update from 3.7 to 3.8

PR:		24371
Submitted by:	MAINTAINER

18 files changed, 706 insertions, 167 deletions

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index 1b1129da1393..9436e26f402b 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -6,7 +6,7 @@
 #
 
 PORTNAME=	tinker
-PORTVERSION=	3.7
+PORTVERSION=	3.8
 CATEGORIES=	biology
 MASTER_SITES=	ftp://dasher.wustl.edu/pub/
 DISTNAME=	${PORTNAME}
@@ -37,6 +37,25 @@ INSTALL_TARGET=	rename
 
 RESTRICTED=	author requests no distribution except from his FTP site
 
+
+.if defined(WANT_VIEWER)
+.if ${XFREE86_VERSION} == 3
+BUILD_DEPENDS+=	imake:${PORTSDIR}/devel/imake
+.elif ${XFREE86_VERSION} == 4
+BUILD_DEPENDS+=	imake:${PORTSDIR}/devel/imake-4
+.endif
+PLIST=		${PKGDIR}/pkg-plist.viewer
+USE_XLIB=	yes
+post-build:
+	${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer
+.else
+pre-extract:
+	@${ECHO} ""
+	@${ECHO} If you would like to also build
+	@${ECHO} the molecular viewer, define WANT_VIEWER.
+	@${ECHO} ""
+.endif
+
 post-install:
 	${MKDIR} ${PREFIX}/share/tinker
 	${MKDIR} ${PREFIX}/share/tinker/params
@@ -44,6 +63,7 @@ post-install:
 ${PREFIX}/share/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/params/* \
 ${PREFIX}/share/tinker/params
+
 .if !defined(NOPORTDOCS)
 	${MKDIR} ${PREFIX}/share/doc/tinker
 	${MKDIR} ${PREFIX}/share/examples/tinker
@@ -51,54 +71,62 @@ ${PREFIX}/share/tinker/params
 	${MKDIR} ${PREFIX}/share/tinker/test
 	${INSTALL_DATA} ${WRKDIR}/tinker/doc/README \
 ${PREFIX}/share/doc/tinker
+	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.gz \
+${PREFIX}/share/doc/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.pdf \
 ${PREFIX}/share/doc/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.ps \
 ${PREFIX}/share/doc/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.Z \
-${PREFIX}/share/doc/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.txt \
 ${PREFIX}/share/doc/tinker
 	${INSTALL_DATA} ${WRKDIR}/tinker/example/README \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/anion.dyn0 \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.1st \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.in* \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.boat \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.key \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.cell \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.log \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.chair \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.dat \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/argon.1st \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.dyn0 \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/crambin.pdb \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.key \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.boat \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.log \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/cyclohex.chair \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.pdb \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/example/formamide.cell \
+	${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \
 ${PREFIX}/share/examples/tinker
 	${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \
 ${PREFIX}/share/examples/tinker
 	${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/*.run \
 ${PREFIX}/share/examples/tinker
-	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.input \
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.dyn0 \
+${PREFIX}/share/tinker/bench
+	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.log \
 ${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.key \
 ${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.xyz \
 ${PREFIX}/share/tinker/bench
-	${INSTALL_DATA} ${WRKDIR}/tinker/bench/water.dyn0 \
-${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/bench/results* \
 ${PREFIX}/share/tinker/bench
 	${INSTALL_SCRIPT} ${WRKDIR}/tinker/bench/*.run \
 ${PREFIX}/share/tinker/bench
 	${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${PREFIX}/share/tinker/test
 .endif
+
+.if defined(WANT_VIEWER)
+	${MKDIR} ${PREFIX}/share/tinker/rasmol
+	${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin 
+	${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp ${PREFIX}/share/tinker/rasmol
+
+.endif
+
 	@${ECHO} ""
 	@${ECHO} "   **********************************************************"
 	@${ECHO} "       The author requests that you return a license form    "
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
index 3f6df0ec8b72..673edd1ec5f2 100644
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@@ -1 +1 @@
-MD5 (tinker.tar.gz) = 057d58a10c3b35370b04f3239fbdce1d
+MD5 (tinker.tar.gz) = e3784b524b5e8acf80b592657c457602
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
index 526ce65e518c..0d3f17e2ce38 100644
--- a/biology/tinker/files/patch-aa
+++ b/biology/tinker/files/patch-aa
@@ -1,5 +1,5 @@
---- ../make/Makefile.orig	Mon Jul 12 10:56:36 1999
-+++ ../make/Makefile	Wed May 31 16:00:31 2000
+--- ../make/Makefile.orig	Mon Jan 15 12:39:52 2001
++++ ../make/Makefile	Mon Jan 15 15:48:37 2001
 @@ -9,8 +9,8 @@
  ##
  ##   1. make all              Build all the TINKER executables
@@ -24,41 +24,36 @@
  
  ####################################################################
  ##  Known Machine Types; Uncomment One of the Following Sections  ##
-@@ -45,13 +45,13 @@
- ##  Compiler: DEC Fortran 77/90, V4.1
+@@ -87,12 +87,12 @@
+ ##  Compiler: GNU g77
  ##
  
--F77 = /usr/bin/f77
--RM = /sbin/rm
+-F77 = /usr/bin/g77
 -LIBS =
 -F77FLAGS = -c
--OPTFLAGS = -fast -tune host
--LIBFLAGS = -rlv
--LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched
-+#F77 = /usr/bin/f77
-+#RM = /sbin/rm
+-OPTFLAGS = -O3 -ffast-math
+-LIBFLAGS = -crusv
+-LINKFLAGS =
++#F77 = /usr/bin/g77
 +#LIBS =
 +#F77FLAGS = -c
-+#OPTFLAGS = -fast -tune host
-+#LIBFLAGS = -rlv
-+#LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched
++#OPTFLAGS = -O3 -ffast-math
++#LIBFLAGS = -crusv
++#LINKFLAGS =
  
  ##
- ##  Machine:  Silicon Graphics
-@@ -104,6 +104,40 @@
- #diagq.o:
- #	${F77} ${F77FLAGS} -ffast-math diagq.f
+ ##  Machine:  IntelPC / Linux
+@@ -108,6 +108,35 @@
+ #LIBFLAGS = -crusv
+ #LINKFLAGS =
  
 +##
-+##  Machine: IntelPC
-+##  CPU Type:        Pentium Pro
-+##  Oper Sys:        FreeBSD 3.0
-+##  Compiler:        f77(f2c/gcc version 2.7.2.1) || egcs g77
-+##
++##  Machine:  IntelPC / FreeBSD
++##  CPU Type: Intel, AMD, Cyrix
++##  Oper Sys: FreeBSD 4.2
++##  Compiler: f77 , aka g77
 +
 +F77 = ${FC}
-+RM = /bin/rm
-+
 +.if ${FC}==f77
 +.if !defined(HAVE_G2C)
 +LIBS = -lU77
@@ -70,32 +65,38 @@
 +LINKFLAGS =
 +.endif
 +.elseif ${FC}==g77
-+LIBS=
++LIBS =
 +F77FLAGS = -Wno-globals -fno-globals -c -w
 +LINKFLAGS =
 +.endif
 +
 +OPTFLAGS = ${FFLAGS} -ffast-math
 +.if ${MACHINE_ARCH} == "i386"
-+OPTFLAGS+= -malign-double
++OPTFLAGS += -malign-double
 +.endif
 +LIBFLAGS = -rcuv
-+diagq.o:
-+	${F77} ${F77FLAGS} -ffast-math diagq.f
 +
  #################################################################
  ##  Should not be Necessary to Change Things Below this Point  ##
  #################################################################
-@@ -775,6 +809,7 @@
-         volume2.o \
-         writeout.o \
-         xyzatm.o
-+	ranlib libtinker.a
+@@ -486,11 +515,13 @@
+            xyzpdb.x \
+            xyzsybyl.x
+ 
++.SUFFIXES: .x
++
+ .f.o:
+ 	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f 
+ 
+-%.x: %.o libtinker.a
+-	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}
++.o.x: libtinker.a
++	${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
+ 
+ all:	${EXEFILES}
  
- alchemy.x:
- 	${F77} ${LINKFLAGS} -o alchemy.x alchemy.o libtinker.a ${LIBS}
-@@ -868,51 +903,51 @@
- 	${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS}
+@@ -501,56 +532,56 @@
+ 	cat *.i *.f > tinker.txt
  
  rename:
 -	mv  alchemy.x    $(BINDIR)/alchemy
@@ -104,6 +105,7 @@
 -	mv  archive.x    $(BINDIR)/archive
 -	mv  correlate.x  $(BINDIR)/correlate
 -	mv  crystal.x    $(BINDIR)/crystal
+-	mv  diffuse.x    $(BINDIR)/diffuse
 -	mv  distgeom.x   $(BINDIR)/distgeom
 -	mv  document.x   $(BINDIR)/document
 -	mv  dynamic.x    $(BINDIR)/dynamic
@@ -112,8 +114,10 @@
 -	mv  intxyz.x     $(BINDIR)/intxyz
 -	mv  minimize.x   $(BINDIR)/minimize
 -	mv  minirot.x    $(BINDIR)/minirot
+-	mv  minrigid.x   $(BINDIR)/minrigid
 -	mv  newton.x     $(BINDIR)/newton
 -	mv  newtrot.x    $(BINDIR)/newtrot
+-	mv  nucleic.x    $(BINDIR)/nucleic
 -	mv  optimize.x   $(BINDIR)/optimize
 -	mv  optirot.x    $(BINDIR)/optirot
 -	mv  optrigid.x   $(BINDIR)/optrigid
@@ -123,10 +127,12 @@
 -	mv  pss.x        $(BINDIR)/pss
 -	mv  pssrigid.x   $(BINDIR)/pssrigid
 -	mv  pssrot.x     $(BINDIR)/pssrot
+-	mv  radial.x     $(BINDIR)/radial
 -	mv  saddle.x     $(BINDIR)/saddle
 -	mv  scan.x       $(BINDIR)/scan
 -	mv  sniffer.x    $(BINDIR)/sniffer
 -	mv  spacefill.x  $(BINDIR)/spacefill
+-	mv  spectrum.x   $(BINDIR)/spectrum
 -	mv  superpose.x  $(BINDIR)/superpose
 -	mv  sybylxyz.x   $(BINDIR)/sybylxyz
 -	mv  testgrad.x   $(BINDIR)/testgrad
@@ -149,6 +155,7 @@
 +	${INSTALL_PROGRAM}  archive.x    $(BINDIR)/archive
 +	${INSTALL_PROGRAM}  correlate.x  $(BINDIR)/correlate
 +	${INSTALL_PROGRAM}  crystal.x    $(BINDIR)/crystal
++	${INSTALL_PROGRAM}  diffuse.x    $(BINDIR)/diffuse
 +	${INSTALL_PROGRAM}  distgeom.x   $(BINDIR)/distgeom
 +	${INSTALL_PROGRAM}  document.x   $(BINDIR)/document
 +	${INSTALL_PROGRAM}  dynamic.x    $(BINDIR)/dynamic
@@ -157,8 +164,10 @@
 +	${INSTALL_PROGRAM}  intxyz.x     $(BINDIR)/intxyz
 +	${INSTALL_PROGRAM}  minimize.x   $(BINDIR)/minimize
 +	${INSTALL_PROGRAM}  minirot.x    $(BINDIR)/minirot
++	${INSTALL_PROGRAM}  minrigid.x   $(BINDIR)/minrigid
 +	${INSTALL_PROGRAM}  newton.x     $(BINDIR)/newton
 +	${INSTALL_PROGRAM}  newtrot.x    $(BINDIR)/newtrot
++	${INSTALL_PROGRAM}  nucleic.x    $(BINDIR)/nucleic
 +	${INSTALL_PROGRAM}  optimize.x   $(BINDIR)/optimize
 +	${INSTALL_PROGRAM}  optirot.x    $(BINDIR)/optirot
 +	${INSTALL_PROGRAM}  optrigid.x   $(BINDIR)/optrigid
@@ -168,10 +177,12 @@
 +	${INSTALL_PROGRAM}  pss.x        $(BINDIR)/pss
 +	${INSTALL_PROGRAM}  pssrigid.x   $(BINDIR)/pssrigid
 +	${INSTALL_PROGRAM}  pssrot.x     $(BINDIR)/pssrot
++	${INSTALL_PROGRAM}  radial.x     $(BINDIR)/radial
 +	${INSTALL_PROGRAM}  saddle.x     $(BINDIR)/saddle
 +	${INSTALL_PROGRAM}  scan.x       $(BINDIR)/scan
 +	${INSTALL_PROGRAM}  sniffer.x    $(BINDIR)/sniffer
 +	${INSTALL_PROGRAM}  spacefill.x  $(BINDIR)/spacefill
++	${INSTALL_PROGRAM}  spectrum.x   $(BINDIR)/spectrum
 +	${INSTALL_PROGRAM}  superpose.x  $(BINDIR)/superpose
 +	${INSTALL_PROGRAM}  sybylxyz.x   $(BINDIR)/sybylxyz
 +	${INSTALL_PROGRAM}  testgrad.x   $(BINDIR)/testgrad
@@ -191,3 +202,13 @@
  
  remove_links:
  	rm -f $(LINKDIR)/alchemy
+@@ -671,8 +702,8 @@
+         bspline.o \
+         calendar.o \
+         center.o \
+-        chkxyz.o \
+         cholesky.o \
++        chkxyz.o \
+         clock.o \
+         cluster.o \
+         column.o \
diff --git a/biology/tinker/files/patch-ab b/biology/tinker/files/patch-ab
deleted file mode 100644
index 5fbcd518580c..000000000000
--- a/biology/tinker/files/patch-ab
+++ /dev/null
@@ -1,12 +0,0 @@
---- ../doc/license.txt.orig	Wed Jun 16 13:54:43 1999
-+++ ../doc/license.txt	Sat Jun 19 14:19:18 1999
-@@ -1,7 +1,7 @@
--         TINKER ­  Software Tools for Molecular Design
-+         TINKER -  Software Tools for Molecular Design
- 
-                     Version 3.7   June 1999  
--          Copyright © 1990-1999   Jay William Ponder
-+          Copyright (c) 1990-1999   Jay William Ponder
- 
- TINKER is a modular program package for molecular mechanics-
- based potential energy calculations, molecular dynamics 
diff --git a/biology/tinker/files/patch-ac b/biology/tinker/files/patch-ac
deleted file mode 100644
index e21d420dce16..000000000000
--- a/biology/tinker/files/patch-ac
+++ /dev/null
@@ -1,13 +0,0 @@
-*** ../doc/summary.txt.orig    Fri Aug 28 23:50:17 1998
---- ../doc/summary.txt Fri Aug 28 23:50:33 1998
-***************
-*** 1,4 ****
-!         TINKER ­ Software Tools for Molecular Design
-  
-        Jay Ponder Lab, Dept. of Biochemistry & Molecular 
-                           Biophysics,
---- 1,4 ----
-!         TINKER - Software Tools for Molecular Design
-  
-        Jay Ponder Lab, Dept. of Biochemistry & Molecular 
-                           Biophysics,
diff --git a/biology/tinker/files/patch-ad b/biology/tinker/files/patch-ad
deleted file mode 100644
index 7171c8290043..000000000000
--- a/biology/tinker/files/patch-ad
+++ /dev/null
@@ -1,7 +0,0 @@
-*** ../bench/crambin.run.orig  Sat Aug 29 21:54:06 1998
---- ../bench/crambin.run       Sat Aug 29 21:54:20 1998
-***************
-*** 1 ****
-! ../bin/timer < crambin.input
---- 1 ----
-! timer < crambin.input
diff --git a/biology/tinker/files/patch-ae b/biology/tinker/files/patch-ae
deleted file mode 100644
index d8d1efdaf941..000000000000
--- a/biology/tinker/files/patch-ae
+++ /dev/null
@@ -1,7 +0,0 @@
-*** ../bench/crystal.run.orig  Sat Aug 29 21:56:20 1998
---- ../bench/crystal.run       Sat Aug 29 21:56:30 1998
-***************
-*** 1 ****
-! ../bin/timer < crystal.input
---- 1 ----
-! timer < crystal.input
diff --git a/biology/tinker/files/patch-af b/biology/tinker/files/patch-af
deleted file mode 100644
index a1fa92a8963a..000000000000
--- a/biology/tinker/files/patch-af
+++ /dev/null
@@ -1,11 +0,0 @@
-*** ../bench/water.run.orig    Sat Aug 29 21:56:44 1998
---- ../bench/water.run Sat Aug 29 21:56:58 1998
-***************
-*** 1,3 ****
-  cp water.dyn0 water.dyn
-! time ../bin/dynamic < water.input
-  rm water.dyn
---- 1,3 ----
-  cp water.dyn0 water.dyn
-! time dynamic < water.input
-  rm water.dyn
diff --git a/biology/tinker/files/patch-ag b/biology/tinker/files/patch-ag
new file mode 100644
index 000000000000..a1084876fe7d
--- /dev/null
+++ b/biology/tinker/files/patch-ag
@@ -0,0 +1,11 @@
+--- sizes.i.orig	Fri Jan 12 11:43:06 2001
++++ sizes.i	Fri Jan 12 11:43:38 2001
+@@ -52,7 +52,7 @@
+       integer maxvar,maxopt,maxhess,maxlight,maxvib,maxgeo,maxcell
+       integer maxring,maxfix,maxbio,maxres,maxamino,maxnuc,maxbnd
+       integer maxang,maxtors,maxpi,maxpib,maxpit
+-      parameter (maxatm=10000)
++      parameter (maxatm=2500)
+       parameter (maxval=4)
+       parameter (maxgrp=100)
+       parameter (maxtyp=1000)
diff --git a/biology/tinker/files/patch-ah b/biology/tinker/files/patch-ah
new file mode 100644
index 000000000000..c3f23dd2e057
--- /dev/null
+++ b/biology/tinker/files/patch-ah
@@ -0,0 +1,5 @@
+--- ../bench/bench-1.run.orig	Tue Jan  9 14:28:53 2001
++++ ../bench/bench-1.run	Tue Jan  9 14:29:19 2001
+@@ -1 +1 @@
+-../bin/timer bench-1 1 y
++timer bench-1 1 y
diff --git a/biology/tinker/files/patch-ai b/biology/tinker/files/patch-ai
new file mode 100644
index 000000000000..643cc82de1ed
--- /dev/null
+++ b/biology/tinker/files/patch-ai
@@ -0,0 +1,5 @@
+--- ../bench/bench-2.run.orig	Tue Jan  9 14:29:26 2001
++++ ../bench/bench-2.run	Tue Jan  9 14:29:33 2001
+@@ -1 +1 @@
+-../bin/timer bench-2 1 y
++timer bench-2 1 y
diff --git a/biology/tinker/files/patch-aj b/biology/tinker/files/patch-aj
new file mode 100644
index 000000000000..1f36c30fe172
--- /dev/null
+++ b/biology/tinker/files/patch-aj
@@ -0,0 +1,5 @@
+--- ../bench/bench-3.run.orig	Tue Jan  9 14:29:40 2001
++++ ../bench/bench-3.run	Tue Jan  9 14:29:53 2001
+@@ -1 +1 @@
+-time ../bin/vibrate bench-3 0
++time vibrate bench-3 0
diff --git a/biology/tinker/files/patch-ak b/biology/tinker/files/patch-ak
new file mode 100644
index 000000000000..d0549d42829d
--- /dev/null
+++ b/biology/tinker/files/patch-ak
@@ -0,0 +1,7 @@
+--- ../bench/bench-4.run.orig	Tue Jan  9 14:29:59 2001
++++ ../bench/bench-4.run	Tue Jan  9 14:30:14 2001
+@@ -1,3 +1,3 @@
+ cp bench-4.dyn0 bench-4.dyn
+-time ../bin/dynamic bench-4 1000 1.0 10.0 2 298.0
++time dynamic bench-4 1000 1.0 10.0 2 298.0
+ rm bench-4.dyn
diff --git a/biology/tinker/files/patch-al b/biology/tinker/files/patch-al
new file mode 100644
index 000000000000..8127254d2daa
--- /dev/null
+++ b/biology/tinker/files/patch-al
@@ -0,0 +1,7 @@
+--- ../bench/bench-5.run.orig	Tue Jan  9 14:30:18 2001
++++ ../bench/bench-5.run	Tue Jan  9 14:30:29 2001
+@@ -1,3 +1,3 @@
+ cp bench-5.dyn0 bench-5.dyn
+-time ../bin/dynamic bench-5 100 1.0 10.0 2 298.0
++time dynamic bench-5 100 1.0 10.0 2 298.0
+ rm bench-5.dyn
diff --git a/biology/tinker/pkg-descr b/biology/tinker/pkg-descr
index eee99649421d..a34d7f69fd53 100644
--- a/biology/tinker/pkg-descr
+++ b/biology/tinker/pkg-descr
@@ -1,10 +1,15 @@
 Tinker is a set of small programs for doing general purpose molecular
-modeling. Tools are included for energy minimizations, geometry
-calculations, and molecular analysis calculations. Tools for converting
-coordinate sets are also provided.
+modeling calculations. Tools are included for energy minimizations,
+geometry calculations, simulated annealing, molecular dynamics, and
+molecular analysis calculations. Tools for converting coordinate sets
+are also provided.  Tinker employs several force fields and minimization
+techniques.
 
-Tinker employs several force fields and minimizaation techniques.
-Simulated annealing and molecular dynamics can be performed with Tinker.
+This port sets the maxatm value to 2500 atoms.  This should be
+sufficient for most molecular systems.  Should you need to work with
+larger systems you can set the maxatm parameter in the sizes.i file
+located in the tinker/source directory and recompile.  Note that if it
+is set too large that tinker programs will abort and core dump.
 
 For more information about Tinker see:
 
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index 012299f88e88..880a1d1110ce 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -4,6 +4,7 @@ bin/anneal
 bin/archive
 bin/correlate
 bin/crystal
+bin/diffuse
 bin/distgeom
 bin/document
 bin/dynamic
@@ -12,8 +13,10 @@ bin/intedit
 bin/intxyz
 bin/minimize
 bin/minirot
+bin/minrigid
 bin/newton
 bin/newtrot
+bin/nucleic
 bin/optimize
 bin/optirot
 bin/optrigid
@@ -23,10 +26,12 @@ bin/protein
 bin/pss
 bin/pssrigid
 bin/pssrot
+bin/radial
 bin/saddle
 bin/scan
 bin/sniffer
 bin/spacefill
+bin/spectrum
 bin/superpose
 bin/sybylxyz
 bin/testgrad
@@ -43,95 +48,92 @@ bin/xyzedit
 bin/xyzint
 bin/xyzpdb
 bin/xyzsybyl
-share/tinker/bench/crambin.input
-share/tinker/bench/crambin.key
-share/tinker/bench/crambin.run
-share/tinker/bench/crambin.xyz
-share/tinker/bench/crystal.input
-share/tinker/bench/crystal.key
-share/tinker/bench/crystal.run
-share/tinker/bench/crystal.xyz
-share/tinker/bench/results-2.3
-share/tinker/bench/results-2.4
-share/tinker/bench/results-2.9
-share/tinker/bench/results-3.1
-share/tinker/bench/results-3.2
-share/tinker/bench/results-3.4
-share/tinker/bench/results-3.5
-share/tinker/bench/results-3.7
-share/tinker/bench/water.dyn0
-share/tinker/bench/water.input
-share/tinker/bench/water.key
-share/tinker/bench/water.run
-share/tinker/bench/water.xyz
 share/doc/tinker/README
+share/doc/tinker/announce.txt
 share/doc/tinker/guide.pdf
-share/doc/tinker/guide.ps.Z
+share/doc/tinker/guide.ps.gz
 share/doc/tinker/guide.txt
 share/doc/tinker/license.pdf
-share/doc/tinker/license.ps.Z
+share/doc/tinker/license.ps
 share/doc/tinker/license.txt
-share/doc/tinker/logo.ps.Z
-share/doc/tinker/spine.ps
+share/doc/tinker/logo.pdf
+share/doc/tinker/logo.ps.gz
 share/doc/tinker/summary.pdf
 share/doc/tinker/summary.ps
 share/doc/tinker/summary.txt
 share/examples/tinker/README
+share/examples/tinker/anion.dat
 share/examples/tinker/anion.dyn0
-share/examples/tinker/anion.in1
-share/examples/tinker/anion.in2
 share/examples/tinker/anion.key
 share/examples/tinker/anion.log
 share/examples/tinker/anion.run
 share/examples/tinker/anion.xyz
 share/examples/tinker/argon.1st
-share/examples/tinker/argon.in1
-share/examples/tinker/argon.in2
 share/examples/tinker/argon.key
 share/examples/tinker/argon.log
 share/examples/tinker/argon.run
 share/examples/tinker/clean.make
-share/examples/tinker/cluster.in1
+share/examples/tinker/cluster.dat
 share/examples/tinker/cluster.key
 share/examples/tinker/cluster.log
 share/examples/tinker/cluster.run
 share/examples/tinker/cluster.xyz
-share/examples/tinker/crambin.in1
-share/examples/tinker/crambin.in2
-share/examples/tinker/crambin.in3
 share/examples/tinker/crambin.key
 share/examples/tinker/crambin.log
 share/examples/tinker/crambin.pdb
 share/examples/tinker/crambin.run
 share/examples/tinker/cyclohex.boat
 share/examples/tinker/cyclohex.chair
-share/examples/tinker/cyclohex.in1
-share/examples/tinker/cyclohex.in2
-share/examples/tinker/cyclohex.in3
 share/examples/tinker/cyclohex.key
 share/examples/tinker/cyclohex.log
 share/examples/tinker/cyclohex.run
-share/examples/tinker/enkephalin.in1
-share/examples/tinker/enkephalin.in2
-share/examples/tinker/enkephalin.in3
+share/examples/tinker/enkephalin.dat
 share/examples/tinker/enkephalin.key
 share/examples/tinker/enkephalin.log
 share/examples/tinker/enkephalin.run
 share/examples/tinker/formamide.cell
-share/examples/tinker/formamide.in1
-share/examples/tinker/formamide.in2
-share/examples/tinker/formamide.in3
-share/examples/tinker/formamide.in4
+share/examples/tinker/formamide.dat
 share/examples/tinker/formamide.key
 share/examples/tinker/formamide.log
 share/examples/tinker/formamide.run
-share/examples/tinker/helix.in1
+share/examples/tinker/helix.1st
 share/examples/tinker/helix.key
 share/examples/tinker/helix.log
 share/examples/tinker/helix.run
-share/examples/tinker/helix.xyz
+share/examples/tinker/salt.cell
+share/examples/tinker/salt.key
+share/examples/tinker/salt.log
+share/examples/tinker/salt.run
+share/tinker/bench/bench-1.key
+share/tinker/bench/bench-1.run
+share/tinker/bench/bench-1.xyz
+share/tinker/bench/bench-2.key
+share/tinker/bench/bench-2.run
+share/tinker/bench/bench-2.xyz
+share/tinker/bench/bench-3.key
+share/tinker/bench/bench-3.run
+share/tinker/bench/bench-3.xyz
+share/tinker/bench/bench-4.dyn0
+share/tinker/bench/bench-4.key
+share/tinker/bench/bench-4.log
+share/tinker/bench/bench-4.run
+share/tinker/bench/bench-4.xyz
+share/tinker/bench/bench-5.dyn0
+share/tinker/bench/bench-5.key
+share/tinker/bench/bench-5.run
+share/tinker/bench/bench-5.xyz
+share/tinker/bench/results-2.3
+share/tinker/bench/results-2.4
+share/tinker/bench/results-2.9
+share/tinker/bench/results-3.1
+share/tinker/bench/results-3.2
+share/tinker/bench/results-3.4
+share/tinker/bench/results-3.5
+share/tinker/bench/results-3.7
+share/tinker/bench/results-3.8
 share/tinker/params/README
 share/tinker/params/amber.prm
+share/tinker/params/amberN.prm
 share/tinker/params/charmm.prm
 share/tinker/params/emr.prm
 share/tinker/params/hoch.prm
@@ -147,19 +149,18 @@ share/tinker/params/water.prm
 share/tinker/test/README
 share/tinker/test/ala20.key
 share/tinker/test/ala20.xyz
-share/tinker/test/annulene.int
-share/tinker/test/annulene.key
-share/tinker/test/annulene.xyz
-share/tinker/test/annulene2.key
-share/tinker/test/annulene2.xyz
-share/tinker/test/annulene3.key
-share/tinker/test/annulene3.xyz
+share/tinker/test/alkane.key
+share/tinker/test/alkane.xyz
 share/tinker/test/arach.int
 share/tinker/test/arach.key
 share/tinker/test/arach.xyz
 share/tinker/test/azulene.int
 share/tinker/test/azulene.key
 share/tinker/test/azulene.xyz
+share/tinker/test/bdna.int
+share/tinker/test/bdna.key
+share/tinker/test/bdna.seq
+share/tinker/test/bdna.xyz
 share/tinker/test/bearing.key
 share/tinker/test/bearing.pdb
 share/tinker/test/bearing.xyz
@@ -169,6 +170,13 @@ share/tinker/test/bearing2.xyz
 share/tinker/test/benzene.int
 share/tinker/test/benzene.key
 share/tinker/test/benzene.xyz
+share/tinker/test/bowl.int
+share/tinker/test/bowl.key
+share/tinker/test/bowl.xyz
+share/tinker/test/bowl2.key
+share/tinker/test/bowl2.xyz
+share/tinker/test/bowl3.key
+share/tinker/test/bowl3.xyz
 share/tinker/test/butane.int
 share/tinker/test/butane.key
 share/tinker/test/butane.xyz
@@ -195,13 +203,20 @@ share/tinker/test/c7ax.xyz
 share/tinker/test/c7eq.key
 share/tinker/test/c7eq.seq
 share/tinker/test/c7eq.xyz
+share/tinker/test/calmodulin.key
+share/tinker/test/calmodulin.pdb
+share/tinker/test/calmodulin.seq
+share/tinker/test/calmodulin.xyz
 share/tinker/test/cpentene.key
 share/tinker/test/cpentene.xyz
 share/tinker/test/crambin.key
+share/tinker/test/crambin.min
 share/tinker/test/crambin.pdb
 share/tinker/test/crambin.seq
+share/tinker/test/crambin.super
 share/tinker/test/crambin.xyz
 share/tinker/test/crambinx.key
+share/tinker/test/crambinx.ray
 share/tinker/test/crambinx.xyz
 share/tinker/test/crown.int
 share/tinker/test/crown.key
@@ -221,12 +236,12 @@ share/tinker/test/diene.xyz
 share/tinker/test/dimethane.key
 share/tinker/test/dimethane.xyz
 share/tinker/test/diwater.key
+share/tinker/test/diwater.lin
+share/tinker/test/diwater.min
 share/tinker/test/diwater.xyz
 share/tinker/test/enkephalin.int
 share/tinker/test/enkephalin.key
 share/tinker/test/enkephalin.make
-share/tinker/test/enkephalin.pdb
-share/tinker/test/enkephalin.run
 share/tinker/test/enkephalin.seq
 share/tinker/test/enkephalin.xyz
 share/tinker/test/ermer.int
@@ -237,14 +252,21 @@ share/tinker/test/ester.xyz
 share/tinker/test/ethane.int
 share/tinker/test/ethane.key
 share/tinker/test/ethane.xyz
+share/tinker/test/ethanol.int
+share/tinker/test/ethanol.key
+share/tinker/test/ethanol.xyz
 share/tinker/test/ethylene.int
 share/tinker/test/ethylene.key
 share/tinker/test/ethylene.xyz
 share/tinker/test/flane.int
 share/tinker/test/flane.key
 share/tinker/test/flane.xyz
-share/tinker/test/formamide.key
-share/tinker/test/formamide.xyz
+share/tinker/test/form.key
+share/tinker/test/form.xyz
+share/tinker/test/formbig.key
+share/tinker/test/formbig.xyz
+share/tinker/test/formbox.key
+share/tinker/test/formbox.xyz
 share/tinker/test/furan.int
 share/tinker/test/furan.key
 share/tinker/test/furan.xyz
@@ -252,6 +274,13 @@ share/tinker/test/glucose.key
 share/tinker/test/glucose.xyz
 share/tinker/test/helix.key
 share/tinker/test/helix.xyz
+share/tinker/test/hexane.int
+share/tinker/test/hexane.key
+share/tinker/test/hexane.xyz
+share/tinker/test/hexanes.dyn
+share/tinker/test/hexanes.key
+share/tinker/test/hexanes.run
+share/tinker/test/hexanes.xyz
 share/tinker/test/imidazole.int
 share/tinker/test/imidazole.key
 share/tinker/test/imidazole.xyz
@@ -260,11 +289,19 @@ share/tinker/test/imine.key
 share/tinker/test/imine.xyz
 share/tinker/test/lactam.key
 share/tinker/test/lactam.xyz
+share/tinker/test/melittin.key
+share/tinker/test/melittin.pdb
+share/tinker/test/melittin.seq
+share/tinker/test/melittin.xyz
 share/tinker/test/methane.int
 share/tinker/test/methane.key
 share/tinker/test/methane.xyz
 share/tinker/test/methanol.key
 share/tinker/test/methanol.xyz
+share/tinker/test/nacl.key
+share/tinker/test/nacl.xyz
+share/tinker/test/naphthalene.key
+share/tinker/test/naphthalene.xyz
 share/tinker/test/nma.int
 share/tinker/test/nma.key
 share/tinker/test/nma.xyz
@@ -287,14 +324,24 @@ share/tinker/test/palmitate.xyz
 share/tinker/test/peptide.int
 share/tinker/test/peptide.key
 share/tinker/test/peptide.make
+share/tinker/test/peptide.min
 share/tinker/test/peptide.pdb
 share/tinker/test/peptide.seq
 share/tinker/test/peptide.xyz
 share/tinker/test/phenanth.key
 share/tinker/test/phenanth.xyz
+share/tinker/test/photo.key
+share/tinker/test/photo.pdb
+share/tinker/test/photo.seq
+share/tinker/test/photo.xyz
+share/tinker/test/propane.key
+share/tinker/test/propane.ray
+share/tinker/test/propane.xyz
 share/tinker/test/propellane.int
 share/tinker/test/propellane.key
 share/tinker/test/propellane.xyz
+share/tinker/test/propyne.key
+share/tinker/test/propyne.xyz
 share/tinker/test/pyridine.int
 share/tinker/test/pyridine.key
 share/tinker/test/pyridine.xyz
@@ -317,6 +364,8 @@ share/tinker/test/thiophene.xyz
 share/tinker/test/thr.int
 share/tinker/test/thr.key
 share/tinker/test/thr.xyz
+share/tinker/test/tip5p.key
+share/tinker/test/tip5p.xyz
 share/tinker/test/water.int
 share/tinker/test/water.key
 share/tinker/test/water.xyz
@@ -337,9 +386,9 @@ share/tinker/test/white.int
 share/tinker/test/white.key
 share/tinker/test/white.xyz
 share/tinker/tinker.txt
-@dirrm share/tinker/bench
 @dirrm share/doc/tinker
 @dirrm share/examples/tinker
+@dirrm share/tinker/bench
 @dirrm share/tinker/params
 @dirrm share/tinker/test
 @dirrm share/tinker
diff --git a/biology/tinker/pkg-plist.viewer b/biology/tinker/pkg-plist.viewer
new file mode 100644
index 000000000000..8cedec932ec5
--- /dev/null
+++ b/biology/tinker/pkg-plist.viewer
@@ -0,0 +1,399 @@
+bin/alchemy
+bin/analyze
+bin/anneal
+bin/archive
+bin/correlate
+bin/crystal
+bin/diffuse
+bin/distgeom
+bin/document
+bin/dynamic
+bin/gda
+bin/intedit
+bin/intxyz
+bin/minimize
+bin/minirot
+bin/minrigid
+bin/newton
+bin/newtrot
+bin/nucleic
+bin/optimize
+bin/optirot
+bin/optrigid
+bin/path
+bin/pdbxyz
+bin/protein
+bin/pss
+bin/pssrigid
+bin/pssrot
+bin/radial
+bin/saddle
+bin/scan
+bin/sniffer
+bin/spacefill
+bin/spectrum
+bin/superpose
+bin/sybylxyz
+bin/testgrad
+bin/testhess
+bin/testlight
+bin/testrot
+bin/timer
+bin/timerot
+bin/tview-8
+bin/tview-16
+bin/tview-32
+bin/vibrate
+bin/vibrot
+bin/xtalfit
+bin/xtalmin
+bin/xyzedit
+bin/xyzint
+bin/xyzpdb
+bin/xyzsybyl
+share/doc/tinker/README
+share/doc/tinker/announce.txt
+share/doc/tinker/guide.pdf
+share/doc/tinker/guide.ps.gz
+share/doc/tinker/guide.txt
+share/doc/tinker/license.pdf
+share/doc/tinker/license.ps
+share/doc/tinker/license.txt
+share/doc/tinker/logo.pdf
+share/doc/tinker/logo.ps.gz
+share/doc/tinker/summary.pdf
+share/doc/tinker/summary.ps
+share/doc/tinker/summary.txt
+share/examples/tinker/README
+share/examples/tinker/anion.dat
+share/examples/tinker/anion.dyn0
+share/examples/tinker/anion.key
+share/examples/tinker/anion.log
+share/examples/tinker/anion.run
+share/examples/tinker/anion.xyz
+share/examples/tinker/argon.1st
+share/examples/tinker/argon.key
+share/examples/tinker/argon.log
+share/examples/tinker/argon.run
+share/examples/tinker/clean.make
+share/examples/tinker/cluster.dat
+share/examples/tinker/cluster.key
+share/examples/tinker/cluster.log
+share/examples/tinker/cluster.run
+share/examples/tinker/cluster.xyz
+share/examples/tinker/crambin.key
+share/examples/tinker/crambin.log
+share/examples/tinker/crambin.pdb
+share/examples/tinker/crambin.run
+share/examples/tinker/cyclohex.boat
+share/examples/tinker/cyclohex.chair
+share/examples/tinker/cyclohex.key
+share/examples/tinker/cyclohex.log
+share/examples/tinker/cyclohex.run
+share/examples/tinker/enkephalin.dat
+share/examples/tinker/enkephalin.key
+share/examples/tinker/enkephalin.log
+share/examples/tinker/enkephalin.run
+share/examples/tinker/formamide.cell
+share/examples/tinker/formamide.dat
+share/examples/tinker/formamide.key
+share/examples/tinker/formamide.log
+share/examples/tinker/formamide.run
+share/examples/tinker/helix.1st
+share/examples/tinker/helix.key
+share/examples/tinker/helix.log
+share/examples/tinker/helix.run
+share/examples/tinker/salt.cell
+share/examples/tinker/salt.key
+share/examples/tinker/salt.log
+share/examples/tinker/salt.run
+share/tinker/bench/bench-1.key
+share/tinker/bench/bench-1.run
+share/tinker/bench/bench-1.xyz
+share/tinker/bench/bench-2.key
+share/tinker/bench/bench-2.run
+share/tinker/bench/bench-2.xyz
+share/tinker/bench/bench-3.key
+share/tinker/bench/bench-3.run
+share/tinker/bench/bench-3.xyz
+share/tinker/bench/bench-4.dyn0
+share/tinker/bench/bench-4.key
+share/tinker/bench/bench-4.log
+share/tinker/bench/bench-4.run
+share/tinker/bench/bench-4.xyz
+share/tinker/bench/bench-5.dyn0
+share/tinker/bench/bench-5.key
+share/tinker/bench/bench-5.run
+share/tinker/bench/bench-5.xyz
+share/tinker/bench/results-2.3
+share/tinker/bench/results-2.4
+share/tinker/bench/results-2.9
+share/tinker/bench/results-3.1
+share/tinker/bench/results-3.2
+share/tinker/bench/results-3.4
+share/tinker/bench/results-3.5
+share/tinker/bench/results-3.7
+share/tinker/bench/results-3.8
+share/tinker/params/README
+share/tinker/params/amber.prm
+share/tinker/params/amberN.prm
+share/tinker/params/charmm.prm
+share/tinker/params/emr.prm
+share/tinker/params/hoch.prm
+share/tinker/params/mm2.prm
+share/tinker/params/mm3.prm
+share/tinker/params/mm3pro.prm
+share/tinker/params/opls.prm
+share/tinker/params/oplsaa.prm
+share/tinker/params/smooth.prm
+share/tinker/params/smoothaa.prm
+share/tinker/params/tinker.prm
+share/tinker/params/water.prm
+share/tinker/rasmol/rasmol.hlp
+share/tinker/test/README
+share/tinker/test/ala20.key
+share/tinker/test/ala20.xyz
+share/tinker/test/alkane.key
+share/tinker/test/alkane.xyz
+share/tinker/test/arach.int
+share/tinker/test/arach.key
+share/tinker/test/arach.xyz
+share/tinker/test/azulene.int
+share/tinker/test/azulene.key
+share/tinker/test/azulene.xyz
+share/tinker/test/bdna.int
+share/tinker/test/bdna.key
+share/tinker/test/bdna.seq
+share/tinker/test/bdna.xyz
+share/tinker/test/bearing.key
+share/tinker/test/bearing.pdb
+share/tinker/test/bearing.xyz
+share/tinker/test/bearing2.key
+share/tinker/test/bearing2.pdb
+share/tinker/test/bearing2.xyz
+share/tinker/test/benzene.int
+share/tinker/test/benzene.key
+share/tinker/test/benzene.xyz
+share/tinker/test/bowl.int
+share/tinker/test/bowl.key
+share/tinker/test/bowl.xyz
+share/tinker/test/bowl2.key
+share/tinker/test/bowl2.xyz
+share/tinker/test/bowl3.key
+share/tinker/test/bowl3.xyz
+share/tinker/test/butane.int
+share/tinker/test/butane.key
+share/tinker/test/butane.xyz
+share/tinker/test/butane2.int
+share/tinker/test/butane2.key
+share/tinker/test/butane2.xyz
+share/tinker/test/butanes.dyn
+share/tinker/test/butanes.key
+share/tinker/test/butanes.xyz
+share/tinker/test/butanex.key
+share/tinker/test/butanex.xyz
+share/tinker/test/butopls.int
+share/tinker/test/butopls.key
+share/tinker/test/butopls.xyz
+share/tinker/test/butopls2.int
+share/tinker/test/butopls2.key
+share/tinker/test/butopls2.xyz
+share/tinker/test/c5.key
+share/tinker/test/c5.seq
+share/tinker/test/c5.xyz
+share/tinker/test/c7ax.key
+share/tinker/test/c7ax.seq
+share/tinker/test/c7ax.xyz
+share/tinker/test/c7eq.key
+share/tinker/test/c7eq.seq
+share/tinker/test/c7eq.xyz
+share/tinker/test/calmodulin.key
+share/tinker/test/calmodulin.pdb
+share/tinker/test/calmodulin.seq
+share/tinker/test/calmodulin.xyz
+share/tinker/test/cpentene.key
+share/tinker/test/cpentene.xyz
+share/tinker/test/crambin.key
+share/tinker/test/crambin.min
+share/tinker/test/crambin.pdb
+share/tinker/test/crambin.seq
+share/tinker/test/crambin.super
+share/tinker/test/crambin.xyz
+share/tinker/test/crambinx.key
+share/tinker/test/crambinx.ray
+share/tinker/test/crambinx.xyz
+share/tinker/test/crown.int
+share/tinker/test/crown.key
+share/tinker/test/crown.xyz
+share/tinker/test/cychept.int
+share/tinker/test/cychept.key
+share/tinker/test/cychept.xyz
+share/tinker/test/cyclo.int
+share/tinker/test/cyclo.key
+share/tinker/test/cyclo.xyz
+share/tinker/test/cyclo2.int
+share/tinker/test/cyclo2.key
+share/tinker/test/cyclo2.xyz
+share/tinker/test/diene.int
+share/tinker/test/diene.key
+share/tinker/test/diene.xyz
+share/tinker/test/dimethane.key
+share/tinker/test/dimethane.xyz
+share/tinker/test/diwater.key
+share/tinker/test/diwater.lin
+share/tinker/test/diwater.min
+share/tinker/test/diwater.xyz
+share/tinker/test/enkephalin.int
+share/tinker/test/enkephalin.key
+share/tinker/test/enkephalin.make
+share/tinker/test/enkephalin.seq
+share/tinker/test/enkephalin.xyz
+share/tinker/test/ermer.int
+share/tinker/test/ermer.key
+share/tinker/test/ermer.xyz
+share/tinker/test/ester.key
+share/tinker/test/ester.xyz
+share/tinker/test/ethane.int
+share/tinker/test/ethane.key
+share/tinker/test/ethane.xyz
+share/tinker/test/ethanol.int
+share/tinker/test/ethanol.key
+share/tinker/test/ethanol.xyz
+share/tinker/test/ethylene.int
+share/tinker/test/ethylene.key
+share/tinker/test/ethylene.xyz
+share/tinker/test/flane.int
+share/tinker/test/flane.key
+share/tinker/test/flane.xyz
+share/tinker/test/form.key
+share/tinker/test/form.xyz
+share/tinker/test/formbig.key
+share/tinker/test/formbig.xyz
+share/tinker/test/formbox.key
+share/tinker/test/formbox.xyz
+share/tinker/test/furan.int
+share/tinker/test/furan.key
+share/tinker/test/furan.xyz
+share/tinker/test/glucose.key
+share/tinker/test/glucose.xyz
+share/tinker/test/helix.key
+share/tinker/test/helix.xyz
+share/tinker/test/hexane.int
+share/tinker/test/hexane.key
+share/tinker/test/hexane.xyz
+share/tinker/test/hexanes.dyn
+share/tinker/test/hexanes.key
+share/tinker/test/hexanes.run
+share/tinker/test/hexanes.xyz
+share/tinker/test/imidazole.int
+share/tinker/test/imidazole.key
+share/tinker/test/imidazole.xyz
+share/tinker/test/imine.int
+share/tinker/test/imine.key
+share/tinker/test/imine.xyz
+share/tinker/test/lactam.key
+share/tinker/test/lactam.xyz
+share/tinker/test/melittin.key
+share/tinker/test/melittin.pdb
+share/tinker/test/melittin.seq
+share/tinker/test/melittin.xyz
+share/tinker/test/methane.int
+share/tinker/test/methane.key
+share/tinker/test/methane.xyz
+share/tinker/test/methanol.key
+share/tinker/test/methanol.xyz
+share/tinker/test/nacl.key
+share/tinker/test/nacl.xyz
+share/tinker/test/naphthalene.key
+share/tinker/test/naphthalene.xyz
+share/tinker/test/nma.int
+share/tinker/test/nma.key
+share/tinker/test/nma.xyz
+share/tinker/test/nmabox.dyn
+share/tinker/test/nmabox.key
+share/tinker/test/nmabox.xyz
+share/tinker/test/nstilbene.int
+share/tinker/test/nstilbene.key
+share/tinker/test/nstilbene.xyz
+share/tinker/test/octane.int
+share/tinker/test/octane.key
+share/tinker/test/octane.xyz
+share/tinker/test/octane2.int
+share/tinker/test/octane2.key
+share/tinker/test/octane2.xyz
+share/tinker/test/octene.key
+share/tinker/test/octene.xyz
+share/tinker/test/palmitate.key
+share/tinker/test/palmitate.xyz
+share/tinker/test/peptide.int
+share/tinker/test/peptide.key
+share/tinker/test/peptide.make
+share/tinker/test/peptide.min
+share/tinker/test/peptide.pdb
+share/tinker/test/peptide.seq
+share/tinker/test/peptide.xyz
+share/tinker/test/phenanth.key
+share/tinker/test/phenanth.xyz
+share/tinker/test/photo.key
+share/tinker/test/photo.pdb
+share/tinker/test/photo.seq
+share/tinker/test/photo.xyz
+share/tinker/test/propane.key
+share/tinker/test/propane.ray
+share/tinker/test/propane.xyz
+share/tinker/test/propellane.int
+share/tinker/test/propellane.key
+share/tinker/test/propellane.xyz
+share/tinker/test/propyne.key
+share/tinker/test/propyne.xyz
+share/tinker/test/pyridine.int
+share/tinker/test/pyridine.key
+share/tinker/test/pyridine.xyz
+share/tinker/test/pyrrole.int
+share/tinker/test/pyrrole.key
+share/tinker/test/pyrrole.xyz
+share/tinker/test/retinoic.key
+share/tinker/test/retinoic.xyz
+share/tinker/test/sterol.key
+share/tinker/test/sterol.xyz
+share/tinker/test/styrene.int
+share/tinker/test/styrene.key
+share/tinker/test/styrene.xyz
+share/tinker/test/thiadiene.int
+share/tinker/test/thiadiene.key
+share/tinker/test/thiadiene.xyz
+share/tinker/test/thiophene.int
+share/tinker/test/thiophene.key
+share/tinker/test/thiophene.xyz
+share/tinker/test/thr.int
+share/tinker/test/thr.key
+share/tinker/test/thr.xyz
+share/tinker/test/tip5p.key
+share/tinker/test/tip5p.xyz
+share/tinker/test/water.int
+share/tinker/test/water.key
+share/tinker/test/water.xyz
+share/tinker/test/waterbig.key
+share/tinker/test/waterbig.xyz
+share/tinker/test/waterbox.dyn
+share/tinker/test/waterbox.key
+share/tinker/test/waterbox.xyz
+share/tinker/test/waterhuge.key
+share/tinker/test/waterhuge.xyz
+share/tinker/test/wateroct.dyn
+share/tinker/test/wateroct.key
+share/tinker/test/wateroct.xyz
+share/tinker/test/watersmall.dyn
+share/tinker/test/watersmall.key
+share/tinker/test/watersmall.xyz
+share/tinker/test/white.int
+share/tinker/test/white.key
+share/tinker/test/white.xyz
+share/tinker/tinker.txt
+@dirrm share/doc/tinker
+@dirrm share/examples/tinker
+@dirrm share/tinker/bench
+@dirrm share/tinker/params
+@dirrm share/tinker/rasmol
+@dirrm share/tinker/test
+@dirrm share/tinker
diff --git a/biology/tinker/scripts/build_viewer b/biology/tinker/scripts/build_viewer
new file mode 100644
index 000000000000..24fb838c4fd0
--- /dev/null
+++ b/biology/tinker/scripts/build_viewer
@@ -0,0 +1,47 @@
+#!/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