15284) @@ -179,7 +179,7 @@ }); } if(menu instanceof JMenu) - jcpPanel.menus.put(key, (JMenu)menu); + jcpPanel.menus.add((JMenu)menu); else if(menu instanceof JChemPaintPopupMenu) jcpPanel.popupmenuitems.put(key, (JChemPaintPopupMenu)menu); return menu; @@ -269,7 +269,7 @@ jcpPanel.undoMenu=mi; if(cmd.equals("redo")) jcpPanel.redoMenu=mi; - jcpPanel.menus.put(cmd, (JMenuItem)mi); + jcpPanel.menus.add((JMenuItem)mi); return mi; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-01-11 14:30:26
|
Revision: 15287 http://cdk.svn.sourceforge.net/cdk/?rev=15287&view=rev Author: shk3 Date: 2010-01-11 14:30:19 +0000 (Mon, 11 Jan 2010) Log Message: ----------- made all dialogs to inherit from JDialog Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/AboutAction.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditAtomContainerPropsAction.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditChemObjectPropsAction.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/AboutDialog.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/PeriodicTablePanel.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/WaitDialog.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/ChemObjectPropertyDialog.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java Removed Paths: ------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/CreateCoordinatesForFileDialog.java Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/AboutAction.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/AboutAction.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/AboutAction.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -28,8 +28,12 @@ */ package org.openscience.jchempaint.action; +import java.awt.Frame; import java.awt.event.ActionEvent; +import javax.swing.JOptionPane; + +import org.openscience.jchempaint.applet.JChemPaintEditorApplet; import org.openscience.jchempaint.dialog.AboutDialog; /** @@ -43,7 +47,8 @@ public void actionPerformed(ActionEvent e) { - AboutDialog ad = new AboutDialog(jcpPanel.getGuistring()); + Frame frame = JOptionPane.getFrameForComponent(jcpPanel); + AboutDialog ad = new AboutDialog(frame, jcpPanel.getGuistring()); ad.pack(); ad.setVisible(true); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditAtomContainerPropsAction.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditAtomContainerPropsAction.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditAtomContainerPropsAction.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -28,8 +28,11 @@ */ package org.openscience.jchempaint.action; +import java.awt.Frame; import java.awt.event.ActionEvent; +import javax.swing.JOptionPane; + import org.openscience.cdk.Atom; import org.openscience.cdk.Bond; import org.openscience.cdk.interfaces.IAtomContainer; @@ -58,7 +61,7 @@ relevantContainer = ChemModelManipulator.getRelevantAtomContainer(jcpPanel.getChemModel(),(Bond)object); editor.setChemObject(relevantContainer); ChemObjectPropertyDialog frame = - new ChemObjectPropertyDialog(jcpPanel.get2DHub(), editor); + new ChemObjectPropertyDialog(JOptionPane.getFrameForComponent(editor), jcpPanel.get2DHub(), editor); frame.pack(); frame.setVisible(true); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditChemObjectPropsAction.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditChemObjectPropsAction.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/action/EditChemObjectPropsAction.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -28,8 +28,11 @@ */ package org.openscience.jchempaint.action; +import java.awt.Frame; import java.awt.event.ActionEvent; +import javax.swing.JOptionPane; + import org.openscience.cdk.Atom; import org.openscience.cdk.PseudoAtom; import org.openscience.cdk.Reaction; @@ -69,7 +72,7 @@ if (editor != null) { editor.setChemObject((org.openscience.cdk.ChemObject)object); ChemObjectPropertyDialog frame = - new ChemObjectPropertyDialog(jcpPanel.get2DHub(),editor); + new ChemObjectPropertyDialog(JOptionPane.getFrameForComponent(editor), jcpPanel.get2DHub(),editor); frame.pack(); frame.setVisible(true); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/applet/JChemPaintAbstractApplet.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -31,6 +31,7 @@ import java.awt.Color; import java.awt.Container; +import java.awt.Frame; import java.awt.event.MouseAdapter; import java.awt.event.MouseEvent; import java.awt.event.WindowAdapter; @@ -44,6 +45,7 @@ import java.util.StringTokenizer; import javax.swing.JApplet; +import javax.swing.JComponent; import javax.vecmath.Point2d; import javax.vecmath.Vector2d; @@ -639,5 +641,13 @@ chemPaintPanel.getChemModel().setMoleculeSet(moleculeSet); chemPaintPanel.get2DHub().updateView(); } + + public Frame getFrame(){ + Container component = this.getParent(); + while(!(component instanceof Frame)){ + component=component.getParent(); + } + return (Frame)component; + } } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/AboutDialog.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/AboutDialog.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/AboutDialog.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -30,11 +30,12 @@ import java.awt.BorderLayout; import java.awt.Color; +import java.awt.Frame; import java.net.URL; import javax.swing.BorderFactory; import javax.swing.ImageIcon; -import javax.swing.JFrame; +import javax.swing.JDialog; import javax.swing.JLabel; import javax.swing.JTextArea; import javax.swing.border.Border; @@ -53,7 +54,7 @@ * * @cdk.created 27. April 2005 */ -public class AboutDialog extends JFrame { +public class AboutDialog extends JDialog { private static final long serialVersionUID = 8890609574363086221L; @@ -61,8 +62,8 @@ LoggingToolFactory.createLoggingTool(AboutDialog.class); /** Displays the About Dialog for JChemPaint. */ - public AboutDialog(String guistring) { - super(JCPMenuTextMaker.getInstance(guistring).getText("about")); + public AboutDialog(Frame owner, String guistring) { + super(owner, JCPMenuTextMaker.getInstance(guistring).getText("about")); doInit(); } Deleted: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/CreateCoordinatesForFileDialog.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/CreateCoordinatesForFileDialog.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/CreateCoordinatesForFileDialog.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -1,206 +0,0 @@ -/* - * $RCSfile$ - * $Author: egonw $ - * $Date: 2007-05-01 20:15:34 +0100 (Tue, 01 May 2007) $ - * $Revision: 8292 $ - * - * Copyright (C) 1997-2007 The JChemPaint project - * - * Contact: jch...@li... - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU Lesser General Public License - * as published by the Free Software Foundation; either version 2.1 - * of the License, or (at your option) any later version. - * All we ask is that proper credit is given for our work, which includes - * - but is not limited to - adding the above copyright notice to the beginning - * of your source code files, and to any copyright notice that you may distribute - * with programs based on this work. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU Lesser General Public License for more details. - * - * You should have received a copy of the GNU Lesser General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA. - */ -package org.openscience.jchempaint.dialog; - -import java.awt.BorderLayout; -import java.awt.Container; -import java.awt.Dimension; -import java.awt.GridLayout; -import java.awt.event.ActionEvent; -import java.util.Iterator; - -import javax.swing.AbstractAction; -import javax.swing.BorderFactory; -import javax.swing.Box; -import javax.swing.BoxLayout; -import javax.swing.ButtonGroup; -import javax.swing.JButton; -import javax.swing.JInternalFrame; -import javax.swing.JLabel; -import javax.swing.JPanel; -import javax.swing.JRadioButton; - -import org.openscience.cdk.geometry.GeometryTools; -import org.openscience.cdk.geometry.Projector; -import org.openscience.cdk.graph.ConnectivityChecker; -import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.interfaces.IChemModel; -import org.openscience.cdk.interfaces.IMoleculeSet; -import org.openscience.cdk.layout.StructureDiagramGenerator; -import org.openscience.cdk.tools.manipulator.ChemModelManipulator; -import org.openscience.jchempaint.controller.ControllerHub; - -/** - * Dialog for coordinate creationg - * - * @cdk.module jchempaint - * @author steinbeck - */ -public class CreateCoordinatesForFileDialog extends JInternalFrame -{ - - private static final long serialVersionUID = 6717348756533287248L; - - private IChemModel chemModel; - private JRadioButton generate2DButton; - private JRadioButton from3DButton; - - - /** - * Constructor for the CreateCoordinatesForFileDialog object - * - *@param model Description of the Parameter - */ - public CreateCoordinatesForFileDialog(IChemModel model) - { - super("Coordinate Creation", true, true, true, true); - - this.chemModel = model; - Container contentPane = getContentPane(); - contentPane.setLayout(new BorderLayout()); - - // options - JPanel radioPanel = new JPanel(); - radioPanel.setLayout(new GridLayout(0, 1)); - ButtonGroup group = new ButtonGroup(); - generate2DButton = new JRadioButton("create with layout algorithm"); - group.add(generate2DButton); - radioPanel.add(generate2DButton); - if (GeometryTools.has3DCoordinates(chemModel)) { - from3DButton = new JRadioButton("create from 3D coordinates in file"); - group.add(from3DButton); - radioPanel.add(from3DButton); - from3DButton.setSelected(true); - } else - { - generate2DButton.setSelected(true); - } - - JPanel optionPane = new JPanel(); - optionPane.setLayout(new GridLayout(0, 1)); - JLabel label = new JLabel("The file does not contain 2D Coordinates or only some. Should I create those?"); - optionPane.add(label); - optionPane.add(radioPanel); - - //buttons - JButton cancelButton = new JButton("Cancel"); - JButton createButton = new JButton("Create"); - cancelButton.addActionListener(new CancelAction()); - createButton.addActionListener(new CreateAction()); - getRootPane().setDefaultButton(createButton); - - //Lay out the buttons from left to right. - JPanel buttonPane = new JPanel(); - buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.X_AXIS)); - buttonPane.setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10)); - buttonPane.add(Box.createHorizontalGlue()); - buttonPane.add(createButton); - buttonPane.add(Box.createRigidArea(new Dimension(10, 0))); - buttonPane.add(cancelButton); - - contentPane.add(optionPane, BorderLayout.CENTER); - contentPane.add(buttonPane, BorderLayout.SOUTH); - pack(); - setVisible(true); - } - - public void closeFrame() - { - dispose(); - } - - class CancelAction extends AbstractAction - { - - private static final long serialVersionUID = -2305492502437164455L; - - CancelAction() - { - super("Cancel"); - } - - public void actionPerformed(ActionEvent event) - { - closeFrame(); - } - } - - - /** - * Description of the Class - * - *@author steinbeck - */ - class CreateAction extends AbstractAction - { - - private static final long serialVersionUID = 7041050310635125218L; - - StructureDiagramGenerator diagramGenerator; - - CreateAction() - { - super("Create"); - this.diagramGenerator = new StructureDiagramGenerator(); - } - - public void actionPerformed(ActionEvent event) - { - if (from3DButton != null && from3DButton.isSelected()) - { - // JOptionPane.showMessageDialog(jchempaint, "Not implemented yet"); - Iterator containers = ChemModelManipulator.getAllAtomContainers(chemModel).iterator(); - while (containers.hasNext()) { - Projector.project2D((IAtomContainer)containers.next()); - } - } else - { - for (IAtomContainer container : - ChemModelManipulator.getAllAtomContainers(chemModel)) { - if (ConnectivityChecker.isConnected(container)) { - ControllerHub.generateNewCoordinates(container); - } else { - // deal with disconnected atom containers - IMoleculeSet molecules = - ConnectivityChecker.partitionIntoMolecules(container); - for (IAtomContainer subContainer : molecules.molecules()) { - ControllerHub.generateNewCoordinates(subContainer); - } - - } - } - ControllerHub.avoidOverlap(chemModel); - } - closeFrame(); - } - - } - -} - Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -36,7 +36,7 @@ import java.awt.event.ActionListener; import javax.swing.JButton; -import javax.swing.JFrame; +import javax.swing.JDialog; import javax.swing.JPanel; import org.openscience.jchempaint.GT; @@ -48,7 +48,7 @@ * Simple Dialog that shows the loaded dictionaries.. * */ -public class ModifyRenderOptionsDialog extends JFrame { +public class ModifyRenderOptionsDialog extends JDialog { private static final long serialVersionUID = -7228371698429720333L; Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/PeriodicTablePanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/PeriodicTablePanel.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/PeriodicTablePanel.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -47,6 +47,7 @@ import javax.swing.BorderFactory; import javax.swing.Box; import javax.swing.JButton; +import javax.swing.JDialog; import javax.swing.JLabel; import javax.swing.JLayeredPane; import javax.swing.JPanel; @@ -66,7 +67,7 @@ * @author Konstantin Tokarev * @author Mark Rijnbeek */ -public class PeriodicTablePanel extends JPanel +public class PeriodicTablePanel extends JDialog { private static final long serialVersionUID = -2539418347261469740L; Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/WaitDialog.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/WaitDialog.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/WaitDialog.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -1,15 +1,12 @@ package org.openscience.jchempaint.dialog; -import javax.swing.JFrame; import java.awt.FlowLayout; +import java.awt.Font; import java.awt.Toolkit; +import javax.swing.JDialog; import javax.swing.JLabel; -import javax.swing.ImageIcon; -import java.awt.Font; -import java.net.URL; - /** * This class is used to display the Wait Dialog. This Dialog is displayed * when the system is busy processing. All the GUI controls in this dialog @@ -20,7 +17,7 @@ * @since 1.0 * @version 1.0 */ -public class WaitDialog extends JFrame { +public class WaitDialog extends JDialog { /** * */ Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/ChemObjectPropertyDialog.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/ChemObjectPropertyDialog.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/ChemObjectPropertyDialog.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -31,11 +31,12 @@ import java.awt.BorderLayout; import java.awt.Color; import java.awt.FlowLayout; +import java.awt.Frame; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; import javax.swing.JButton; -import javax.swing.JFrame; +import javax.swing.JDialog; import javax.swing.JOptionPane; import javax.swing.JPanel; @@ -45,7 +46,7 @@ * Simple Dialog that shows the loaded dictionaries. * */ -public class ChemObjectPropertyDialog extends JFrame { +public class ChemObjectPropertyDialog extends JDialog { private static final long serialVersionUID = 1850053536210317644L; @@ -55,8 +56,8 @@ /** * Displays the Info Dialog for JChemPaint. */ - public ChemObjectPropertyDialog(ControllerHub hub, ChemObjectEditor editor) { - super("IChemObject Props Dialog"); + public ChemObjectPropertyDialog(Frame frame, ControllerHub hub, ChemObjectEditor editor) { + super(frame,"IChemObject Props Dialog"); this.editor = editor; this.hub=hub; createDialog(); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java 2010-01-08 15:43:19 UTC (rev 15286) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java 2010-01-11 14:30:19 UTC (rev 15287) @@ -33,28 +33,25 @@ import java.awt.event.ActionListener; import java.util.Properties; +import javax.swing.BoxLayout; import javax.swing.ButtonGroup; import javax.swing.JButton; import javax.swing.JCheckBox; import javax.swing.JColorChooser; import javax.swing.JComboBox; +import javax.swing.JDialog; import javax.swing.JFrame; import javax.swing.JLabel; -import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.JRadioButton; import javax.swing.JSeparator; import javax.swing.JSlider; import javax.swing.JTextField; -import javax.swing.BoxLayout; import org.openscience.jchempaint.GT; import org.openscience.jchempaint.JCPPropertyHandler; -import org.openscience.jchempaint.JChemPaintMenuHelper; import org.openscience.jchempaint.JChemPaintPanel; -import org.openscience.jchempaint.action.ModifySettingsAction; -import org.openscience.jchempaint.applet.JChemPaintEditorApplet; import org.openscience.jchempaint.dialog.FieldTablePanel; import org.openscience.jchempaint.dialog.ModifyRenderOptionsDialog; import org.openscience.jchempaint.renderer.RendererModel; @@ -123,7 +120,7 @@ private Color currentColor; - private JFrame frame; + private JDialog frame; private JChemPaintPanel jcpPanel; @@ -139,7 +136,7 @@ private int tabtoshow; - public PropertiesModelEditor(JFrame frame, JChemPaintPanel jcpPanel, int tabtoshow) { + public PropertiesModelEditor(JDialog frame, JChemPaintPanel jcpPanel, int tabtoshow) { super(true); this.frame = frame; this.jcpPanel = jcpPanel; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-01-11 15:07:50
|
Revision: 15288 http://cdk.svn.sourceforge.net/cdk/?rev=15288&view=rev Author: shk3 Date: 2010-01-11 15:07:44 +0000 (Mon, 11 Jan 2010) Log Message: ----------- fixes bug #2905692 Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/SwingPopupModule.java Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java 2010-01-11 14:30:19 UTC (rev 15287) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JChemPaintMenuHelper.java 2010-01-11 15:07:44 UTC (rev 15288) @@ -140,10 +140,9 @@ public void menuSelected(MenuEvent arg0) { menu.removeAll(); - if((jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection()!=null && jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().isFilled() && jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().getAtomCount()==1) - || jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getHighlightedAtom()!=null){ + if(SwingPopupModule.lastAtomPopupedFor.getSymbol()!=null){ try { - IIsotope[] isotopes = IsotopeFactory.getInstance(jcpPanel.getChemModel().getBuilder()).getIsotopes(jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getHighlightedAtom()!=null ? jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getHighlightedAtom().getSymbol() : jcpPanel.getRenderPanel().getRenderer().getRenderer2DModel().getSelection().getConnectedAtomContainer().getAtom(0).getSymbol()); + IIsotope[] isotopes = IsotopeFactory.getInstance(jcpPanel.getChemModel().getBuilder()).getIsotopes(SwingPopupModule.lastAtomPopupedFor.getSymbol()); for(int i=0;i<isotopes.length;i++){ String cmd=isotopes[i].getSymbol()+isotopes[i].getMassNumber(); JMenuItem mi = new JMenuItem(cmd); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/SwingPopupModule.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/SwingPopupModule.java 2010-01-11 14:30:19 UTC (rev 15287) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/SwingPopupModule.java 2010-01-11 15:07:44 UTC (rev 15288) @@ -33,6 +33,7 @@ import javax.vecmath.Point2d; +import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IChemObject; import org.openscience.cdk.interfaces.IReactionSet; import org.openscience.cdk.tools.ILoggingTool; @@ -52,6 +53,8 @@ private RenderPanel rendererPanel; private String ID; + + public static IAtom lastAtomPopupedFor = null; public SwingPopupModule(RenderPanel renderer,IChemModelRelay chemModelRelay) { super(chemModelRelay); @@ -125,6 +128,8 @@ if (objectInRange == null) objectInRange = chemModelRelay.getIChemModel(); + if (objectInRange instanceof IAtom) + lastAtomPopupedFor = (IAtom)objectInRange; JChemPaintPopupMenu popupMenu = getPopupMenu(objectInRange.getClass()); if (popupMenu != null) { This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-02-11 16:19:02
|
Revision: 15384 http://cdk.svn.sourceforge.net/cdk/?rev=15384&view=rev Author: shk3 Date: 2010-02-11 16:17:50 +0000 (Thu, 11 Feb 2010) Log Message: ----------- Added templates by Witek Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/TemplateBrowser.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JCPGUI_application.properties jchempaint/branches/3_0/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties Added Paths: ----------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alanine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alanine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alloc.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/arginine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/arginine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/asparagine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/asparagine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/aspartic_acid.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/aspartic_acid.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/citruline.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/citruline.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/cysteine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/cysteine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamic_acid.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamic_acid.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glycine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glycine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/histidine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/histidine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/isoleucine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/isoleucine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/leucine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/leucine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/lysine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/lysine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/methionine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/methionine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ornithine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ornithine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/phenylalanine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/phenylalanine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/proline.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/proline.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/serine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/serine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/threonine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/threonine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tryptophan.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tryptophan.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tyrosine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tyrosine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/valine.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/valine.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/alloc.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/alloc.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/boc.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/boc.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/cbz.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/cbz.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/dmt.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/dmt.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/fmoc.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/fmoc.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/pht.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/pht.png jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/trt.mol jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/trt.png Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2010-02-11 15:17:29 UTC (rev 15383) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/JCPMenuTextMaker.java 2010-02-11 16:17:50 UTC (rev 15384) @@ -313,6 +313,7 @@ entries.put("selectProducts", GT._("Select Products")); entries.put("reactionMenuTitle", GT._("Reaction Popup Menu")); entries.put("alkaloids", GT._("Alkaloids")); + entries.put("amino_acids", GT._("Amino Acids")); entries.put("beta_lactams", GT._("Beta Lactams")); entries.put("carbohydrates", GT._("Carbohydrates")); entries.put("inositols", GT._("Inositols")); @@ -320,6 +321,7 @@ entries.put("miscellaneous", GT._("Miscellaneous")); entries.put("nucleosides", GT._("Nucleosides")); entries.put("porphyrins", GT._("Porphyrins")); + entries.put("protecting_groups", GT._("Protecting Groups")); entries.put("steroids", GT._("Steroids")); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/TemplateBrowser.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/TemplateBrowser.java 2010-02-11 15:17:29 UTC (rev 15383) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/TemplateBrowser.java 2010-02-11 16:17:50 UTC (rev 15384) @@ -158,7 +158,7 @@ allPanel.add(allButton); } tabbedPane.addTab(GT.getStringNoExtraction(key.replace('_', ' ')), panel ); - if(tabToSelect.equals(key.replace('_',' '))){ + if(tabToSelect.equals(key)){ tabbedPane.setSelectedIndex(count+1); } count++; @@ -234,7 +234,7 @@ if(withsubdirs){ for(int k=0;k<dir.list().length;k++){ if(dir.listFiles()[k].getName().indexOf(".mol")>-1){ - MDLV2000Reader reader = new MDLV2000Reader(new FileInputStream(dir.listFiles()[k]), Mode.STRICT); + MDLV2000Reader reader = new MDLV2000Reader(new FileInputStream(dir.listFiles()[k]), Mode.RELAXED); IMolecule cdkmol = (IMolecule)reader.read(DefaultChemObjectBuilder.getInstance().newMolecule()); entriesMol.get(dir.getName()).add(cdkmol); entriesMolName.put(cdkmol,dir.listFiles()[k].getName().substring(0,dir.listFiles()[k].getName().length()-4)); Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alanine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alanine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alanine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,16 @@ +Alanine + CDK 1/19/10,15:9 + + 6 5 0 0 0 0 0 0 0 0999 V2000 + 104.0000 133.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 147.3010 108.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 190.6030 133.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 190.6030 183.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 233.9040 108.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 147.3010 58.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 6 1 0 0 0 0 + 3 4 2 0 0 0 0 + 3 5 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alanine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alanine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alloc.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/alloc.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/arginine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/arginine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/arginine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,29 @@ +Arginine + CDK 1/19/10,16:38 + + 12 11 0 0 0 0 0 0 0 0999 V2000 + 1.1180 2.9689 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.1138 4.4689 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4107 5.2226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.1873 5.2153 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.7119 4.4762 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4065 6.7225 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4843 4.4616 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7854 5.2080 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0823 4.4544 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.3835 5.2007 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.6804 4.4470 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -5.3877 6.7007 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 12 1 0 0 0 0 +M CHG 1 12 1 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/arginine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/arginine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/asparagine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/asparagine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/asparagine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,22 @@ +Asparagine + CDK 1/19/10,15:44 + + 9 8 0 0 0 0 0 0 0 0999 V2000 + -0.6443 1.1268 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6485 2.6269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6485 3.3805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9496 3.3732 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9496 2.6341 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6442 4.8804 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2466 2.6195 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.5477 3.3659 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2423 1.1196 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/asparagine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/asparagine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/aspartic_acid.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/aspartic_acid.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/aspartic_acid.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,22 @@ +Aspartic Acid + CDK 1/19/10,15:46 + + 9 8 0 0 0 0 0 0 0 0999 V2000 + -1.3568 0.9768 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3610 2.4768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0640 3.2305 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6621 3.2232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2371 2.4841 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0682 4.7305 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9590 2.4695 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.2602 3.2159 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9548 0.9695 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/aspartic_acid.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/aspartic_acid.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/citruline.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/citruline.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/citruline.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,28 @@ +L-Citrulline + CDK 2/11/10,12:47 + + 12 11 0 0 0 0 0 0 0 0999 V2000 + -2.5981 -7.6250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2990 -6.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 -7.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2990 -5.3750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0000 -9.1250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2991 -6.8750 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5981 -4.6250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5981 -3.1250 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8971 -2.3750 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8971 -0.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1961 -0.1250 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5981 -0.1250 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 1 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 + 10 11 2 0 0 0 0 + 10 12 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/citruline.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/citruline.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/cysteine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/cysteine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/cysteine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,18 @@ +Cysteine + CDK 1/19/10,15:47 + + 7 6 0 0 0 0 0 0 0 0999 V2000 + -1.9900 0.6492 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2176 1.9350 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2822 1.9090 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9449 3.2469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0096 0.5972 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0546 3.1949 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4447 3.2729 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/cysteine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/cysteine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamic_acid.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamic_acid.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamic_acid.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,24 @@ +Glutamic Acid + CDK 1/19/10,15:48 + + 10 9 0 0 0 0 0 0 0 0999 V2000 + -0.3383 1.3061 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3285 2.8061 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9755 3.5476 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6226 3.5646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2695 2.7890 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9853 5.0475 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.9265 2.8232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2206 3.5817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.5245 2.8403 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2107 5.0817 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 8 10 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamic_acid.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamic_acid.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,24 @@ +Glutamine + CDK 1/19/10,15:49 + + 10 9 0 0 0 0 0 0 0 0999 V2000 + -0.2997 1.3245 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3180 2.8244 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9718 3.5902 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6261 3.5585 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2799 2.8560 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9536 5.0901 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.9159 2.7928 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2239 3.5269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.5137 2.7611 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2422 5.0268 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 8 10 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glutamine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glycine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glycine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glycine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,14 @@ +Glycine + OpenBabel01191015072D + + 5 4 0 0 0 0 0 0 0 0999 V2000 + 104.0000 133.0000 0.0000 N 0 0 0 0 0 + 147.3010 108.0000 0.0000 C 0 0 0 0 0 + 190.6030 133.0000 0.0000 C 0 0 0 0 0 + 190.6030 183.0000 0.0000 O 0 0 0 0 0 + 233.9040 108.0000 0.0000 O 0 0 0 0 0 + 1 2 1 0 0 0 + 2 3 1 0 0 0 + 3 4 2 0 0 0 + 3 5 1 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glycine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/glycine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/histidine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/histidine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/histidine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,27 @@ +Histidine + CDK 1/19/10,15:51 + + 11 11 0 0 0 0 0 0 0 0999 V2000 + 2.0415 1.6037 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.4690 0.1659 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9279 -0.1827 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.4376 -0.9232 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.9593 0.9064 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.3554 -1.6205 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0213 -0.5746 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5968 0.8106 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1609 -1.5500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.4407 -0.7676 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0921 0.6914 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 2 0 0 0 0 + 8 11 1 0 0 0 0 + 9 10 1 0 0 0 0 + 11 10 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/histidine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/histidine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/isoleucine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/isoleucine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/isoleucine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,22 @@ +Isoleucine + CDK 1/19/10,16:20 + + 9 8 0 0 0 0 0 0 0 0999 V2000 + -0.2723 0.5701 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3046 2.0697 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9779 2.8475 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2928 2.1257 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9456 4.3472 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6195 2.7915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6519 4.2912 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.9021 2.0137 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.2170 2.7356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 6 1 0 0 0 0 + 3 4 2 0 0 0 0 + 3 5 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 + 8 9 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/isoleucine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/isoleucine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/leucine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/leucine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/leucine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,22 @@ +Leucine + CDK 1/19/10,16:21 + + 9 8 0 0 0 0 0 0 0 0999 V2000 + -0.6093 1.1394 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.6416 2.6391 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6410 3.4169 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.9559 2.6951 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.6087 4.9166 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9565 3.3609 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2391 2.5831 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.5540 3.3049 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.2067 1.0834 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 6 1 0 0 0 0 + 3 4 2 0 0 0 0 + 3 5 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 9 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/leucine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/leucine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/lysine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/lysine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/lysine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,24 @@ +Lysine + CDK 1/19/10,16:22 + + 10 9 0 0 0 0 0 0 0 0999 V2000 + 0.3874 1.6429 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3832 3.1429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6801 3.8965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.9179 3.8892 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9813 3.1501 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6759 5.3965 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2148 3.1356 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5160 3.8819 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.8129 3.1283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -6.1140 3.8747 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/lysine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/lysine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/methionine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/methionine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/methionine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,22 @@ +Methionine + CDK 1/19/10,16:22 + + 9 8 0 0 0 0 0 0 0 0999 V2000 + -0.0023 2.0760 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0357 3.5755 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3533 4.2924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.6329 3.5097 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3913 5.7919 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2439 4.3582 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5616 3.6413 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8412 4.4239 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1588 3.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 6 1 0 0 0 0 + 3 4 2 0 0 0 0 + 3 5 1 0 0 0 0 + 6 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/methionine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/methionine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ornithine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ornithine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ornithine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,22 @@ +L-Ornithine + CDK 2/11/10,12:47 + + 9 8 0 0 0 0 0 0 0 0999 V2000 + -3.8250 -4.8333 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5259 -4.0833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2269 -4.8333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.5259 -2.5833 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2269 -6.3333 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0722 -4.0833 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8250 -1.8333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8250 -0.3333 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.1240 0.4167 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 1 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 8 9 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ornithine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/ornithine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/phenylalanine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/phenylalanine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/phenylalanine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,29 @@ +Phenylalanine + CDK 1/19/10,16:23 + + 12 12 0 0 0 0 0 0 0 0999 V2000 + 2.2153 -2.2839 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.2111 -0.7839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5080 -0.0302 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9099 -0.0375 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8091 -0.7766 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.5038 1.4698 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3870 -0.7911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6881 -0.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.9851 -0.7984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.9809 -2.2984 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.6797 -3.0448 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.3828 -2.2911 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 12 7 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 11 12 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/phenylalanine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/phenylalanine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/proline.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/proline.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/proline.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,23 @@ +Proline + CDK 1/19/10,16:23 + + 9 9 0 0 0 0 0 0 0 0999 V2000 + -0.4080 0.1074 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7902 0.6900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7715 -0.4445 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9957 -1.7283 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5350 -1.3872 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0651 -0.1751 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0269 1.5429 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0 + 2.0464 0.9594 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5570 -1.5922 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 5 1 1 0 0 0 0 + 1 6 1 0 0 0 0 + 1 7 1 0 0 0 0 + 2 3 1 0 0 0 0 + 3 4 1 0 0 0 0 + 4 5 1 0 0 0 0 + 6 8 1 0 0 0 0 + 6 9 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/proline.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/proline.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/serine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/serine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/serine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,18 @@ +Serine + CDK 1/19/10,16:24 + + 7 6 0 0 0 0 0 0 0 0999 V2000 + -1.9597 0.6244 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2116 1.9245 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2884 1.9266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.9634 3.2224 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0403 0.6286 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0366 3.2266 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.4634 3.2203 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/serine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/serine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/threonine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/threonine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/threonine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,20 @@ +Threonine + CDK 1/19/10,16:24 + + 8 7 0 0 0 0 0 0 0 0999 V2000 + -0.4060 0.0741 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4102 1.5741 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8867 2.3277 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7113 2.3204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.1879 1.5814 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.8825 3.8277 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0083 1.5668 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7155 3.8204 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 4 8 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/threonine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/threonine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tryptophan.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tryptophan.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tryptophan.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,36 @@ +Tryptophan + CDK 1/19/10,16:25 + + 15 16 0 0 0 0 0 0 0 0999 V2000 + 2.8093 -1.9600 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 2.8356 -0.4602 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1476 0.2669 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.5500 0.3125 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 5.4333 -0.5058 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 4.1739 1.7667 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2380 -0.4146 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.1214 0.2194 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.1445 -0.8775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.0550 -1.9034 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.4174 -2.1895 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6061 -0.5400 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -4.0445 0.8945 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.0214 1.9915 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5599 1.6539 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 1 0 0 0 0 + 7 10 2 0 0 0 0 + 8 9 1 0 0 0 0 + 15 8 2 0 0 0 0 + 9 11 1 0 0 0 0 + 9 12 2 0 0 0 0 + 11 10 1 0 0 0 0 + 12 13 1 0 0 0 0 + 13 14 2 0 0 0 0 + 14 15 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tryptophan.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tryptophan.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tyrosine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tyrosine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tyrosine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,31 @@ +Tyrosine + CDK 1/19/10,16:26 + + 13 13 0 0 0 0 0 0 0 0999 V2000 + 0.9092 -2.7648 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6816 -1.4790 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.1814 -1.5050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.9543 -0.1671 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9087 -2.8169 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 3.9538 -0.2192 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5455 -0.1411 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.2729 1.1707 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.7726 1.1968 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.5451 -0.0891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.8177 -1.4009 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3179 -1.4269 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -5.0448 -0.0630 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 3 5 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 12 7 1 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 10 13 1 0 0 0 0 + 11 12 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tyrosine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/tyrosine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/valine.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/valine.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/valine.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,20 @@ +Valine + CDK 1/19/10,16:26 + + 8 7 0 0 0 0 0 0 0 0999 V2000 + -0.8119 0.8028 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.7880 2.3027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5229 3.0318 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8098 2.2612 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 0.5468 4.5317 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0749 3.0733 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.3857 2.3441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.0510 4.5731 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 6 1 0 0 0 0 + 3 4 2 0 0 0 0 + 3 5 1 0 0 0 0 + 6 7 1 0 0 0 0 + 6 8 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/valine.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Amino_Acids/valine.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/alloc.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/alloc.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/alloc.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,18 @@ +Alloc + CDK 2/11/10,13:24 + + 7 6 0 0 0 0 0 0 0 0999 V2000 + 2.5788 0.3376 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0122 1.0533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6980 1.4569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9066 2.8276 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2809 1.4569 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -0.2868 0.3033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.5446 0.9924 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 1 3 1 0 0 0 0 + 3 4 2 0 0 0 0 + 3 5 1 0 0 0 0 + 2 6 1 0 0 0 0 + 6 7 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/alloc.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/alloc.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/boc.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/boc.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/boc.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,20 @@ +Boc + CDK 2/11/10,13:23 + + 8 7 0 0 0 0 0 0 0 0999 V2000 + -0.8515 1.7494 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2766 1.4869 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.2390 -0.1256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6516 3.1558 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.8335 1.5619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.2677 0.6301 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.5238 -0.7406 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.8506 0.6301 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 2 4 1 0 0 0 0 + 2 5 1 0 0 0 0 + 1 6 1 0 0 0 0 + 6 7 2 0 0 0 0 + 6 8 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/boc.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/boc.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/cbz.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/cbz.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/cbz.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,27 @@ +Cbz + CDK 2/11/10,13:23 + + 11 11 0 0 0 0 0 0 0 0999 V2000 + 2.5788 0.3376 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1.0122 1.0533 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4032 0.5251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.6980 1.4569 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.9066 2.8276 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 5.2809 1.4569 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7857 1.3233 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1681 0.5251 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.1681 -1.0712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.7857 -1.8694 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -0.4032 -1.0712 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 0 0 0 + 2 3 1 0 0 0 0 + 1 4 1 0 0 0 0 + 4 5 2 0 0 0 0 + 4 6 1 0 0 0 0 + 3 7 1 0 0 0 0 + 7 8 2 0 0 0 0 + 8 9 1 0 0 0 0 + 9 10 2 0 0 0 0 + 10 11 1 0 0 0 0 + 11 3 2 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/cbz.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/cbz.png ___________________________________________________________________ Added: svn:mime-type + application/octet-stream Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/dmt.mol =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/dmt.mol (rev 0) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/dmt.mol 2010-02-11 16:17:50 UTC (rev 15384) @@ -0,0 +1,55 @@ +Dimethoxytrityl + CDK 2/11/10,13:26 + + 24 26 0 0 0 0 0 0 0 0999 V2000 + -0.0048 -2.0839 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3241 -1.3167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3336 -1.3167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.3241 0.2177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.3336 0.2177 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.6625 -2.0839 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -0.0048 0.9849 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.3933 1.4768 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -3.9913 -1.3167 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4942 2.4745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6433 2.7758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4540 0.4161 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 + 3.4942 4.0089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8231 1.7073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3145 2.0086 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.6433 4.3102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 4.8231 4.7761 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1519 2.4745 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0144 2.7758 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 0.3145 5.0775 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 6.1519 4.0089 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -1.0144 4.3102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + -2.3464 5.0793 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + -3.6784 4.3102 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 2 0 0 0 0 + 3 1 1 0 0 0 0 + 2 4 1 0 0 0 0 + 5 3 2 0 0 0 0 + 3 6 1 0 0 0 0 + 4 7 2 0 0 0 0 + 8 4 1 0 0 0 0 + 7 5 1 0 0 0 0 + 6 9 1 0 0 0 0 + 8 10 1 0 0 0 0 + 8 11 1 0 0 0 0 + 8 12 1 0 0 0 0 + 13 10 2 0 0 0 0 + 10 14 1 0 0 0 0 + 15 11 2 0 0 0 0 + 11 16 1 0 0 0 0 + 17 13 1 0 0 0 0 + 14 18 2 0 0 0 0 + 19 15 1 0 0 0 0 + 16 20 2 0 0 0 0 + 21 17 2 0 0 0 0 + 18 21 1 0 0 0 0 + 22 19 2 0 0 0 0 + 20 22 1 0 0 0 0 + 22 23 1 0 0 0 0 + 23 24 1 0 0 0 0 +M END Added: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/templates/Protecting_Groups/dmt.png =================================================================== (Binary files differ) Property changes on: jchempaint/branches/3_0/src... [truncated message content] |
From: <sh...@us...> - 2010-02-24 16:11:10
|
Revision: 15436 http://cdk.svn.sourceforge.net/cdk/?rev=15436&view=rev Author: shk3 Date: 2010-02-24 15:31:00 +0000 (Wed, 24 Feb 2010) Log Message: ----------- solves bug #75 Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/controller/ControllerHub.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/controller/ControllerHub.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/controller/ControllerHub.java 2010-02-24 14:52:22 UTC (rev 15435) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/controller/ControllerHub.java 2010-02-24 15:31:00 UTC (rev 15436) @@ -425,6 +425,7 @@ //OK TODO this could do with less partitioning public IAtomContainer removeAtom(IAtom atom) { IAtomContainer ac = removeAtomWithoutUndo(atom); + removeEmptyContainers(chemModel); if(getUndoRedoFactory()!=null && getUndoRedoHandler()!=null){ IUndoRedoable undoredo = getUndoRedoFactory().getRemoveAtomsAndBondsEdit(getIChemModel(), ac, "Remove Atom",this); getUndoRedoHandler().postEdit(undoredo); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java 2010-02-24 14:52:22 UTC (rev 15435) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/FieldTablePanel.java 2010-02-24 15:31:00 UTC (rev 15436) @@ -62,6 +62,7 @@ if(hasTabs){ setLayout(new BorderLayout()); tabbedPane = new JTabbedPane(); + tabbedPane.setName("tabs"); add( tabbedPane, BorderLayout.CENTER ); }else{ setLayout(new GridBagLayout()); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java 2010-02-24 14:52:22 UTC (rev 15435) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/ModifyRenderOptionsDialog.java 2010-02-24 15:31:00 UTC (rev 15436) @@ -82,6 +82,7 @@ JPanel buttonPanel = new JPanel(); buttonPanel.setLayout ( new FlowLayout(FlowLayout.RIGHT) ); JButton ok = new JButton(GT._("OK")); + ok.setName("ok"); ok.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { OKPressed(); @@ -90,6 +91,7 @@ buttonPanel.add( ok ); getRootPane().setDefaultButton(ok); JButton apply = new JButton(GT._("Apply")); + apply.setName("apply"); apply.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { ApplyPressed(false); @@ -97,6 +99,7 @@ ); buttonPanel.add( apply ); JButton cancel = new JButton(GT._("Cancel")); + cancel.setName("cancel"); cancel.addActionListener(new ActionListener() { public void actionPerformed(ActionEvent e) { closeFrame(); Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java 2010-02-24 14:52:22 UTC (rev 15435) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/dialog/editor/PropertiesModelEditor.java 2010-02-24 15:31:00 UTC (rev 15436) @@ -317,6 +317,7 @@ languagesstrings[i] = gtlanguages[i].language; } language = new JComboBox(languagesstrings); + language.setName("language"); for(int i=0;i<languagesstrings.length;i++){ if(gtlanguages[i].code.equals(GT.getLanguage())) language.setSelectedIndex(i); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <sh...@us...> - 2010-04-16 11:18:44
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Revision: 15520 http://cdk.svn.sourceforge.net/cdk/?rev=15520&view=rev Author: shk3 Date: 2010-04-16 11:18:38 +0000 (Fri, 16 Apr 2010) Log Message: ----------- Some changes which fixes stuff which got broken while adopting to new cdk (mainly usage of IAtomContainer instead of IMolecule) Modified Paths: -------------- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java jchempaint/branches/3_0/src/main/org/openscience/jchempaint/renderer/Renderer.java Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java 2010-04-16 11:18:06 UTC (rev 15519) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/application/JChemPaint.java 2010-04-16 11:18:38 UTC (rev 15520) @@ -189,7 +189,7 @@ .newInstance(IChemModel.class); chemModel.setMoleculeSet(chemModel.getBuilder().newInstance(IMoleculeSet.class)); chemModel.getMoleculeSet().addAtomContainer( - chemModel.getBuilder().newInstance(IAtomContainer.class)); + chemModel.getBuilder().newInstance(IMolecule.class)); showInstance(chemModel, GT._("Untitled-") + (instancecounter++), debug); } Modified: jchempaint/branches/3_0/src/main/org/openscience/jchempaint/renderer/Renderer.java =================================================================== --- jchempaint/branches/3_0/src/main/org/openscience/jchempaint/renderer/Renderer.java 2010-04-16 11:18:06 UTC (rev 15519) +++ jchempaint/branches/3_0/src/main/org/openscience/jchempaint/renderer/Renderer.java 2010-04-16 11:18:38 UTC (rev 15520) @@ -320,7 +320,7 @@ return paintMoleculeSet(moleculeSet, drawVisitor); } - if (moleculeSet != null && reactionSet != null) { + if (moleculeSet != null && moleculeSet.getAtomContainerCount()>0 && reactionSet != null) { Rectangle2D totalBounds = Renderer.calculateBounds(reactionSet); totalBounds = totalBounds.createUnion( Renderer.calculateBounds(moleculeSet)); This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |