7 files changed, 387 insertions, 0 deletions

diff --git a/biology/spdbv/Makefile b/biology/spdbv/Makefile
new file mode 100644
index 000000000000..003a5ce0d540
--- /dev/null
+++ b/biology/spdbv/Makefile
@@ -0,0 +1,38 @@
+# New ports collection makefile for:	spdbv
+# Date created:				15 Jan 2002
+# Whom:					chuynh@biolateral.com.au
+#
+# $FreeBSD$
+#
+
+PORTNAME=	spdbv
+PORTVERSION=	37b2
+CATEGORIES=	biology
+MASTER_SITES=	http://au.expasy.org/spdbv/program/ \
+				http://www.expasy.org/spdbv/program/ \
+				http://tw.expasy.org/spdbv/program/ \
+				http://cn.expasy.org/spdbv/program/ \
+				http://ca.expasy.org/spdbv/program/ \
+				http://kr.expasy.org/spdbv/program/ \
+				http://inn-prot.weizmann.ac.il/spdbv/program/\
+				http://www.usm.maine.edu/spdbv/program/ \
+				http://www.genebee.msu.ru/spdbv/program/
+DISTNAME=	${PORTNAME}${PORTVERSION}_IRIX_Linux
+
+MAINTAINER=	chuynh@biolateral.com.au
+
+RUN_DEPENDS=	${LINUXBASE}${X11BASE}/lib/libMesaGL.so.3:${PORTSDIR}/graphics/linux_mesa3
+
+SPDBV=	SPDBV
+
+WRKSRC=		${WRKDIR}/SPDBV_DISTRIBUTION
+
+NO_BUILD=	yes
+NO_CDROM=	"Must be downloaded direct from Expasy via www interface"
+
+do-install:
+	@cd ${WRKSRC}; ${SETENV} PREFIX=${PREFIX} ./install.sh
+
+# PLIST_SUB=	PORTVERSION="${PORTVERSION}"
+
+.include <bsd.port.mk>
diff --git a/biology/spdbv/distinfo b/biology/spdbv/distinfo
new file mode 100644
index 000000000000..3b3ba8302d96
--- /dev/null
+++ b/biology/spdbv/distinfo
@@ -0,0 +1 @@
+MD5 (spdbv37b2_IRIX_Linux.tar.gz) = 28513cb85c8e09493d8be535e76076a3
diff --git a/biology/spdbv/files/patch-aa b/biology/spdbv/files/patch-aa
new file mode 100644
index 000000000000..125c1dd245b8
--- /dev/null
+++ b/biology/spdbv/files/patch-aa
@@ -0,0 +1,118 @@
+--- install.sh.orig	Mon Dec  4 21:31:45 2000
++++ install.sh	Thu Dec 20 10:15:42 2001
+@@ -7,10 +7,9 @@
+ SPDBVNEEDOSbis="Linux"
+ 
+ SPDBVUSERDIR="$HOME"
+-SPDBVSHAREDIR="/usr/share"
+ SPDBVDIR="SPDBV"
+ SPDBVSTUFF="_stuff_"
+-SPDBVDEST=""
++SPDBVDEST="${PREFIX}"
+ SPDBVOSVERSION=`uname -r`
+ SPDBVOS=`uname -s`
+ if [ $SPDBVOS = IRIX64 ]; then
+@@ -27,20 +26,8 @@
+     echo "Will install the shared files in $SPDBVDEST."
+     if [  -d $SPDBVDEST/$SPDBVDIR ]; then
+         echo "Shared files are already installed on this system."
+-        echo "Delete old files and reinstall (Y/N)?"
+-        read INP
+-        if [ $INP = "Y" -o $INP = "y" ]; then
+-            echo " "
+-            echo "will reinstall"
+-	    if [ -w $SPDBVDEST/$SPDBVDIR ]; then
+-		rm -r $SPDBVDEST/$SPDBVDIR
+-	    else
+-	        echo "Could not delete shared files."
+-		abort
+-	    fi
+-        else
+-            abort
+-        fi
++        echo " "
++        echo "will reinstall"
+     fi
+     mkdir $SPDBVDEST/$SPDBVDIR #2> /dev/null
+     if [ ! -d $SPDBVDEST/$SPDBVDIR ]; then
+@@ -64,11 +51,11 @@
+     chmod ugo+rx $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh
+ 
+     #try to make link from /usr/bin/spdbv to ./spdbv.sh
+-    if [ ! -w /usr/bin/ ]; then
++    if [ ! -w ${SPDBVDEST}/bin/ ]; then
+        echo " "
+-       echo "Can't make a link from /usr/bin/spdbv to spdbv.sh"
++       echo "Can't make a link from ${SPDBVDEST}/bin/spdbv to spdbv.sh"
+     else
+-       ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh /usr/bin/spdbv
++       ln -sf $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh ${SPDBVDEST}/bin/spdbv
+     fi
+ }
+ 
+@@ -82,65 +69,18 @@
+    echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)"
+    echo " " 
+    echo " " 
+-   echo " Please follow the instructions below."
+-   echo " "
+-   echo "Where do you want me to install the files:"
+-   echo "globally in /usr/share/SPDBV  ->  G"
+-   echo "or just locally in ~/SPDBV    ->  L"
+-   echo "something different           ->  O"
+-   echo "(G/L/O)?"
+-   read DEST
+-
+-   SPDBVDEST=""
+-   if [ $DEST = "G" -o $DEST = "g" ]; then
+-       SPDBVDEST=$SPDBVSHAREDIR
+-   elif [ $DEST = "L" -o $DEST = "l" ]; then
+-       SPDBVDEST=$SPDBVUSERDIR
+-   elif [ $DEST = "O" -o $DEST = "o" ]; then
+-       echo "enter target Path where to install directory SPDBV:"
+-       read SPDBVDEST
+-   fi
+-
+-   if [ -z $SPDBVDEST ]; then
+-       echo ""
+-       echo "$SPDBVDEST is not a valid answer. 1"
+-       echo ""
+-       echo "continue .. hit any key"
+-       read DEST
+-       mainmenu
+-   fi
+-   if [ ! '(' -d $SPDBVDEST ')' ]; then
+-       echo ""
+-       echo "$SPDBVDEST is not a valid answer. 2"
+-       echo ""
+-       echo "continue .. hit any key"
+-       read DEST
+-       mainmenu
+-   fi
+ 
+    makesharedinst
+ 
+-#   clear
+-
+    echo " "
+    echo " SPDBV - Swiss PDB Viewer" 
+    echo " Installation script for Release $SPDBVVERSION ($SPDBVNEEDOS)"
+    echo " "
+    echo "Installation completed."
+-   echo "Start your copy of SPDBV with the script $SPDBVDEST/$SPDBVDIR/bin/spdbv.sh"
+    echo ""
+    echo "ENJOY SPDBV!"
+    exit
+ }
+-
+-# test for the right os
+-if [ $SPDBVOS != $SPDBVNEEDOS ]; then
+-  if [ $SPDBVOS != $SPDBVNEEDOSbis ]; then 
+-    echo "SPDBV $SPDBVVERSION ($SPDBVNEEDOS) is intended to run on hardware under $SPDBVNEEDOS."
+-    abort
+-    exit
+-  fi
+-fi
+ 
+ # start up the mainmenu
+ mainmenu 
diff --git a/biology/spdbv/files/patch-ab b/biology/spdbv/files/patch-ab
new file mode 100644
index 000000000000..48bb1215f83d
--- /dev/null
+++ b/biology/spdbv/files/patch-ab
@@ -0,0 +1,20 @@
+--- SPDBV/bin/spdbv-orig.sh.orig	Thu Dec 20 10:11:25 2001
++++ SPDBV/bin/spdbv-orig.sh	Thu Dec 20 10:26:00 2001
+@@ -1,6 +1,8 @@
+ ARCH=`uname -s`
+ if [ $ARCH = IRIX64 ]; then
+ 	ARCH=IRIX
++elif [ $ARCH = FreeBSD ]; then
++	ARCH=Linux
+ fi
+ SPDBV_TEMP=$HOME/SPDBV/temp
+ SPDBV_DOWNLOAD=$HOME/SPDBV/download
+@@ -38,7 +40,5 @@
+ #xrdb -override $SPDBV_BASE/app-defaults/Spdbv
+ 
+ #start the SPDBV, reroute stderr to nirvana
+-{
+-   $SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $*
+-} 2> /dev/null
++$SPDBV_BASE/bin/$SPDBV_RELEASE.$ARCH $*
+ #done.
diff --git a/biology/spdbv/pkg-comment b/biology/spdbv/pkg-comment
new file mode 100644
index 000000000000..5f9f33b5bb79
--- /dev/null
+++ b/biology/spdbv/pkg-comment
@@ -0,0 +1 @@
+Deep View Swiss-PdbViewer is a Protein viewer and analysis tool
diff --git a/biology/spdbv/pkg-descr b/biology/spdbv/pkg-descr
new file mode 100644
index 000000000000..c35f6ac20ac5
--- /dev/null
+++ b/biology/spdbv/pkg-descr
@@ -0,0 +1,24 @@
+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/
diff --git a/biology/spdbv/pkg-plist b/biology/spdbv/pkg-plist
new file mode 100644
index 000000000000..80d6959e803e
--- /dev/null
+++ b/biology/spdbv/pkg-plist
@@ -0,0 +1,185 @@
+SPDBV/_stuff_/AlignWnd.hlp
+SPDBV/_stuff_/CavitInf.hlp
+SPDBV/_stuff_/CtrlPanl.hlp
+SPDBV/_stuff_/DispWnd.hlp
+SPDBV/_stuff_/LayerInf.hlp
+SPDBV/_stuff_/RamaWnd.hlp
+SPDBV/_stuff_/Rotolib.aa
+SPDBV/_stuff_/Rotolib1.aa
+SPDBV/_stuff_/Rotolib2.aa
+SPDBV/_stuff_/SM_req.htm
+SPDBV/_stuff_/SM_templ.htm
+SPDBV/_stuff_/XtalInf.hlp
+SPDBV/_stuff_/_loopDB_
+SPDBV/_stuff_/crystmov.txt
+SPDBV/_stuff_/crystsym.txt
+SPDBV/_stuff_/default.PP
+SPDBV/_stuff_/grmparam/angles.prm
+SPDBV/_stuff_/grmparam/bonds.prm
+SPDBV/_stuff_/grmparam/improper.prm
+SPDBV/_stuff_/grmparam/nbondsel.prm
+SPDBV/_stuff_/grmparam/nonbonds.prm
+SPDBV/_stuff_/grmparam/torsion.prm
+SPDBV/_stuff_/grmtopol/ALA.tpl
+SPDBV/_stuff_/grmtopol/ARG.tpl
+SPDBV/_stuff_/grmtopol/ARGN.tpl
+SPDBV/_stuff_/grmtopol/ASN.tpl
+SPDBV/_stuff_/grmtopol/ASP.tpl
+SPDBV/_stuff_/grmtopol/ASPH.tpl
+SPDBV/_stuff_/grmtopol/CA2.tpl
+SPDBV/_stuff_/grmtopol/CL.tpl
+SPDBV/_stuff_/grmtopol/CU.tpl
+SPDBV/_stuff_/grmtopol/CU1.tpl
+SPDBV/_stuff_/grmtopol/CYS.tpl
+SPDBV/_stuff_/grmtopol/CYS1.tpl
+SPDBV/_stuff_/grmtopol/CYS2.tpl
+SPDBV/_stuff_/grmtopol/CYSH.tpl
+SPDBV/_stuff_/grmtopol/FE.tpl
+SPDBV/_stuff_/grmtopol/GLN.tpl
+SPDBV/_stuff_/grmtopol/GLU.tpl
+SPDBV/_stuff_/grmtopol/GLUH.tpl
+SPDBV/_stuff_/grmtopol/GLY.tpl
+SPDBV/_stuff_/grmtopol/H2O.tpl
+SPDBV/_stuff_/grmtopol/HHT.tpl
+SPDBV/_stuff_/grmtopol/HIS1.tpl
+SPDBV/_stuff_/grmtopol/HISA.tpl
+SPDBV/_stuff_/grmtopol/HISB.tpl
+SPDBV/_stuff_/grmtopol/HISH.tpl
+SPDBV/_stuff_/grmtopol/ILE.tpl
+SPDBV/_stuff_/grmtopol/LEU.tpl
+SPDBV/_stuff_/grmtopol/LYS.tpl
+SPDBV/_stuff_/grmtopol/LYSH.tpl
+SPDBV/_stuff_/grmtopol/MET.tpl
+SPDBV/_stuff_/grmtopol/MG.tpl
+SPDBV/_stuff_/grmtopol/MN.tpl
+SPDBV/_stuff_/grmtopol/MSE.tpl
+SPDBV/_stuff_/grmtopol/NA.tpl
+SPDBV/_stuff_/grmtopol/OXT.tpl
+SPDBV/_stuff_/grmtopol/PHE.tpl
+SPDBV/_stuff_/grmtopol/PRO.tpl
+SPDBV/_stuff_/grmtopol/SEP.tpl
+SPDBV/_stuff_/grmtopol/SER.tpl
+SPDBV/_stuff_/grmtopol/SO42.tpl
+SPDBV/_stuff_/grmtopol/THR.tpl
+SPDBV/_stuff_/grmtopol/TPO.tpl
+SPDBV/_stuff_/grmtopol/TRP.tpl
+SPDBV/_stuff_/grmtopol/TYR.tpl
+SPDBV/_stuff_/grmtopol/VAL.tpl
+SPDBV/_stuff_/grmtopol/ZN.tpl
+SPDBV/_stuff_/images/1bnhsmal.gif
+SPDBV/_stuff_/images/1crnE.gif
+SPDBV/_stuff_/images/1crnE2.gif
+SPDBV/_stuff_/images/1ldbcont.gif
+SPDBV/_stuff_/images/1ldbfull.gif
+SPDBV/_stuff_/images/1ldbyell.gif
+SPDBV/_stuff_/images/6pticell.gif
+SPDBV/_stuff_/images/6ptiwat.gif
+SPDBV/_stuff_/images/FASL.gif
+SPDBV/_stuff_/images/activsit.gif
+SPDBV/_stuff_/images/align.gif
+SPDBV/_stuff_/images/balstick.gif
+SPDBV/_stuff_/images/bg.gif
+SPDBV/_stuff_/images/control.gif
+SPDBV/_stuff_/images/edm.gif
+SPDBV/_stuff_/images/edm2.gif
+SPDBV/_stuff_/images/hb.gif
+SPDBV/_stuff_/images/hb_inter.jpg
+SPDBV/_stuff_/images/hb_light.jpg
+SPDBV/_stuff_/images/hb_pov.jpg
+SPDBV/_stuff_/images/hb_std.gif
+SPDBV/_stuff_/images/hb_wire.gif
+SPDBV/_stuff_/images/home.gif
+SPDBV/_stuff_/images/ldb61_65.gif
+SPDBV/_stuff_/images/logo.gif
+SPDBV/_stuff_/images/mixed.gif
+SPDBV/_stuff_/images/model1.gif
+SPDBV/_stuff_/images/model2.gif
+SPDBV/_stuff_/images/pov3labl.gif
+SPDBV/_stuff_/images/rama.gif
+SPDBV/_stuff_/images/rib1.gif
+SPDBV/_stuff_/images/rib2.gif
+SPDBV/_stuff_/images/rib3.gif
+SPDBV/_stuff_/images/rib3b.gif
+SPDBV/_stuff_/images/smooth3.jpg
+SPDBV/_stuff_/images/smooth3m.jpg
+SPDBV/_stuff_/images/smooth6.jpg
+SPDBV/_stuff_/images/smooth6m.jpg
+SPDBV/_stuff_/images/spacefil.gif
+SPDBV/_stuff_/images/sticks.gif
+SPDBV/_stuff_/images/sup1.gif
+SPDBV/_stuff_/images/sup2.gif
+SPDBV/_stuff_/images/thread1.gif
+SPDBV/_stuff_/images/thread2.gif
+SPDBV/_stuff_/images/tools1.gif
+SPDBV/_stuff_/images/tools2.gif
+SPDBV/_stuff_/images/tools3.gif
+SPDBV/_stuff_/images/ucell.gif
+SPDBV/_stuff_/images/wind.gif
+SPDBV/_stuff_/initloop.txt
+SPDBV/_stuff_/mainpage.htm
+SPDBV/_stuff_/manual.htm
+SPDBV/_stuff_/text/activsit.htm
+SPDBV/_stuff_/text/amber_pl.htm
+SPDBV/_stuff_/text/ambertut.htm
+SPDBV/_stuff_/text/build.htm
+SPDBV/_stuff_/text/charm_pl.htm
+SPDBV/_stuff_/text/charmtut.htm
+SPDBV/_stuff_/text/color.htm
+SPDBV/_stuff_/text/cshrc.htm
+SPDBV/_stuff_/text/ctrlpanl.htm
+SPDBV/_stuff_/text/disclaim.htm
+SPDBV/_stuff_/text/display.htm
+SPDBV/_stuff_/text/distort.htm
+SPDBV/_stuff_/text/edm.htm
+SPDBV/_stuff_/text/edmtut.htm
+SPDBV/_stuff_/text/fabp.htm
+SPDBV/_stuff_/text/feedback.htm
+SPDBV/_stuff_/text/files.htm
+SPDBV/_stuff_/text/gallery.htm
+SPDBV/_stuff_/text/gromo_pl.htm
+SPDBV/_stuff_/text/gromotut.htm
+SPDBV/_stuff_/text/hew.htm
+SPDBV/_stuff_/text/index.htm
+SPDBV/_stuff_/text/pov.htm
+SPDBV/_stuff_/text/loop.htm
+SPDBV/_stuff_/text/main.htm
+SPDBV/_stuff_/text/minim.htm
+SPDBV/_stuff_/text/modeling.htm
+SPDBV/_stuff_/text/moving.htm
+SPDBV/_stuff_/text/mutation.htm
+SPDBV/_stuff_/text/phipsi.htm
+SPDBV/_stuff_/text/povscene.htm
+SPDBV/_stuff_/text/prefs.htm
+SPDBV/_stuff_/text/rama.htm
+SPDBV/_stuff_/text/refs.htm
+SPDBV/_stuff_/text/rendcomp.htm
+SPDBV/_stuff_/text/render.htm
+SPDBV/_stuff_/text/ribbon.htm
+SPDBV/_stuff_/text/select.htm
+SPDBV/_stuff_/text/selmenu.htm
+SPDBV/_stuff_/text/superpos.htm
+SPDBV/_stuff_/text/tips.htm
+SPDBV/_stuff_/text/toolmenu.htm
+SPDBV/_stuff_/text/tools.htm
+SPDBV/_stuff_/text/torsion.htm
+SPDBV/_stuff_/text/transfo.htm
+SPDBV/_stuff_/text/tutorial.htm
+SPDBV/_stuff_/text/xsymtut.htm
+SPDBV/_stuff_/readme.txt
+SPDBV/_stuff_/smalloop.txt
+SPDBV/_stuff_/tinyloop.txt
+SPDBV/bin/spdbv.IRIX
+SPDBV/bin/spdbv.Linux
+SPDBV/bin/spdbv.sh
+SPDBV/readme.txt
+SPDBV/spdbv37b1.txt
+SPDBV/spdbv37b2.txt
+SPDBV/user.tar.gz
+bin/spdbv
+@dirrm SPDBV/_stuff_/grmparam
+@dirrm SPDBV/_stuff_/grmtopol
+@dirrm SPDBV/_stuff_/images
+@dirrm SPDBV/_stuff_/text
+@dirrm SPDBV/_stuff_
+@dirrm SPDBV/bin
+@dirrm SPDBV