ports/123631: [NEW PORT] science/jmol : An Open-Source Java Viewer for Chemical Structures in 3D

Wen Heping wenheping at gmail.com
Tue May 13 16:10:03 UTC 2008 

>Number:         123631
>Category:       ports
>Synopsis:       [NEW PORT] science/jmol : An Open-Source Java Viewer for Chemical Structures in 3D
>Confidential:   no
>Severity:       non-critical
>Priority:       low
>Responsible:    freebsd-ports-bugs
>State:          open
>Quarter:        
>Keywords:       
>Date-Required:
>Class:          change-request
>Submitter-Id:   current-users
>Arrival-Date:   Tue May 13 16:10:02 UTC 2008
>Closed-Date:
>Last-Modified:
>Originator:     Wen Heping
>Release:        FreeBSD 7.0 release
>Organization:
ChangAn Middle School
>Environment:
FreeBSD fb7.wenjing.com 7.0-RELEASE FreeBSD 7.0-RELEASE #0: Sun Feb 24 19:59:52 UTC 2008     root at logan.cse.buffalo.edu:/usr/obj/usr/src/sys/GENERIC  i386

>Description:
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/

>How-To-Repeat:

>Fix:


Patch attached with submission follows:

# This is a shell archive.  Save it in a file, remove anything before
# this line, and then unpack it by entering "sh file".  Note, it may
# create directories; files and directories will be owned by you and
# have default permissions.
#
# This archive contains:
#
#	/usr/ports/science/jmol
#	/usr/ports/science/jmol/Makefile
#	/usr/ports/science/jmol/pkg-descr
#	/usr/ports/science/jmol/distinfo
#	/usr/ports/science/jmol/pkg-plist
#
echo c - /usr/ports/science/jmol
mkdir -p /usr/ports/science/jmol > /dev/null 2>&1
echo x - /usr/ports/science/jmol/Makefile
sed 's/^X//' >/usr/ports/science/jmol/Makefile << 'END-of-/usr/ports/science/jmol/Makefile'
X# Ports collection makefile for:	jmol
X# Date created:			May 11, 2008
X# Whom:				Wen heping <wenheping at gmail.com>
X#
X# $FreeBSD$
X#
X
XPORTNAME=	jmol
XPORTVERSION=	11.4.2
XCATEGORIES=	science java
XMASTER_SITES=	SF:source1 \
X		http://jmol.svn.sourceforge.net/viewvc/*checkout*/jmol/trunk/Jmol/selfSignedCertificate/:source2
XDISTFILES=	${PORTNAME}-${PORTVERSION}-full.tar.gz:source1 \
X		selfSignedCertificate.cer:source2 \
X		selfSignedCertificate.store:source2
XEXTRACT_ONLY=	${PORTNAME}-${PORTVERSION}-full.tar.gz
X
XMAINTAINER=	wenheping at gmail.com
XCOMMENT=	An Open-Source Java Viewer for Chemical Structures in 3D
X
XUSE_JAVA=	yes
XJAVA_VERSION=	1.4+
XWRKSRC=		${WRKDIR}/${PORTNAME}-${PORTVERSION}
XJMOL_FILES=	Jmol.jar JmolApplet.jar JmolApplet0.jar \
X		JmolApplet0_Core.jar JmolApplet0_Jars.jar \
X		JmolApplet0_Jvxl.jar JmolApplet0_Main.jar \
X		JmolApplet0_Popup.jar JmolApplet0_Quantum.jar \
X		JmolApplet0_ReadersCifPdb.jar JmolApplet0_ReadersMolXyz.jar \
X		JmolApplet0_ReadersMore.jar JmolApplet0_ReadersXml.jar \
X		JmolApplet0_ShapeBio.jar JmolApplet0_ShapeSpecial.jar \
X		JmolApplet0_Smiles.jar JmolApplet0_Viewer.jar \
X		JmolApplet0_i18n.jar
XJMOL_FILES_EXT=	Jmol.js
XSIGN_DIR=	${WRKSRC}/selfSignedCertificate
X
X.if !defined(WITHOUT_COMPILE)
XUSE_ANT=	yes
XALL_TARGET=	all
X.if !defined(NOPORTDOCS)
XALL_TARGET=	main
X.endif
X.else
XNO_BUILD=	yes
X.endif
X
X.include <bsd.port.pre.mk>
X
Xpre-fetch:
X	@${ECHO_MSG} ""
X	@${ECHO_MSG} "You may use the following build options:"
X	@${ECHO_MSG} ""
X	@${ECHO_MSG} "    WITHOUT_COMPILE=yes    Install the pre-compiled .jar file"
X	@${ECHO_MSG} ""
X
Xpost-extract:
X	@${MKDIR} ${SIGN_DIR}
X	@${CP} ${DISTDIR}/selfSignedCertificate.cer ${SIGN_DIR}
X	@${CP} ${DISTDIR}/selfSignedCertificate.store ${SIGN_DIR}
X
Xdo-install:
X.for j in ${JMOL_FILES_EXT}
X	${INSTALL_DATA} ${WRKSRC}/${j} ${JAVAJARDIR}
X.endfor
X
X.if !defined(WITHOUT_COMPILE)
X.for j in ${JMOL_FILES}
X	${INSTALL_DATA} ${WRKSRC}/build/${j} ${JAVAJARDIR}
X.endfor
X.else
X.for j in ${JMOL_FILES}
X	${INSTALL_DATA} ${WRKSRC}/${j} ${JAVAJARDIR}
X.endfor
X.endif
X
X.if !defined(NOPORTDOCS)
X	@${ECHO_MSG} -n ">> Installing documentation in ${DOCSDIR}..."
X	@cd ${WRKSRC}/doc && ${FIND} . -type d -exec ${MKDIR} ${DOCSDIR}/{} \;
X	@cd ${WRKSRC}/doc && ${FIND} . -type f -exec \
X		${INSTALL_DATA} {} ${DOCSDIR}/{} \;
X	@${ECHO_MSG} " [DONE]"
X.endif
X
X.include <bsd.port.post.mk>
END-of-/usr/ports/science/jmol/Makefile
echo x - /usr/ports/science/jmol/pkg-descr
sed 's/^X//' >/usr/ports/science/jmol/pkg-descr << 'END-of-/usr/ports/science/jmol/pkg-descr'
XJmol is a Java molecular viewer for 
Xthree-dimensional chemical structures. 
XFeatures include reading a variety 
Xof file types and output from quantum 
Xchemistry programs, and animation of 
Xmulti-frame files and computed normal 
Xmodes from quantum programs.
X
XWWW:  http://sourceforge.net/projects/jmol/
END-of-/usr/ports/science/jmol/pkg-descr
echo x - /usr/ports/science/jmol/distinfo
sed 's/^X//' >/usr/ports/science/jmol/distinfo << 'END-of-/usr/ports/science/jmol/distinfo'
XMD5 (jmol-11.4.2-full.tar.gz) = 58b0cd6a38be0c94d4943c1e74a7d8b5
XSHA256 (jmol-11.4.2-full.tar.gz) = 8890805394a8d0d0260739e230b30bbd3eb6c915fd5c6c6fc21478be9e29ecaf
XSIZE (jmol-11.4.2-full.tar.gz) = 15926387
XMD5 (selfSignedCertificate.cer) = ec6c4b413be88a8fab584399cc931d55
XSHA256 (selfSignedCertificate.cer) = 0fa14fd5f21593a328ba4439ac17b3b507969d71a2734e392239b83ae8ec2920
XSIZE (selfSignedCertificate.cer) = 735
XMD5 (selfSignedCertificate.store) = bf2be32212c831e4fa369809a639b75d
XSHA256 (selfSignedCertificate.store) = 81b69722530d94dc599ce79382a3386cce518baa7ab79fbb530d13483b51bed5
XSIZE (selfSignedCertificate.store) = 1516
END-of-/usr/ports/science/jmol/distinfo
echo x - /usr/ports/science/jmol/pkg-plist
sed 's/^X//' >/usr/ports/science/jmol/pkg-plist << 'END-of-/usr/ports/science/jmol/pkg-plist'
X%%DOCSDIR%%/JmolAppletGuide.html
X%%DOCSDIR%%/JmolDevelopersGuide.html
X%%DOCSDIR%%/JmolUserGuide/ch01.html
X%%DOCSDIR%%/JmolUserGuide/ch02.html
X%%DOCSDIR%%/JmolUserGuide/ch02s02.html
X%%DOCSDIR%%/JmolUserGuide/ch02s03.html
X%%DOCSDIR%%/JmolUserGuide/ch02s04.html
X%%DOCSDIR%%/JmolUserGuide/ch02s05.html
X%%DOCSDIR%%/JmolUserGuide/ch02s06.html
X%%DOCSDIR%%/JmolUserGuide/ch02s07.html
X%%DOCSDIR%%/JmolUserGuide/ch03.html
X%%DOCSDIR%%/JmolUserGuide/ch03s02.html
X%%DOCSDIR%%/JmolUserGuide/ch03s03.html
X%%DOCSDIR%%/JmolUserGuide/ch03s04.html
X%%DOCSDIR%%/JmolUserGuide/ch03s05.html
X%%DOCSDIR%%/JmolUserGuide/ch04.html
X%%DOCSDIR%%/JmolUserGuide/index.html
X%%DOCSDIR%%/docbook-xml-4.4.zip
X%%DOCSDIR%%/docbook-xsl-1.73.2.tar.gz
X%%DOCSDIR%%/ibm.license.html
X%%DOCSDIR%%/jcfl-1.2.6-source.tar.gz
X%%DOCSDIR%%/jpegEncoder.license
X%%DOCSDIR%%/lgpl.license
X%%DOCSDIR%%/rasmol26.license
X%%DOCSDIR%%/source/JmolAppletGuide.docbook.xml
X%%DOCSDIR%%/source/JmolAppletGuide_de.docbook.xml
X%%DOCSDIR%%/source/JmolAppletGuide_fr.docbook.xml
X%%DOCSDIR%%/source/JmolDevelopersGuide.docbook.xml
X%%DOCSDIR%%/source/JmolDevelopersGuide_de.docbook.xml
X%%DOCSDIR%%/source/JmolDevelopersGuide_fr.docbook.xml
X%%DOCSDIR%%/source/JmolGuide.docbook.xml
X%%DOCSDIR%%/source/JmolGuide_de.docbook.xml
X%%DOCSDIR%%/source/JmolGuide_fr.docbook.xml
X%%DOCSDIR%%/source/JmolHistory.xml
X%%DOCSDIR%%/source/JmolHistoryToHtml.xsl
X%%DOCSDIR%%/source/JmolHistory_fr.xml
X%%DOCSDIR%%/source/JmolHistory_nl.xml
X%%DOCSDIR%%/source/applet/browsers.docbook.xml
X%%DOCSDIR%%/source/applet/browsers_fr.docbook.xml
X%%DOCSDIR%%/source/applet/hardware.docbook.xml
X%%DOCSDIR%%/source/applet/hardware_fr.docbook.xml
X%%DOCSDIR%%/source/applet/intro.docbook.xml
X%%DOCSDIR%%/source/applet/intro_fr.docbook.xml
X%%DOCSDIR%%/source/applet/serverconfig.docbook.xml
X%%DOCSDIR%%/source/applet/serverconfig_fr.docbook.xml
X%%DOCSDIR%%/source/applet/usage.docbook.xml
X%%DOCSDIR%%/source/applet/usage_fr.docbook.xml
X%%DOCSDIR%%/source/guide/commandline.docbook.xml
X%%DOCSDIR%%/source/guide/commandline_fr.docbook.xml
X%%DOCSDIR%%/source/guide/intro.docbook.xml
X%%DOCSDIR%%/source/guide/intro_fr.docbook.xml
X%%DOCSDIR%%/source/guide/menus.docbook.xml
X%%DOCSDIR%%/source/guide/menus_fr.docbook.xml
X%%DOCSDIR%%/source/guide/scriptCommands.docbook.xml
X%%DOCSDIR%%/source/guide/scripts.docbook.xml
X%%DOCSDIR%%/source/guide/scripts_fr.docbook.xml
X%%DOCSDIR%%/source/history/changes.xml
X%%DOCSDIR%%/source/history/changes_fr.xml
X%%DOCSDIR%%/source/history/changes_nl.xml
X%%DOCSDIR%%/source/history/contributors.xml
X%%DOCSDIR%%/source/po/JmolAppletGuide.de.po
X%%DOCSDIR%%/source/po/JmolAppletGuide.pot
X%%DOCSDIR%%/source/po/JmolDevelopersGuide.de.po
X%%DOCSDIR%%/source/po/JmolDevelopersGuide.pot
X%%DOCSDIR%%/source/po/JmolGuide.de.po
X%%DOCSDIR%%/source/po/JmolGuide.pot
X%%DOCSDIR%%/source/xml2po-modes/docbook.py
X%%DOCSDIR%%/source/xml2po-modes/empty.py
X%%DOCSDIR%%/source/xml2po-modes/gs.py
X%%DOCSDIR%%/source/xml2po.bat
X%%DOCSDIR%%/source/xml2po.py
X%%DOCSDIR%%/source/xml2po.sh
X%%DOCSDIR%%/splash.ai
X%%JAVAJARDIR%%/Jmol.jar
X%%JAVAJARDIR%%/Jmol.js
X%%JAVAJARDIR%%/JmolApplet.jar
X%%JAVAJARDIR%%/JmolApplet0.jar
X%%JAVAJARDIR%%/JmolApplet0_Core.jar
X%%JAVAJARDIR%%/JmolApplet0_Jars.jar
X%%JAVAJARDIR%%/JmolApplet0_Jvxl.jar
X%%JAVAJARDIR%%/JmolApplet0_Main.jar
X%%JAVAJARDIR%%/JmolApplet0_Popup.jar
X%%JAVAJARDIR%%/JmolApplet0_Quantum.jar
X%%JAVAJARDIR%%/JmolApplet0_ReadersCifPdb.jar
X%%JAVAJARDIR%%/JmolApplet0_ReadersMolXyz.jar
X%%JAVAJARDIR%%/JmolApplet0_ReadersMore.jar
X%%JAVAJARDIR%%/JmolApplet0_ReadersXml.jar
X%%JAVAJARDIR%%/JmolApplet0_ShapeBio.jar
X%%JAVAJARDIR%%/JmolApplet0_ShapeSpecial.jar
X%%JAVAJARDIR%%/JmolApplet0_Smiles.jar
X%%JAVAJARDIR%%/JmolApplet0_Viewer.jar
X%%JAVAJARDIR%%/JmolApplet0_i18n.jar
X at dirrm %%DOCSDIR%%/source/xml2po-modes
X at dirrm %%DOCSDIR%%/source/po
X at dirrm %%DOCSDIR%%/source/history
X at dirrm %%DOCSDIR%%/source/guide
X at dirrm %%DOCSDIR%%/source/applet
X at dirrm %%DOCSDIR%%/source
X at dirrm %%DOCSDIR%%/JmolUserGuide
X at dirrm %%DOCSDIR%%
END-of-/usr/ports/science/jmol/pkg-plist
exit



>Release-Note:
>Audit-Trail:
>Unformatted:

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