Date: Tue, 15 Jan 2002 10:19:19 +1100 (EST) From: Camson Huynh <chuynh@biolateral.com.au> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/33902: New Port: biology/spdbv Message-ID: <200201142319.g0ENJJo21186@gateway.biolateral.com.au>
next in thread | raw e-mail | index | archive | help
>Number: 33902 >Category: ports >Synopsis: New Port: biology/spdbv >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Mon Jan 14 15:20:01 PST 2002 >Closed-Date: >Last-Modified: >Originator: Camson Huynh >Release: FreeBSD 4.5-PRERELEASE i386 >Organization: BioLateral Pty Ltd >Environment: System: FreeBSD oasis.bio 4.5-PRERELEASE FreeBSD 4.5-PRERELEASE #2: Mon Dec 24 11:32:35 EST 2001 root@oasis.bio:/usr/obj/usr/src/sys/OASIS i386 >Description: Swiss-PdbViewer is an application that provides a user friendly interface allowing to analyse several proteins at the same time. The proteins can be superimposed in order to deduce structural alignments and compare their active sites or any other relevant parts. Amino acid mutations, H-bonds, angles and distances between atoms are easy to obtain thanks to the intuitive graphic and menu interface. Moreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated homology modelling server developped at Glaxo Welcome Experimental Research in Geneva. Working with these two programs greatly reduces the amount of work necessary to generate models, as it is possible to thread a protein primary sequence onto a 3D template and get an immediate feedback of how well the threaded protein will be accepted by the reference structure before submitting a request to build missing loops and refine sidechain packing. Swiss-PdbViewer can also read electron density maps, and provides various tools to build into the density. In addition, various modelling tools are integrated and command files for popular energy minimisation packages can be generated. Finally, as a special bonus, POV-Ray scenes can be generated from the current view in order to make stunning ray-traced quality images. WWW: http://www.expasy.ch/spdbv/ >How-To-Repeat: >Fix: # 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: # # spdbv # spdbv/files # spdbv/files/patch-aa # spdbv/files/patch-ab # spdbv/pkg-descr # spdbv/pkg-comment # spdbv/distinfo # spdbv/Makefile # spdbv/pkg-plist # echo c - spdbv mkdir -p spdbv > /dev/null 2>&1 echo c - spdbv/files mkdir -p spdbv/files > /dev/null 2>&1 echo x - spdbv/files/patch-aa sed 's/^X//' >spdbv/files/patch-aa << 'END-of-spdbv/files/patch-aa' X--- install.sh.orig Mon Dec 4 21:31:45 2000 X+++ install.sh Thu Dec 20 10:15:42 2001 X@@ -7,10 +7,9 @@ X SPDBVNEEDOSbis="Linux" X X SPDBVUSERDIR="$HOME" X-SPDBVSHAREDIR="/usr/share" X SPDBVDIR="SPDBV" X SPDBVSTUFF="_stuff_" X-SPDBVDEST="" X+SPDBVDEST="${PREFIX}" X SPDBVOSVERSION=`uname -r` X SPDBVOS=`uname -s` X if [ $SPDBVOS = IRIX64 ]; then X@@ -27,20 +26,8 @@ X echo "Will install the shared files in $SPDBVDEST." X if [ -d $SPDBVDEST/$SPDBVDIR ]; then X echo "Shared files are already installed on this system." X- echo "Delete old files and reinstall (Y/N)?" X- read INP X- if [ $INP = "Y" -o $INP = "y" ]; then X- echo " " X- echo "will reinstall" X- if [ -w $SPDBVDEST/$SPDBVDIR ]; then X- rm -r $SPDBVDEST/$SPDBVDIR X- else X- echo "Could not delete shared files." X- abort X- fi X- else X- abort X- fi X+ echo " " X+ echo "will reinstall" X fi X mkdir $SPDBVDEST/$SPDBVDIR #2> /dev/null X if [ ! -d $SPDBVDEST/$SPDBVDIR ]; then X@@ -64,11 +51,11 @@ X chmod ugo+rx $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh X X #try to make link from /usr/bin/spdbv to ./spdbv.sh X- if [ ! -w /usr/bin/ ]; then X+ if [ ! -w ${SPDBVDEST}/bin/ ]; then X echo " " X- echo "Can't make a link from /usr/bin/spdbv to spdbv.sh" X+ echo "Can't make a link from ${SPDBVDEST}/bin/spdbv to spdbv.sh" X else X- ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh /usr/bin/spdbv X+ ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh ${SPDBVDEST}/bin/spdbv X fi X } X X@@ -82,65 +69,18 @@ X echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)" X echo " " X echo " " X- echo " Please follow the instructions below." X- echo " " X- echo "Where do you want me to install the files:" X- echo "globally in /usr/share/SPDBV -> G" X- echo "or just locally in ~/SPDBV -> L" X- echo "something different -> O" X- echo "(G/L/O)?" X- read DEST X- X- SPDBVDEST="" X- if [ $DEST = "G" -o $DEST = "g" ]; then X- SPDBVDEST=$SPDBVSHAREDIR X- elif [ $DEST = "L" -o $DEST = "l" ]; then X- SPDBVDEST=$SPDBVUSERDIR X- elif [ $DEST = "O" -o $DEST = "o" ]; then X- echo "enter target Path where to install directory SPDBV:" X- read SPDBVDEST X- fi X- X- if [ -z $SPDBVDEST ]; then X- echo "" X- echo "$SPDBVDEST is not a valid answer. 1" X- echo "" X- echo "continue .. hit any key" X- read DEST X- mainmenu X- fi X- if [ ! '(' -d $SPDBVDEST ')' ]; then X- echo "" X- echo "$SPDBVDEST is not a valid answer. 2" X- echo "" X- echo "continue .. hit any key" X- read DEST X- mainmenu X- fi X X makesharedinst X X-# clear X- X echo " " X echo " SPDBV - Swiss PDB Viewer" X echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)" X echo " " X echo "Installation completed." X- echo "Start your copy of SPDBV with the script $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh" X echo "" X echo "ENJOY SPDBV!" X exit X } X- X-# test for the right os X-if [ $SPDBVOS != $SPDBVNEEDOS ]; then X- if [ $SPDBVOS != $SPDBVNEEDOSbis ]; then X- echo "SPDBV $SPDBVVERSION ($SPDBVNEEDOS) is intended to run on hardware under $SPDBVNEEDOS." X- abort X- exit X- fi X-fi X X # start up the mainmenu X mainmenu END-of-spdbv/files/patch-aa echo x - spdbv/files/patch-ab sed 's/^X//' >spdbv/files/patch-ab << 'END-of-spdbv/files/patch-ab' X--- SPDBV/bin/spdbv-orig.sh.orig Thu Dec 20 10:11:25 2001 X+++ SPDBV/bin/spdbv-orig.sh Thu Dec 20 10:26:00 2001 X@@ -1,6 +1,8 @@ X ARCH=`uname -s` X if [ $ARCH = IRIX64 ]; then X ARCH=IRIX X+elif [ $ARCH = FreeBSD ]; then X+ ARCH=Linux X fi X SPDBV_TEMP=$HOME/SPDBV/temp X SPDBV_DOWNLOAD=$HOME/SPDBV/download X@@ -38,7 +40,5 @@ X #xrdb -override $SPDBV_BASE/app-defaults/Spdbv X X #start the SPDBV, reroute stderr to nirvana X-{ X- $SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $* X-} 2> /dev/null X+$SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $* X #done. END-of-spdbv/files/patch-ab echo x - spdbv/pkg-descr sed 's/^X//' >spdbv/pkg-descr << 'END-of-spdbv/pkg-descr' XSwiss-PdbViewer is an application that provides a user friendly interface Xallowing to analyse several proteins at the same time. The proteins can be Xsuperimposed in order to deduce structural alignments and compare their Xactive sites or any other relevant parts. Amino acid mutations, H-bonds, Xangles and distances between atoms are easy to obtain thanks to the Xintuitive graphic and menu interface. X XMoreover, Swiss-PdbViewer is tightly linked to Swiss-Model, an automated Xhomology modelling server developped at Glaxo Welcome Experimental Research Xin Geneva. Working with these two programs greatly reduces the amount of work Xnecessary to generate models, as it is possible to thread a protein primary Xsequence onto a 3D template and get an immediate feedback of how well the Xthreaded protein will be accepted by the reference structure before Xsubmitting a request to build missing loops and refine sidechain packing. X XSwiss-PdbViewer can also read electron density maps, and provides various Xtools to build into the density. In addition, various modelling tools are Xintegrated and command files for popular energy minimisation packages can be Xgenerated. X XFinally, as a special bonus, POV-Ray scenes can be generated from the Xcurrent view in order to make stunning ray-traced quality images. X XWWW: http://www.expasy.ch/spdbv/ END-of-spdbv/pkg-descr echo x - spdbv/pkg-comment sed 's/^X//' >spdbv/pkg-comment << 'END-of-spdbv/pkg-comment' XDeep View Swiss-PdbViewer is a Protein viewer and analysis tool END-of-spdbv/pkg-comment echo x - spdbv/distinfo sed 's/^X//' >spdbv/distinfo << 'END-of-spdbv/distinfo' XMD5 (spdbv37b2_IRIX_Linux.tar.gz) = 28513cb85c8e09493d8be535e76076a3 END-of-spdbv/distinfo echo x - spdbv/Makefile sed 's/^X//' >spdbv/Makefile << 'END-of-spdbv/Makefile' X# New ports collection makefile for: spdbv X# Date created: 15 Jan 2002 X# Whom: chuynh@biolateral.com.au X# X# $FreeBSD$ X# X XPORTNAME= spdbv XPORTVERSION= 37b2 XCATEGORIES= biology XMASTER_SITES= http://au.expasy.org/spdbv/program/ \ X http://www.expasy.org/spdbv/program/ \ X http://tw.expasy.org/spdbv/program/ \ X http://cn.expasy.org/spdbv/program/ \ X http://ca.expasy.org/spdbv/program/ \ X http://kr.expasy.org/spdbv/program/ \ X http://inn-prot.weizmann.ac.il/spdbv/program/\ X http://www.usm.maine.edu/spdbv/program/ \ X http://www.genebee.msu.ru/spdbv/program/ XDISTNAME= ${PORTNAME}${PORTVERSION}_IRIX_Linux X XMAINTAINER= chuynh@biolateral.com.au X XRUN_DEPENDS= ${LINUXBASE}${X11BASE}/lib/libMesaGL.so.3:${PORTSDIR}/graphics/linux_mesa3 X XSPDBV= SPDBV X XWRKSRC= ${WRKDIR}/SPDBV_DISTRIBUTION X XNO_BUILD= yes XNO_CDROM= "Must be downloaded direct from Expasy via www interface" X Xdo-install: X @cd ${WRKSRC}; ${SETENV} PREFIX=${PREFIX} ./install.sh X X# PLIST_SUB= PORTVERSION="${PORTVERSION}" X X.include <bsd.port.mk> END-of-spdbv/Makefile echo x - spdbv/pkg-plist sed 's/^X//' >spdbv/pkg-plist << 'END-of-spdbv/pkg-plist' XSPDBV/_stuff_/AlignWnd.hlp XSPDBV/_stuff_/CavitInf.hlp XSPDBV/_stuff_/CtrlPanl.hlp XSPDBV/_stuff_/DispWnd.hlp XSPDBV/_stuff_/LayerInf.hlp XSPDBV/_stuff_/RamaWnd.hlp XSPDBV/_stuff_/Rotolib.aa XSPDBV/_stuff_/Rotolib1.aa XSPDBV/_stuff_/Rotolib2.aa XSPDBV/_stuff_/SM_req.htm XSPDBV/_stuff_/SM_templ.htm XSPDBV/_stuff_/XtalInf.hlp XSPDBV/_stuff_/_loopDB_ XSPDBV/_stuff_/crystmov.txt XSPDBV/_stuff_/crystsym.txt XSPDBV/_stuff_/default.PP XSPDBV/_stuff_/grmparam/angles.prm XSPDBV/_stuff_/grmparam/bonds.prm XSPDBV/_stuff_/grmparam/improper.prm XSPDBV/_stuff_/grmparam/nbondsel.prm XSPDBV/_stuff_/grmparam/nonbonds.prm XSPDBV/_stuff_/grmparam/torsion.prm XSPDBV/_stuff_/grmtopol/ALA.tpl XSPDBV/_stuff_/grmtopol/ARG.tpl XSPDBV/_stuff_/grmtopol/ARGN.tpl XSPDBV/_stuff_/grmtopol/ASN.tpl XSPDBV/_stuff_/grmtopol/ASP.tpl XSPDBV/_stuff_/grmtopol/ASPH.tpl XSPDBV/_stuff_/grmtopol/CA2.tpl XSPDBV/_stuff_/grmtopol/CL.tpl XSPDBV/_stuff_/grmtopol/CU.tpl XSPDBV/_stuff_/grmtopol/CU1.tpl XSPDBV/_stuff_/grmtopol/CYS.tpl XSPDBV/_stuff_/grmtopol/CYS1.tpl XSPDBV/_stuff_/grmtopol/CYS2.tpl XSPDBV/_stuff_/grmtopol/CYSH.tpl XSPDBV/_stuff_/grmtopol/FE.tpl XSPDBV/_stuff_/grmtopol/GLN.tpl XSPDBV/_stuff_/grmtopol/GLU.tpl XSPDBV/_stuff_/grmtopol/GLUH.tpl XSPDBV/_stuff_/grmtopol/GLY.tpl XSPDBV/_stuff_/grmtopol/H2O.tpl XSPDBV/_stuff_/grmtopol/HHT.tpl XSPDBV/_stuff_/grmtopol/HIS1.tpl XSPDBV/_stuff_/grmtopol/HISA.tpl XSPDBV/_stuff_/grmtopol/HISB.tpl XSPDBV/_stuff_/grmtopol/HISH.tpl XSPDBV/_stuff_/grmtopol/ILE.tpl XSPDBV/_stuff_/grmtopol/LEU.tpl XSPDBV/_stuff_/grmtopol/LYS.tpl XSPDBV/_stuff_/grmtopol/LYSH.tpl XSPDBV/_stuff_/grmtopol/MET.tpl XSPDBV/_stuff_/grmtopol/MG.tpl XSPDBV/_stuff_/grmtopol/MN.tpl XSPDBV/_stuff_/grmtopol/MSE.tpl XSPDBV/_stuff_/grmtopol/NA.tpl XSPDBV/_stuff_/grmtopol/OXT.tpl XSPDBV/_stuff_/grmtopol/PHE.tpl XSPDBV/_stuff_/grmtopol/PRO.tpl XSPDBV/_stuff_/grmtopol/SEP.tpl XSPDBV/_stuff_/grmtopol/SER.tpl XSPDBV/_stuff_/grmtopol/SO42.tpl XSPDBV/_stuff_/grmtopol/THR.tpl XSPDBV/_stuff_/grmtopol/TPO.tpl XSPDBV/_stuff_/grmtopol/TRP.tpl XSPDBV/_stuff_/grmtopol/TYR.tpl XSPDBV/_stuff_/grmtopol/VAL.tpl XSPDBV/_stuff_/grmtopol/ZN.tpl XSPDBV/_stuff_/images/1bnhsmal.gif XSPDBV/_stuff_/images/1crnE.gif XSPDBV/_stuff_/images/1crnE2.gif XSPDBV/_stuff_/images/1ldbcont.gif XSPDBV/_stuff_/images/1ldbfull.gif XSPDBV/_stuff_/images/1ldbyell.gif XSPDBV/_stuff_/images/6pticell.gif XSPDBV/_stuff_/images/6ptiwat.gif XSPDBV/_stuff_/images/FASL.gif XSPDBV/_stuff_/images/activsit.gif XSPDBV/_stuff_/images/align.gif XSPDBV/_stuff_/images/balstick.gif XSPDBV/_stuff_/images/bg.gif XSPDBV/_stuff_/images/control.gif XSPDBV/_stuff_/images/edm.gif XSPDBV/_stuff_/images/edm2.gif XSPDBV/_stuff_/images/hb.gif XSPDBV/_stuff_/images/hb_inter.jpg XSPDBV/_stuff_/images/hb_light.jpg XSPDBV/_stuff_/images/hb_pov.jpg XSPDBV/_stuff_/images/hb_std.gif XSPDBV/_stuff_/images/hb_wire.gif XSPDBV/_stuff_/images/home.gif XSPDBV/_stuff_/images/ldb61_65.gif XSPDBV/_stuff_/images/logo.gif XSPDBV/_stuff_/images/mixed.gif XSPDBV/_stuff_/images/model1.gif XSPDBV/_stuff_/images/model2.gif XSPDBV/_stuff_/images/pov3labl.gif XSPDBV/_stuff_/images/rama.gif XSPDBV/_stuff_/images/rib1.gif XSPDBV/_stuff_/images/rib2.gif XSPDBV/_stuff_/images/rib3.gif XSPDBV/_stuff_/images/rib3b.gif XSPDBV/_stuff_/images/smooth3.jpg XSPDBV/_stuff_/images/smooth3m.jpg XSPDBV/_stuff_/images/smooth6.jpg XSPDBV/_stuff_/images/smooth6m.jpg XSPDBV/_stuff_/images/spacefil.gif XSPDBV/_stuff_/images/sticks.gif XSPDBV/_stuff_/images/sup1.gif XSPDBV/_stuff_/images/sup2.gif XSPDBV/_stuff_/images/thread1.gif XSPDBV/_stuff_/images/thread2.gif XSPDBV/_stuff_/images/tools1.gif XSPDBV/_stuff_/images/tools2.gif XSPDBV/_stuff_/images/tools3.gif XSPDBV/_stuff_/images/ucell.gif XSPDBV/_stuff_/images/wind.gif XSPDBV/_stuff_/initloop.txt XSPDBV/_stuff_/mainpage.htm XSPDBV/_stuff_/manual.htm XSPDBV/_stuff_/text/activsit.htm XSPDBV/_stuff_/text/amber_pl.htm XSPDBV/_stuff_/text/ambertut.htm XSPDBV/_stuff_/text/build.htm XSPDBV/_stuff_/text/charm_pl.htm XSPDBV/_stuff_/text/charmtut.htm XSPDBV/_stuff_/text/color.htm XSPDBV/_stuff_/text/cshrc.htm XSPDBV/_stuff_/text/ctrlpanl.htm XSPDBV/_stuff_/text/disclaim.htm XSPDBV/_stuff_/text/display.htm XSPDBV/_stuff_/text/distort.htm XSPDBV/_stuff_/text/edm.htm XSPDBV/_stuff_/text/edmtut.htm XSPDBV/_stuff_/text/fabp.htm XSPDBV/_stuff_/text/feedback.htm XSPDBV/_stuff_/text/files.htm XSPDBV/_stuff_/text/gallery.htm XSPDBV/_stuff_/text/gromo_pl.htm XSPDBV/_stuff_/text/gromotut.htm XSPDBV/_stuff_/text/hew.htm XSPDBV/_stuff_/text/index.htm XSPDBV/_stuff_/text/pov.htm XSPDBV/_stuff_/text/loop.htm XSPDBV/_stuff_/text/main.htm XSPDBV/_stuff_/text/minim.htm XSPDBV/_stuff_/text/modeling.htm XSPDBV/_stuff_/text/moving.htm XSPDBV/_stuff_/text/mutation.htm XSPDBV/_stuff_/text/phipsi.htm XSPDBV/_stuff_/text/povscene.htm XSPDBV/_stuff_/text/prefs.htm XSPDBV/_stuff_/text/rama.htm XSPDBV/_stuff_/text/refs.htm XSPDBV/_stuff_/text/rendcomp.htm XSPDBV/_stuff_/text/render.htm XSPDBV/_stuff_/text/ribbon.htm XSPDBV/_stuff_/text/select.htm XSPDBV/_stuff_/text/selmenu.htm XSPDBV/_stuff_/text/superpos.htm XSPDBV/_stuff_/text/tips.htm XSPDBV/_stuff_/text/toolmenu.htm XSPDBV/_stuff_/text/tools.htm XSPDBV/_stuff_/text/torsion.htm XSPDBV/_stuff_/text/transfo.htm XSPDBV/_stuff_/text/tutorial.htm XSPDBV/_stuff_/text/xsymtut.htm XSPDBV/_stuff_/readme.txt XSPDBV/_stuff_/smalloop.txt XSPDBV/_stuff_/tinyloop.txt XSPDBV/bin/spdbv.IRIX XSPDBV/bin/spdbv.Linux XSPDBV/bin/spdbv.sh XSPDBV/readme.txt XSPDBV/spdbv37b1.txt XSPDBV/spdbv37b2.txt XSPDBV/user.tar.gz Xbin/spdbv X@dirrm SPDBV/_stuff_/grmparam X@dirrm SPDBV/_stuff_/grmtopol X@dirrm SPDBV/_stuff_/images X@dirrm SPDBV/_stuff_/text X@dirrm SPDBV/_stuff_ X@dirrm SPDBV/bin X@dirrm SPDBV END-of-spdbv/pkg-plist exit >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
Want to link to this message? Use this URL: <https://mail-archive.FreeBSD.org/cgi/mid.cgi?200201142319.g0ENJJo21186>