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[Bioclipse-commit] SF.net SVN: bioclipse:[7408] bioclipse2/trunk
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From: <eg...@us...> - 2008-10-24 14:56:51
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Revision: 7408
http://bioclipse.svn.sourceforge.net/bioclipse/?rev=7408&view=rev
Author: egonw
Date: 2008-10-24 14:56:46 +0000 (Fri, 24 Oct 2008)
Log Message:
-----------
Added jmol.minimize
Modified Paths:
--------------
bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.core/src/org/openscience/cdk/config/IsotopeFactory.java
bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/IJmolManager.java
bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/JmolManager.java
bioclipse2/trunk/plugins/net.bioclipse.ui/bioclipse.product
Modified: bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.core/src/org/openscience/cdk/config/IsotopeFactory.java
===================================================================
--- bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.core/src/org/openscience/cdk/config/IsotopeFactory.java 2008-10-24 14:33:00 UTC (rev 7407)
+++ bioclipse2/trunk/cdk-externals/trunk/org.openscience.cdk.core/src/org/openscience/cdk/config/IsotopeFactory.java 2008-10-24 14:56:46 UTC (rev 7408)
@@ -88,7 +88,7 @@
String errorMessage = "There was a problem getting org.openscience.cdk." +
"config.isotopes.xml as a stream";
try {
- String configFile = "org/openscience/cdk/config/data/isotopes.xml";
+ String configFile = "/org/openscience/cdk/config/data/isotopes.xml";
if (debug) logger.debug("Getting stream for ", configFile);
ins = this.getClass().getClassLoader().getResourceAsStream(configFile);
} catch (Exception exception) {
Modified: bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/IJmolManager.java
===================================================================
--- bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/IJmolManager.java 2008-10-24 14:33:00 UTC (rev 7407)
+++ bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/IJmolManager.java 2008-10-24 14:56:46 UTC (rev 7408)
@@ -16,6 +16,7 @@
import net.bioclipse.core.PublishedMethod;
import net.bioclipse.core.Recorded;
import net.bioclipse.core.business.IBioclipseManager;
+import net.bioclipse.core.jobs.Job;
public interface IJmolManager extends IBioclipseManager{
@@ -61,4 +62,9 @@
@PublishedMethod( methodSummary = "Causes active jmol to stop " +
"spinning molecule" )
public void spinOff();
+
+ @Recorded
+ @Job
+ @PublishedMethod(methodSummary = "Optimizes the geometry of the structure in the active JmolEditor" )
+ public void minimize();
}
Modified: bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/JmolManager.java
===================================================================
--- bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/JmolManager.java 2008-10-24 14:33:00 UTC (rev 7407)
+++ bioclipse2/trunk/plugins/net.bioclipse.jmol/src/net/bioclipse/jmol/business/JmolManager.java 2008-10-24 14:56:46 UTC (rev 7408)
@@ -130,4 +130,8 @@
public void spinOn() {
run( "spin" );
}
+
+ public void minimize() {
+ run("minimize");
+ }
}
Modified: bioclipse2/trunk/plugins/net.bioclipse.ui/bioclipse.product
===================================================================
--- bioclipse2/trunk/plugins/net.bioclipse.ui/bioclipse.product 2008-10-24 14:33:00 UTC (rev 7407)
+++ bioclipse2/trunk/plugins/net.bioclipse.ui/bioclipse.product 2008-10-24 14:56:46 UTC (rev 7408)
@@ -78,49 +78,49 @@
<plugin id="org.eclipse.core.expressions"/>
<plugin id="org.eclipse.core.filebuffers"/>
<plugin id="org.eclipse.core.filesystem"/>
- <plugin id="org.eclipse.core.filesystem.hpux.ia64_32" fragment="true"/>
- <plugin id="org.eclipse.core.filesystem.linux.ppc" fragment="true"/>
+ <plugin id="org.eclipse.core.filesystem.hpux.ia64_32"/>
+ <plugin id="org.eclipse.core.filesystem.linux.ppc"/>
<plugin id="org.eclipse.core.filesystem.linux.x86" fragment="true"/>
- <plugin id="org.eclipse.core.filesystem.linux.x86_64" fragment="true"/>
- <plugin id="org.eclipse.core.filesystem.macosx" fragment="true"/>
- <plugin id="org.eclipse.core.filesystem.solaris.sparc" fragment="true"/>
- <plugin id="org.eclipse.core.filesystem.win32.x86" fragment="true"/>
+ <plugin id="org.eclipse.core.filesystem.linux.x86_64"/>
+ <plugin id="org.eclipse.core.filesystem.macosx"/>
+ <plugin id="org.eclipse.core.filesystem.solaris.sparc"/>
+ <plugin id="org.eclipse.core.filesystem.win32.x86"/>
<plugin id="org.eclipse.core.jobs"/>
<plugin id="org.eclipse.core.net"/>
<plugin id="org.eclipse.core.net.linux.x86" fragment="true"/>
- <plugin id="org.eclipse.core.net.win32.x86" fragment="true"/>
+ <plugin id="org.eclipse.core.net.win32.x86"/>
<plugin id="org.eclipse.core.resources"/>
<plugin id="org.eclipse.core.resources.compatibility" fragment="true"/>
- <plugin id="org.eclipse.core.resources.win32.x86" fragment="true"/>
+ <plugin id="org.eclipse.core.resources.win32.x86"/>
<plugin id="org.eclipse.core.runtime"/>
- <plugin id="org.eclipse.core.runtime.compatibility.registry"/>
+ <plugin id="org.eclipse.core.runtime.compatibility.registry" fragment="true"/>
<plugin id="org.eclipse.equinox.app"/>
<plugin id="org.eclipse.equinox.common"/>
<plugin id="org.eclipse.equinox.preferences"/>
<plugin id="org.eclipse.equinox.registry"/>
<plugin id="org.eclipse.equinox.security"/>
- <plugin id="org.eclipse.equinox.security.macosx" fragment="true"/>
- <plugin id="org.eclipse.equinox.security.win32.x86" fragment="true"/>
+ <plugin id="org.eclipse.equinox.security.macosx"/>
+ <plugin id="org.eclipse.equinox.security.win32.x86"/>
<plugin id="org.eclipse.help"/>
<plugin id="org.eclipse.jface"/>
<plugin id="org.eclipse.jface.databinding"/>
<plugin id="org.eclipse.jface.text"/>
<plugin id="org.eclipse.osgi"/>
<plugin id="org.eclipse.swt"/>
- <plugin id="org.eclipse.swt.carbon.macosx" fragment="true"/>
- <plugin id="org.eclipse.swt.gtk.linux.ppc" fragment="true"/>
+ <plugin id="org.eclipse.swt.carbon.macosx"/>
+ <plugin id="org.eclipse.swt.gtk.linux.ppc"/>
<plugin id="org.eclipse.swt.gtk.linux.x86" fragment="true"/>
- <plugin id="org.eclipse.swt.gtk.linux.x86_64" fragment="true"/>
- <plugin id="org.eclipse.swt.gtk.solaris.sparc" fragment="true"/>
- <plugin id="org.eclipse.swt.motif.aix.ppc" fragment="true"/>
- <plugin id="org.eclipse.swt.motif.hpux.ia64_32" fragment="true"/>
- <plugin id="org.eclipse.swt.win32.win32.x86" fragment="true"/>
- <plugin id="org.eclipse.swt.win32.win32.x86_64" fragment="true"/>
- <plugin id="org.eclipse.swt.wpf.win32.x86" fragment="true"/>
+ <plugin id="org.eclipse.swt.gtk.linux.x86_64"/>
+ <plugin id="org.eclipse.swt.gtk.solaris.sparc"/>
+ <plugin id="org.eclipse.swt.motif.aix.ppc"/>
+ <plugin id="org.eclipse.swt.motif.hpux.ia64_32"/>
+ <plugin id="org.eclipse.swt.win32.win32.x86"/>
+ <plugin id="org.eclipse.swt.win32.win32.x86_64"/>
+ <plugin id="org.eclipse.swt.wpf.win32.x86"/>
<plugin id="org.eclipse.text"/>
<plugin id="org.eclipse.ui"/>
<plugin id="org.eclipse.ui.browser"/>
- <plugin id="org.eclipse.ui.carbon" fragment="true"/>
+ <plugin id="org.eclipse.ui.carbon"/>
<plugin id="org.eclipse.ui.cheatsheets"/>
<plugin id="org.eclipse.ui.editors"/>
<plugin id="org.eclipse.ui.forms"/>
@@ -131,13 +131,13 @@
<plugin id="org.eclipse.ui.net"/>
<plugin id="org.eclipse.ui.views"/>
<plugin id="org.eclipse.ui.views.properties.tabbed"/>
- <plugin id="org.eclipse.ui.win32" fragment="true"/>
+ <plugin id="org.eclipse.ui.win32"/>
<plugin id="org.eclipse.ui.workbench"/>
<plugin id="org.eclipse.ui.workbench.texteditor"/>
<plugin id="org.eclipse.update.configurator"/>
<plugin id="org.eclipse.update.core"/>
<plugin id="org.eclipse.update.core.linux" fragment="true"/>
- <plugin id="org.eclipse.update.core.win32" fragment="true"/>
+ <plugin id="org.eclipse.update.core.win32"/>
<plugin id="org.eclipse.update.ui"/>
<plugin id="org.springframework.bundle.osgi.core"/>
<plugin id="org.springframework.bundle.osgi.extender"/>
@@ -154,8 +154,8 @@
</plugins>
<features>
- <feature id="net.bioclipse_feature" version="2.0.0.A20080808"/>
- <feature id="net.bioclipse.chemoinformatics_feature" version="2.0.0.A20080903"/>
+ <feature id="net.bioclipse.chemoinformatics_feature" version="2.0.0.A20081022"/>
+ <feature id="net.bioclipse_feature" version="2.0.0.A20081022"/>
</features>
</product>
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