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-rw-r--r--sci-chemistry/jmol/ChangeLog12
-rw-r--r--sci-chemistry/jmol/Manifest36
-rw-r--r--sci-chemistry/jmol/files/caffeine.xyz26
-rw-r--r--sci-chemistry/jmol/files/digest-jmol-11.0.33
-rw-r--r--sci-chemistry/jmol/files/index.html14
-rw-r--r--sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch96
-rw-r--r--sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch266
-rw-r--r--sci-chemistry/jmol/files/selfSignedCertificate.storebin0 -> 1516 bytes
-rw-r--r--sci-chemistry/jmol/jmol-11.0.3.ebuild120
-rw-r--r--sci-chemistry/jmol/metadata.xml10
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
Binary files differ
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>
+