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[Cdk-commits] SF.net SVN: cdk:[14732] jchempaint/trunk
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From: <sh...@us...> - 2009-08-17 17:06:50
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Revision: 14732
http://cdk.svn.sourceforge.net/cdk/?rev=14732&view=rev
Author: shk3
Date: 2009-08-17 17:06:44 +0000 (Mon, 17 Aug 2009)
Log Message:
-----------
everyting in jcp needed for the undefined stereo stuff
Modified Paths:
--------------
jchempaint/trunk/.classpath
jchempaint/trunk/src/main/org/openscience/jchempaint/action/ChangeModeAction.java
jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties
Added Paths:
-----------
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/small-bin/undefined_bond.gif
jchempaint/trunk/src/main/org/openscience/jchempaint/resources/small-bin/undefined_stereo_bond.gif
Modified: jchempaint/trunk/.classpath
===================================================================
--- jchempaint/trunk/.classpath 2009-08-17 14:45:41 UTC (rev 14731)
+++ jchempaint/trunk/.classpath 2009-08-17 17:06:44 UTC (rev 14732)
@@ -12,6 +12,6 @@
<classpathentry kind="lib" path="lib/fest-util-1.1.jar"/>
<classpathentry kind="lib" path="lib/fest-assert-1.1.jar"/>
<classpathentry kind="lib" path="lib/fest-reflect-1.1.jar"/>
- <classpathentry combineaccessrules="false" kind="src" path="/org.openscience.cdk"/>
+ <classpathentry combineaccessrules="false" kind="src" path="/jchempaint-primary"/>
<classpathentry kind="output" path="bin"/>
</classpath>
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/action/ChangeModeAction.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/action/ChangeModeAction.java 2009-08-17 14:45:41 UTC (rev 14731)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/action/ChangeModeAction.java 2009-08-17 17:06:44 UTC (rev 14732)
@@ -107,6 +107,14 @@
hub.setActiveDrawModule(new AlterBondStereoModule(
hub, Direction.DOWN));
hub.getController2DModel().setDrawElement("C");
+ } else if (type.equals("undefined_bond")) {
+ hub.setActiveDrawModule(new AlterBondStereoModule(
+ hub, Direction.UNDEFINED));
+ hub.getController2DModel().setDrawElement("C");
+ } else if (type.equals("undefined_stereo_bond")) {
+ hub.setActiveDrawModule(new AlterBondStereoModule(
+ hub, Direction.EZ_UNDEFINED));
+ hub.getController2DModel().setDrawElement("C");
} else if (type.equals("triangle")) {
hub.setActiveDrawModule(new AddRingModule(hub, 3, false));
hub.getController2DModel().setDrawElement("C");
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2009-08-17 14:45:41 UTC (rev 14731)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/action/CopyPasteAction.java 2009-08-17 17:06:44 UTC (rev 14732)
@@ -64,6 +64,7 @@
import org.openscience.cdk.interfaces.IMolecule;
import org.openscience.cdk.interfaces.IReaction;
import org.openscience.cdk.io.IChemObjectWriter;
+import org.openscience.cdk.io.INChIPlainTextReader;
import org.openscience.cdk.io.ISimpleChemObjectReader;
import org.openscience.cdk.io.MDLV2000Reader;
import org.openscience.cdk.io.MDLWriter;
@@ -193,23 +194,21 @@
);
sdg.generateCoordinates();
} catch (Exception ex) {
- if (content.startsWith("InChI")) { // handle it as an InChI
+ if (content.indexOf("INChI")>-1) { // handle it as an InChI
try {
- InChIGeneratorFactory inchiFactory = new InChIGeneratorFactory();
- InChIToStructure inchiToStructure = inchiFactory.getInChIToStructure(content,jcpPanel.getChemModel().getBuilder());
- INCHI_RET status = inchiToStructure.getReturnStatus();
- if (status == INCHI_RET.OKAY) {
- IAtomContainer atomContainer = inchiToStructure.getAtomContainer();
- toPaste = atomContainer.getBuilder().newMolecule(atomContainer);
- StructureDiagramGenerator sdg =
- new StructureDiagramGenerator((IMolecule)toPaste);
+ StringReader sr = new StringReader(content);
+ INChIPlainTextReader inchireader = new INChIPlainTextReader(sr);
+ IChemFile mol = DefaultChemObjectBuilder.getInstance().newChemFile();
+ toPaste = ((IChemFile) inchireader.read(mol)).getChemSequence(0).getChemModel(0).getMoleculeSet().getMolecule(0);
+ StructureDiagramGenerator sdg =
+ new StructureDiagramGenerator((IMolecule)toPaste);
- sdg.setTemplateHandler(
- new TemplateHandler(toPaste.getBuilder())
- );
- sdg.generateCoordinates(); }
- } catch (Exception e2) {
- //we do nothing
+ sdg.setTemplateHandler(
+ new TemplateHandler(toPaste.getBuilder())
+ );
+ sdg.generateCoordinates();
+ } catch (Exception e2) {
+ e2.printStackTrace();
}
}
}
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2009-08-17 14:45:41 UTC (rev 14731)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_applet.properties 2009-08-17 17:06:44 UTC (rev 14732)
@@ -103,6 +103,6 @@
uppertoolbar=select lasso eraser undo redo zoomin zoomout plus minus move
righttoolbar=periodictable enterelement C H O N P S F Cl Br I
lowertoolbar=triangle square pentagon hexagon heptagon octagon benzene
-lefttoolbar=bond up_bond down_bond
+lefttoolbar=bond up_bond down_bond undefined_bond undefined_stereo_bond
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-08-17 14:45:41 UTC (rev 14731)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JCPGUI_stable.properties 2009-08-17 17:06:44 UTC (rev 14732)
@@ -100,10 +100,10 @@
# toolbar definition #
#######################################################
-uppertoolbar=select lasso eraser undo redo plus minus move
+uppertoolbar=select lasso eraser undo redo zoomin zoomout plus minus move
righttoolbar=periodictable enterelement C H O N P S F Cl Br I
lowertoolbar=triangle square pentagon hexagon heptagon octagon benzene
-lefttoolbar=bond up_bond down_bond
+lefttoolbar=bond up_bond down_bond undefined_bond undefined_stereo_bond
#open saveAs cyclesymbol move cleanup atomatommapping
Modified: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties
===================================================================
--- jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties 2009-08-17 14:45:41 UTC (rev 14731)
+++ jchempaint/trunk/src/main/org/openscience/jchempaint/resources/JChemPaintResources.properties 2009-08-17 17:06:44 UTC (rev 14732)
@@ -64,6 +64,8 @@
rotationImage=resources/small-bin/rotation.gif
up_bondImage=resources/small-bin/up_bond.gif
down_bondImage=resources/small-bin/down_bond.gif
+undefined_bondImage=resources/small-bin/undefined_bond.gif
+undefined_stereo_bondImage=resources/small-bin/undefined_stereo_bond.gif
normalizeImage=resources/small-bin/normalize.gif
undoImage=resources/small-bin/undo.gif
redoImage=resources/small-bin/redo.gif
@@ -211,6 +213,8 @@
benzeneAction=org.openscience.jchempaint.action.ChangeModeAction@benzene
up_bondAction=org.openscience.jchempaint.action.ChangeModeAction@up_bond
down_bondAction=org.openscience.jchempaint.action.ChangeModeAction@down_bond
+undefined_bondAction=org.openscience.jchempaint.action.ChangeModeAction@undefined_bond
+undefined_stereo_bondAction=org.openscience.jchempaint.action.ChangeModeAction@undefined_stereo_bond
atomatommappingAction=org.openscience.jchempaint.action.ChangeModeAction@atomatommapping
#######################################################
@@ -238,6 +242,8 @@
rotationLabel=rotation
up_bondLabel=up_bond
down_bondLabel=down_bond
+undefined_bondLabel=undefined_bond
+undefined_stereo_bondLabel=undefined_stereo_bond
normalizeLabel=normalize
undoLabel=undo
redoLabel=redo
Added: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/small-bin/undefined_bond.gif
===================================================================
(Binary files differ)
Property changes on: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/small-bin/undefined_bond.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/small-bin/undefined_stereo_bond.gif
===================================================================
(Binary files differ)
Property changes on: jchempaint/trunk/src/main/org/openscience/jchempaint/resources/small-bin/undefined_stereo_bond.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
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