Undelete Jmol

9 files changed, 602 insertions, 0 deletions

diff --git a/sci-chemistry/jmol/ChangeLog b/sci-chemistry/jmol/ChangeLog
new file mode 100644
index 000000000..5c8defcb9
--- /dev/null
+++ b/sci-chemistry/jmol/ChangeLog
@@ -0,0 +1,51 @@
+# ChangeLog for sci-chemistry/jmol
+# Copyright 1999-2009 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+*jmol-11.6 (23 Apr 2009)
+
+  23 Apr 2009; Justin Lecher (jlec) <jlec@j-schmitz.net>
+  +files/jmol-11.6-manifest.patch, +files/jmol-11.6-nointl.patch,
+  +files/caffeine.xyz, +files/index.html,
+  +files/selfSignedCertificate.store, +metadata.xml, +jmol-11.6.ebuild:
+  version bump
+
+  05 Oct 2008; Petteri Räty <betelgeuse@gentoo.org> jmol-11.0.3-r1.ebuild:
+  Add slot deps.
+
+  06 Aug 2008; Ulrich Mueller <ulm@gentoo.org> metadata.xml:
+  Add USE flag description to metadata wrt GLEP 56.
+
+  15 Apr 2008; Donnie Berkholz <dberkholz@gentoo.org>;
+  jmol-11.0.3-r1.ebuild:
+  Fix conditional webapp to not pull in webapp-config when it's unneeded.
+
+  31 Dec 2007; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
+  Fixing my email address.
+
+  02 Sep 2007; <je_fro@gentoo.org> jmol-11.0.3-r1.ebuild:
+  Fix conditional code moving netscape.jar wrt bug #191032
+
+  05 Jul 2007; Jeff Gardner <je_fro@gentoo.org> jmol-11.0.3-r1.ebuild:
+  Protecting netscape.jar from removal on amd64.
+
+  22 Jun 2007; Jeff Gardner <je_fro@gentoo.org> jmol-11.0.3-r1.ebuild:
+  Removing ~amd64 for jmol-11.0.3-r1 because the bundled netscape.jar is still
+  required on this arch.
+
+*jmol-11.0.3-r1 (22 Jun 2007)
+
+  22 Jun 2007; Vlastimil Babka <caster@gentoo.org> jmol-11.0.3.ebuild,
+  +jmol-11.0.3-r1.ebuild:
+  Revbump for java-related fixes - install jars we've built and not the
+  bundled ones, don't absorb dependencies' classes, depend only on what's
+  actually needed, use java dolauncher instead of supplied one. Keyword ~x86.
+
+*jmol-11.0.3 (15 Jun 2007)
+
+  15 Jun 2007; Jeff Gardner <je_fro@gentoo.org>
+  +files/jmol-11.0.3-manifest.patch, +files/jmol-11.0.3-nointl.patch,
+  +files/caffeine.xyz, +files/index.html,
+  +files/selfSignedCertificate.store, +jmol-11.0.3.ebuild:
+  Initial import of jmol-11.0.3.
+
diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest
new file mode 100644
index 000000000..483a9e0fa
--- /dev/null
+++ b/sci-chemistry/jmol/Manifest
@@ -0,0 +1,9 @@
+AUX caffeine.xyz 1116 RMD160 92b432c6584cd927fa1bfb155ea41011ab7a82d8 SHA1 d0f35a447b333b8ea51c15ab0ac67d887556e43c SHA256 45a9afac0b247780595944a98f8e1076a7e7e0dbb3e02cb54cecb0764b1cb67f
+AUX index.html 328 RMD160 60d2a573c228e018a864fd7d9cfc7554264ccd6b SHA1 7ab256d768d3a4da43b5e497dfb1c3a53a8068a9 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451
+AUX jmol-11.6-manifest.patch 3726 RMD160 03e1e11fdd29fb63de15934fff166348577084b0 SHA1 925a957bc30e1fbab9fd773dc07f83411f667d30 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd
+AUX jmol-11.6-nointl.patch 11528 RMD160 3d36d42b4cf07330f7fac6357c84d2a08e220294 SHA1 9d9588b2179871bf07438acb8f7e3a99dcf2f234 SHA256 c16cd2d14434f273ba99ec03209814e1028e8ff2425d9ef8789f196c38aa5d5d
+AUX selfSignedCertificate.store 1516 RMD160 583b7bab5578e1e32f649388b7009dc654df1199 SHA1 88d9123bdc1a376ba00e00c8abef4751adefe3a5 SHA256 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5
+DIST jmol-11.6-full.tar.gz 26294021 RMD160 6f7f86b8debcfd1c89f5c40d902713e5ae2da0a3 SHA1 50e9be1b8cdb1f3f29f97a9ad97611348d2308a1 SHA256 ffabdbcb9d656fe365136da1ad5f40830a4882d355a9efde93fa29383d2bb70f
+EBUILD jmol-11.6.ebuild 3205 RMD160 4b94f8dc026684d7720c74a2d2868df87ad18123 SHA1 7e120bbc6e353301ca503d5d7767fbbf10e79651 SHA256 4172ab00b35ba277a137411a90dcba949d728221cf4cd70a6602fcc55692f1fa
+MISC ChangeLog 1897 RMD160 b6291e1d06084a8b942b98922cecb88e20a2a2bd SHA1 ced7fc44560413b7e85e4102a7fc0126b6eee216 SHA256 f998872cd30a470d0e9a8dd2b350e61de877245f2950be64be08eb33ba80a237
+MISC metadata.xml 355 RMD160 2c279aeab8c72ba2ac5573ccd72a69726166c638 SHA1 3cf53d45ceec1ed494d8c7312f60933657356e48 SHA256 a26dbd57c95fd7f37b7ade989dca90933da7f75fe7c27ac54c030d275edf12b4
diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz
new file mode 100644
index 000000000..f0325b049
--- /dev/null
+++ b/sci-chemistry/jmol/files/caffeine.xyz
@@ -0,0 +1,26 @@
+24
+Caffeine
+H      -3.3804130    -1.1272367     0.5733036
+N       0.9668296    -1.0737425    -0.8198227
+C       0.0567293     0.8527195     0.3923156
+N      -1.3751742    -1.0212243    -0.0570552
+C      -1.2615018     0.2590713     0.5234135
+C      -0.3068337    -1.6836331    -0.7169344
+C       1.1394235     0.1874122    -0.2700900
+N       0.5602627     2.0839095     0.8251589
+O      -0.4926797    -2.8180554    -1.2094732
+C      -2.6328073    -1.7303959    -0.0060953
+O      -2.2301338     0.7988624     1.0899730
+H       2.5496990     2.9734977     0.6229590
+C       2.0527432    -1.7360887    -1.4931279
+H      -2.4807715    -2.7269528     0.4882631
+H      -3.0089039    -1.9025254    -1.0498023
+H       2.9176101    -1.8481516    -0.7857866
+H       2.3787863    -1.1211917    -2.3743655
+H       1.7189877    -2.7489920    -1.8439205
+C      -0.1518450     3.0970046     1.5348347
+C       1.8934096     2.1181245     0.4193193
+N       2.2861252     0.9968439    -0.2440298
+H      -0.1687028     4.0436553     0.9301094
+H       0.3535322     3.2979060     2.5177747
+H      -1.2074498     2.7537592     1.7203047
diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html
new file mode 100644
index 000000000..35a5d4921
--- /dev/null
+++ b/sci-chemistry/jmol/files/index.html
@@ -0,0 +1,14 @@
+<html>
+  <head>
+    <title>Jmol Test Page</title>
+      <div align="center"> <b>All the Sugar and Twice the Caffeine.</b> <br><br>
+      <script src="./Jmol.js"></script>
+  </head>
+  <body>
+    <script>
+      jmolInitialize("./"); // REQUIRED
+      jmolApplet(400, "load ./caffeine.xyz");
+    </script></div>
+  </body>
+</html>
+
diff --git a/sci-chemistry/jmol/files/jmol-11.6-manifest.patch b/sci-chemistry/jmol/files/jmol-11.6-manifest.patch
new file mode 100644
index 000000000..3b43c219d
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-11.6-manifest.patch
@@ -0,0 +1,96 @@
+diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt
+--- jmol-11.0.3-orig/manifest/applet0.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet0.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,6 @@
++Main-Class: JmolApplet

++Sealed: true

++

++Name: org/jmol/api/

++Sealed: false

++

+diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt
+--- jmol-11.0.3-orig/manifest/applet1.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet1.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,6 @@
++Name: org/jmol/api/

++Sealed: false

++

++Name: org/jmol/applet/

++Sealed: true

++

+diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt
+--- jmol-11.0.3-orig/manifest/applet2.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet2.txt	2007-05-16 01:56:19.000000000 -0500
+@@ -0,0 +1,3 @@
++Name: javax/vecmath/
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt
+--- jmol-11.0.3-orig/manifest/applet3.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet3.txt	2007-05-16 01:56:47.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/g3d/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt
+--- jmol-11.0.3-orig/manifest/applet4.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet4.txt	2007-05-16 01:57:05.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/adapter/smarter/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt
+--- jmol-11.0.3-orig/manifest/applet5.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet5.txt	2007-05-16 01:57:23.000000000 -0500
+@@ -0,0 +1,4 @@
++Name: org/openscience/jmol/ui/
++Sealed: true
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt
+--- jmol-11.0.3-orig/manifest/applet6.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet6.txt	2007-05-16 01:57:46.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/viewer/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt
+--- jmol-11.0.3-orig/manifest/appletMain.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/appletMain.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,5 @@
++Manifest-Version: 1.0

++Sealed: true

++

++Name: org/jmol/api/

++Sealed: false

+diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt
+--- jmol-11.0.3-orig/manifest/appletMonolithic.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/appletMonolithic.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,7 @@
++Main-Class: JmolApplet

++Sealed: true

++

++Name: org/jmol/api/

++Sealed: false

++

++

+diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt
+--- jmol-11.0.3-orig/manifest/applet.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,2 @@
++Manifest-Version: 1.0

++Sealed: true

+\ No newline at end of file
+diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt
+--- jmol-11.0.3-orig/manifest/application.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/application.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1 @@
++Main-Class: org.openscience.jmol.app.Jmol

+diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt
+--- jmol-11.0.3-orig/manifest/jvxl.txt	1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/jvxl.txt	2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1 @@
++Main-Class: org.openscience.jvxl.Jvxl

diff --git a/sci-chemistry/jmol/files/jmol-11.6-nointl.patch b/sci-chemistry/jmol/files/jmol-11.6-nointl.patch
new file mode 100644
index 000000000..351093faf
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-11.6-nointl.patch
@@ -0,0 +1,274 @@
+--- jmol-11.6/build.xml	2008-10-08 19:03:17.000000000 +0200
++++ jmol-11.6/build.xml.new	2009-04-23 11:05:58.000000000 +0200
+@@ -100,10 +100,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -113,14 +109,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />

+-        </uptodate>

+       </and>

+     </condition>

+     

+@@ -130,14 +118,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolDevelopersGuide.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolDevelopersGuide_fr.docbook.xml"/>

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolDevelopersGuide_de.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -147,14 +127,6 @@
+           <srcfiles dir="doc/source"

+                     includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>

+         </uptodate>

+-        <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>

+-        </uptodate>

+-        <uptodate targetfile="build/doc/JmolAppletGuide_de.html">

+-          <srcfiles dir="doc/source"

+-                    includes="JmolAppletGuide_de.docbook.xml"/>

+-        </uptodate>

+       </and>

+     </condition>

+ 

+@@ -348,17 +320,12 @@
+   </target>

+ 

+   <target name="jar" id="jar"

+-          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">

++          depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">

+     <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >

+       <fileset dir="build/doc/JmolUserGuide">

+         <include name="**/*.html" />

+       </fileset>

+     </copy>

+-    <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >

+-      <fileset dir="build/doc/JmolUserGuide_fr">

+-        <include name="**/*.html" />

+-      </fileset>

+-    </copy>

+     <copy todir="${classes.dir}/org/openscience/jmol/Data" >

+       <fileset dir="build/doc/JmolHistory">

+         <include name="**/*.html" />

+@@ -505,11 +472,6 @@
+ 	      </fileset>

+ 	      <fileset dir="${appletjars.dir}" includes="**/*"/>

+ 	    </jar>	

+-  	    <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" manifest="manifest/applet_i18n.txt" >

+-	      <fileset dir="${applet.classes.dir}">

+-	        <include name="org/jmol/translation/**" />

+-	      </fileset>

+-	    </jar>

+ 	  	<jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">

+ 	      <fileset dir="${applet.classes.dir}">

+ 	        <include name="org/jmol/minimize/**" />

+@@ -606,7 +568,6 @@
+   		<include name="org/jmol/bspt/**" />

+ 		<include name="org/jmol/g3d/**" />

+ 		<include name="org/jmol/geodesic/**" />

+-   		<include name="org/jmol/i18n/**" />

+   		<include name="org/jmol/modelset/**" />

+   		<include name="org/jmol/shape/**" />

+ 		<include name="org/jmol/util/**" />

+@@ -628,7 +589,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />

+-        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_i18n.jar" />

+       </indexjars>

+     </jar>

+     <!-- changes to this must be replicated below for the signed applet -->

+@@ -713,11 +673,6 @@
+              keystore="selfSignedCertificate/selfSignedCertificate.store"

+              storepass="selfSignedCertificate" alias="selfSignedCertificate" />

+     	  	

+-  	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n.jar"

+-             signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar"

+-             keystore="selfSignedCertificate/selfSignedCertificate.store"

+-             storepass="selfSignedCertificate" alias="selfSignedCertificate" />

+-

+     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->

+     <!-- this one must be treated specially because of jar indexing

+          we cannot simply rename the jar file, because the index has

+@@ -743,7 +698,6 @@
+ 		<include name="org/jmol/shape/**" />

+ 		<include name="org/jmol/viewer/**" />

+ 		<include name="org/jmol/util/**" />

+-		<include name="org/jmol/i18n/**" />

+       </fileset>    	

+       <indexjars>

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Popup.jar" />

+@@ -757,7 +711,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />

+-        <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_i18n.jar" />

+       </indexjars>

+     </jar>

+     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"

+@@ -767,7 +720,7 @@
+   </target>

+ 

+   <target name="dist" id="dist"

+-          depends="doc,main-i18n,main,signed-applet">

++          depends="doc,main,signed-applet">

+     <!-- first build binary distribution -->

+     <delete dir="build/dist/jmol-${version}"/>

+     <mkdir dir="build/dist/jmol-${version}"/>

+@@ -824,7 +777,6 @@
+       <fileset dir=".">

+         <include name="applet.classes" />

+         <include name="build.xml" />

+-        <include name="build-i18n.xml" />

+       </fileset>

+     </copy>

+ 

+@@ -903,7 +855,6 @@
+       <fileset dir=".">

+         <include name="apisio.classes" />

+         <include name="build.xml" />

+-        <include name="build-i18n.xml" />

+       </fileset>

+     </copy>

+ 

+@@ -995,7 +946,7 @@
+   <target name="xclean" id="xclean">

+   </target>

+ 

+-  <target name="spotless" id="spotless" depends="clean,spotless-i18n">

++  <target name="spotless" id="spotless" depends="clean">

+     <delete dir="build"/>

+     <delete dir="${javadoc.dir}"/>

+     <delete dir="packaging/rpm/dist"/>

+@@ -1058,16 +1009,6 @@
+       <arg value="../../../doc/source/JmolGuide.docbook.xml" />

+       <arg value="../../${docbook-xsl}/html/chunk.xsl" />

+     </java>

+-    <echo message="Generating user's guide (fr)" />

+-    <mkdir dir="build/doc/JmolUserGuide_fr" />

+-    <java fork="true" dir="build/doc/JmolUserGuide_fr"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <jvmarg value="${proxyHost}" />

+-      <jvmarg value="${proxyPort}" />

+-      <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />

+-      <arg value="../../${docbook-xsl}/html/chunk.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolHistory" id="jmolHistory"

+@@ -1082,26 +1023,6 @@
+       <arg value="../../../doc/source/JmolHistory.xml" />

+       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+     </java>

+-    <echo message="Generating history of changes (fr)" />

+-    <java fork="true" dir="build/doc/JmolHistory"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="ChangeLog_fr.html" />

+-      <arg value="../../../doc/source/JmolHistory_fr.xml" />

+-      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+-      <arg value="lang=fr" />

+-    </java>

+-    <echo message="Generating history of changes (nl)" />

+-    <java fork="true" dir="build/doc/JmolHistory"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="ChangeLog_nl.html" />

+-      <arg value="../../../doc/source/JmolHistory_nl.xml" />

+-      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />

+-      <arg value="lang=nl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"

+@@ -1115,24 +1036,6 @@
+       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />

+       <arg value="../${docbook-xsl}/html/docbook.xsl" />

+     </java>

+-    <echo message="Generating developer's guide (fr)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolDevelopersGuide_fr.html" />

+-      <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+-    <echo message="Generating developer's guide (de)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolDevelopersGuide_de.html" />

+-      <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"

+@@ -1146,24 +1049,6 @@
+       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />

+       <arg value="../${docbook-xsl}/html/docbook.xsl" />

+     </java>

+-    <echo message="Generating applet guide (fr)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolAppletGuide_fr.html" />

+-      <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+-    <echo message="Generating applet guide (de)" />

+-    <java fork="true" dir="build/doc"

+-          classname="com.icl.saxon.StyleSheet"

+-          classpath="${lib.dir}/saxon.jar" >

+-      <arg value="-o" />

+-      <arg value="JmolAppletGuide_de.html" />

+-      <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />

+-      <arg value="../${docbook-xsl}/html/docbook.xsl" />

+-    </java>

+   </target>

+ 

+   <target name="test" id="test" depends="main,compile-tests">

+@@ -1195,12 +1080,4 @@
+     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />

+   </target>

+ 

+-  <!-- i18n stuff -->

+-  <target name="main-i18n" depends="classes">

+-    <ant antfile="build-i18n.xml" target="main-i18n"/>

+-  </target>

+-  <target name="spotless-i18n">

+-    <ant antfile="build-i18n.xml" target="spotless-i18n"/>

+-  </target>

+-

+ </project>

diff --git a/sci-chemistry/jmol/files/selfSignedCertificate.store b/sci-chemistry/jmol/files/selfSignedCertificate.store
new file mode 100644
index 000000000..a7b0ccb86
--- /dev/null
+++ b/sci-chemistry/jmol/files/selfSignedCertificate.store
diff --git a/sci-chemistry/jmol/jmol-11.6.ebuild b/sci-chemistry/jmol/jmol-11.6.ebuild
new file mode 100644
index 000000000..1409f461e
--- /dev/null
+++ b/sci-chemistry/jmol/jmol-11.6.ebuild
@@ -0,0 +1,119 @@
+# Copyright 1999-2009 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+EAPI=1
+WEBAPP_OPTIONAL="yes"
+
+inherit eutils webapp java-pkg-2 java-ant-2
+
+DESCRIPTION="Jmol is a java molecular viever for 3-D chemical structures."
+SRC_URI="mirror://sourceforge/${PN}/${P}-full.tar.gz"
+HOMEPAGE="http://jmol.sourceforge.net/"
+KEYWORDS="~x86 ~amd64"
+LICENSE="LGPL-2.1"
+
+IUSE="client-only vhosts"
+
+WEBAPP_MANUAL_SLOT="yes"
+SLOT="0"
+
+COMMON_DEP="dev-java/commons-cli:1
+	dev-java/itext:0
+	sci-libs/jmol-acme:0
+	sci-libs/vecmath-objectclub:0"
+
+RDEPEND=">=virtual/jre-1.4
+	${COMMON_DEP}"
+DEPEND=">=virtual/jdk-1.4
+	!client-only? ( ${WEBAPP_DEPEND} )
+	${COMMON_DEP}"
+
+pkg_setup() {
+
+	if ! use client-only ; then
+		webapp_pkg_setup || die "Failed to setup webapp"
+	fi
+
+	java-pkg-2_pkg_setup
+
+}
+
+src_unpack() {
+
+	unpack ${A}
+	epatch "${FILESDIR}"/${P}-nointl.patch
+	epatch "${FILESDIR}"/${P}-manifest.patch
+
+	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
+	cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
+		|| die "Failed to install Cert file."
+
+	rm -v "${S}"/*.jar "${S}"/plugin-jars/*.jar || die
+	cd "${S}/jars"
+
+# We still have to use netscape.jar on amd64 until a nice way to include plugin.jar comes along.
+	if use amd64; then
+		mv -v netscape.jar netscape.tempjar || die "Failed to move netscape.jar."
+		rm -v *.jar *.tar.gz || die "Failed to remove jars."
+		mv -v netscape.tempjar netscape.jar || die "Failed to move netscape.tempjar."
+	fi
+
+	java-pkg_jar-from vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar
+	java-pkg_jar-from itext iText.jar itext-1.4.5.jar
+	java-pkg_jar-from jmol-acme jmol-acme.jar Acme.jar
+	java-pkg_jar-from commons-cli-1 commons-cli.jar commons-cli-1.0.jar
+
+	mkdir -p "${S}/build/appjars" || die
+}
+
+src_compile() {
+	# prevent absorbing dep's classes
+	eant -Dlibjars.uptodate=true main
+}
+
+src_install() {
+
+	java-pkg_dojar build/Jmol.jar
+	dohtml -r  build/doc/* || die "Failed to install html docs."
+	dodoc *.txt doc/*license* || die "Failed to install licenses."
+
+	java-pkg_dolauncher ${PN} --main org.openscience.jmol.app.Jmol \
+		--java_args "-Xmx512m"
+
+	if ! use client-only ; then
+		webapp_src_preinst || die "Failed webapp_src_preinst."
+		cmd="cp Jmol.js build/Jmol.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp build/JmolApplet*.jar "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp applet.classes "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp -r build/classes/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp -r build/appletjars/* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp "${FILESDIR}"/caffeine.xyz "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp "${FILESDIR}"/index.html "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+
+		webapp_src_install || die "Failed running webapp_src_install"
+	fi
+}
+
+pkg_postinst() {
+
+	if ! use client-only ; then
+		webapp_pkg_postinst || die "webapp_pkg_postinst failed"
+	fi
+
+}
+
+pkg_prerm() {
+
+	if ! use client-only ; then
+		webapp_pkg_prerm || die "webapp_pkg_prerm failed"
+	fi
+
+}
diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml
new file mode 100644
index 000000000..ee65d2c2a
--- /dev/null
+++ b/sci-chemistry/jmol/metadata.xml
@@ -0,0 +1,13 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+<herd>sci-chemistry</herd>
+<maintainer>
+<email>je_fro@gentoo.org</email>
+<name>Jeff Gardner</name>
+</maintainer>
+<use>
+  <flag name='client-only'>Install the viewer only, no applet files for httpd
+    </flag>
+</use>
+</pkgmetadata>