Initial import of jmol.

git-svn-id: http://overlays.gentoo.org/svn/proj/science/overlay@396 32389bae-6d03-0410-99cf-db05cde120eb
author: je_fro <je_fro@32389bae-6d03-0410-99cf-db05cde120eb> 2006-10-31 12:00:10 +0000
committer: je_fro <je_fro@32389bae-6d03-0410-99cf-db05cde120eb> 2006-10-31 12:00:10 +0000
commit: 372246a4929eb64f9794be1c15d3606f7c89e576 (patch)
tree: 1a787f3e49eebde0f229ef6d6c8c42324b684ded /sci-chemistry/jmol
parent: Minor fix to comment. (diff)
download: sci-372246a4929eb64f9794be1c15d3606f7c89e576.tar.gz
sci-372246a4929eb64f9794be1c15d3606f7c89e576.tar.bz2
sci-372246a4929eb64f9794be1c15d3606f7c89e576.zip
9 files changed, 432 insertions, 0 deletions
diff --git a/sci-chemistry/jmol/ChangeLog b/sci-chemistry/jmol/ChangeLog
new file mode 100644
index 000000000..72184868f
--- /dev/null
+++ b/sci-chemistry/jmol/ChangeLog
@@ -0,0 +1,7 @@
+# ChangeLog for sci-chemistry/jmol
+# Copyright 1999-2006 Gentoo Foundation; Distributed under the GPL v2
+# $Header: $
+
+  31 Oct 2006; Jeff Gardner <je_fro@gentoo.org> ChangeLog:
+  Initial import of jmol-10.2.0.
+
diff --git a/sci-chemistry/jmol/files/caffeine.xyz b/sci-chemistry/jmol/files/caffeine.xyz
new file mode 100644
index 000000000..f0325b049
--- /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-10.2.0 b/sci-chemistry/jmol/files/digest-jmol-10.2.0
new file mode 100644
index 000000000..b5030f31e
--- /dev/null
+++ b/sci-chemistry/jmol/files/digest-jmol-10.2.0
@@ -0,0 +1,3 @@
+MD5 687d4cdb0b12f22b40835fd82a064a70 jmol-10.2.0-full.tar.gz 10551595
+RMD160 23fa2847f7dd2e6a5ae0ff36a788c5789bc2d043 jmol-10.2.0-full.tar.gz 10551595
+SHA256 b47134cd6da869099dcb5f052ca7e3fd6438cdeb255e58a3572bf490d4ca2b35 jmol-10.2.0-full.tar.gz 10551595
diff --git a/sci-chemistry/jmol/files/index.html b/sci-chemistry/jmol/files/index.html
new file mode 100644
index 000000000..35a5d4921
--- /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-10.2.0-manifest.patch b/sci-chemistry/jmol/files/jmol-10.2.0-manifest.patch
new file mode 100644
index 000000000..b4d195a67
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-10.2.0-manifest.patch
@@ -0,0 +1,69 @@
+diff -aurN manifest/applet0.txt manifest/applet0.txt
+--- manifest/applet0.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet0.txt	2006-10-18 18:03:05.980019000 -0500
+@@ -0,0 +1,5 @@
++Main-Class: JmolApplet
++
++Name: org/jmol/appletwrapper/
++Sealed: true
++
+diff -aurN manifest/applet1.txt manifest/applet1.txt
+--- manifest/applet1.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet1.txt	2006-10-18 18:03:05.948019000 -0500
+@@ -0,0 +1,6 @@
++Name: org/jmol/api/
++Sealed: false
++
++Name: org/jmol/applet/
++Sealed: true
++
+diff -aurN manifest/applet2.txt manifest/applet2.txt
+--- manifest/applet2.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet2.txt	2006-10-18 18:03:05.960019000 -0500
+@@ -0,0 +1,2 @@
++Name: javax/vecmath/
++
+diff -aurN manifest/applet3.txt manifest/applet3.txt
+--- manifest/applet3.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet3.txt	2006-10-18 18:03:05.960019000 -0500
+@@ -0,0 +1,3 @@
++
++Name: org/jmol/g3d/
++Sealed: true
+diff -aurN manifest/applet4.txt manifest/applet4.txt
+--- manifest/applet4.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet4.txt	2006-10-18 18:03:05.964019000 -0500
+@@ -0,0 +1,3 @@
++
++Name: org/jmol/adapter/smarter/
++Sealed: true
+diff -aurN manifest/applet5.txt manifest/applet5.txt
+--- manifest/applet5.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet5.txt	2006-10-18 18:03:05.964019000 -0500
+@@ -0,0 +1,6 @@
++
++Name: org/openscience/jmol/ui/
++Sealed: true
++
++Name: org/jmol/bspt/
++Sealed: true
+diff -aurN manifest/applet6.txt manifest/applet6.txt
+--- manifest/applet6.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet6.txt	2006-10-18 18:03:05.964019000 -0500
+@@ -0,0 +1,3 @@
++
++Name: org/jmol/viewer/
++Sealed: true
+diff -aurN manifest/applet_i18n.txt manifest/applet_i18n.txt
+--- manifest/applet_i18n.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/applet_i18n.txt	2006-10-18 18:03:05.964019000 -0500
+@@ -0,0 +1,3 @@
++
++Name: org/jmol/translation/
++Sealed: true
+diff -aurN manifest/application.txt manifest/application.txt
+--- manifest/application.txt	1969-12-31 18:00:00.000000000 -0600
++++ manifest/application.txt	2006-10-18 18:03:05.936019000 -0500
+@@ -0,0 +1,2 @@
++Main-Class: org.openscience.jmol.app.Jmol
++
diff --git a/sci-chemistry/jmol/files/jmol-10.2.0-nointl.patch b/sci-chemistry/jmol/files/jmol-10.2.0-nointl.patch
new file mode 100644
index 000000000..039fe3bfc
--- /dev/null
+++ b/sci-chemistry/jmol/files/jmol-10.2.0-nointl.patch
@@ -0,0 +1,211 @@
+--- jmol-10.2.0-orig/build.xml	2006-10-18 12:10:44.016019000 -0500
++++ jmol-10.2.0/build.xml	2006-10-18 17:58:42.640019000 -0500
+@@ -96,10 +96,6 @@
+           <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>
+ 
+@@ -109,14 +105,6 @@
+           <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>
+     
+@@ -126,14 +114,6 @@
+           <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>
+ 
+@@ -143,14 +123,6 @@
+           <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>
+ 
+@@ -326,17 +298,12 @@
+   </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="${classes.dir}/org/openscience/jmol/Data" >
+       <fileset dir="build/doc/JmolHistory">
+         <include name="**/*.html" />
+@@ -571,7 +538,7 @@
+   </target>
+ 
+   <target name="dist" id="dist"
+-          depends="doc,main-i18n,main,signed-applet">
++          depends="doc,main,signed-applet">
+     <!-- first build binary distribution -->
+     <delete dir="build/dist/jmol-${version}"/>
+     <mkdir dir="build/dist/jmol-${version}"/>
+@@ -711,7 +678,6 @@
+       <fileset dir=".">
+         <include name="apisio.classes" />
+         <include name="build.xml" />
+-        <include name="build-i18n.xml" />
+       </fileset>
+     </copy>
+ 
+@@ -801,7 +767,7 @@
+     </delete>
+   </target>
+ 
+-  <target name="spotless" id="spotless" depends="clean,spotless-i18n">
++  <target name="spotless" id="spotless" depends="clean">
+     <delete dir="build"/>
+     <delete dir="${javadoc.dir}"/>
+     <delete dir="packaging/rpm/dist"/>
+@@ -862,16 +828,6 @@
+       <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="../../${docbook-xsl}/html/chunk.xsl" />
+-    </java>
+   </target>
+ 
+   <target name="jmolHistory" id="jmolHistory"
+@@ -886,26 +842,6 @@
+       <arg value="../../../doc/source/JmolHistory.xml" />
+       <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+     </java>
+-    <echo message="Generating history of changes (fr)" />
+-    <java fork="true" dir="build/doc/JmolHistory"
+-          classname="com.icl.saxon.StyleSheet"
+-          classpath="${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="${lib.dir}/saxon.jar" >
+-      <arg value="-o" />
+-      <arg value="ChangeLog_nl.html" />
+-      <arg value="../../../doc/source/JmolHistory_nl.xml" />
+-      <arg value="../../../doc/source/JmolHistoryToHtml.xsl" />
+-      <arg value="lang=nl" />
+-    </java>
+   </target>
+ 
+   <target name="jmolDevelopersGuide" id="jmolDevelopersGuide"
+@@ -919,24 +855,6 @@
+       <arg value="../../doc/source/JmolDevelopersGuide.docbook.xml" />
+       <arg value="../${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"
+@@ -950,24 +868,6 @@
+       <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="../${docbook-xsl}/html/docbook.xsl" />
+-    </java>
+   </target>
+ 
+   <target name="test" id="test" depends="main,compile-tests">
+@@ -998,12 +898,6 @@
+     <jar destfile="Tests.jar" basedir="${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>
++  <!-- i18n stuff je_fro says - this isn't working in 10.2, only in svn -->
+ 
+ </project>
diff --git a/sci-chemistry/jmol/files/selfSignedCertificate.store b/sci-chemistry/jmol/files/selfSignedCertificate.store
new file mode 100644
index 000000000..a7b0ccb86
--- /dev/null
+++ b/sci-chemistry/jmol/files/selfSignedCertificate.store
diff --git a/sci-chemistry/jmol/jmol-10.2.0.ebuild b/sci-chemistry/jmol/jmol-10.2.0.ebuild
new file mode 100644
index 000000000..a537a6965
--- /dev/null
+++ b/sci-chemistry/jmol/jmol-10.2.0.ebuild
@@ -0,0 +1,93 @@
+# Copyright 1999-2006 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+# $Header: $
+
+inherit eutils java-pkg-2 webapp
+
+DESCRIPTION="Jmol is a java molecular viever for 3-D chemical structures."
+SRC_URI="mirror://sourceforge.net/${PN}/${P}-full.tar.gz"
+HOMEPAGE="http://jmol.sourceforge.net/"
+KEYWORDS="~amd64"
+LICENSE="LGPL-2.1"
+
+IUSE=""
+
+RDEPEND=">=virtual/jre-1.4"
+DEPEND=">=virtual/jre-1.4
+	dev-java/ant-core
+	vhosts? app-admin/webapp-config"
+
+
+pkg_setup() {
+	
+	if use vhosts ; then
+		webapp_pkg_setup
+	fi
+
+}
+
+src_unpack() {
+
+	unpack ${A}
+	cd "${S}"
+
+# i18n is broken without files from svn.
+	epatch "${FILESDIR}"/${P}-nointl.patch
+
+	epatch "${FILESDIR}"/${P}-manifest.patch
+
+	sed -i "s/${PN}/${P}\/lib/" "${PN}" || die "Failed running sed."
+
+	mkdir "${S}"/selfSignedCertificate || die "Failed to create Cert directory."
+	cp "${FILESDIR}"/selfSignedCertificate.store "${S}"/selfSignedCertificate/ \
+		|| die "Failed to install Cert file."
+
+}
+
+src_compile() {
+
+	ant || die "Compilation problem"
+
+}
+
+
+src_install() {
+
+	java-pkg_dojar   Jmol.jar JmolApplet.* || die "Failed to install jars."
+	dohtml -r  build/doc/* || die "Failed to install html docs."
+	dodoc  *.txt doc/*license* || die "Failed to install licenses."
+	edos2unix jmol || die "Failed to convert jmol from DOS format."
+	dobin   jmol || die "Failed to install startup script."
+
+	if use vhosts ; then
+		webapp_src_preinst || die 
+		cp Jmol.* "${D}${MY_HTDOCSDIR}" || die "Failed installing webapp files."
+		cp jmol "${D}${MY_HTDOCSDIR}" || die "Failed installing webapp files."
+		cp JmolApplet.* "${D}${MY_HTDOCSDIR}" die
+		cp applet.classes "${D}${MY_HTDOCSDIR}" || die
+		cp -r build/classes/* "${D}${MY_HTDOCSDIR}" || die 
+		cp -r build/appjars/* "${D}${MY_HTDOCSDIR}" || die 
+		cp "${FILESDIR}"/caffeine.xyz "${D}${MY_HTDOCSDIR}" || die
+		cp "${FILESDIR}"/index.html "${D}${MY_HTDOCSDIR}" || die
+
+		webapp_src_install || die "Failed running webapp_src_install"
+	fi
+	
+}
+
+pkg_postinst() {
+	
+	if use vhosts ; then
+		webapp_pkg_postinst || die "pkg_postinst failed"
+	fi
+
+}
+
+pkg_prerm() {
+
+	if use vhosts ; then
+		webapp_pkg_prerm || die "pkg_prerm failed"
+	fi
+
+}
+
diff --git a/sci-chemistry/jmol/metadata.xml b/sci-chemistry/jmol/metadata.xml
new file mode 100644
index 000000000..6fe1b5ffa
--- /dev/null
+++ b/sci-chemistry/jmol/metadata.xml
@@ -0,0 +1,9 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+  <herd>sci</herd>
+  <maintainer>
+    <email>je_fro@gentoo.org</email>
+    <name>Jeff Gardner</name>
+  </maintainer>
+</pkgmetadata>
author	je_fro <je_fro@32389bae-6d03-0410-99cf-db05cde120eb>	2006-10-31 12:00:10 +0000
committer	je_fro <je_fro@32389bae-6d03-0410-99cf-db05cde120eb>	2006-10-31 12:00:10 +0000
commit	372246a4929eb64f9794be1c15d3606f7c89e576 (patch)
tree	1a787f3e49eebde0f229ef6d6c8c42324b684ded /sci-chemistry/jmol
parent	Minor fix to comment. (diff)
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