Initial import sci-chemistry/jmol.

Package-Manager: portage-2.1.2.7

10 files changed, 583 insertions, 0 deletions

diff --git a/sci-chemistry/jmol/ChangeLog b/sci-chemistry/jmol/ChangeLog
new file mode 100644
index 000000000000..3c689643f275
--- /dev/null
+++ b/sci-chemistry/jmol/ChangeLog
@@ -0,0 +1,12 @@
+# ChangeLog for sci-chemistry/jmol
+# Copyright 1999-2007 Gentoo Foundation; Distributed under the GPL v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/jmol/ChangeLog,v 1.1 2007/06/15 08:21:59 je_fro Exp $
+
+*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 000000000000..c9ac852275b2
--- /dev/null
+++ b/sci-chemistry/jmol/Manifest
@@ -0,0 +1,36 @@
+AUX caffeine.xyz 1116 RMD160 92b432c6584cd927fa1bfb155ea41011ab7a82d8 SHA1 d0f35a447b333b8ea51c15ab0ac67d887556e43c SHA256 45a9afac0b247780595944a98f8e1076a7e7e0dbb3e02cb54cecb0764b1cb67f
+MD5 c0204ee82eba27bc55b8856ba8cdf6a4 files/caffeine.xyz 1116
+RMD160 92b432c6584cd927fa1bfb155ea41011ab7a82d8 files/caffeine.xyz 1116
+SHA256 45a9afac0b247780595944a98f8e1076a7e7e0dbb3e02cb54cecb0764b1cb67f files/caffeine.xyz 1116
+AUX index.html 328 RMD160 60d2a573c228e018a864fd7d9cfc7554264ccd6b SHA1 7ab256d768d3a4da43b5e497dfb1c3a53a8068a9 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451
+MD5 fe4402e54486534640b0863007ad4877 files/index.html 328
+RMD160 60d2a573c228e018a864fd7d9cfc7554264ccd6b files/index.html 328
+SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451 files/index.html 328
+AUX jmol-11.0.3-manifest.patch 3726 RMD160 03e1e11fdd29fb63de15934fff166348577084b0 SHA1 925a957bc30e1fbab9fd773dc07f83411f667d30 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd
+MD5 79677cfda8337f3de16e14053ccf022e files/jmol-11.0.3-manifest.patch 3726
+RMD160 03e1e11fdd29fb63de15934fff166348577084b0 files/jmol-11.0.3-manifest.patch 3726
+SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd files/jmol-11.0.3-manifest.patch 3726
+AUX jmol-11.0.3-nointl.patch 11109 RMD160 ea8808469e488c3c7d8a75d2273fefdae32c3011 SHA1 891b83352cdf940c0da2d903b1cf6a9da31f67d7 SHA256 56ad460779a0ecfb90ad61cf4cfae2fad9b017f9f78581a720241e4ea208b49a
+MD5 1084c3836521b45d5c3e786f445e2a74 files/jmol-11.0.3-nointl.patch 11109
+RMD160 ea8808469e488c3c7d8a75d2273fefdae32c3011 files/jmol-11.0.3-nointl.patch 11109
+SHA256 56ad460779a0ecfb90ad61cf4cfae2fad9b017f9f78581a720241e4ea208b49a files/jmol-11.0.3-nointl.patch 11109
+AUX selfSignedCertificate.store 1516 RMD160 583b7bab5578e1e32f649388b7009dc654df1199 SHA1 88d9123bdc1a376ba00e00c8abef4751adefe3a5 SHA256 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5
+MD5 bf2be32212c831e4fa369809a639b75d files/selfSignedCertificate.store 1516
+RMD160 583b7bab5578e1e32f649388b7009dc654df1199 files/selfSignedCertificate.store 1516
+SHA256 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5 files/selfSignedCertificate.store 1516
+DIST jmol-11.0.3-full.tar.gz 13578526 RMD160 53e34c52d6085635daea74cd9c5787da67ef483e SHA1 35dc9d3d3cfe08cbe3076a6939f62361b2c59c86 SHA256 210eb7d119e53ed0b7f41939321bcfcdb4d7312761d8002e340c83ff49664616
+EBUILD jmol-11.0.3.ebuild 3499 RMD160 235f612e9bf9401f401dd00df0c614b8bf128520 SHA1 412646ad1ad960ca85b57f89f54b45eeee894ac6 SHA256 6c2e3e22fb81c6b74c28b3b5e9218fb0283915d2ea8bec715601be626510d339
+MD5 b1aa3cdd36b89f69371bec1f966b9c36 jmol-11.0.3.ebuild 3499
+RMD160 235f612e9bf9401f401dd00df0c614b8bf128520 jmol-11.0.3.ebuild 3499
+SHA256 6c2e3e22fb81c6b74c28b3b5e9218fb0283915d2ea8bec715601be626510d339 jmol-11.0.3.ebuild 3499
+MISC ChangeLog 490 RMD160 8b150559040a0a8d9b22b5e14aab365f4bd67886 SHA1 6bacf5c4709b50bc52ba7c9851b6eff857d6a8b5 SHA256 7b3fc9de6719787f23d91c358c7b56d3e42f29dd395b14440284fa98f6993428
+MD5 2004fc280250e2474470e95e8d675e6d ChangeLog 490
+RMD160 8b150559040a0a8d9b22b5e14aab365f4bd67886 ChangeLog 490
+SHA256 7b3fc9de6719787f23d91c358c7b56d3e42f29dd395b14440284fa98f6993428 ChangeLog 490
+MISC metadata.xml 253 RMD160 59050ef726d30aa457b0dabb61494f8386687bd6 SHA1 f5ea0ad09e8f7647830e3b912eafa71f28b054a0 SHA256 f20f704428c998a9fa8511f02730d72435a0a2e168c6f6ef5c6005bc1608841a
+MD5 5a3da73e18cd061fb7f74cfc718a90d3 metadata.xml 253
+RMD160 59050ef726d30aa457b0dabb61494f8386687bd6 metadata.xml 253
+SHA256 f20f704428c998a9fa8511f02730d72435a0a2e168c6f6ef5c6005bc1608841a metadata.xml 253
+MD5 4474d7ff73147d373b76fc7cc9361806 files/digest-jmol-11.0.3 256
+RMD160 f8d2a3980cf89147b84f30dd195c898ee07e258b files/digest-jmol-11.0.3 256
+SHA256 8c5917e259cefb8aae76765625422987300243e5e698c0149db9bf8ad3dcb3a1 files/digest-jmol-11.0.3 256
diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz
new file mode 100644
index 000000000000..f0325b049f3c
--- /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/digest-jmol-11.0.3 b/sci-chemistry/jmol/files/digest-jmol-11.0.3
new file mode 100644
index 000000000000..8a749a8f3cc5
--- /dev/null
+++ b/sci-chemistry/jmol/files/digest-jmol-11.0.3
@@ -0,0 +1,3 @@
+MD5 09a589e1fc1099a522b96a7bda16fdd0 jmol-11.0.3-full.tar.gz 13578526
+RMD160 53e34c52d6085635daea74cd9c5787da67ef483e jmol-11.0.3-full.tar.gz 13578526
+SHA256 210eb7d119e53ed0b7f41939321bcfcdb4d7312761d8002e340c83ff49664616 jmol-11.0.3-full.tar.gz 13578526
diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html
new file mode 100644
index 000000000000..35a5d49217e2
--- /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-11.0.3-manifest.patch b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch
new file mode 100644
index 000000000000..3b43c219d94f
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-11.0.3-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-11.0.3-nointl.patch b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch
new file mode 100644
index 000000000000..25fd17e36c68
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch
@@ -0,0 +1,266 @@
+--- jmol-11.0.3-orig/build.xml	2007-05-17 09:35:04.000000000 -0500
++++ jmol-11.0.3/build.xml	2007-05-17 09:40:21.000000000 -0500
+@@ -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>

+ 

+@@ -332,17 +304,12 @@
+   </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" />

+@@ -462,7 +429,6 @@
+         <!-- note that this class is included in JmolApplet0.jar -->

+         <exclude name="org/jmol/api/JmolAppletInterface.class" />

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

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

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

+       </fileset>

+     </jar>

+@@ -502,12 +468,6 @@
+       </fileset>

+     </jar>

+ 

+-    <jar destfile="${jmol.applet.build.dir}/JmolApplet_i18n.jar" manifest="manifest/applet_i18n.txt" >

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

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

+-      </fileset>

+-    </jar>

+-

+     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->

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

+     <jar destfile="${jmol.applet.build.dir}/JmolApplet0.jar"

+@@ -527,7 +487,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet4.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet5.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolApplet6.jar" />

+-        <pathelement path="${jmol.applet.build.dir}/JmolApplet_i18n.jar" />

+       </indexjars>

+     </jar>

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

+@@ -564,10 +523,6 @@
+              signedjar="${jmol.applet.build.dir}/JmolAppletSigned6.jar"

+              keystore="selfSignedCertificate/selfSignedCertificate.store"

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

+-    <signjar jar="${jmol.applet.build.dir}/JmolApplet_i18n.jar"

+-             signedjar="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar"

+-             keystore="selfSignedCertificate/selfSignedCertificate.store"

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

+ 

+     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->

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

+@@ -589,7 +544,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned4.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned5.jar" />

+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned6.jar" />

+-        <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar" />

+       </indexjars>

+     </jar>

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

+@@ -599,7 +553,7 @@
+   </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}"/>

+@@ -655,7 +609,6 @@
+       <fileset dir=".">

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

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

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

+       </fileset>

+     </copy>

+ 

+@@ -744,7 +697,6 @@
+       <fileset dir=".">

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

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

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

+       </fileset>

+     </copy>

+ 

+@@ -839,7 +791,7 @@
+   <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"/>

+@@ -900,16 +852,6 @@
+       <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"

+@@ -924,26 +866,6 @@
+       <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"

+@@ -957,24 +879,6 @@
+       <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"

+@@ -988,24 +892,6 @@
+       <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">

+@@ -1036,12 +922,4 @@
+     <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 000000000000..a7b0ccb86e12
--- /dev/null
+++ b/sci-chemistry/jmol/files/selfSignedCertificate.store
diff --git a/sci-chemistry/jmol/jmol-11.0.3.ebuild b/sci-chemistry/jmol/jmol-11.0.3.ebuild
new file mode 100644
index 000000000000..4fbd59bfddf2
--- /dev/null
+++ b/sci-chemistry/jmol/jmol-11.0.3.ebuild
@@ -0,0 +1,120 @@
+# Copyright 1999-2007 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: /var/cvsroot/gentoo-x86/sci-chemistry/jmol/jmol-11.0.3.ebuild,v 1.1 2007/06/15 08:21:59 je_fro Exp $
+
+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="~amd64"
+LICENSE="LGPL-2.1"
+
+IUSE="client-only vhosts"
+
+WEBAPP_MANUAL_SLOT="yes"
+SLOT="0"
+SAXON_SLOT="6.5"
+
+RDEPEND=">=virtual/jre-1.4"
+DEPEND=">=virtual/jdk-1.4
+	dev-java/ant-core
+	dev-java/ant-contrib
+	dev-java/commons-cli
+	dev-java/itext
+	dev-java/junit
+	dev-java/gnu-jaxp
+	dev-java/sax
+	=dev-java/saxon-6.5.5
+	sci-libs/jmol-acme
+	sci-libs/vecmath-objectclub
+	vhosts? ( app-admin/webapp-config )"
+
+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}"/${P}-manifest.patch
+
+	sed -i -e '/^command=java/a source \/etc\/env.d\/java\/30jmol' "${S}/${PN}" || die "sed failed"
+
+	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
+	cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
+		|| die "Failed to install Cert file."
+
+# The only bundled jar we still rely on is netscape.jar.
+	cd "${S}/jars"
+
+	java-pkg_jar-from --build-only ant-contrib
+	java-pkg_jar-from --build-only itext iText.jar itext-1.4.5.jar
+	java-pkg_jar-from --build-only junit
+	java-pkg_jar-from --build-only gnu-jaxp
+	java-pkg_jar-from --build-only saxon-${SAXON_SLOT} saxon.jar saxon.jar
+	java-pkg_jar-from --build-only commons-cli-1 commons-cli.jar commons-cli-1.0.jar
+	java-pkg_jar-from --build-only jmol-acme jmol-acme.jar Acme.jar
+	java-pkg_jar-from --build-only vecmath-objectclub vecmath-objectclub.jar vecmath1.2-1.14.jar
+	java-pkg_jar-from --build-only gnu-jaxp gnujaxp.jar gnujaxp-onlysax.jar
+
+}
+
+src_install() {
+
+	java-pkg_dojar Jmol.jar JmolApplet.jar
+	dohtml -r  build/doc/* || die "Failed to install html docs."
+	dodoc *.txt doc/*license* || die "Failed to install licenses."
+	edos2unix jmol || die "Failed to convert jmol from DOS format."
+	dobin jmol || die "Failed to install startup script."
+
+	dodir /etc/env.d/java
+	cat >> "${D}"/etc/env.d/java/30jmol << EOF
+JMOL_HOME=/usr/share/${PN}/lib
+EOF
+
+	if ! use client-only ; then
+		webapp_src_preinst || die "Failed webapp_src_preinst."
+		cmd="cp Jmol.* "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp jmol "${D}${MY_HTDOCSDIR}"" ; ${cmd} \
+		|| die "${cmd} failed."
+		cmd="cp JmolApplet.* "${D}${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/appjars/* "${D}${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 000000000000..adf0aa95b029
--- /dev/null
+++ b/sci-chemistry/jmol/metadata.xml
@@ -0,0 +1,10 @@
+<?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>
+</pkgmetadata>
+