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/

PR:		33902
Submitted by:	chuynh@biolateral.com.au

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