gentoo resync : 15.09.2019

10 files changed, 0 insertions, 1003 deletions

diff --git a/sci-chemistry/Manifest.gz b/sci-chemistry/Manifest.gz
index ede7d91dbca9..5b26b8dc8f79 100644
--- a/sci-chemistry/Manifest.gz
+++ b/sci-chemistry/Manifest.gz
diff --git a/sci-chemistry/jmol/Manifest b/sci-chemistry/jmol/Manifest
deleted file mode 100644
index 8077f60fe4f5..000000000000
--- a/sci-chemistry/jmol/Manifest
+++ /dev/null
@@ -1,11 +0,0 @@
-AUX 12.0.45/jmol-manifest.patch 3726 BLAKE2B e12ae62b240186f1644a679acff1ab0ec5e833629665f9bdd0842ca377574f5dad18495b6cddc3206d89bd95e00e3e2959532cb323cbbb8b740f50c1c77dceda SHA512 016e57a3c3e55d89fe2a72447160c0b6359affec305c6b4949892ddec3b4a648bad96b87ff0aa5cb0c5187f59e825b441cbbe60e6936a14df536ed0095f67112
-AUX 12.0.45/jmol-nointl.patch 13315 BLAKE2B bf9801273d477476fc9b9091ce661037e11810451f933c916cb9a182d96bb36ee5bbfc0ed1e2277fde80b36ac2a9adc9ebd1f6f4ec52298e2d28408fb84c0e8e SHA512 deb54c7f94e3fd4b43a701d58c992edbc80f650397feea97594a8f00cdc14463a19e2314fa616fb3a0ca42af8b70770c0426b8eacfe1d81a30b53c566e6342c0
-AUX caffeine.xyz 1116 BLAKE2B ae08271e144b0eb7a0c03324faf612b8fb428a7b677c45f22b92f04325d22721a76bcc2a65dab3bc60a1a267fce0d60d469df3d9f1f54aeed1b609b1394d122a SHA512 863ee4a327b2d765ed042cf24055c708d3970a20c3c3b2ee45b46096390be11a7c02915faedb30ee6cb69101faa5942fcfb19fe2b530afb93460a2cd167c3688
-AUX index.html 328 BLAKE2B 203b1ccfd41ecb23e2f4f7ddc221a43b02ab742cbc6bc5db1646746f6049713c09810c3b7a85239ed29c4a44d5570e004d12477fc20c069086755b5677d6ee2c SHA512 e89c62ba91ecebb38d6f9c88cc1f257600bd7d6005df97713f2715036d3308dee53f7b838ca749c1acc810cc4701c384525f2763b96ac2f1d6802e639cd1961b
-AUX jmol-12.2.27-nointl.patch 13821 BLAKE2B f7d3731fcf0916cbd3f274f89c23ea5bbc4049c326a20e822aa70392a0b3e18c6e50edc7a68628eda9635f4786a2db93c9a83ee315c8a511c27d8acb42608649 SHA512 6ad196dfd6d38a086fad461f8170340f8ef3beb7ae69916e0285d8e30ce8a40efc278e461a3d0ae0da71611529f4a0e58c9a73336319764b1fef62d75336a8dc
-DIST Jmol-12.0.45-full.tar.gz 26501382 BLAKE2B 68db22b79ecfca719ac4dc6e971e5f3fbfc1c66cd669ea5e823e18da0fca28279afaf9cc8999398849df9d718a6efcbd975f913c62e0b558de5b785f63d62045 SHA512 b0e999335c039e5bde5e261c076f3eb75dd0c33a351445d5c086995d32b3fd03795b3a11dc57a06bf8ac39e74945f3c9f4547ecfbf18b56d827b9a42f5208c11
-DIST Jmol-12.2.27-full.tar.gz 29493780 BLAKE2B 8e4dc9334348847fe0b54baea1c0575d70a2e564a194474e8e007ec6dc60fdb46a8d139f5dad1686b32f23a4be11a76dfc6578e015d65a532a891bf24425c20e SHA512 a8608e64dc06b6d3b0cb7e911f0a224456a65bdc15c51d6b420ee6abf8d82cdcec9f54f6b1a51cfe032e2e074f173f50a88bcff783311de19ce9b95ad990ebca
-DIST jmol-selfSignedCertificate.store.tar 10240 BLAKE2B 04dc1504bc751d2a9829b12fe64f851885d308ffee170cffc871d59552d46bff8ab211e5bdb4ed00b596b3882a359669bf4ebf170cca37d518d76f140294d1e6 SHA512 2c3e9d1183a0b174273346d0fba0729caa415ef53fe01629a4c47daa2393c9e18ca3f57984911e6340197429cf0ee581c64bb9b6072db902102976030d9f2c23
-EBUILD jmol-12.0.45-r1.ebuild 2923 BLAKE2B 441f20bdd786caa3334402d8fc91ce636c44226ebd4a4332e5e4c0ae3bdbfc7f27cfa0f0f3a18b636e4155976c707d8e4f2163e65866ef1c0e681ddcf5a18daa SHA512 6336b5293150abcf0f8349ebd80088b26b4b6da3633f00ac53a9396569e65f1736f2fa14cd69f65ea16838e3507d0050734c71c23734311cefe41dc1bd3d0974
-EBUILD jmol-12.2.27-r1.ebuild 2780 BLAKE2B 12edd8bcc1d51022ed8054253cbc7b28d3756d95da05c404569d043318b14e9834cbf3c1b70e05de444f439e6de7e88189bcc644574f55dfe1d8b234c3d169b3 SHA512 ff56e4624e925ce5692b7a6b9240fd1d39ed354c138049e475f71f839485bc84ca9f7b3d3d14fc632dfb5dc4a011d8e4aa95c0a454ace418beb3928f06276e14
-MISC metadata.xml 458 BLAKE2B 63e371d7d578efe778790b6dc3c6631bdfc36149b4cb0bca928dd098466a45da507e347dd59694af53146ec198d90c306a09c44a9275e94500cc02c25eb189a3 SHA512 2808cc38baa2aefa5fb873cab1f2f96d52125c41f969d37cf9405b19c16883aa0bec82895fc40001acc1eb9b7b02ceb5fb03b9a517b887e56ea13d3889dd9012
diff --git a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch b/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
deleted file mode 100644
index 3b43c219d94f..000000000000
--- a/sci-chemistry/jmol/files/12.0.45/jmol-manifest.patch
+++ /dev/null
@@ -1,96 +0,0 @@
-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
deleted file mode 100644
index c1b22e83c615..000000000000
--- a/sci-chemistry/jmol/files/12.0.45/jmol-nointl.patch
+++ /dev/null
@@ -1,313 +0,0 @@
---- 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
deleted file mode 100644
index f0325b049f3c..000000000000
--- a/sci-chemistry/jmol/files/caffeine.xyz
+++ /dev/null
@@ -1,26 +0,0 @@
-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
deleted file mode 100644
index 35a5d49217e2..000000000000
--- a/sci-chemistry/jmol/files/index.html
+++ /dev/null
@@ -1,14 +0,0 @@
-<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-12.2.27-nointl.patch b/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
deleted file mode 100644
index 0a43faaf653d..000000000000
--- a/sci-chemistry/jmol/files/jmol-12.2.27-nointl.patch
+++ /dev/null
@@ -1,330 +0,0 @@
---- 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
deleted file mode 100644
index 589cc469b42f..000000000000
--- a/sci-chemistry/jmol/jmol-12.0.45-r1.ebuild
+++ /dev/null
@@ -1,100 +0,0 @@
-# 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
deleted file mode 100644
index a109067c1d7d..000000000000
--- a/sci-chemistry/jmol/jmol-12.2.27-r1.ebuild
+++ /dev/null
@@ -1,98 +0,0 @@
-# Copyright 1999-2019 Gentoo Authors
-# 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="~amd64 ~x86"
-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
deleted file mode 100644
index 888f06b55ce5..000000000000
--- a/sci-chemistry/jmol/metadata.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?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>