7 files changed, 508 insertions, 470 deletions

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index 2a09fa51a1b0..bc7a92323892 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -6,14 +6,9 @@
 #
 
 PORTNAME=	tinker
-PORTVERSION=	4.2.20040908
-PORTREVISION=	5
+PORTVERSION=	5.1.09
 CATEGORIES=	biology
-MASTER_SITES=	ftp://ftp.tu-chemnitz.de/.SAN0/pub/FreeBSD/ports/distfiles/RESTRICTED/${PORTNAME}-${PORTVERSION}/\
-		ftp://ftp.tw.freebsd.org/pub/ports/distfiles/${PORTNAME}-${PORTVERSION}/ \
-		ftp://ftp.uvsq.fr/pub/FreeBSD/ports/distfiles/RESTRICTED/${PORTNAME}-${PORTVERSION}/
-DISTNAME=	${PORTNAME}
-DIST_SUBDIR=	${PORTNAME}-${PORTVERSION}
+MASTER_SITES=	http://dasher.wustl.edu/tinker/downloads/
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A general purpose molecular modelling package
@@ -27,10 +22,9 @@ ALL_TARGET=	all listing
 INSTALL_TARGET=	rename
 RESTRICTED=	author requests no distribution except from his FTP site
 
-DOCS=		README *.pdf *.txt release*
-SAMPLES=	README clean.make *.1st *.boat *.cell *.chair *.dat *.dyn0	\
-		*.key *.log *.pdb *.run *.xyz
-BENCHES=	README *.dyn0 *.log *.key *.run *.xyz results*
+DOCS=		0README *.pdf *.txt announce/release*
+SAMPLES=	0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.run *.xyz
+BENCHES=	0README *.dyn0 *.log *.key *.run *.xyz results*
 
 .include <bsd.port.pre.mk>
 
@@ -43,21 +37,6 @@ FFLAGS+=	-mfancy-math-387 -malign-double
 .endif # i386
 .endif
 
-.if defined(WITH_VIEWER)
-BUILD_DEPENDS+=	imake:${PORTSDIR}/devel/imake
-USE_XORG=	x11 xext xi
-PLIST_SUB+=	WITH_VIEWER=""
-post-build:
-	@${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer
-.else
-PLIST_SUB+=	WITH_VIEWER="@comment "
-pre-extract:
-	@${ECHO_MSG} ""
-	@${ECHO_MSG} If you would like to also build
-	@${ECHO_MSG} the molecular viewer, define WITH_VIEWER.
-	@${ECHO_MSG} ""
-.endif
-
 pre-everything::
 .if !defined(WITH_OPTIMIZED_FLAGS)
 	@${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
@@ -85,13 +64,6 @@ post-install:
 	@${INSTALL_DATA} ${BENCHES:S|^|${WRKDIR}/tinker/bench/|} ${DATADIR}/bench
 	@${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${DATADIR}/test
 .endif
-.if defined(WITH_VIEWER)
-	@${MKDIR} ${DATADIR}/rasmol
-	@${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin
-	@${INSTALL_SCRIPT} ${FILESDIR}/tview ${PREFIX}/bin
-	@${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp \
-		${DATADIR}/rasmol
-.endif
 	@${ECHO_MSG} ""
 	@${ECHO_MSG} "   **********************************************************"
 	@${ECHO_MSG} "       The author requests that you return a license form    "
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
index 42d584ef4d26..d441f5ba5b8a 100644
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@@ -1,3 +1,2 @@
-MD5 (tinker-4.2.20040908/tinker.tar.gz) = 5618d8a373896f00e452b137200223fd
-SHA256 (tinker-4.2.20040908/tinker.tar.gz) = ad0cc9782dabdb0cce490fe26508761a36078e741f019090cbaa3e6cacf71055
-SIZE (tinker-4.2.20040908/tinker.tar.gz) = 8177555
+SHA256 (tinker-5.1.09.tar.gz) = 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183
+SIZE (tinker-5.1.09.tar.gz) = 14071638
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
index 9bb922e07cf5..e68ae52123d0 100644
--- a/biology/tinker/files/patch-aa
+++ b/biology/tinker/files/patch-aa
@@ -1,5 +1,5 @@
---- ../make/Makefile.orig	Thu Aug 19 17:37:44 2004
-+++ ../make/Makefile	Thu Aug 19 22:52:41 2004
+--- ../make/Makefile.orig	2010-08-25 00:58:16.000000000 +0400
++++ ../make/Makefile	2011-01-22 01:12:41.000000000 +0300
 @@ -9,8 +9,8 @@
  ##
  ##   1. make all              Build all the TINKER executables
@@ -15,7 +15,7 @@
  ##  LINKDIR      Linked Copies of TINKER Executables
  ##
  
--TINKERDIR = /user/ponder/tinker
+-TINKERDIR = /Users/ponder/tinker
 -BINDIR = $(TINKERDIR)/bin
 -LINKDIR = /usr/local/bin
 +TINKERDIR = ${WRKDIR}
@@ -24,11 +24,10 @@
  
  ####################################################################
  ##  Known Machine Types; Uncomment One of the Following Sections  ##
-@@ -122,6 +122,20 @@
- #LIBFLAGS = -crusv
- #LINKFLAGS =
+@@ -40,6 +40,20 @@
+ ####################################################################
  
-+##
+ ##
 +##  Machine:  IntelPC / FreeBSD
 +##  CPU Type: Intel, AMD, Cyrix
 +##  Oper Sys: FreeBSD 4.2
@@ -42,10 +41,30 @@
 +OPTFLAGS = 
 +LIBFLAGS = -rcuv
 +
- #################################################################
- ##  Should not be Necessary to Change Things Below this Point  ##
- #################################################################
-@@ -529,11 +543,13 @@
++##
+ ##  Machine:  Generic Linux
+ ##  CPU Type: Intel x86 Compatible
+ ##  Oper Sys: Fedora Core
+@@ -102,12 +116,12 @@
+ ##  Compiler: Intel Fortran for Mac 11
+ ##
+ 
+-F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort
+-LIBS =
+-F77FLAGS = -c -axSSSE3 -vec-report0
+-OPTFLAGS = -O3 -no-ipo -no-prec-div
+-LIBFLAGS = -crusv
+-LINKFLAGS = -static-intel -mmacosx-version-min=10.4
++#F77 = /opt/intel/Compiler/11.1/058/bin/intel64/ifort
++#LIBS =
++#F77FLAGS = -c -axSSSE3 -vec-report0
++#OPTFLAGS = -O3 -no-ipo -no-prec-div
++#LIBFLAGS = -crusv
++#LINKFLAGS = -static-intel -mmacosx-version-min=10.4
+ 
+ ##
+ ##  Machine:  Macintosh (PPC)
+@@ -584,6 +598,8 @@
             xyzpdb.x \
             xyzsybyl.x
  
@@ -54,6 +73,10 @@
  .f.o:
  	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f 
  
+@@ -596,8 +612,8 @@
+ server.o:
+ 	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
+ 
 -%.x: %.o libtinker.a
 -	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}
 +.o.x: libtinker.a
@@ -61,7 +84,7 @@
  
  all:	${EXEFILES}
  
-@@ -544,59 +560,59 @@
+@@ -608,63 +624,63 @@
  	cat *.i *.f > tinker.txt
  
  rename:
@@ -91,6 +114,8 @@
 -	mv  path.x       $(BINDIR)/path
 -	mv  pdbxyz.x     $(BINDIR)/pdbxyz
 -	mv  polarize.x   $(BINDIR)/polarize
+-	mv  poledit.x    $(BINDIR)/poledit
+-	mv  potential.x  $(BINDIR)/potential
 -	mv  prmedit.x    $(BINDIR)/prmedit
 -	mv  protein.x    $(BINDIR)/protein
 -	mv  pss.x        $(BINDIR)/pss
@@ -106,10 +131,12 @@
 -	mv  sybylxyz.x   $(BINDIR)/sybylxyz
 -	mv  testgrad.x   $(BINDIR)/testgrad
 -	mv  testhess.x   $(BINDIR)/testhess
--	mv  testlight.x  $(BINDIR)/testlight
+-	mv  testpair.x   $(BINDIR)/testpair
 -	mv  testrot.x    $(BINDIR)/testrot
 -	mv  timer.x      $(BINDIR)/timer
 -	mv  timerot.x    $(BINDIR)/timerot
+-	mv  valence.x    $(BINDIR)/valence
+-	mv  vibbig.x     $(BINDIR)/vibbig
 -	mv  vibrate.x    $(BINDIR)/vibrate
 -	mv  vibrot.x     $(BINDIR)/vibrot
 -	mv  xtalfit.x    $(BINDIR)/xtalfit
@@ -144,6 +171,8 @@
 +	${INSTALL_PROGRAM}  path.x       $(BINDIR)/path
 +	${INSTALL_PROGRAM}  pdbxyz.x     $(BINDIR)/pdbxyz
 +	${INSTALL_PROGRAM}  polarize.x   $(BINDIR)/polarize
++	${INSTALL_PROGRAM}  poledit.x    $(BINDIR)/poledit
++	${INSTALL_PROGRAM}  potential.x  $(BINDIR)/potential
 +	${INSTALL_PROGRAM}  prmedit.x    $(BINDIR)/prmedit
 +	${INSTALL_PROGRAM}  protein.x    $(BINDIR)/protein
 +	${INSTALL_PROGRAM}  pss.x        $(BINDIR)/pss
@@ -159,10 +188,12 @@
 +	${INSTALL_PROGRAM}  sybylxyz.x   $(BINDIR)/sybylxyz
 +	${INSTALL_PROGRAM}  testgrad.x   $(BINDIR)/testgrad
 +	${INSTALL_PROGRAM}  testhess.x   $(BINDIR)/testhess
-+	${INSTALL_PROGRAM}  testlight.x  $(BINDIR)/testlight
++	${INSTALL_PROGRAM}  testpair.x   $(BINDIR)/testpair
 +	${INSTALL_PROGRAM}  testrot.x    $(BINDIR)/testrot
 +	${INSTALL_PROGRAM}  timer.x      $(BINDIR)/timer
 +	${INSTALL_PROGRAM}  timerot.x    $(BINDIR)/timerot
++	${INSTALL_PROGRAM}  valence.x    $(BINDIR)/valence
++	${INSTALL_PROGRAM}  vibbig.x     $(BINDIR)/vibbig
 +	${INSTALL_PROGRAM}  vibrate.x    $(BINDIR)/vibrate
 +	${INSTALL_PROGRAM}  vibrot.x     $(BINDIR)/vibrot
 +	${INSTALL_PROGRAM}  xtalfit.x    $(BINDIR)/xtalfit
diff --git a/biology/tinker/files/patch-al b/biology/tinker/files/patch-al
index e85fd419c12f..4fa7ddb6faf4 100644
--- a/biology/tinker/files/patch-al
+++ b/biology/tinker/files/patch-al
@@ -1,7 +1,7 @@
---- ../bench/bench5.run.orig	Tue Jul 24 14:02:20 2001
-+++ ../bench/bench5.run	Wed Sep  5 14:03:07 2001
+--- ../bench/bench5.run.orig	2010-08-25 00:58:15.000000000 +0400
++++ ../bench/bench5.run	2011-01-26 23:35:18.000000000 +0300
 @@ -1,3 +1,3 @@
  cp bench5.dyn0 bench5.dyn
--time ../bin/dynamic bench5 100 1.0 10.0 2 298.0
-+time dynamic bench5 100 1.0 10.0 2 298.0
+-time ../bin/dynamic bench5 1000 1.0 10.0 2 298.0
++time dynamic bench5 1000 1.0 10.0 2 298.0
  rm bench5.dyn
diff --git a/biology/tinker/files/tview b/biology/tinker/files/tview
deleted file mode 100644
index 834dd72ba166..000000000000
--- a/biology/tinker/files/tview
+++ /dev/null
@@ -1,21 +0,0 @@
-#!/bin/sh
-
-# Determine if X is running
-if [ -z $DISPLAY ]; then
-	echo You must be running X for this.
-else
-# Try to determine the color depth of the X server
-
-	DEPTH=`xwininfo -root | grep Depth | awk '{print $2}'`
-
-	if [ $DEPTH = 24 -o $DEPTH = 32 ]; then
-		PROGRAM=tview-32
-	elif [ $DEPTH = 16 ]; then
-		PROGRAM=tview-16
-	elif [ $DEPTH = 8 ]; then
-		PROGRAM=tview-8
-	else
-		echo Can not determine color depth of Display $DISPLAY
-	fi
-	exec $PROGRAM $@
-fi
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index f9e728d8df1c..a83b64406249 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -24,6 +24,8 @@ bin/optrigid
 bin/path
 bin/pdbxyz
 bin/polarize
+bin/poledit
+bin/potential
 bin/prmedit
 bin/protein
 bin/pss
@@ -39,14 +41,12 @@ bin/superpose
 bin/sybylxyz
 bin/testgrad
 bin/testhess
-bin/testlight
+bin/testpair
 bin/testrot
 bin/timer
 bin/timerot
-%%WITH_VIEWER%%bin/tview
-%%WITH_VIEWER%%bin/tview-8
-%%WITH_VIEWER%%bin/tview-16
-%%WITH_VIEWER%%bin/tview-32
+bin/valence
+bin/vibbig
 bin/vibrate
 bin/vibrot
 bin/xtalfit
@@ -55,7 +55,7 @@ bin/xyzedit
 bin/xyzint
 bin/xyzpdb
 bin/xyzsybyl
-%%PORTDOCS%%%%DOCSDIR%%/README
+%%PORTDOCS%%%%DOCSDIR%%/0README
 %%PORTDOCS%%%%DOCSDIR%%/ffe-guide.pdf
 %%PORTDOCS%%%%DOCSDIR%%/guide.pdf
 %%PORTDOCS%%%%DOCSDIR%%/guide.txt
@@ -71,54 +71,366 @@ bin/xyzsybyl
 %%PORTDOCS%%%%DOCSDIR%%/release-4.2
 %%PORTDOCS%%%%DOCSDIR%%/summary.pdf
 %%PORTDOCS%%%%DOCSDIR%%/summary.txt
-%%PORTDOCS%%share/examples/tinker/README
-%%PORTDOCS%%share/examples/tinker/anion.dat
-%%PORTDOCS%%share/examples/tinker/anion.dyn0
-%%PORTDOCS%%share/examples/tinker/anion.key
-%%PORTDOCS%%share/examples/tinker/anion.log
-%%PORTDOCS%%share/examples/tinker/anion.run
-%%PORTDOCS%%share/examples/tinker/anion.xyz
-%%PORTDOCS%%share/examples/tinker/argon.1st
-%%PORTDOCS%%share/examples/tinker/argon.key
-%%PORTDOCS%%share/examples/tinker/argon.log
-%%PORTDOCS%%share/examples/tinker/argon.run
-%%PORTDOCS%%share/examples/tinker/clean.make
-%%PORTDOCS%%share/examples/tinker/cluster.dat
-%%PORTDOCS%%share/examples/tinker/cluster.key
-%%PORTDOCS%%share/examples/tinker/cluster.log
-%%PORTDOCS%%share/examples/tinker/cluster.run
-%%PORTDOCS%%share/examples/tinker/cluster.xyz
-%%PORTDOCS%%share/examples/tinker/crambin.key
-%%PORTDOCS%%share/examples/tinker/crambin.log
-%%PORTDOCS%%share/examples/tinker/crambin.pdb
-%%PORTDOCS%%share/examples/tinker/crambin.run
-%%PORTDOCS%%share/examples/tinker/cyclohex.boat
-%%PORTDOCS%%share/examples/tinker/cyclohex.chair
-%%PORTDOCS%%share/examples/tinker/cyclohex.key
-%%PORTDOCS%%share/examples/tinker/cyclohex.log
-%%PORTDOCS%%share/examples/tinker/cyclohex.run
-%%PORTDOCS%%share/examples/tinker/dialanine.key
-%%PORTDOCS%%share/examples/tinker/dialanine.log
-%%PORTDOCS%%share/examples/tinker/dialanine.run
-%%PORTDOCS%%share/examples/tinker/dialanine.xyz
-%%PORTDOCS%%share/examples/tinker/enkephalin.dat
-%%PORTDOCS%%share/examples/tinker/enkephalin.key
-%%PORTDOCS%%share/examples/tinker/enkephalin.log
-%%PORTDOCS%%share/examples/tinker/enkephalin.run
-%%PORTDOCS%%share/examples/tinker/formamide.cell
-%%PORTDOCS%%share/examples/tinker/formamide.dat
-%%PORTDOCS%%share/examples/tinker/formamide.key
-%%PORTDOCS%%share/examples/tinker/formamide.log
-%%PORTDOCS%%share/examples/tinker/formamide.run
-%%PORTDOCS%%share/examples/tinker/helix.1st
-%%PORTDOCS%%share/examples/tinker/helix.key
-%%PORTDOCS%%share/examples/tinker/helix.log
-%%PORTDOCS%%share/examples/tinker/helix.run
-%%PORTDOCS%%share/examples/tinker/salt.cell
-%%PORTDOCS%%share/examples/tinker/salt.key
-%%PORTDOCS%%share/examples/tinker/salt.log
-%%PORTDOCS%%share/examples/tinker/salt.run
-%%PORTDOCS%%%%DATADIR%%/bench/README
+%%PORTDOCS%%%%EXAMPLESDIR%%/0README
+%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/alatet.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/alkane.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/ammonia.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/amoeba.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/arach.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/arach.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/arach.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/azulene.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.make
+%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/bdna.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/bearing.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/bearing.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/bearing2.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/benzamidine.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/benzamidine.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/benzbox.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/benzbox.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/benzene.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/benzene.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/benzene.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/bowl.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/bowl.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/bowl.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/bowl2.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/bowl2.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/bowl3.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/bowl3.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/bucky.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/bucky.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/bucky.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/butane.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/butane.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/butane.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/butane2.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/butane2.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/butane2.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/butanes.dyn
+%%PORTDOCS%%%%EXAMPLESDIR%%/butanes.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/butanes.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/butanex.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/butanex.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/butopls.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/butopls.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/butopls.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/butopls2.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/butopls2.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/butopls2.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/c5.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/c5.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/c5.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/c5.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7a.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7a.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7a.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7a.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7e.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7e.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7e.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/c7e.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/calmodulin.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/calmodulin.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/calmodulin.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/calmodulin.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/cawater.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/cawater.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/copper.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/copper.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/cpentene.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/cpentene.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/crambin.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/crambin.pdb
+%%PORTDOCS%%%%EXAMPLESDIR%%/crambin.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/crambin.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/crambinx.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/crambinx.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/crown.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/crown.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/crown.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/cychept.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/cychept.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/cychept.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/cyclo.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/cyclo.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/cyclo.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/cyclo2.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/cyclo2.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/cyclo2.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/cycprop.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/cycprop.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/dang.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/dang.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/deltorphin.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/deltorphin.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/deltorphin.make
+%%PORTDOCS%%%%EXAMPLESDIR%%/deltorphin.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/deltorphin.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr.run
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr2.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr2.run
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr2.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/dhfr2.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/diamond.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/diamond.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/diene.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/diene.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/diene.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/dimethane.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/dimethane.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/dmp.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/dmp.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/enkephalin.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/enkephalin.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/enkephalin.make
+%%PORTDOCS%%%%EXAMPLESDIR%%/enkephalin.seq
+%%PORTDOCS%%%%EXAMPLESDIR%%/enkephalin.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/ermer.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/ermer.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/ermer.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/ester.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/ester.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/ethane.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/ethane.key
+%%PORTDOCS%%%%EXAMPLESDIR%%/ethane.xyz
+%%PORTDOCS%%%%EXAMPLESDIR%%/ethanol.int
+%%PORTDOCS%%%%EXAMPLESDIR%%/ethanol.key
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-%%PORTDOCS%%%%DATADIR%%/test/flane.key
-%%PORTDOCS%%%%DATADIR%%/test/flane.xyz
-%%PORTDOCS%%%%DATADIR%%/test/form.key
-%%PORTDOCS%%%%DATADIR%%/test/form.xyz
-%%PORTDOCS%%%%DATADIR%%/test/formbig.key
-%%PORTDOCS%%%%DATADIR%%/test/formbig.xyz
-%%PORTDOCS%%%%DATADIR%%/test/formbox.dyn
-%%PORTDOCS%%%%DATADIR%%/test/formbox.key
-%%PORTDOCS%%%%DATADIR%%/test/formbox.xyz
-%%PORTDOCS%%%%DATADIR%%/test/furan.int
-%%PORTDOCS%%%%DATADIR%%/test/furan.key
-%%PORTDOCS%%%%DATADIR%%/test/furan.xyz
-%%PORTDOCS%%%%DATADIR%%/test/glucose.key
-%%PORTDOCS%%%%DATADIR%%/test/glucose.xyz
-%%PORTDOCS%%%%DATADIR%%/test/glycerol.dyn
-%%PORTDOCS%%%%DATADIR%%/test/glycerol.key
-%%PORTDOCS%%%%DATADIR%%/test/glycerol.xyz
-%%PORTDOCS%%%%DATADIR%%/test/graphite.key
-%%PORTDOCS%%%%DATADIR%%/test/graphite.xyz
-%%PORTDOCS%%%%DATADIR%%/test/helix.dyn
+%%PORTDOCS%%%%DATADIR%%/test/enkephalin.log
+%%PORTDOCS%%%%DATADIR%%/test/enkephalin.run
+%%PORTDOCS%%%%DATADIR%%/test/formamide.cell
+%%PORTDOCS%%%%DATADIR%%/test/formamide.dat
+%%PORTDOCS%%%%DATADIR%%/test/formamide.key
+%%PORTDOCS%%%%DATADIR%%/test/formamide.log
+%%PORTDOCS%%%%DATADIR%%/test/formamide.run
+%%PORTDOCS%%%%DATADIR%%/test/gpcr.blk
+%%PORTDOCS%%%%DATADIR%%/test/gpcr.key
+%%PORTDOCS%%%%DATADIR%%/test/gpcr.log
+%%PORTDOCS%%%%DATADIR%%/test/gpcr.run
+%%PORTDOCS%%%%DATADIR%%/test/gpcr.xyz
+%%PORTDOCS%%%%DATADIR%%/test/helix.1st
 %%PORTDOCS%%%%DATADIR%%/test/helix.key
-%%PORTDOCS%%%%DATADIR%%/test/helix.xyz
-%%PORTDOCS%%%%DATADIR%%/test/heme.key
-%%PORTDOCS%%%%DATADIR%%/test/heme.xyz
-%%PORTDOCS%%%%DATADIR%%/test/hexane.int
-%%PORTDOCS%%%%DATADIR%%/test/hexane.key
-%%PORTDOCS%%%%DATADIR%%/test/hexane.xyz
-%%PORTDOCS%%%%DATADIR%%/test/hexanes.dyn
-%%PORTDOCS%%%%DATADIR%%/test/hexanes.key
-%%PORTDOCS%%%%DATADIR%%/test/hexanes.xyz
-%%PORTDOCS%%%%DATADIR%%/test/imidazole.int
-%%PORTDOCS%%%%DATADIR%%/test/imidazole.key
-%%PORTDOCS%%%%DATADIR%%/test/imidazole.xyz
-%%PORTDOCS%%%%DATADIR%%/test/imine.int
-%%PORTDOCS%%%%DATADIR%%/test/imine.key
-%%PORTDOCS%%%%DATADIR%%/test/imine.xyz
-%%PORTDOCS%%%%DATADIR%%/test/lactam.key
-%%PORTDOCS%%%%DATADIR%%/test/lactam.xyz
-%%PORTDOCS%%%%DATADIR%%/test/lipid.key
-%%PORTDOCS%%%%DATADIR%%/test/lipid.xyz
-%%PORTDOCS%%%%DATADIR%%/test/melittin.key
-%%PORTDOCS%%%%DATADIR%%/test/melittin.pdb
-%%PORTDOCS%%%%DATADIR%%/test/melittin.seq
-%%PORTDOCS%%%%DATADIR%%/test/melittin.xyz
-%%PORTDOCS%%%%DATADIR%%/test/membrane.key
-%%PORTDOCS%%%%DATADIR%%/test/membrane.xyz
-%%PORTDOCS%%%%DATADIR%%/test/methane.int
-%%PORTDOCS%%%%DATADIR%%/test/methane.key
-%%PORTDOCS%%%%DATADIR%%/test/methane.xyz
-%%PORTDOCS%%%%DATADIR%%/test/methanol.key
-%%PORTDOCS%%%%DATADIR%%/test/methanol.xyz
-%%PORTDOCS%%%%DATADIR%%/test/mm3.key
-%%PORTDOCS%%%%DATADIR%%/test/mm3.xyz
-%%PORTDOCS%%%%DATADIR%%/test/nacl.key
-%%PORTDOCS%%%%DATADIR%%/test/nacl.xyz
-%%PORTDOCS%%%%DATADIR%%/test/nada.key
-%%PORTDOCS%%%%DATADIR%%/test/nada.xyz
-%%PORTDOCS%%%%DATADIR%%/test/naphthalene.int
-%%PORTDOCS%%%%DATADIR%%/test/naphthalene.key
-%%PORTDOCS%%%%DATADIR%%/test/naphthalene.xyz
-%%PORTDOCS%%%%DATADIR%%/test/nitrogen.dyn
-%%PORTDOCS%%%%DATADIR%%/test/nitrogen.key
-%%PORTDOCS%%%%DATADIR%%/test/nitrogen.xyz
-%%PORTDOCS%%%%DATADIR%%/test/nma.int
-%%PORTDOCS%%%%DATADIR%%/test/nma.key
-%%PORTDOCS%%%%DATADIR%%/test/nma.xyz
-%%PORTDOCS%%%%DATADIR%%/test/nmabox.dyn
-%%PORTDOCS%%%%DATADIR%%/test/nmabox.key
-%%PORTDOCS%%%%DATADIR%%/test/nmabox.xyz
-%%PORTDOCS%%%%DATADIR%%/test/nstilbene.int
-%%PORTDOCS%%%%DATADIR%%/test/nstilbene.key
-%%PORTDOCS%%%%DATADIR%%/test/nstilbene.xyz
-%%PORTDOCS%%%%DATADIR%%/test/octane.int
-%%PORTDOCS%%%%DATADIR%%/test/octane.key
-%%PORTDOCS%%%%DATADIR%%/test/octane.xyz
-%%PORTDOCS%%%%DATADIR%%/test/octane2.int
-%%PORTDOCS%%%%DATADIR%%/test/octane2.key
-%%PORTDOCS%%%%DATADIR%%/test/octane2.xyz
-%%PORTDOCS%%%%DATADIR%%/test/octene.key
-%%PORTDOCS%%%%DATADIR%%/test/octene.xyz
-%%PORTDOCS%%%%DATADIR%%/test/palmitate.int
-%%PORTDOCS%%%%DATADIR%%/test/palmitate.key
-%%PORTDOCS%%%%DATADIR%%/test/palmitate.xyz
-%%PORTDOCS%%%%DATADIR%%/test/peptide.int
-%%PORTDOCS%%%%DATADIR%%/test/peptide.key
-%%PORTDOCS%%%%DATADIR%%/test/peptide.make
-%%PORTDOCS%%%%DATADIR%%/test/peptide.pdb
-%%PORTDOCS%%%%DATADIR%%/test/peptide.seq
-%%PORTDOCS%%%%DATADIR%%/test/peptide.xyz
-%%PORTDOCS%%%%DATADIR%%/test/phenanth.key
-%%PORTDOCS%%%%DATADIR%%/test/phenanth.xyz
-%%PORTDOCS%%%%DATADIR%%/test/photo.key
-%%PORTDOCS%%%%DATADIR%%/test/photo.pdb
-%%PORTDOCS%%%%DATADIR%%/test/photo.seq
-%%PORTDOCS%%%%DATADIR%%/test/photo.xyz
-%%PORTDOCS%%%%DATADIR%%/test/pol3.key
-%%PORTDOCS%%%%DATADIR%%/test/pol3.xyz
-%%PORTDOCS%%%%DATADIR%%/test/polyala.key
-%%PORTDOCS%%%%DATADIR%%/test/polyala.xyz
-%%PORTDOCS%%%%DATADIR%%/test/propane.key
-%%PORTDOCS%%%%DATADIR%%/test/propane.ray
-%%PORTDOCS%%%%DATADIR%%/test/propane.xyz
-%%PORTDOCS%%%%DATADIR%%/test/propellane.int
-%%PORTDOCS%%%%DATADIR%%/test/propellane.key
-%%PORTDOCS%%%%DATADIR%%/test/propellane.xyz
-%%PORTDOCS%%%%DATADIR%%/test/propyne.key
-%%PORTDOCS%%%%DATADIR%%/test/propyne.xyz
-%%PORTDOCS%%%%DATADIR%%/test/pyridine.int
-%%PORTDOCS%%%%DATADIR%%/test/pyridine.key
-%%PORTDOCS%%%%DATADIR%%/test/pyridine.xyz
-%%PORTDOCS%%%%DATADIR%%/test/pyrrole.int
-%%PORTDOCS%%%%DATADIR%%/test/pyrrole.key
-%%PORTDOCS%%%%DATADIR%%/test/pyrrole.xyz
-%%PORTDOCS%%%%DATADIR%%/test/retinoic.key
-%%PORTDOCS%%%%DATADIR%%/test/retinoic.xyz
-%%PORTDOCS%%%%DATADIR%%/test/skunk.key
-%%PORTDOCS%%%%DATADIR%%/test/skunk.xyz
-%%PORTDOCS%%%%DATADIR%%/test/spc.key
-%%PORTDOCS%%%%DATADIR%%/test/spc.xyz
-%%PORTDOCS%%%%DATADIR%%/test/sterol.key
-%%PORTDOCS%%%%DATADIR%%/test/sterol.xyz
-%%PORTDOCS%%%%DATADIR%%/test/styrene.int
-%%PORTDOCS%%%%DATADIR%%/test/styrene.key
-%%PORTDOCS%%%%DATADIR%%/test/styrene.xyz
-%%PORTDOCS%%%%DATADIR%%/test/terphenyl.key
-%%PORTDOCS%%%%DATADIR%%/test/terphenyl.xyz
-%%PORTDOCS%%%%DATADIR%%/test/tfe.key
-%%PORTDOCS%%%%DATADIR%%/test/tfe.xyz
-%%PORTDOCS%%%%DATADIR%%/test/thiadiene.int
-%%PORTDOCS%%%%DATADIR%%/test/thiadiene.key
-%%PORTDOCS%%%%DATADIR%%/test/thiadiene.xyz
-%%PORTDOCS%%%%DATADIR%%/test/thiophene.int
-%%PORTDOCS%%%%DATADIR%%/test/thiophene.key
-%%PORTDOCS%%%%DATADIR%%/test/thiophene.xyz
-%%PORTDOCS%%%%DATADIR%%/test/thr.int
-%%PORTDOCS%%%%DATADIR%%/test/thr.key
-%%PORTDOCS%%%%DATADIR%%/test/thr.xyz
-%%PORTDOCS%%%%DATADIR%%/test/tip3f.key
-%%PORTDOCS%%%%DATADIR%%/test/tip3f.xyz
-%%PORTDOCS%%%%DATADIR%%/test/tip3p.key
-%%PORTDOCS%%%%DATADIR%%/test/tip3p.xyz
-%%PORTDOCS%%%%DATADIR%%/test/tip4f.key
-%%PORTDOCS%%%%DATADIR%%/test/tip4f.xyz
-%%PORTDOCS%%%%DATADIR%%/test/tip4p.key
-%%PORTDOCS%%%%DATADIR%%/test/tip4p.xyz
-%%PORTDOCS%%%%DATADIR%%/test/tip5p.key
-%%PORTDOCS%%%%DATADIR%%/test/tip5p.xyz
-%%PORTDOCS%%%%DATADIR%%/test/trpcage.key
-%%PORTDOCS%%%%DATADIR%%/test/trpcage.pdb
-%%PORTDOCS%%%%DATADIR%%/test/trpcage.seq
-%%PORTDOCS%%%%DATADIR%%/test/trpcage.xyz
-%%PORTDOCS%%%%DATADIR%%/test/water.int
+%%PORTDOCS%%%%DATADIR%%/test/helix.log
+%%PORTDOCS%%%%DATADIR%%/test/helix.run
+%%PORTDOCS%%%%DATADIR%%/test/salt.cell
+%%PORTDOCS%%%%DATADIR%%/test/salt.key
+%%PORTDOCS%%%%DATADIR%%/test/salt.log
+%%PORTDOCS%%%%DATADIR%%/test/salt.run
+%%PORTDOCS%%%%DATADIR%%/test/tetraala.dat
+%%PORTDOCS%%%%DATADIR%%/test/tetraala.key
+%%PORTDOCS%%%%DATADIR%%/test/tetraala.log
+%%PORTDOCS%%%%DATADIR%%/test/tetraala.run
 %%PORTDOCS%%%%DATADIR%%/test/water.key
+%%PORTDOCS%%%%DATADIR%%/test/water.log
+%%PORTDOCS%%%%DATADIR%%/test/water.pot
+%%PORTDOCS%%%%DATADIR%%/test/water.run
 %%PORTDOCS%%%%DATADIR%%/test/water.xyz
-%%PORTDOCS%%%%DATADIR%%/test/waterbig.key
-%%PORTDOCS%%%%DATADIR%%/test/waterbig.xyz
-%%PORTDOCS%%%%DATADIR%%/test/waterbox.dyn
-%%PORTDOCS%%%%DATADIR%%/test/waterbox.key
-%%PORTDOCS%%%%DATADIR%%/test/waterbox.xyz
-%%PORTDOCS%%%%DATADIR%%/test/waterdot.dyn
-%%PORTDOCS%%%%DATADIR%%/test/waterdot.key
-%%PORTDOCS%%%%DATADIR%%/test/waterdot.xyz
-%%PORTDOCS%%%%DATADIR%%/test/waterhuge.key
-%%PORTDOCS%%%%DATADIR%%/test/waterhuge.xyz
-%%PORTDOCS%%%%DATADIR%%/test/watersmall.dyn
-%%PORTDOCS%%%%DATADIR%%/test/watersmall.key
-%%PORTDOCS%%%%DATADIR%%/test/watersmall.xyz
-%%PORTDOCS%%%%DATADIR%%/test/watertiny.dyn
-%%PORTDOCS%%%%DATADIR%%/test/watertiny.key
-%%PORTDOCS%%%%DATADIR%%/test/watertiny.xyz
-%%PORTDOCS%%%%DATADIR%%/test/white.int
-%%PORTDOCS%%%%DATADIR%%/test/white.key
-%%PORTDOCS%%%%DATADIR%%/test/white.xyz
 %%DATADIR%%/tinker.txt
-%%PORTDOCS%%@dirrm %%DOCSDIR%%
-%%PORTDOCS%%@dirrm share/examples/tinker
-%%PORTDOCS%%@dirrm %%DATADIR%%/bench
-@dirrm %%DATADIR%%/params
-%%WITH_VIEWER%%@dirrm %%DATADIR%%/rasmol
 %%PORTDOCS%%@dirrm %%DATADIR%%/test
+@dirrm %%DATADIR%%/params
+%%PORTDOCS%%@dirrm %%DATADIR%%/bench
 @dirrm %%DATADIR%%
+%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
+%%PORTDOCS%%@dirrm %%DOCSDIR%%
diff --git a/biology/tinker/scripts/build_viewer b/biology/tinker/scripts/build_viewer
deleted file mode 100644
index 24fb838c4fd0..000000000000
--- a/biology/tinker/scripts/build_viewer
+++ /dev/null
@@ -1,47 +0,0 @@
-#!/bin/sh
-
-# This builds the molecular viewer for tinker files.  It is a modified
-# version of rasmol.  One of the problems with rasmol is that is only
-# works at one color depth.  This script will build three viewers at
-# different color depths, 8-bit, 16-bit, and 32-bit.  The binaries are
-# called tview-8, tview-16, and tview-32 respectively.
-
-cd ${WRKSRC}/../rasmol
-
-cp Imakefile Imakefile.orig
-
-sed s@/user/ponder@${PREFIX}/share@ Imakefile > Imakefile.temp
-
-sed s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-32)'@ \
-    Imakefile.temp > Imakefile
-
-xmkmf -a
-
-make clean && make
-
-sed -e s@'DEPTHDEF = -DTHIRTYTWOBIT'@'# DEPTHDEF = -DTHIRTYTWOBIT'@ \
-    -e s@'# DEPTHDEF = -DSIXTEENBIT'@'DEPTHDEF = -DSIXTEENBIT'@ \
-    -e s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-16)'@ \
-       Imakefile.temp > Imakefile
-
-xmkmf -a
-
-make clean && make
-
-sed -e s@'DEPTHDEF = -DTHIRTYTWOBIT'@'# DEPTHDEF = -DTHIRTYTWOBIT'@ \
-    -e s@'# DEPTHDEF = -DEIGHTBIT'@'DEPTHDEF = -DEIGHTBIT'@ \
-    -e s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-8)'@ \
-       Imakefile.temp > Imakefile
-
-xmkmf -a
-
-make clean && make
-
-# Restore Imakefile to original state so that rerunning this script does
-# the right thing.
-rm Imakefile.temp
-mv Imakefile.orig Imakefile
-xmkmf -a
-make clean
-
-exit 0