- Update to version 6.1.01

- Add MAKE_JOBS_SAFE
- Convert to optionsng
- Trim Makefile header

PR:           ports/171971
Submitted by: KATO Tsuguru <tkato432 _at_ yahoo.com>
Approved by:  beat (mentor)
Feature safe: yes

15 files changed, 788 insertions, 753 deletions

diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index 7035071bbaf..3e3fb3a2899 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -1,76 +1,74 @@
-# New ports collection makefile for:   tinker
-# Date Created:                26 August 1998
-# Whom:                        Glenn Johnson
-#
+# Created by: Glenn Johnson
 # $FreeBSD$
-#
 
 PORTNAME=	tinker
-PORTVERSION=	5.1.09
+PORTVERSION=	6.1.01
 CATEGORIES=	biology
 MASTER_SITES=	http://dasher.wustl.edu/tinker/downloads/
 
 MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A general purpose molecular modelling package
 
-MAKE_ENV+=	HAVE_G2C=yes INSTALL_PROGRAM="${INSTALL_PROGRAM}"
+RESTRICTED=	author requests no distribution except from his FTP site
+
+OPTIONS_DEFINE=	OPTIMIZED_FFLAGS DATA DOCS EXAMPLES
+OPTIONS_DEFAULT=DATA
+OPTIMIZED_FFLAGS_DESC=	compilation optimizations
 
-WRKSRC=		${WRKDIR}/tinker/source
+WRKSRC=		${WRKDIR}/${PORTNAME}
+BUILD_WRKSRC=	${WRKSRC}/source
+INSTALL_WRKSRC=	${WRKSRC}/source
 
-MAKEFILE=	${WRKDIR}/tinker/make/Makefile
+USE_FORTRAN=	yes
+MAKE_ENV=	HAVE_G2C=yes
+MAKEFILE=	${WRKSRC}/make/Makefile
 ALL_TARGET=	all listing
 INSTALL_TARGET=	rename
-RESTRICTED=	author requests no distribution except from his FTP site
+MAKE_JOBS_SAFE=	yes
 
-DOCS=		0README *.pdf *.txt announce/release*
-SAMPLES=	0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.run *.xyz
+SUB_FILES=	pkg-message
+
+DOCS=		0README *.pdf *.txt
+SAMPLES=	0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz
 BENCHES=	0README *.dyn0 *.log *.key *.run *.xyz results*
 
 .include <bsd.port.pre.mk>
 
-USE_FORTRAN=	yes
-
-.if defined(WITH_OPTIMIZED_FLAGS)
+.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS}
 FFLAGS+=	-O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations
 .if (${ARCH} == "i386")
 FFLAGS+=	-mfancy-math-387 -malign-double
 .endif # i386
 .endif
 
-pre-everything::
-.if !defined(WITH_OPTIMIZED_FLAGS)
-	@${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
+.if empty(PORT_OPTIONS:MDATA)
+NOPORTDATA=	yes
 .endif
 
 post-extract:
-	${CHMOD} -R u+w ${WRKDIR}/tinker
-
-post-patch:
-	@${REINPLACE_CMD} -e 's|%%FFLAGS%%|${FFLAGS}|g' ${WRKSRC}/../make/Makefile
+	@${CHMOD} -R u+w ${WRKSRC}
 
 post-install:
+	@${MKDIR} ${DATADIR}
+	${INSTALL_DATA} ${INSTALL_WRKSRC}/tinker.txt ${DATADIR}
 	@${MKDIR} ${DATADIR}/params
-	@${INSTALL_DATA} ${WRKDIR}/tinker/source/tinker.txt \
-		${DATADIR}
-	@${INSTALL_DATA} ${WRKDIR}/tinker/params/* \
-		${DATADIR}/params
-.if !defined(NOPORTDOCS)
-	@${MKDIR} ${DOCSDIR}
-	@${MKDIR} ${EXAMPLESDIR}
+	${INSTALL_DATA} ${WRKSRC}/params/* ${DATADIR}/params
+.if ${PORT_OPTIONS:MDATA}
 	@${MKDIR} ${DATADIR}/bench
+	${INSTALL_DATA} ${BENCHES:S|^|${WRKSRC}/bench/|} ${DATADIR}/bench
 	@${MKDIR} ${DATADIR}/test
-	@${INSTALL_DATA} ${DOCS:S|^|${WRKDIR}/tinker/doc/|} ${DOCSDIR}
-	@${INSTALL_DATA} ${SAMPLES:S|^|${WRKDIR}/tinker/example/|} ${EXAMPLESDIR}
-	@${INSTALL_DATA} ${BENCHES:S|^|${WRKDIR}/tinker/bench/|} ${DATADIR}/bench
-	@${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${DATADIR}/test
+	${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test
+.endif
+.if ${PORT_OPTIONS:MDOCS}
+	@${MKDIR} ${DOCSDIR}
+	${INSTALL_DATA} ${DOCS:S|^|${WRKSRC}/doc/|} ${DOCSDIR}
+.endif
+.if ${PORT_OPTIONS:MEXAMPLES}
+	@${MKDIR} ${EXAMPLESDIR}
+	${INSTALL_DATA} ${SAMPLES:S|^|${WRKSRC}/example/|} ${EXAMPLESDIR}
 .endif
-	@${ECHO_MSG} ""
-	@${ECHO_MSG} "   **********************************************************"
-	@${ECHO_MSG} "       The author requests that you return a license form    "
-	@${ECHO_MSG} "       to him if you find Tinker to be useful.               "
-	@${ECHO_MSG} "                                                             "
-	@${ECHO_MSG} "       See ${DOCSDIR} for license forms.     "
-	@${ECHO_MSG} "   **********************************************************"
-	@${ECHO_MSG} ""
+	@${ECHO_CMD}
+	@${CAT} ${PKGMESSAGE}
+	@${ECHO_CMD}
 
 .include <bsd.port.post.mk>
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
index d441f5ba5b8..2971eb29303 100644
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@@ -1,2 +1,2 @@
-SHA256 (tinker-5.1.09.tar.gz) = 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183
-SIZE (tinker-5.1.09.tar.gz) = 14071638
+SHA256 (tinker-6.1.01.tar.gz) = fa287c381fd866822b19396fa152406b8463421f0a27902867cdbbf6b67233e4
+SIZE (tinker-6.1.01.tar.gz) = 19478639
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
deleted file mode 100644
index e68ae52123d..00000000000
--- a/biology/tinker/files/patch-aa
+++ /dev/null
@@ -1,207 +0,0 @@
---- ../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
- ##   2. make rename           Move the executables to BINDIR
--##   3. make remove_links     Create soft links in LINKDIR
--##   4. make create_links     Remove soft links from LINKDIR
-+##   3. make remove_links     Remove soft links in LINKDIR
-+##   4. make create_links     Create soft links from LINKDIR
- ##   6. make listing          Concatenate source to tinker.txt
- ##   5. make clean            Delete objects and executables
- ##
-@@ -30,9 +30,9 @@
- ##  LINKDIR      Linked Copies of TINKER Executables
- ##
- 
--TINKERDIR = /Users/ponder/tinker
--BINDIR = $(TINKERDIR)/bin
--LINKDIR = /usr/local/bin
-+TINKERDIR = ${WRKDIR}
-+BINDIR = ${PREFIX}/bin
-+#LINKDIR = /usr/local/bin
- 
- ####################################################################
- ##  Known Machine Types; Uncomment One of the Following Sections  ##
-@@ -40,6 +40,20 @@
- ####################################################################
- 
- ##
-+##  Machine:  IntelPC / FreeBSD
-+##  CPU Type: Intel, AMD, Cyrix
-+##  Oper Sys: FreeBSD 4.2
-+##  Compiler: f77 , aka g77
-+##
-+
-+F77 = ${FC}
-+LIBS =
-+F77FLAGS = -c %%FFLAGS%%
-+LINKFLAGS =
-+OPTFLAGS = 
-+LIBFLAGS = -rcuv
-+
-+##
- ##  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
- 
-+.SUFFIXES: .x
-+
- .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
-+	${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
- 
- all:	${EXEFILES}
- 
-@@ -608,63 +624,63 @@
- 	cat *.i *.f > tinker.txt
- 
- rename:
--	mv  alchemy.x    $(BINDIR)/alchemy
--	mv  analyze.x    $(BINDIR)/analyze
--	mv  anneal.x     $(BINDIR)/anneal
--	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
--	mv  gda.x        $(BINDIR)/gda
--	mv  intedit.x    $(BINDIR)/intedit
--	mv  intxyz.x     $(BINDIR)/intxyz
--	mv  minimize.x   $(BINDIR)/minimize
--	mv  minirot.x    $(BINDIR)/minirot
--	mv  minrigid.x   $(BINDIR)/minrigid
--	mv  monte.x      $(BINDIR)/monte
--	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
--	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
--	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
--	mv  testhess.x   $(BINDIR)/testhess
--	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
--	mv  xtalmin.x    $(BINDIR)/xtalmin
--	mv  xyzedit.x    $(BINDIR)/xyzedit
--	mv  xyzint.x     $(BINDIR)/xyzint
--	mv  xyzpdb.x     $(BINDIR)/xyzpdb
--	mv  xyzsybyl.x   $(BINDIR)/xyzsybyl
-+	${INSTALL_PROGRAM}  alchemy.x    $(BINDIR)/alchemy
-+	${INSTALL_PROGRAM}  analyze.x    $(BINDIR)/analyze
-+	${INSTALL_PROGRAM}  anneal.x     $(BINDIR)/anneal
-+	${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
-+	${INSTALL_PROGRAM}  gda.x        $(BINDIR)/gda
-+	${INSTALL_PROGRAM}  intedit.x    $(BINDIR)/intedit
-+	${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}  monte.x      $(BINDIR)/monte
-+	${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
-+	${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
-+	${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
-+	${INSTALL_PROGRAM}  testhess.x   $(BINDIR)/testhess
-+	${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
-+	${INSTALL_PROGRAM}  xtalmin.x    $(BINDIR)/xtalmin
-+	${INSTALL_PROGRAM}  xyzedit.x    $(BINDIR)/xyzedit
-+	${INSTALL_PROGRAM}  xyzint.x     $(BINDIR)/xyzint
-+	${INSTALL_PROGRAM}  xyzpdb.x     $(BINDIR)/xyzpdb
-+	${INSTALL_PROGRAM}  xyzsybyl.x   $(BINDIR)/xyzsybyl
- 
- remove_links:
- 	rm -f $(LINKDIR)/alchemy
diff --git a/biology/tinker/files/patch-ah b/biology/tinker/files/patch-ah
deleted file mode 100644
index 12bd7c9ac00..00000000000
--- a/biology/tinker/files/patch-ah
+++ /dev/null
@@ -1,5 +0,0 @@
---- ../bench/bench1.run.orig	Tue Jul 24 14:02:20 2001
-+++ ../bench/bench1.run	Wed Sep  5 13:57:02 2001
-@@ -1 +1 @@
--../bin/timer bench1 1 y
-+timer bench1 1 y
diff --git a/biology/tinker/files/patch-ai b/biology/tinker/files/patch-ai
deleted file mode 100644
index e5a6559bb29..00000000000
--- a/biology/tinker/files/patch-ai
+++ /dev/null
@@ -1,5 +0,0 @@
---- ../bench/bench2.run.orig	Tue Jul 24 14:02:20 2001
-+++ ../bench/bench2.run	Wed Sep  5 13:58:47 2001
-@@ -1 +1 @@
--../bin/timer bench2 1 y
-+timer bench2 1 y
diff --git a/biology/tinker/files/patch-aj b/biology/tinker/files/patch-aj
deleted file mode 100644
index 3e18d09b507..00000000000
--- a/biology/tinker/files/patch-aj
+++ /dev/null
@@ -1,5 +0,0 @@
---- ../bench/bench3.run.orig	Wed Sep  5 14:00:09 2001
-+++ ../bench/bench3.run	Wed Sep  5 14:01:27 2001
-@@ -1 +1 @@
--time ../bin/vibrate bench3 0
-+time vibrate bench3 0
diff --git a/biology/tinker/files/patch-bench__bench1.run b/biology/tinker/files/patch-bench__bench1.run
new file mode 100644
index 00000000000..7b728a8884f
--- /dev/null
+++ b/biology/tinker/files/patch-bench__bench1.run
@@ -0,0 +1,5 @@
+--- bench/bench1.run.orig	Tue Jul 24 14:02:20 2001
++++ bench/bench1.run	Wed Sep  5 13:57:02 2001
+@@ -1 +1 @@
+-../bin/timer bench1 1 y
++timer bench1 1 y
diff --git a/biology/tinker/files/patch-bench__bench2.run b/biology/tinker/files/patch-bench__bench2.run
new file mode 100644
index 00000000000..b9f70cc453d
--- /dev/null
+++ b/biology/tinker/files/patch-bench__bench2.run
@@ -0,0 +1,5 @@
+--- bench/bench2.run.orig	Tue Jul 24 14:02:20 2001
++++ bench/bench2.run	Wed Sep  5 13:58:47 2001
+@@ -1 +1 @@
+-../bin/timer bench2 1 y
++timer bench2 1 y
diff --git a/biology/tinker/files/patch-bench__bench3.run b/biology/tinker/files/patch-bench__bench3.run
new file mode 100644
index 00000000000..fc1db99f32d
--- /dev/null
+++ b/biology/tinker/files/patch-bench__bench3.run
@@ -0,0 +1,5 @@
+--- bench/bench3.run.orig	Wed Sep  5 14:00:09 2001
++++ bench/bench3.run	Wed Sep  5 14:01:27 2001
+@@ -1 +1 @@
+-time ../bin/vibrate bench3 0
++time vibrate bench3 0
diff --git a/biology/tinker/files/patch-ak b/biology/tinker/files/patch-bench__bench4.run
index 9a415fcd0f3..177ddfb84e3 100644
--- a/biology/tinker/files/patch-ak
+++ b/biology/tinker/files/patch-bench__bench4.run
@@ -1,5 +1,5 @@
---- ../bench/bench4.run.orig	Tue Jul 24 14:02:20 2001
-+++ ../bench/bench4.run	Wed Sep  5 14:02:17 2001
+--- bench/bench4.run.orig	Tue Jul 24 14:02:20 2001
++++ bench/bench4.run	Wed Sep  5 14:02:17 2001
 @@ -1,3 +1,3 @@
  cp bench4.dyn0 bench4.dyn
 -time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0
diff --git a/biology/tinker/files/patch-al b/biology/tinker/files/patch-bench__bench5.run
index 4fa7ddb6faf..c047178b3ec 100644
--- a/biology/tinker/files/patch-al
+++ b/biology/tinker/files/patch-bench__bench5.run
@@ -1,5 +1,5 @@
---- ../bench/bench5.run.orig	2010-08-25 00:58:15.000000000 +0400
-+++ ../bench/bench5.run	2011-01-26 23:35:18.000000000 +0300
+--- 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 1000 1.0 10.0 2 298.0
diff --git a/biology/tinker/files/patch-make__Makefile b/biology/tinker/files/patch-make__Makefile
new file mode 100644
index 00000000000..47ea46a155c
--- /dev/null
+++ b/biology/tinker/files/patch-make__Makefile
@@ -0,0 +1,211 @@
+--- make/Makefile.orig	2012-06-29 14:51:42.000000000 +0900
++++ make/Makefile	2012-11-10 00:12:19.000000000 +0900
+@@ -9,8 +9,8 @@
+ ##
+ ##   1. make all              Build all the TINKER executables
+ ##   2. make rename           Move the executables to BINDIR
+-##   3. make remove_links     Create soft links in LINKDIR
+-##   4. make create_links     Remove soft links from LINKDIR
++##   3. make remove_links     Remove soft links in LINKDIR
++##   4. make create_links     Create soft links from LINKDIR
+ ##   6. make listing          Concatenate source to tinker.txt
+ ##   5. make clean            Delete objects and executables
+ ##
+@@ -30,9 +30,9 @@
+ ##  LINKDIR      Linked Copies of TINKER Executables
+ ##
+ 
+-TINKERDIR = /Users/ponder/tinker
+-BINDIR = $(TINKERDIR)/bin
+-LINKDIR = /usr/local/bin
++TINKERDIR = ${WRKDIR}
++BINDIR = ${PREFIX}/bin
++#LINKDIR = /usr/local/bin
+ 
+ ####################################################################
+ ##  Known Machine Types; Uncomment One of the Following Sections  ##
+@@ -40,6 +40,20 @@
+ ####################################################################
+ 
+ ##
++##  Machine:  IntelPC / FreeBSD
++##  CPU Type: Intel, AMD, Cyrix
++##  Oper Sys: FreeBSD 4.2
++##  Compiler: f77 , aka g77
++##
++
++F77 = ${FC}
++LIBS = 
++F77FLAGS = -c ${FFLAGS}
++LINKFLAGS = ${LDFLAGS}
++OPTFLAGS = 
++LIBFLAGS = -rcuv
++
++##
+ ##  Machine:  Generic Linux
+ ##  CPU Type: Intel x86 Compatible
+ ##  Oper Sys: Fedora Core
+@@ -104,12 +118,12 @@
+ ##  Parallel: OpenMP
+ ##
+ 
+-F77 = /opt/intel/bin/ifort
+-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3
+-F77FLAGS = -c -axSSSE3 -assume cc_omp
+-OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
+-LIBFLAGS = -crusv
+-LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
++#F77 = /opt/intel/bin/ifort
++#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3
++#F77FLAGS = -c -axSSSE3 -assume cc_omp
++#OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp
++#LIBFLAGS = -crusv
++#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4
+ 
+ ##
+ ##  Machine:  Macintosh
+@@ -592,6 +606,8 @@
+            xyzpdb.x \
+            xyzsybyl.x
+ 
++.SUFFIXES: .x
++
+ .f.o:
+ 	${F77} ${F77FLAGS} ${OPTFLAGS} $*.f 
+ 
+@@ -601,8 +617,8 @@
+ server.o:
+ 	${F77} ${F77FLAGS} ${OPTFLAGS} server.f
+ 
+-%.x: %.o libtinker.a
+-	${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@
++.o.x: libtinker.a
++	${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS}
+ 
+ all:	${EXEFILES}
+ 
+@@ -613,65 +629,65 @@
+ 	cat *.i *.f *.c > tinker.txt
+ 
+ rename:
+-	mv  alchemy.x    $(BINDIR)/alchemy
+-	mv  analyze.x    $(BINDIR)/analyze
+-	mv  anneal.x     $(BINDIR)/anneal
+-	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
+-	mv  gda.x        $(BINDIR)/gda
+-	mv  intedit.x    $(BINDIR)/intedit
+-	mv  intxyz.x     $(BINDIR)/intxyz
+-	mv  minimize.x   $(BINDIR)/minimize
+-	mv  minirot.x    $(BINDIR)/minirot
+-	mv  minrigid.x   $(BINDIR)/minrigid
+-	mv  molxyz.x     $(BINDIR)/molxyz
+-	mv  monte.x      $(BINDIR)/monte
+-	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
+-	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
+-	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
+-	mv  testhess.x   $(BINDIR)/testhess
+-	mv  testpair.x   $(BINDIR)/testpair
+-	mv  testrot.x    $(BINDIR)/testrot
+-	mv  timer.x      $(BINDIR)/timer
+-	mv  timerot.x    $(BINDIR)/timerot
+-	mv  torsfit.x    $(BINDIR)/torsfit
+-	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
+-	mv  xtalmin.x    $(BINDIR)/xtalmin
+-	mv  xyzedit.x    $(BINDIR)/xyzedit
+-	mv  xyzint.x     $(BINDIR)/xyzint
+-	mv  xyzpdb.x     $(BINDIR)/xyzpdb
+-	mv  xyzsybyl.x   $(BINDIR)/xyzsybyl
++	${BSD_INSTALL_PROGRAM}  alchemy.x    $(BINDIR)/alchemy
++	${BSD_INSTALL_PROGRAM}  analyze.x    $(BINDIR)/analyze
++	${BSD_INSTALL_PROGRAM}  anneal.x     $(BINDIR)/anneal
++	${BSD_INSTALL_PROGRAM}  archive.x    $(BINDIR)/archive
++	${BSD_INSTALL_PROGRAM}  correlate.x  $(BINDIR)/correlate
++	${BSD_INSTALL_PROGRAM}  crystal.x    $(BINDIR)/crystal
++	${BSD_INSTALL_PROGRAM}  diffuse.x    $(BINDIR)/diffuse
++	${BSD_INSTALL_PROGRAM}  distgeom.x   $(BINDIR)/distgeom
++	${BSD_INSTALL_PROGRAM}  document.x   $(BINDIR)/document
++	${BSD_INSTALL_PROGRAM}  dynamic.x    $(BINDIR)/dynamic
++	${BSD_INSTALL_PROGRAM}  gda.x        $(BINDIR)/gda
++	${BSD_INSTALL_PROGRAM}  intedit.x    $(BINDIR)/intedit
++	${BSD_INSTALL_PROGRAM}  intxyz.x     $(BINDIR)/intxyz
++	${BSD_INSTALL_PROGRAM}  minimize.x   $(BINDIR)/minimize
++	${BSD_INSTALL_PROGRAM}  minirot.x    $(BINDIR)/minirot
++	${BSD_INSTALL_PROGRAM}  minrigid.x   $(BINDIR)/minrigid
++	${BSD_INSTALL_PROGRAM}  molxyz.x     $(BINDIR)/molxyz
++	${BSD_INSTALL_PROGRAM}  monte.x      $(BINDIR)/monte
++	${BSD_INSTALL_PROGRAM}  newton.x     $(BINDIR)/newton
++	${BSD_INSTALL_PROGRAM}  newtrot.x    $(BINDIR)/newtrot
++	${BSD_INSTALL_PROGRAM}  nucleic.x    $(BINDIR)/nucleic
++	${BSD_INSTALL_PROGRAM}  optimize.x   $(BINDIR)/optimize
++	${BSD_INSTALL_PROGRAM}  optirot.x    $(BINDIR)/optirot
++	${BSD_INSTALL_PROGRAM}  optrigid.x   $(BINDIR)/optrigid
++	${BSD_INSTALL_PROGRAM}  path.x       $(BINDIR)/path
++	${BSD_INSTALL_PROGRAM}  pdbxyz.x     $(BINDIR)/pdbxyz
++	${BSD_INSTALL_PROGRAM}  polarize.x   $(BINDIR)/polarize
++	${BSD_INSTALL_PROGRAM}  poledit.x    $(BINDIR)/poledit
++	${BSD_INSTALL_PROGRAM}  potential.x  $(BINDIR)/potential
++	${BSD_INSTALL_PROGRAM}  prmedit.x    $(BINDIR)/prmedit
++	${BSD_INSTALL_PROGRAM}  protein.x    $(BINDIR)/protein
++	${BSD_INSTALL_PROGRAM}  pss.x        $(BINDIR)/pss
++	${BSD_INSTALL_PROGRAM}  pssrigid.x   $(BINDIR)/pssrigid
++	${BSD_INSTALL_PROGRAM}  pssrot.x     $(BINDIR)/pssrot
++	${BSD_INSTALL_PROGRAM}  radial.x     $(BINDIR)/radial
++	${BSD_INSTALL_PROGRAM}  saddle.x     $(BINDIR)/saddle
++	${BSD_INSTALL_PROGRAM}  scan.x       $(BINDIR)/scan
++	${BSD_INSTALL_PROGRAM}  sniffer.x    $(BINDIR)/sniffer
++	${BSD_INSTALL_PROGRAM}  spacefill.x  $(BINDIR)/spacefill
++	${BSD_INSTALL_PROGRAM}  spectrum.x   $(BINDIR)/spectrum
++	${BSD_INSTALL_PROGRAM}  superpose.x  $(BINDIR)/superpose
++	${BSD_INSTALL_PROGRAM}  sybylxyz.x   $(BINDIR)/sybylxyz
++	${BSD_INSTALL_PROGRAM}  testgrad.x   $(BINDIR)/testgrad
++	${BSD_INSTALL_PROGRAM}  testhess.x   $(BINDIR)/testhess
++	${BSD_INSTALL_PROGRAM}  testpair.x   $(BINDIR)/testpair
++	${BSD_INSTALL_PROGRAM}  testrot.x    $(BINDIR)/testrot
++	${BSD_INSTALL_PROGRAM}  timer.x      $(BINDIR)/timer
++	${BSD_INSTALL_PROGRAM}  timerot.x    $(BINDIR)/timerot
++	${BSD_INSTALL_PROGRAM}  torsfit.x    $(BINDIR)/torsfit
++	${BSD_INSTALL_PROGRAM}  valence.x    $(BINDIR)/valence
++	${BSD_INSTALL_PROGRAM}  vibbig.x     $(BINDIR)/vibbig
++	${BSD_INSTALL_PROGRAM}  vibrate.x    $(BINDIR)/vibrate
++	${BSD_INSTALL_PROGRAM}  vibrot.x     $(BINDIR)/vibrot
++	${BSD_INSTALL_PROGRAM}  xtalfit.x    $(BINDIR)/xtalfit
++	${BSD_INSTALL_PROGRAM}  xtalmin.x    $(BINDIR)/xtalmin
++	${BSD_INSTALL_PROGRAM}  xyzedit.x    $(BINDIR)/xyzedit
++	${BSD_INSTALL_PROGRAM}  xyzint.x     $(BINDIR)/xyzint
++	${BSD_INSTALL_PROGRAM}  xyzpdb.x     $(BINDIR)/xyzpdb
++	${BSD_INSTALL_PROGRAM}  xyzsybyl.x   $(BINDIR)/xyzsybyl
+ 
+ remove_links:
+ 	rm -f $(LINKDIR)/alchemy
diff --git a/biology/tinker/files/patch-openend.f b/biology/tinker/files/patch-source_openend.f
index ad2afdc47ad..5745f93d0a8 100644
--- a/biology/tinker/files/patch-openend.f
+++ b/biology/tinker/files/patch-source_openend.f
@@ -1,8 +1,8 @@
 
 $FreeBSD$
 
---- openend.f.orig	Fri Apr 18 13:31:51 2003
-+++ openend.f	Mon Jul 21 13:36:11 2003
+--- source/openend.f.orig	Fri Apr 18 13:31:51 2003
++++ source/openend.f	Mon Jul 21 13:36:11 2003
 @@ -29,11 +29,11 @@
  c
  c     standard Fortran 90, unavailable in some Fortran 77 compilers
diff --git a/biology/tinker/files/pkg-message.in b/biology/tinker/files/pkg-message.in
new file mode 100644
index 00000000000..97777e8a5a2
--- /dev/null
+++ b/biology/tinker/files/pkg-message.in
@@ -0,0 +1,6 @@
+**********************************************************
+   The author requests that you return a license form
+   to him if you find Tinker to be useful.
+
+   See %%DOCSDIR%% for license forms.
+**********************************************************"
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index a83b6440624..9b6dc9d419a 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -14,6 +14,7 @@ bin/intxyz
 bin/minimize
 bin/minirot
 bin/minrigid
+bin/molxyz
 bin/monte
 bin/newton
 bin/newtrot
@@ -45,6 +46,7 @@ bin/testpair
 bin/testrot
 bin/timer
 bin/timerot
+bin/torsfit
 bin/valence
 bin/vibbig
 bin/vibrate
@@ -58,424 +60,429 @@ bin/xyzsybyl
 %%PORTDOCS%%%%DOCSDIR%%/0README
 %%PORTDOCS%%%%DOCSDIR%%/ffe-guide.pdf
 %%PORTDOCS%%%%DOCSDIR%%/guide.pdf
-%%PORTDOCS%%%%DOCSDIR%%/guide.txt
 %%PORTDOCS%%%%DOCSDIR%%/license.pdf
 %%PORTDOCS%%%%DOCSDIR%%/license.txt
-%%PORTDOCS%%%%DOCSDIR%%/release-3.2
-%%PORTDOCS%%%%DOCSDIR%%/release-3.6
-%%PORTDOCS%%%%DOCSDIR%%/release-3.7
-%%PORTDOCS%%%%DOCSDIR%%/release-3.8
-%%PORTDOCS%%%%DOCSDIR%%/release-3.9
-%%PORTDOCS%%%%DOCSDIR%%/release-4.0
-%%PORTDOCS%%%%DOCSDIR%%/release-4.1
-%%PORTDOCS%%%%DOCSDIR%%/release-4.2
 %%PORTDOCS%%%%DOCSDIR%%/summary.pdf
 %%PORTDOCS%%%%DOCSDIR%%/summary.txt
-%%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
-%%PORTDOCS%%%%EXAMPLESDIR%%/ethanol.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/ether.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/ether.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/etherbox.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/etherbox.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/etherbox.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/ethylene.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/ethylene.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/ethylene.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/flane.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/flane.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/flane.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/form.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/form.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/formbig.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/formbig.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/formbox.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/formbox.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/formbox.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/formopls.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/formopls.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/formopls.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/furan.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/furan.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/furan.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/glucose.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/glucose.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/glycerol.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/glycerol.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/glycerol.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/graphite.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/graphite.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/helix.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/helix.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/helix.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/heme.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/heme.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/hexane.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/hexane.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/hexane.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/hexanes.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/hexanes.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/hexanes.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/imidazole.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/imidazole.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/imidazole.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/imine.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/imine.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/imine.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/indole.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/indole.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/lactam.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/lactam.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/lipid.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/lipid.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/lj38.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/lj38.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.pdb
-%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.seq
-%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/membrane.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/membrane.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/meohbox.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/meohbox.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/meohbox.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/methane.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/methane.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/methane.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/methanol.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/methanol.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/mgwater.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/mgwater.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/mm3.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/mm3.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/nacl.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/nacl.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/nada.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/nada.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/naphthalene.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/naphthalene.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/naphthalene.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/naphthax.frac
-%%PORTDOCS%%%%EXAMPLESDIR%%/naphthax.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/naphthax.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/nitrogen.dyn
-%%PORTDOCS%%%%EXAMPLESDIR%%/nitrogen.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/nitrogen.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/nma.int
-%%PORTDOCS%%%%EXAMPLESDIR%%/nma.key
-%%PORTDOCS%%%%EXAMPLESDIR%%/nma.xyz
-%%PORTDOCS%%%%EXAMPLESDIR%%/nmabox.dyn
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 %%DATADIR%%/params/0README
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 %%DATADIR%%/params/amber94.prm
 %%DATADIR%%/params/amber96.prm
 %%DATADIR%%/params/amber98.prm
@@ -493,6 +500,7 @@ bin/xyzsybyl
 %%DATADIR%%/params/mm2.prm
 %%DATADIR%%/params/mm3.prm
 %%DATADIR%%/params/mm3pro.prm
+%%DATADIR%%/params/mmff.prm
 %%DATADIR%%/params/oplsaa.prm
 %%DATADIR%%/params/oplsaal.prm
 %%DATADIR%%/params/oplsua.prm
@@ -500,76 +508,95 @@ bin/xyzsybyl
 %%DATADIR%%/params/smoothua.prm
 %%DATADIR%%/params/tiny.prm
 %%DATADIR%%/params/water.prm
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 %%DATADIR%%/tinker.txt
-%%PORTDOCS%%@dirrm %%DATADIR%%/test
+%%PORTDATA%%@dirrm %%DATADIR%%/test
 @dirrm %%DATADIR%%/params
-%%PORTDOCS%%@dirrm %%DATADIR%%/bench
+%%PORTDATA%%@dirrm %%DATADIR%%/bench
 @dirrm %%DATADIR%%
-%%PORTDOCS%%@dirrm %%EXAMPLESDIR%%
+%%PORTEXAMPLES%%@dirrm %%EXAMPLESDIR%%
 %%PORTDOCS%%@dirrm %%DOCSDIR%%