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Date:      Sat, 1 Dec 2012 00:00:43 +0000 (UTC)
From:      Armin Pirkovitsch <sperber@FreeBSD.org>
To:        ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org
Subject:   svn commit: r308054 - in head/biology/tinker: . files
Message-ID:  <201212010000.qB100huw082519@svn.freebsd.org>

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Author: sperber
Date: Sat Dec  1 00:00:43 2012
New Revision: 308054
URL: http://svnweb.freebsd.org/changeset/ports/308054

Log:
  - 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

Added:
  head/biology/tinker/files/patch-bench__bench1.run   (contents, props changed)
  head/biology/tinker/files/patch-bench__bench2.run   (contents, props changed)
  head/biology/tinker/files/patch-bench__bench3.run   (contents, props changed)
  head/biology/tinker/files/patch-bench__bench4.run   (contents, props changed)
  head/biology/tinker/files/patch-bench__bench5.run   (contents, props changed)
  head/biology/tinker/files/patch-make__Makefile   (contents, props changed)
  head/biology/tinker/files/patch-source_openend.f   (contents, props changed)
  head/biology/tinker/files/pkg-message.in   (contents, props changed)
Deleted:
  head/biology/tinker/files/patch-aa
  head/biology/tinker/files/patch-ah
  head/biology/tinker/files/patch-ai
  head/biology/tinker/files/patch-aj
  head/biology/tinker/files/patch-ak
  head/biology/tinker/files/patch-al
  head/biology/tinker/files/patch-openend.f
Modified:
  head/biology/tinker/Makefile   (contents, props changed)
  head/biology/tinker/distinfo   (contents, props changed)
  head/biology/tinker/pkg-plist   (contents, props changed)

Modified: head/biology/tinker/Makefile
==============================================================================
--- head/biology/tinker/Makefile	Sat Dec  1 00:00:33 2012	(r308053)
+++ head/biology/tinker/Makefile	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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
 
-WRKSRC=		${WRKDIR}/tinker/source
+OPTIONS_DEFINE=	OPTIMIZED_FFLAGS DATA DOCS EXAMPLES
+OPTIONS_DEFAULT=DATA
+OPTIMIZED_FFLAGS_DESC=	compilation optimizations
+
+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
+
+SUB_FILES=	pkg-message
 
-DOCS=		0README *.pdf *.txt announce/release*
-SAMPLES=	0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.run *.xyz
+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>

Modified: head/biology/tinker/distinfo
==============================================================================
--- head/biology/tinker/distinfo	Sat Dec  1 00:00:33 2012	(r308053)
+++ head/biology/tinker/distinfo	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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

Added: head/biology/tinker/files/patch-bench__bench1.run
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/patch-bench__bench1.run	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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

Added: head/biology/tinker/files/patch-bench__bench2.run
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/patch-bench__bench2.run	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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

Added: head/biology/tinker/files/patch-bench__bench3.run
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/patch-bench__bench3.run	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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

Added: head/biology/tinker/files/patch-bench__bench4.run
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/patch-bench__bench4.run	Sat Dec  1 00:00:43 2012	(r308054)
@@ -0,0 +1,7 @@
+--- 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
++time dynamic bench4 1000 1.0 10.0 2 298.0
+ rm bench4.dyn

Added: head/biology/tinker/files/patch-bench__bench5.run
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/patch-bench__bench5.run	Sat Dec  1 00:00:43 2012	(r308054)
@@ -0,0 +1,7 @@
+--- 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
++time dynamic bench5 1000 1.0 10.0 2 298.0
+ rm bench5.dyn

Added: head/biology/tinker/files/patch-make__Makefile
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/patch-make__Makefile	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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

Added: head/biology/tinker/files/patch-source_openend.f
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/patch-source_openend.f	Sat Dec  1 00:00:43 2012	(r308054)
@@ -0,0 +1,19 @@
+
+$FreeBSD$
+
+--- 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
+ c
+-      open (unit=iunit,file=name,status='old',position='append')
++c     open (unit=iunit,file=name,status='old',position='append')
+ c
+ c     common extension supported by many Fortran 77 compilers
+ c
+-c     open (unit=iunit,file=name,status='old',access='append')
++      open (unit=iunit,file=name,status='old',access='append')
+ c
+ c     some Fortran 77 compilers open files for append by default
+ c

Added: head/biology/tinker/files/pkg-message.in
==============================================================================
--- /dev/null	00:00:00 1970	(empty, because file is newly added)
+++ head/biology/tinker/files/pkg-message.in	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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.
+**********************************************************"

Modified: head/biology/tinker/pkg-plist
==============================================================================
--- head/biology/tinker/pkg-plist	Sat Dec  1 00:00:33 2012	(r308053)
+++ head/biology/tinker/pkg-plist	Sat Dec  1 00:00:43 2012	(r308054)
@@ -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
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 %%PORTDOCS%%%%DOCSDIR%%/license.pdf
 %%PORTDOCS%%%%DOCSDIR%%/license.txt
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 %%PORTDOCS%%%%DOCSDIR%%/summary.pdf
 %%PORTDOCS%%%%DOCSDIR%%/summary.txt
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+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.make
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing2.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzamidine.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzamidine.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzbox.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzbox.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/book.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/book.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.dyn
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cage.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cage.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.make
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.make
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.pdb
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dimethane.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dimethane.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dmp.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/dmp.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.make
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.seq
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/enkephalin.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ermer.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ester.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ester.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.int
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.key
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethane.xyz
+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethanol.int

*** DIFF OUTPUT TRUNCATED AT 1000 LINES ***



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