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authorJeffrey Gardner <je_fro@gentoo.org>2007-06-15 08:21:59 +0000
committerJeffrey Gardner <je_fro@gentoo.org>2007-06-15 08:21:59 +0000
commit338d7d10630c446d0c1eeec68681657d2821bb83 (patch)
treead0e216a147f5af189d47e6bc8c2cb76943a8e44 /sci-chemistry/jmol/files
parentAdding vhosts and client-only USE flags for sci-chemistry/jmol. (diff)
downloadhistorical-338d7d10630c446d0c1eeec68681657d2821bb83.tar.gz
historical-338d7d10630c446d0c1eeec68681657d2821bb83.tar.bz2
historical-338d7d10630c446d0c1eeec68681657d2821bb83.zip
Initial import sci-chemistry/jmol.
Package-Manager: portage-2.1.2.7
Diffstat (limited to 'sci-chemistry/jmol/files')
-rw-r--r--sci-chemistry/jmol/files/caffeine.xyz26
-rw-r--r--sci-chemistry/jmol/files/digest-jmol-11.0.33
-rw-r--r--sci-chemistry/jmol/files/index.html14
-rw-r--r--sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch96
-rw-r--r--sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch266
-rw-r--r--sci-chemistry/jmol/files/selfSignedCertificate.storebin0 -> 1516 bytes
6 files changed, 405 insertions, 0 deletions
diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz
new file mode 100644
index 000000000000..f0325b049f3c
--- /dev/null
+++ b/sci-chemistry/jmol/files/caffeine.xyz
@@ -0,0 +1,26 @@
+24
+Caffeine
+H -3.3804130 -1.1272367 0.5733036
+N 0.9668296 -1.0737425 -0.8198227
+C 0.0567293 0.8527195 0.3923156
+N -1.3751742 -1.0212243 -0.0570552
+C -1.2615018 0.2590713 0.5234135
+C -0.3068337 -1.6836331 -0.7169344
+C 1.1394235 0.1874122 -0.2700900
+N 0.5602627 2.0839095 0.8251589
+O -0.4926797 -2.8180554 -1.2094732
+C -2.6328073 -1.7303959 -0.0060953
+O -2.2301338 0.7988624 1.0899730
+H 2.5496990 2.9734977 0.6229590
+C 2.0527432 -1.7360887 -1.4931279
+H -2.4807715 -2.7269528 0.4882631
+H -3.0089039 -1.9025254 -1.0498023
+H 2.9176101 -1.8481516 -0.7857866
+H 2.3787863 -1.1211917 -2.3743655
+H 1.7189877 -2.7489920 -1.8439205
+C -0.1518450 3.0970046 1.5348347
+C 1.8934096 2.1181245 0.4193193
+N 2.2861252 0.9968439 -0.2440298
+H -0.1687028 4.0436553 0.9301094
+H 0.3535322 3.2979060 2.5177747
+H -1.2074498 2.7537592 1.7203047
diff --git a/sci-chemistry/jmol/files/digest-jmol-11.0.3 b/sci-chemistry/jmol/files/digest-jmol-11.0.3
new file mode 100644
index 000000000000..8a749a8f3cc5
--- /dev/null
+++ b/sci-chemistry/jmol/files/digest-jmol-11.0.3
@@ -0,0 +1,3 @@
+MD5 09a589e1fc1099a522b96a7bda16fdd0 jmol-11.0.3-full.tar.gz 13578526
+RMD160 53e34c52d6085635daea74cd9c5787da67ef483e jmol-11.0.3-full.tar.gz 13578526
+SHA256 210eb7d119e53ed0b7f41939321bcfcdb4d7312761d8002e340c83ff49664616 jmol-11.0.3-full.tar.gz 13578526
diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html
new file mode 100644
index 000000000000..35a5d49217e2
--- /dev/null
+++ b/sci-chemistry/jmol/files/index.html
@@ -0,0 +1,14 @@
+<html>
+ <head>
+ <title>Jmol Test Page</title>
+ <div align="center"> <b>All the Sugar and Twice the Caffeine.</b> <br><br>
+ <script src="./Jmol.js"></script>
+ </head>
+ <body>
+ <script>
+ jmolInitialize("./"); // REQUIRED
+ jmolApplet(400, "load ./caffeine.xyz");
+ </script></div>
+ </body>
+</html>
+
diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch
new file mode 100644
index 000000000000..3b43c219d94f
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-11.0.3-manifest.patch
@@ -0,0 +1,96 @@
+diff -aurN jmol-11.0.3-orig/manifest/applet0.txt jmol-11.0.3/manifest/applet0.txt
+--- jmol-11.0.3-orig/manifest/applet0.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet0.txt 2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,6 @@
++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
+diff -aurN jmol-11.0.3-orig/manifest/applet1.txt jmol-11.0.3/manifest/applet1.txt
+--- jmol-11.0.3-orig/manifest/applet1.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet1.txt 2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,6 @@
++Name: org/jmol/api/
++Sealed: false
++
++Name: org/jmol/applet/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet2.txt jmol-11.0.3/manifest/applet2.txt
+--- jmol-11.0.3-orig/manifest/applet2.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet2.txt 2007-05-16 01:56:19.000000000 -0500
+@@ -0,0 +1,3 @@
++Name: javax/vecmath/
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet3.txt jmol-11.0.3/manifest/applet3.txt
+--- jmol-11.0.3-orig/manifest/applet3.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet3.txt 2007-05-16 01:56:47.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/g3d/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet4.txt jmol-11.0.3/manifest/applet4.txt
+--- jmol-11.0.3-orig/manifest/applet4.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet4.txt 2007-05-16 01:57:05.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/adapter/smarter/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/applet5.txt jmol-11.0.3/manifest/applet5.txt
+--- jmol-11.0.3-orig/manifest/applet5.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet5.txt 2007-05-16 01:57:23.000000000 -0500
+@@ -0,0 +1,4 @@
++Name: org/openscience/jmol/ui/
++Sealed: true
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet6.txt jmol-11.0.3/manifest/applet6.txt
+--- jmol-11.0.3-orig/manifest/applet6.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet6.txt 2007-05-16 01:57:46.000000000 -0500
+@@ -0,0 +1,4 @@
++
++Name: org/jmol/viewer/
++Sealed: true
++
+diff -aurN jmol-11.0.3-orig/manifest/appletMain.txt jmol-11.0.3/manifest/appletMain.txt
+--- jmol-11.0.3-orig/manifest/appletMain.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/appletMain.txt 2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,5 @@
++Manifest-Version: 1.0
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
+diff -aurN jmol-11.0.3-orig/manifest/appletMonolithic.txt jmol-11.0.3/manifest/appletMonolithic.txt
+--- jmol-11.0.3-orig/manifest/appletMonolithic.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/appletMonolithic.txt 2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,7 @@
++Main-Class: JmolApplet
++Sealed: true
++
++Name: org/jmol/api/
++Sealed: false
++
++
+diff -aurN jmol-11.0.3-orig/manifest/applet.txt jmol-11.0.3/manifest/applet.txt
+--- jmol-11.0.3-orig/manifest/applet.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/applet.txt 2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1,2 @@
++Manifest-Version: 1.0
++Sealed: true
+\ No newline at end of file
+diff -aurN jmol-11.0.3-orig/manifest/application.txt jmol-11.0.3/manifest/application.txt
+--- jmol-11.0.3-orig/manifest/application.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/application.txt 2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1 @@
++Main-Class: org.openscience.jmol.app.Jmol
+diff -aurN jmol-11.0.3-orig/manifest/jvxl.txt jmol-11.0.3/manifest/jvxl.txt
+--- jmol-11.0.3-orig/manifest/jvxl.txt 1969-12-31 18:00:00.000000000 -0600
++++ jmol-11.0.3/manifest/jvxl.txt 2007-05-16 01:54:10.000000000 -0500
+@@ -0,0 +1 @@
++Main-Class: org.openscience.jvxl.Jvxl
diff --git a/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch
new file mode 100644
index 000000000000..25fd17e36c68
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-11.0.3-nointl.patch
@@ -0,0 +1,266 @@
+--- jmol-11.0.3-orig/build.xml 2007-05-17 09:35:04.000000000 -0500
++++ jmol-11.0.3/build.xml 2007-05-17 09:40:21.000000000 -0500
+@@ -100,10 +100,6 @@
+ <srcfiles dir="doc/source"
+ includes="JmolGuide.docbook.xml, guide/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolUserGuide_fr/index.html">
+- <srcfiles dir="doc/source"
+- includes="JmolGuide_fr.docbook.xml, guide/*_fr.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -113,14 +109,6 @@
+ <srcfiles dir="doc/source"
+ includes="JmolHistory.xml,JmolHistoryToHtml.xsl,history/changes.xml" />
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_fr.xml,JmolHistoryToHtml.xsl,history/changes_fr.xml" />
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolHistory/ChangeLog_nl.html">
+- <srcfiles dir="doc/source"
+- includes="JmolHistory_nl.xml,JmolHistoryToHtml.xsl,history/changes_nl.xml" />
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -130,14 +118,6 @@
+ <srcfiles dir="doc/source"
+ includes="JmolDevelopersGuide.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolDevelopersGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolDevelopersGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -147,14 +127,6 @@
+ <srcfiles dir="doc/source"
+ includes="JmolAppletGuide.docbook.xml, applet/*.docbook.xml"/>
+ </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_fr.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_fr.docbook.xml, applet/*_fr.docbook.xml"/>
+- </uptodate>
+- <uptodate targetfile="build/doc/JmolAppletGuide_de.html">
+- <srcfiles dir="doc/source"
+- includes="JmolAppletGuide_de.docbook.xml"/>
+- </uptodate>
+ </and>
+ </condition>
+
+@@ -332,17 +304,12 @@
+ </target>
+
+ <target name="jar" id="jar"
+- depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars,main-i18n">
++ depends="init,classes,jmolGuide,jmolHistory,jmolDevelopersGuide,libjars">
+ <copy todir="${classes.dir}/org/openscience/jmol/Data/guide" >
+ <fileset dir="build/doc/JmolUserGuide">
+ <include name="**/*.html" />
+ </fileset>
+ </copy>
+- <copy todir="${classes.dir}/org/openscience/jmol/Data/guide_fr" >
+- <fileset dir="build/doc/JmolUserGuide_fr">
+- <include name="**/*.html" />
+- </fileset>
+- </copy>
+ <copy todir="${classes.dir}/org/openscience/jmol/Data" >
+ <fileset dir="build/doc/JmolHistory">
+ <include name="**/*.html" />
+@@ -462,7 +429,6 @@
+ <!-- note that this class is included in JmolApplet0.jar -->
+ <exclude name="org/jmol/api/JmolAppletInterface.class" />
+ <include name="org/jmol/applet/**" />
+- <include name="org/jmol/i18n/**" />
+ <include name="org/jmol/popup/**" />
+ </fileset>
+ </jar>
+@@ -502,12 +468,6 @@
+ </fileset>
+ </jar>
+
+- <jar destfile="${jmol.applet.build.dir}/JmolApplet_i18n.jar" manifest="manifest/applet_i18n.txt" >
+- <fileset dir="${applet.classes.dir}">
+- <include name="org/jmol/translation/**" />
+- </fileset>
+- </jar>
+-
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- changes to this must be replicated below for the signed applet -->
+ <jar destfile="${jmol.applet.build.dir}/JmolApplet0.jar"
+@@ -527,7 +487,6 @@
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolApplet6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolApplet_i18n.jar" />
+ </indexjars>
+ </jar>
+ <!-- changes to this must be replicated below for the signed applet -->
+@@ -564,10 +523,6 @@
+ signedjar="${jmol.applet.build.dir}/JmolAppletSigned6.jar"
+ keystore="selfSignedCertificate/selfSignedCertificate.store"
+ storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+- <signjar jar="${jmol.applet.build.dir}/JmolApplet_i18n.jar"
+- signedjar="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar"
+- keystore="selfSignedCertificate/selfSignedCertificate.store"
+- storepass="selfSignedCertificate" alias="selfSignedCertificate" />
+
+ <!-- vvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvvv -->
+ <!-- this one must be treated specially because of jar indexing
+@@ -589,7 +544,6 @@
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned4.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned5.jar" />
+ <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned6.jar" />
+- <pathelement path="${jmol.applet.build.dir}/JmolAppletSigned_i18n.jar" />
+ </indexjars>
+ </jar>
+ <signjar jar="${jmol.applet.build.dir}/JmolAppletSigned0.jar"
+@@ -599,7 +553,7 @@
+ </target>
+
+ <target name="dist" id="dist"
+- depends="doc,main-i18n,main,signed-applet">
++ depends="doc,main,signed-applet">
+ <!-- first build binary distribution -->
+ <delete dir="build/dist/jmol-${version}"/>
+ <mkdir dir="build/dist/jmol-${version}"/>
+@@ -655,7 +609,6 @@
+ <fileset dir=".">
+ <include name="applet.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -744,7 +697,6 @@
+ <fileset dir=".">
+ <include name="apisio.classes" />
+ <include name="build.xml" />
+- <include name="build-i18n.xml" />
+ </fileset>
+ </copy>
+
+@@ -839,7 +791,7 @@
+ <target name="xclean" id="xclean">
+ </target>
+
+- <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++ <target name="spotless" id="spotless" depends="clean">
+ <delete dir="build"/>
+ <delete dir="${javadoc.dir}"/>
+ <delete dir="packaging/rpm/dist"/>
+@@ -900,16 +852,6 @@
+ <arg value="../../../doc/source/JmolGuide.docbook.xml" />
+ <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+ </java>
+- <echo message="Generating user's guide (fr)" />
+- <mkdir dir="build/doc/JmolUserGuide_fr" />
+- <java fork="true" dir="build/doc/JmolUserGuide_fr"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <jvmarg value="${proxyHost}" />
+- <jvmarg value="${proxyPort}" />
+- <arg value="../../../doc/source/JmolGuide_fr.docbook.xml" />
+- <arg value="../../${docbook-xsl}/html/chunk.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolHistory" id="jmolHistory"
+@@ -924,26 +866,6 @@
+ <arg value="../../../doc/source/JmolHistory.xml" />
+ <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+ </java>
+- <echo message="Generating history of changes (fr)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_fr.html" />
+- <arg value="../../../doc/source/JmolHistory_fr.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=fr" />
+- </java>
+- <echo message="Generating history of changes (nl)" />
+- <java fork="true" dir="build/doc/JmolHistory"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="ChangeLog_nl.html" />
+- <arg value="../../../doc/source/JmolHistory_nl.xml" />
+- <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+- <arg value="lang=nl" />
+- </java>
+ </target>
+
+ <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -957,24 +879,6 @@
+ <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating developer's guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_fr.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating developer's guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolDevelopersGuide_de.html" />
+- <arg value="../../doc/source/JmolDevelopersGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="jmolAppletGuide" id="jmolAppletGuide" depends="initdoc"
+@@ -988,24 +892,6 @@
+ <arg value="../../doc/source/JmolAppletGuide.docbook.xml" />
+ <arg value="../${docbook-xsl}/html/docbook.xsl" />
+ </java>
+- <echo message="Generating applet guide (fr)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_fr.html" />
+- <arg value="../../doc/source/JmolAppletGuide_fr.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+- <echo message="Generating applet guide (de)" />
+- <java fork="true" dir="build/doc"
+- classname="com.icl.saxon.StyleSheet"
+- classpath="${lib.dir}/saxon.jar" >
+- <arg value="-o" />
+- <arg value="JmolAppletGuide_de.html" />
+- <arg value="../../doc/source/JmolAppletGuide_de.docbook.xml" />
+- <arg value="../${docbook-xsl}/html/docbook.xsl" />
+- </java>
+ </target>
+
+ <target name="test" id="test" depends="main,compile-tests">
+@@ -1036,12 +922,4 @@
+ <jar destfile="${tests.dir}/Tests.jar" basedir="${test-classes.dir}" />
+ </target>
+
+- <!-- i18n stuff -->
+- <target name="main-i18n" depends="classes">
+- <ant antfile="build-i18n.xml" target="main-i18n"/>
+- </target>
+- <target name="spotless-i18n">
+- <ant antfile="build-i18n.xml" target="spotless-i18n"/>
+- </target>
+-
+ </project>
diff --git a/sci-chemistry/jmol/files/selfSignedCertificate.store b/sci-chemistry/jmol/files/selfSignedCertificate.store
new file mode 100644
index 000000000000..a7b0ccb86e12
--- /dev/null
+++ b/sci-chemistry/jmol/files/selfSignedCertificate.store
Binary files differ