From 4f2d7949f03e1c198bc888f2d05f421d35c57e21 Mon Sep 17 00:00:00 2001
From: V3n3RiX <venerix@redcorelinux.org>
Date: Mon, 9 Oct 2017 18:53:29 +0100
Subject: reinit the tree, so we can have metadata

---
 sci-chemistry/jmol/Manifest                        |  15 +
 .../jmol/files/12.0.45/jmol-manifest.patch         |  96 ++++++
 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch | 313 +++++++++++++++++++
 sci-chemistry/jmol/files/caffeine.xyz              |  26 ++
 sci-chemistry/jmol/files/index.html                |  14 +
 .../jmol/files/jmol-11.0.3-manifest.patch          |  96 ++++++
 sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch  | 266 +++++++++++++++++
 sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch | 330 +++++++++++++++++++++
 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild          | 100 +++++++
 sci-chemistry/jmol/jmol-12.2.27-r1.ebuild          |  98 ++++++
 sci-chemistry/jmol/metadata.xml                    |  15 +
 11 files changed, 1369 insertions(+)
 create mode 100644 sci-chemistry/jmol/Manifest
 create mode 100644 sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
 create mode 100644 sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
 create mode 100644 sci-chemistry/jmol/files/caffeine.xyz
 create mode 100644 sci-chemistry/jmol/files/index.html
 create mode 100644 sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch
 create mode 100644 sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch
 create mode 100644 sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
 create mode 100644 sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
 create mode 100644 sci-chemistry/jmol/jmol-12.2.27-r1.ebuild
 create mode 100644 sci-chemistry/jmol/metadata.xml

(limited to 'sci-chemistry/jmol')

diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest
new file mode 100644
index 000000000000..b47b85f09a7c
--- /dev/null
+++ b/sci-chemistry/jmol/Manifest
@@ -0,0 +1,15 @@
+AUX 12.0.45/jmol-manifest.patch 3726 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd SHA512 016e57a3c3e55d89fe2a72447160c0b6359affec305c6b4949892ddec3b4a648bad96b87ff0aa5cb0c5187f59e825b441cbbe60e6936a14df536ed0095f67112 WHIRLPOOL abb250bc77d15a5f3e0a441dd0ffd8809642d8959f896c1ae394b85695b74bd4578013ad99b38abca822ad5db514562b121ad6b2f0265090653d7e359ee85a2f
+AUX 12.0.45/jmol-nointl.patch 13315 SHA256 6bbf13c59bc3633dc089346c1133ad2b3d0614463abdf364f5ec2e2ccd658df0 SHA512 deb54c7f94e3fd4b43a701d58c992edbc80f650397feea97594a8f00cdc14463a19e2314fa616fb3a0ca42af8b70770c0426b8eacfe1d81a30b53c566e6342c0 WHIRLPOOL 570e359517e1011ba76447161e6c03925db0e6533d262f11f13d9553f75989faa27a0ae5f39352dad19ec53e804e8e39e76bbc79f1b44b495fe948e7b8633472
+AUX caffeine.xyz 1116 SHA256 45a9afac0b247780595944a98f8e1076a7e7e0dbb3e02cb54cecb0764b1cb67f SHA512 863ee4a327b2d765ed042cf24055c708d3970a20c3c3b2ee45b46096390be11a7c02915faedb30ee6cb69101faa5942fcfb19fe2b530afb93460a2cd167c3688 WHIRLPOOL 18df972f5cbafc35be4bf20de29ad8049e7c6f921a668f0c80cd9aff2c3ede32b9b30e830f2629be2136923c554c3711b809915d45ea1bd1da854d8768d6e254
+AUX index.html 328 SHA256 8cba2c5eb7f25c0ecf23bc007eb61549a7d2177ac327db6c1e5f51f333ae2451 SHA512 e89c62ba91ecebb38d6f9c88cc1f257600bd7d6005df97713f2715036d3308dee53f7b838ca749c1acc810cc4701c384525f2763b96ac2f1d6802e639cd1961b WHIRLPOOL 0b407f950f4f2523d21c03b6e4f20f9ef4009e54d666ad3a222b87b0e49576816f3940e4fe076e55e9fda9832170c54f17ed543420333fe489f45f4d7296ee79
+AUX jmol-11.0.3-manifest.patch 3726 SHA256 74cdf274352161ffdf155b34b8d9110dad9c4a15720467f73d301104005566bd SHA512 016e57a3c3e55d89fe2a72447160c0b6359affec305c6b4949892ddec3b4a648bad96b87ff0aa5cb0c5187f59e825b441cbbe60e6936a14df536ed0095f67112 WHIRLPOOL abb250bc77d15a5f3e0a441dd0ffd8809642d8959f896c1ae394b85695b74bd4578013ad99b38abca822ad5db514562b121ad6b2f0265090653d7e359ee85a2f
+AUX jmol-11.0.3-nointl.patch 11109 SHA256 56ad460779a0ecfb90ad61cf4cfae2fad9b017f9f78581a720241e4ea208b49a SHA512 0fe07fb53d989298f7395be39c6ee75f56ab59fc096e956d8481c38581706b17f799e745fcd5b6652c4f1115d4425e7ff9ebef454b606d8de7829e07e26b27e2 WHIRLPOOL daf992208b99fec51f5f0b26ca22d520ebd820a22d439c7baa2b84f2b4b3829ac7139d7d3c48076dd4681af1296fd5e61badd91332efa03cc97e58027b21697a
+AUX jmol-12.2.27-nointl.patch 13821 SHA256 330a911405f00552d37a9c241c4a18b9d3e6812ce858933dbc4574df8248e345 SHA512 6ad196dfd6d38a086fad461f8170340f8ef3beb7ae69916e0285d8e30ce8a40efc278e461a3d0ae0da71611529f4a0e58c9a73336319764b1fef62d75336a8dc WHIRLPOOL 94be437d33ec73ed53c8461e78a7799c2aa34c9b606e309554da191ff74a465fe2243f4953a615aca790d3558e2b69b7edd122526f900475f5b05bb20d98d0fe
+DIST Jmol-12.0.45-full.tar.gz 26501382 SHA256 f9a3fe242841f9b56a718f8da2efe4130e497afe2c12d77f2e68344c62d7f70e SHA512 b0e999335c039e5bde5e261c076f3eb75dd0c33a351445d5c086995d32b3fd03795b3a11dc57a06bf8ac39e74945f3c9f4547ecfbf18b56d827b9a42f5208c11 WHIRLPOOL d0bbae1fc5c96ddfb4dd29f6e09701e496a333a2f44ba266e2a24c60de2d36d73c2184bd9b8f6054b0955535d49856154d6101644ef0297b825c4f6745cfe3bb
+DIST Jmol-12.2.27-full.tar.gz 29493780 SHA256 f2ca3b810ea16a488f6f57003d2a407c8ac040d610479a7ae6d95631157db801 SHA512 a8608e64dc06b6d3b0cb7e911f0a224456a65bdc15c51d6b420ee6abf8d82cdcec9f54f6b1a51cfe032e2e074f173f50a88bcff783311de19ce9b95ad990ebca WHIRLPOOL ae0826eab7eb364acb4f30eb77850450b871a24d8940eaabaf8fe9f3770efc39deb604e3c5f875a695c0d33b516ad47d523982c7a6460f2421f961f50a7680bf
+DIST jmol-selfSignedCertificate.store.tar 10240 SHA256 416744934991ef4f1fa298c0afc8e855d43771de2f2278ed3fbc60f707ea46b2 SHA512 2c3e9d1183a0b174273346d0fba0729caa415ef53fe01629a4c47daa2393c9e18ca3f57984911e6340197429cf0ee581c64bb9b6072db902102976030d9f2c23 WHIRLPOOL 79dc2b2c95b304569f44bb986af3aa25150b0c5f8a9fc9b1698a979647800e60d0f20a7a4abbc89533a21f3d7f4b93a430840eed71bbe04b1cc0bdbcfae7fe63
+EBUILD jmol-12.0.45-r1.ebuild 2923 SHA256 6fb9b443fcfbe680b0e120d0233b0531116351a91bee3bf8d398a921480cfad9 SHA512 6336b5293150abcf0f8349ebd80088b26b4b6da3633f00ac53a9396569e65f1736f2fa14cd69f65ea16838e3507d0050734c71c23734311cefe41dc1bd3d0974 WHIRLPOOL c7890e2d7a8b8ebbf082d2fb65b18923ffad36c0f9ebc95bf00039f6f7b70cbe32bb3773b0e09c1f88146e8d1c19cb9c7099ccb97482c8e43b9f437571a5b07e
+EBUILD jmol-12.2.27-r1.ebuild 2783 SHA256 41f0fbe61872ec8763ff3887f3f574bf9e3ed12751cd44fa7355968c78fea2fc SHA512 dd81a4edccc022a8f7aab66a8a8005feb68eec7e2e3a1a2278f9565c8b3bec364b5dcb0f994c1202a3fb97491ca31b11941ed41501e0a485d9238f233d9e0940 WHIRLPOOL 93d2ea57d5fec5229770ecc2f3e1df317ede5cb97eb4036e81bddd390311fa4df4e587254ae4627094eb323013626cf9a5084a9c884dc4e2ca8e16b50093894e
+MISC ChangeLog 2878 SHA256 18b594c9d1d7ef41e2292dd65768c5847c18ed35c3bc4c65b83fef7f8326b075 SHA512 918cc2877676a207b037b56c1b2400b6b700c8bc367e2399fd4bf4f367ae81dddeaa7cfbbc3d9b73b1d3771ecff22b19e1031753e1ae579f2aeb3cba72c51a66 WHIRLPOOL cf0834fc982455bac386a8b1d9c8e05f2204a8a448579bc09f376a2eb14302c0d7bbc5864a47c8699e06d3b459c56273afb22feb7e96cf9ebe2bcfedd7b38ddb
+MISC ChangeLog-2015 2982 SHA256 bf3153e33aa2d74e25570ecf4fec84e9bee42ad661c18791e1aacdb1e17e1f1a SHA512 fed110fe8de1074909ef53be8d8eb9f576946987e98cccb44540cedd990c37dd85dac54c2af67ba3c460b3a0c083582c883b621d8fe8c8a21b464eb3f3cdff10 WHIRLPOOL 6f7dc08ffcf2644bd452668f256f93f3fad41908fe5ae65cdc3230175fdaab984b82a25103e3181afa427a50ced58f278b2642439dbe3f894c6bbf268008e332
+MISC metadata.xml 458 SHA256 d1ff80e0cb82997846dd7daa0fb55428e4c29dd60645273cb29bd148c625d3e7 SHA512 2808cc38baa2aefa5fb873cab1f2f96d52125c41f969d37cf9405b19c16883aa0bec82895fc40001acc1eb9b7b02ceb5fb03b9a517b887e56ea13d3889dd9012 WHIRLPOOL a9e37b078f979bd05d2c86fa3d5b33b16ebb5f6c853001e95f3c3e26fb460427e20750241194b17709706263ccffbe8d85d5c8b3df793475a64cd43792942571
diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
new file mode 100644
index 000000000000..3b43c219d94f
--- /dev/null
+++ b/sci-chemistry/jmol/files/12.0.45/jmol-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/12.0.45/jmol-nointl.patch b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
new file mode 100644
index 000000000000..c1b22e83c615
--- /dev/null
+++ b/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
@@ -0,0 +1,313 @@
+--- build.xml	2011-02-25 12:59:43.000000000 -0600
++++ build.xml.new	2011-02-27 12:16:02.398959959 -0600
+@@ -110,10 +110,6 @@
+           <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>
+ 
+@@ -123,14 +119,6 @@
+           <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>
+     
+@@ -140,14 +128,6 @@
+           <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>
+ 
+@@ -157,14 +137,6 @@
+           <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>
+ 
+@@ -385,17 +357,12 @@
+   </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="${classes.dir}/org/openscience/jmol/Data" >
+       <fileset dir="build/doc/JmolHistory">
+         <include name="**/*.html" />
+@@ -587,18 +554,6 @@
+       <fileset dir="${appletjars.dir}" includes="**/*"/>
+     </jar>
+ 
+-    <for list="${all.JmolApplet.languages}" delimiter=","
+-         param="current.Jmol.language">
+-      <sequential>
+-        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+-             manifest="manifest/applet_i18n.txt" >
+-          <fileset dir="${applet.classes.dir}">
+-            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+-          </fileset>
+-        </jar>
+-      </sequential>
+-    </for>
+-
+     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+       <fileset dir="${applet.classes.dir}">
+         <include name="org/jmol/minimize/**" />
+@@ -712,7 +667,6 @@
+         <include name="org/jmol/bspt/**" />
+         <include name="org/jmol/g3d/**" />
+         <include name="org/jmol/geodesic/**" />
+-        <include name="org/jmol/i18n/**" />
+         <include name="org/jmol/modelset/**" />
+         <include name="org/jmol/script/**" />
+         <include name="org/jmol/shape/**" />
+@@ -738,7 +692,6 @@
+         <pathelement path="${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" />
+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+       </indexjars>
+     </jar>
+     <!-- changes to this must be replicated below for the signed applet -->
+@@ -851,16 +804,6 @@
+              keystore="selfSignedCertificate/selfSignedCertificate.store"
+              storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+ 
+-    <for list="${all.JmolApplet.languages}" delimiter=","
+-         param="current.Jmol.language">
+-      <sequential>
+-      	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+-                 signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
+-                 keystore="selfSignedCertificate/selfSignedCertificate.store"
+-                 storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+-      </sequential>
+-    </for>
+-
+     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+     <!-- this one must be treated specially because of jar indexing
+          we cannot simply rename the jar file, because the index has
+@@ -906,7 +849,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
+       </indexjars>
+     </jar>
+     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -944,18 +886,6 @@
+ 	      </fileset>
+ 	    </jar>
+ 
+-	    <for list="${all.JmolApplet.languages}" delimiter=","
+-	         param="current.Jmol.language">
+-	      <sequential>
+-	        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+-	             manifest="manifest/applet_i18n.txt" >
+-	          <fileset dir="${applet.classes.dir}">
+-	            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+-	          </fileset>
+-	        </jar>
+-	      </sequential>
+-	    </for>
+-
+ 	    <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+ 	      <fileset dir="${applet.classes.dir}">
+ 	        <include name="org/jmol/minimize/**" />
+@@ -1069,7 +999,6 @@
+ 	        <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/script/**" />
+ 	        <include name="org/jmol/shape/**" />
+@@ -1095,7 +1024,6 @@
+ 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+ 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+ 	        <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+-	        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+ 	      </indexjars>
+ 	    </jar>
+ 	    <!-- changes to this must be replicated below for the signed applet -->
+@@ -1104,7 +1032,7 @@
+ 	  </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}"/>
+@@ -1163,7 +1091,6 @@
+       <fileset dir=".">
+         <include name="applet.classes" />
+         <include name="build.xml" />
+-        <include name="build-i18n.xml" />
+       </fileset>
+     </copy>
+ 
+@@ -1246,7 +1173,6 @@
+       <fileset dir=".">
+         <include name="apisio.classes" />
+         <include name="build.xml" />
+-        <include name="build-i18n.xml" />
+       </fileset>
+     </copy>
+ 
+@@ -1342,7 +1268,7 @@
+   <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="${javadoc.dir}"/>
+     <delete dir="packaging/rpm/dist"/>
+@@ -1406,16 +1332,6 @@
+       <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+       <arg value="../../${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"
+@@ -1430,26 +1346,6 @@
+       <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"
+@@ -1463,24 +1359,6 @@
+       <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="../${docbook-xsl}/html/docbook.xsl" />
+-    </java>
+   </target>
+ 
+   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -1494,24 +1372,6 @@
+       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+       <arg value="../${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">
+@@ -1543,12 +1403,4 @@
+     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+   </target>
+ 
+-  <!-- i18n stuff -->
+-  <target name="main-i18n" depends="classes">
+-    <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
+-  </target>
+-  <target name="spotless-i18n">
+-    <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
+-  </target>
+-
+ </project>
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/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/jmol-12.2.27-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
new file mode 100644
index 000000000000..0a43faaf653d
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
@@ -0,0 +1,330 @@
+--- orig-build.xml	2012-05-31 13:42:43.943062427 -0500
++++ build.xml	2012-05-31 14:01:01.691982062 -0500
+@@ -52,8 +52,6 @@
+ 
+   <property file="proxy.properties" />
+ 
+-  <import file="tools/build-i18n.xml"/>
+-
+   <path id="project.class.path">
+     <fileset dir="${lib.dir}">
+       <include name="*.jar" />
+@@ -111,10 +109,6 @@
+           <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>
+ 
+@@ -124,14 +118,6 @@
+           <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>
+     
+@@ -141,14 +127,6 @@
+           <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>
+ 
+@@ -158,14 +136,6 @@
+           <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>
+ 
+@@ -388,17 +358,12 @@
+   </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" />
+@@ -603,18 +568,6 @@
+       <fileset dir="${appletjars.dir}" includes="**/*"/>
+     </jar>
+ 
+-    <for list="${all.JmolApplet.languages}" delimiter=","
+-         param="current.Jmol.language">
+-      <sequential>
+-        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+-             manifest="manifest/applet_i18n.txt" >
+-          <fileset dir="${applet.classes.dir}">
+-            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+-          </fileset>
+-        </jar>
+-      </sequential>
+-    </for>
+-
+     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+       <fileset dir="${applet.classes.dir}">
+         <include name="org/jmol/minimize/**" />
+@@ -729,7 +682,6 @@
+         <include name="org/jmol/constant/**" />
+         <include name="org/jmol/g3d/**" />
+         <include name="org/jmol/geodesic/**" />
+-        <include name="org/jmol/i18n/**" />
+         <include name="org/jmol/modelset/**" />
+         <include name="org/jmol/script/**" />
+         <include name="org/jmol/shape/**" />
+@@ -755,7 +707,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+       </indexjars>
+     </jar>
+     <!-- changes to this must be replicated below for the signed applet -->
+@@ -868,16 +819,6 @@
+              keystore="selfSignedCertificate/selfSignedCertificate.store"
+              storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+ 
+-    <for list="${all.JmolApplet.languages}" delimiter=","
+-         param="current.Jmol.language">
+-      <sequential>
+-      	<signjar jar="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+-                 signedjar="${jmol.applet.build.dir}/JmolAppletSigned0_i18n_@{current.Jmol.language}.jar"
+-                 keystore="selfSignedCertificate/selfSignedCertificate.store"
+-                 storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+-      </sequential>
+-    </for>
+-
+     <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+     <!-- this one must be treated specially because of jar indexing
+          we cannot simply rename the jar file, because the index has
+@@ -905,7 +846,6 @@
+ 		<include name="org/jmol/shape/**" />
+ 		<include name="org/jmol/viewer/**" />
+ 		<include name="org/jmol/util/**" />
+-		<include name="org/jmol/i18n/**" />
+       </fileset>    	
+       <indexjars>
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Console.jar" />
+@@ -924,7 +864,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_ShapeSurface.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Smiles.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned0_Symmetry.jar" />
+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolAppletSigned0_i18n_*.jar" />
+       </indexjars>
+     </jar>
+     <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -963,18 +902,6 @@
+       </fileset>
+     </jar>
+ 
+-    <for list="${all.JmolApplet.languages}" delimiter=","
+-         param="current.Jmol.language">
+-      <sequential>
+-        <jar destfile="${jmol.applet.build.dir}/JmolApplet0_i18n_@{current.Jmol.language}.jar"
+-             manifest="manifest/applet_i18n.txt" >
+-          <fileset dir="${applet.classes.dir}">
+-            <include name="org/jmol/translation/JmolApplet/@{current.Jmol.language}/**" />
+-          </fileset>
+-        </jar>
+-      </sequential>
+-    </for>
+-
+     <jar destfile="${jmol.applet.build.dir}/JmolApplet0_Minimize.jar" manifest="manifest/applet.txt">
+       <fileset dir="${applet.classes.dir}">
+         <include name="org/jmol/minimize/**" />
+@@ -1088,7 +1015,6 @@
+         <include name="org/jmol/constant/**" />
+         <include name="org/jmol/g3d/**" />
+         <include name="org/jmol/geodesic/**" />
+-        <include name="org/jmol/i18n/**" />
+         <include name="org/jmol/modelset/**" />
+         <include name="org/jmol/script/**" />
+         <include name="org/jmol/shape/**" />
+@@ -1114,7 +1040,6 @@
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_ShapeSurface.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Smiles.jar" />
+         <pathelement path="${jmol.applet.build.dir}/JmolApplet0_Symmetry.jar" />
+-        <fileset dir="${jmol.applet.build.dir}" includes="JmolApplet0_i18n_*.jar" />
+       </indexjars>
+     </jar>
+     <!-- changes to this must be replicated below for the signed applet -->
+@@ -1123,7 +1048,7 @@
+   </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}"/>
+@@ -1183,7 +1108,6 @@
+       <fileset dir=".">
+         <include name="applet.classes" />
+         <include name="build.xml" />
+-        <include name="build-i18n.xml" />
+       </fileset>
+     </copy>
+ 
+@@ -1278,7 +1202,6 @@
+       <fileset dir=".">
+         <include name="apisio.classes" />
+         <include name="build.xml" />
+-        <include name="build-i18n.xml" />
+       </fileset>
+     </copy>
+ 
+@@ -1374,7 +1297,7 @@
+   <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="${javadoc.dir}"/>
+     <delete dir="packaging/rpm/dist"/>
+@@ -1438,16 +1361,6 @@
+       <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+       <arg value="../../${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"
+@@ -1462,26 +1375,6 @@
+       <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"
+@@ -1495,24 +1388,6 @@
+       <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="../${docbook-xsl}/html/docbook.xsl" />
+-    </java>
+   </target>
+ 
+   <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -1526,24 +1401,6 @@
+       <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+       <arg value="../${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">
+@@ -1575,12 +1432,4 @@
+     <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+   </target>
+ 
+-  <!-- i18n stuff -->
+-  <target name="main-i18n" depends="classes">
+-    <ant antfile="tools/build-i18n.xml" target="main-i18n"/>
+-  </target>
+-  <target name="spotless-i18n">
+-    <ant antfile="tools/build-i18n.xml" target="spotless-i18n"/>
+-  </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
new file mode 100644
index 000000000000..589cc469b42f
--- /dev/null
+++ b/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
@@ -0,0 +1,100 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+WEBAPP_OPTIONAL="yes"
+
+inherit eutils webapp java-pkg-2 java-ant-2
+
+MY_P=Jmol
+
+DESCRIPTION="Java molecular viever for 3-D chemical structures"
+HOMEPAGE="http://jmol.sourceforge.net/"
+SRC_URI="
+	mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz
+	https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar"
+
+WEBAPP_MANUAL_SLOT="yes"
+SLOT="0"
+KEYWORDS="~amd64 ~x86"
+LICENSE="LGPL-2.1"
+IUSE="client-only vhosts"
+
+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} )
+	${COMMON_DEP}"
+
+pkg_setup() {
+	use client-only || webapp_pkg_setup
+	java-pkg-2_pkg_setup
+}
+
+src_prepare() {
+	epatch \
+		"${FILESDIR}"/${PV}/${PN}-nointl.patch \
+		"${FILESDIR}"/${PV}/${PN}-manifest.patch
+
+	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
+	cp "${WORKDIR}"/selfSignedCertificate.store "${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 ${PN} --main org.openscience.jmol.app.Jmol \
+		--java_args "-Xmx512m"
+
+	if ! use client-only ; then
+		webapp_src_preinst
+		cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+
+		webapp_src_install
+	fi
+}
+
+pkg_postinst() {
+	use client-only || webapp_pkg_postinst
+}
+
+pkg_prerm() {
+	use client-only || webapp_pkg_prerm
+}
diff --git a/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild
new file mode 100644
index 000000000000..2b78a243a22d
--- /dev/null
+++ b/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild
@@ -0,0 +1,98 @@
+# Copyright 1999-2014 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=5
+WEBAPP_OPTIONAL="yes"
+
+inherit eutils webapp java-pkg-2 java-ant-2
+
+MY_P=Jmol
+
+DESCRIPTION="Java molecular viever for 3-D chemical structures"
+HOMEPAGE="http://jmol.sourceforge.net/"
+SRC_URI="
+	mirror://sourceforge/${PN}/${MY_P}-${PV}-full.tar.gz
+	https://dev.gentoo.org/~jlec/distfiles/${PN}-selfSignedCertificate.store.tar"
+
+LICENSE="LGPL-2.1"
+KEYWORDS="~x86 ~amd64"
+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
+	sci-libs/naga"
+RDEPEND=">=virtual/jre-1.5
+	${COMMON_DEP}"
+DEPEND=">=virtual/jdk-1.5
+	dev-java/saxon:6.5
+	!client-only? ( ${WEBAPP_DEPEND} )
+	${COMMON_DEP}"
+
+pkg_setup() {
+	use client-only || webapp_pkg_setup
+	java-pkg-2_pkg_setup
+}
+
+src_prepare() {
+	epatch "${FILESDIR}"/${P}-nointl.patch
+
+	rm -v "${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
+	java-pkg_jar-from naga
+	java-pkg_jar-from --build-only saxon-6.5 saxon.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 ${PN} --main org.openscience.jmol.app.Jmol \
+		--java_args "-Xmx512m"
+
+	if ! use client-only ; then
+		webapp_src_preinst
+		cp Jmol.js build/Jmol.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp build/JmolApplet*.jar "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp applet.classes "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp -r build/classes/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp -r build/appletjars/* "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp "${FILESDIR}"/caffeine.xyz "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+		cp "${FILESDIR}"/index.html "${ED}"${MY_HTDOCSDIR} || die "${cmd} failed."
+
+		webapp_src_install
+	fi
+}
+
+pkg_postinst() {
+	use client-only || webapp_pkg_postinst
+}
+
+pkg_prerm() {
+	use client-only || webapp_pkg_prerm
+}
diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml
new file mode 100644
index 000000000000..888f06b55ce5
--- /dev/null
+++ b/sci-chemistry/jmol/metadata.xml
@@ -0,0 +1,15 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <maintainer type="project">
+    <email>sci-chemistry@gentoo.org</email>
+    <name>Gentoo Chemistry Project</name>
+  </maintainer>
+  <use>
+    <flag name="client-only">Install the viewer only, no applet files for httpd
+    </flag>
+  </use>
+  <upstream>
+    <remote-id type="sourceforge">jmol</remote-id>
+  </upstream>
+</pkgmetadata>
-- 
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