Jmol is a Java molecular viewer for

three-dimensional chemical structures.
Features include reading a variety
of file types and output from quantum
chemistry programs, and animation of
multi-frame files and computed normal
modes from quantum programs.

WWW:  http://sourceforge.net/projects/jmol/

PR:		ports/123631
Submitted by:	Wen heping <wenheping at gmail.com>

5 files changed, 202 insertions, 0 deletions

diff --git a/science/Makefile b/science/Makefile
index 66fe71d6530b..7ad58ae89d76 100644
--- a/science/Makefile
+++ b/science/Makefile
@@ -62,6 +62,7 @@
     SUBDIR += hdf5
     SUBDIR += ics
     SUBDIR += isaac-cfd
+    SUBDIR += jmol
     SUBDIR += kmovisto
     SUBDIR += kst
     SUBDIR += lamprop
diff --git a/science/jmol/Makefile b/science/jmol/Makefile
new file mode 100644
index 000000000000..0d362d6fd9a1
--- /dev/null
+++ b/science/jmol/Makefile
@@ -0,0 +1,83 @@
+# Ports collection makefile for:	jmol
+# Date created:			May 11, 2008
+# Whom:				Wen heping <wenheping@gmail.com>
+#
+# $FreeBSD$
+#
+
+PORTNAME=	jmol
+PORTVERSION=	11.4.2
+CATEGORIES=	science java
+MASTER_SITES=	SF:source1 \
+		http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/selfSignedCertificate/:source2
+DISTFILES=	${PORTNAME}-${PORTVERSION}-full.tar.gz:source1 \
+		selfSignedCertificate.cer:source2 \
+		selfSignedCertificate.store:source2
+EXTRACT_ONLY=	${PORTNAME}-${PORTVERSION}-full.tar.gz
+
+MAINTAINER=	wenheping@gmail.com
+COMMENT=	An Open-Source Java Viewer for Chemical Structures in 3D
+
+USE_JAVA=	yes
+JAVA_VERSION=	1.4+
+WRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
+JMOL_FILES=	Jmol.jar JmolApplet.jar JmolApplet0.jar \
+		JmolApplet0_Core.jar JmolApplet0_Jars.jar \
+		JmolApplet0_Jvxl.jar JmolApplet0_Main.jar \
+		JmolApplet0_Popup.jar JmolApplet0_Quantum.jar \
+		JmolApplet0_ReadersCifPdb.jar JmolApplet0_ReadersMolXyz.jar \
+		JmolApplet0_ReadersMore.jar JmolApplet0_ReadersXml.jar \
+		JmolApplet0_ShapeBio.jar JmolApplet0_ShapeSpecial.jar \
+		JmolApplet0_Smiles.jar JmolApplet0_Viewer.jar \
+		JmolApplet0_i18n.jar
+JMOL_FILES_EXT=	Jmol.js
+SIGN_DIR=	${WRKSRC}/selfSignedCertificate
+
+.if !defined(WITHOUT_COMPILE)
+USE_ANT=	yes
+ALL_TARGET=	all
+.if !defined(NOPORTDOCS)
+ALL_TARGET=	main
+.endif
+.else
+NO_BUILD=	yes
+.endif
+
+.include <bsd.port.pre.mk>
+
+pre-fetch:
+	@${ECHO_MSG} ""
+	@${ECHO_MSG} "You may use the following build options:"
+	@${ECHO_MSG} ""
+	@${ECHO_MSG} "    WITHOUT_COMPILE=yes    Install the pre-compiled .jar file"
+	@${ECHO_MSG} ""
+
+post-extract:
+	@${MKDIR} ${SIGN_DIR}
+	@${CP} ${DISTDIR}/selfSignedCertificate.cer ${SIGN_DIR}
+	@${CP} ${DISTDIR}/selfSignedCertificate.store ${SIGN_DIR}
+
+do-install:
+.for j in ${JMOL_FILES_EXT}
+	${INSTALL_DATA} ${WRKSRC}/${j} ${JAVAJARDIR}
+.endfor
+
+.if defined(WITHOUT_COMPILE)
+.for j in ${JMOL_FILES}
+	${INSTALL_DATA} ${WRKSRC}/build/${j} ${JAVAJARDIR}
+.endfor
+.else
+.for j in ${JMOL_FILES}
+	${INSTALL_DATA} ${WRKSRC}/${j} ${JAVAJARDIR}
+.endfor
+.endif
+
+.if !defined(NOPORTDOCS)
+	@${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..."
+	@cd ${WRKSRC}/doc && ${FIND} . -type d -exec ${MKDIR} ${DOCSDIR}/{} \;
+	@cd ${WRKSRC}/doc && ${FIND} . -type f -exec \
+		${INSTALL_DATA} {} ${DOCSDIR}/{} \;
+	@${ECHO_MSG} " [DONE]"
+.endif
+
+.include <bsd.port.post.mk>
diff --git a/science/jmol/distinfo b/science/jmol/distinfo
new file mode 100644
index 000000000000..9799cd25f1f9
--- /dev/null
+++ b/science/jmol/distinfo
@@ -0,0 +1,9 @@
+MD5 (jmol-11.4.2-full.tar.gz) = 58b0cd6a38be0c94d4943c1e74a7d8b5
+SHA256 (jmol-11.4.2-full.tar.gz) = 8890805394a8d0d0260739e230b30bbd3eb6c915fd5c6c6fc21478be9e29ecaf
+SIZE (jmol-11.4.2-full.tar.gz) = 15926387
+MD5 (selfSignedCertificate.cer) = ec6c4b413be88a8fab584399cc931d55
+SHA256 (selfSignedCertificate.cer) = 0fa14fd5f21593a328ba4439ac17b3b507969d71a2734e392239b83ae8ec2920
+SIZE (selfSignedCertificate.cer) = 735
+MD5 (selfSignedCertificate.store) = bf2be32212c831e4fa369809a639b75d
+SHA256 (selfSignedCertificate.store) = 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5
+SIZE (selfSignedCertificate.store) = 1516
diff --git a/science/jmol/pkg-descr b/science/jmol/pkg-descr
new file mode 100644
index 000000000000..cb5cca96ba7e
--- /dev/null
+++ b/science/jmol/pkg-descr
@@ -0,0 +1,9 @@
+Jmol is a Java molecular viewer for
+three-dimensional chemical structures.
+Features include reading a variety
+of file types and output from quantum
+chemistry programs, and animation of
+multi-frame files and computed normal
+modes from quantum programs.
+
+WWW:  http://sourceforge.net/projects/jmol/
diff --git a/science/jmol/pkg-plist b/science/jmol/pkg-plist
new file mode 100644
index 000000000000..c0e8119d369b
--- /dev/null
+++ b/science/jmol/pkg-plist
@@ -0,0 +1,100 @@
+%%DOCSDIR%%/JmolAppletGuide.html
+%%DOCSDIR%%/JmolDevelopersGuide.html
+%%DOCSDIR%%/JmolUserGuide/ch01.html
+%%DOCSDIR%%/JmolUserGuide/ch02.html
+%%DOCSDIR%%/JmolUserGuide/ch02s02.html
+%%DOCSDIR%%/JmolUserGuide/ch02s03.html
+%%DOCSDIR%%/JmolUserGuide/ch02s04.html
+%%DOCSDIR%%/JmolUserGuide/ch02s05.html
+%%DOCSDIR%%/JmolUserGuide/ch02s06.html
+%%DOCSDIR%%/JmolUserGuide/ch02s07.html
+%%DOCSDIR%%/JmolUserGuide/ch03.html
+%%DOCSDIR%%/JmolUserGuide/ch03s02.html
+%%DOCSDIR%%/JmolUserGuide/ch03s03.html
+%%DOCSDIR%%/JmolUserGuide/ch03s04.html
+%%DOCSDIR%%/JmolUserGuide/ch03s05.html
+%%DOCSDIR%%/JmolUserGuide/ch04.html
+%%DOCSDIR%%/JmolUserGuide/index.html
+%%DOCSDIR%%/docbook-xml-4.4.zip
+%%DOCSDIR%%/docbook-xsl-1.73.2.tar.gz
+%%DOCSDIR%%/ibm.license.html
+%%DOCSDIR%%/jcfl-1.2.6-source.tar.gz
+%%DOCSDIR%%/jpegEncoder.license
+%%DOCSDIR%%/lgpl.license
+%%DOCSDIR%%/rasmol26.license
+%%DOCSDIR%%/source/JmolAppletGuide.docbook.xml
+%%DOCSDIR%%/source/JmolAppletGuide_de.docbook.xml
+%%DOCSDIR%%/source/JmolAppletGuide_fr.docbook.xml
+%%DOCSDIR%%/source/JmolDevelopersGuide.docbook.xml
+%%DOCSDIR%%/source/JmolDevelopersGuide_de.docbook.xml
+%%DOCSDIR%%/source/JmolDevelopersGuide_fr.docbook.xml
+%%DOCSDIR%%/source/JmolGuide.docbook.xml
+%%DOCSDIR%%/source/JmolGuide_de.docbook.xml
+%%DOCSDIR%%/source/JmolGuide_fr.docbook.xml
+%%DOCSDIR%%/source/JmolHistory.xml
+%%DOCSDIR%%/source/JmolHistoryToHtml.xsl
+%%DOCSDIR%%/source/JmolHistory_fr.xml
+%%DOCSDIR%%/source/JmolHistory_nl.xml
+%%DOCSDIR%%/source/applet/browsers.docbook.xml
+%%DOCSDIR%%/source/applet/browsers_fr.docbook.xml
+%%DOCSDIR%%/source/applet/hardware.docbook.xml
+%%DOCSDIR%%/source/applet/hardware_fr.docbook.xml
+%%DOCSDIR%%/source/applet/intro.docbook.xml
+%%DOCSDIR%%/source/applet/intro_fr.docbook.xml
+%%DOCSDIR%%/source/applet/serverconfig.docbook.xml
+%%DOCSDIR%%/source/applet/serverconfig_fr.docbook.xml
+%%DOCSDIR%%/source/applet/usage.docbook.xml
+%%DOCSDIR%%/source/applet/usage_fr.docbook.xml
+%%DOCSDIR%%/source/guide/commandline.docbook.xml
+%%DOCSDIR%%/source/guide/commandline_fr.docbook.xml
+%%DOCSDIR%%/source/guide/intro.docbook.xml
+%%DOCSDIR%%/source/guide/intro_fr.docbook.xml
+%%DOCSDIR%%/source/guide/menus.docbook.xml
+%%DOCSDIR%%/source/guide/menus_fr.docbook.xml
+%%DOCSDIR%%/source/guide/scriptCommands.docbook.xml
+%%DOCSDIR%%/source/guide/scripts.docbook.xml
+%%DOCSDIR%%/source/guide/scripts_fr.docbook.xml
+%%DOCSDIR%%/source/history/changes.xml
+%%DOCSDIR%%/source/history/changes_fr.xml
+%%DOCSDIR%%/source/history/changes_nl.xml
+%%DOCSDIR%%/source/history/contributors.xml
+%%DOCSDIR%%/source/po/JmolAppletGuide.de.po
+%%DOCSDIR%%/source/po/JmolAppletGuide.pot
+%%DOCSDIR%%/source/po/JmolDevelopersGuide.de.po
+%%DOCSDIR%%/source/po/JmolDevelopersGuide.pot
+%%DOCSDIR%%/source/po/JmolGuide.de.po
+%%DOCSDIR%%/source/po/JmolGuide.pot
+%%DOCSDIR%%/source/xml2po-modes/docbook.py
+%%DOCSDIR%%/source/xml2po-modes/empty.py
+%%DOCSDIR%%/source/xml2po-modes/gs.py
+%%DOCSDIR%%/source/xml2po.bat
+%%DOCSDIR%%/source/xml2po.py
+%%DOCSDIR%%/source/xml2po.sh
+%%DOCSDIR%%/splash.ai
+%%JAVAJARDIR%%/Jmol.jar
+%%JAVAJARDIR%%/Jmol.js
+%%JAVAJARDIR%%/JmolApplet.jar
+%%JAVAJARDIR%%/JmolApplet0.jar
+%%JAVAJARDIR%%/JmolApplet0_Core.jar
+%%JAVAJARDIR%%/JmolApplet0_Jars.jar
+%%JAVAJARDIR%%/JmolApplet0_Jvxl.jar
+%%JAVAJARDIR%%/JmolApplet0_Main.jar
+%%JAVAJARDIR%%/JmolApplet0_Popup.jar
+%%JAVAJARDIR%%/JmolApplet0_Quantum.jar
+%%JAVAJARDIR%%/JmolApplet0_ReadersCifPdb.jar
+%%JAVAJARDIR%%/JmolApplet0_ReadersMolXyz.jar
+%%JAVAJARDIR%%/JmolApplet0_ReadersMore.jar
+%%JAVAJARDIR%%/JmolApplet0_ReadersXml.jar
+%%JAVAJARDIR%%/JmolApplet0_ShapeBio.jar
+%%JAVAJARDIR%%/JmolApplet0_ShapeSpecial.jar
+%%JAVAJARDIR%%/JmolApplet0_Smiles.jar
+%%JAVAJARDIR%%/JmolApplet0_Viewer.jar
+%%JAVAJARDIR%%/JmolApplet0_i18n.jar
+@dirrm %%DOCSDIR%%/source/xml2po-modes
+@dirrm %%DOCSDIR%%/source/po
+@dirrm %%DOCSDIR%%/source/history
+@dirrm %%DOCSDIR%%/source/guide
+@dirrm %%DOCSDIR%%/source/applet
+@dirrm %%DOCSDIR%%/source
+@dirrm %%DOCSDIR%%/JmolUserGuide
+@dirrm %%DOCSDIR%%