Date: Wed, 26 Sep 2012 02:21:06 +0900 From: KATO Tsuguru <tkato432@yahoo.com> To: FreeBSD-gnats-submit@FreeBSD.org Subject: ports/171971: biology/tinker: Update to version 6.0.01 Message-ID: <20120926022106.b56680bc0637210172c61cd0@yahoo.com> Resent-Message-ID: <201209251810.q8PIADTM017818@freefall.freebsd.org>
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>Number: 171971 >Category: ports >Synopsis: biology/tinker: Update to version 6.0.01 >Confidential: no >Severity: non-critical >Priority: low >Responsible: freebsd-ports-bugs >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Tue Sep 25 18:10:13 UTC 2012 >Closed-Date: >Last-Modified: >Originator: KATO Tsuguru >Release: FreeBSD 7.4-RELEASE-p10 i386 >Organization: >Environment: >Description: - Update to version 6.0.01 New file: files/patch-bench__bench1.run files/patch-bench__bench2.run files/patch-bench__bench3.run files/patch-bench__bench4.run files/patch-bench__bench5.run files/patch-make__Makefile files/pkg-message.in Remove file: files/patch-aa files/patch-ah files/patch-ai files/patch-aj files/patch-ak files/patch-al >How-To-Repeat: >Fix: diff -urN /usr/ports/biology/tinker/Makefile biology/tinker/Makefile --- /usr/ports/biology/tinker/Makefile 2011-10-11 05:17:22.000000000 +0900 +++ biology/tinker/Makefile 2012-09-25 03:17:32.000000000 +0900 @@ -1,76 +1,74 @@ -# New ports collection makefile for: tinker -# Date Created: 26 August 1998 -# Whom: Glenn Johnson -# +# Created by: Glenn Johnson # $FreeBSD: ports/biology/tinker/Makefile,v 1.43 2011/10/10 20:17:22 pav Exp $ -# PORTNAME= tinker -PORTVERSION= 5.1.09 +PORTVERSION= 6.0.01 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> diff -urN /usr/ports/biology/tinker/distinfo biology/tinker/distinfo --- /usr/ports/biology/tinker/distinfo 2011-01-31 20:45:44.000000000 +0900 +++ biology/tinker/distinfo 2011-11-23 05:30:20.000000000 +0900 @@ -1,2 +1,2 @@ -SHA256 (tinker-5.1.09.tar.gz) = 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183 -SIZE (tinker-5.1.09.tar.gz) = 14071638 +SHA256 (tinker-6.0.01.tar.gz) = 98f4ffdec889944e5bbe10196ac2c9a7888a3708db3998027ffc65cb6e39dd71 +SIZE (tinker-6.0.01.tar.gz) = 18093304 diff -urN /usr/ports/biology/tinker/files/patch-aa biology/tinker/files/patch-aa --- /usr/ports/biology/tinker/files/patch-aa 2011-01-31 20:45:44.000000000 +0900 +++ biology/tinker/files/patch-aa 1970-01-01 09:00:00.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/files/patch-ah biology/tinker/files/patch-ah --- /usr/ports/biology/tinker/files/patch-ah 2001-09-13 10:13:52.000000000 +0900 +++ biology/tinker/files/patch-ah 1970-01-01 09:00:00.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/files/patch-ai biology/tinker/files/patch-ai --- /usr/ports/biology/tinker/files/patch-ai 2001-09-13 10:13:52.000000000 +0900 +++ biology/tinker/files/patch-ai 1970-01-01 09:00:00.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/files/patch-aj biology/tinker/files/patch-aj --- /usr/ports/biology/tinker/files/patch-aj 2001-09-13 10:13:52.000000000 +0900 +++ biology/tinker/files/patch-aj 1970-01-01 09:00:00.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/files/patch-ak biology/tinker/files/patch-ak --- /usr/ports/biology/tinker/files/patch-ak 2001-09-13 10:13:52.000000000 +0900 +++ biology/tinker/files/patch-ak 1970-01-01 09:00:00.000000000 +0900 @@ -1,7 +0,0 @@ ---- ../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 diff -urN /usr/ports/biology/tinker/files/patch-al biology/tinker/files/patch-al --- /usr/ports/biology/tinker/files/patch-al 2011-01-31 20:45:44.000000000 +0900 +++ biology/tinker/files/patch-al 1970-01-01 09:00:00.000000000 +0900 @@ -1,7 +0,0 @@ ---- ../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 diff -urN /usr/ports/biology/tinker/files/patch-bench__bench1.run biology/tinker/files/patch-bench__bench1.run --- /usr/ports/biology/tinker/files/patch-bench__bench1.run 1970-01-01 09:00:00.000000000 +0900 +++ biology/tinker/files/patch-bench__bench1.run 2012-07-26 14:38:23.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/files/patch-bench__bench2.run biology/tinker/files/patch-bench__bench2.run --- /usr/ports/biology/tinker/files/patch-bench__bench2.run 1970-01-01 09:00:00.000000000 +0900 +++ biology/tinker/files/patch-bench__bench2.run 2012-07-26 14:38:58.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/files/patch-bench__bench3.run biology/tinker/files/patch-bench__bench3.run --- /usr/ports/biology/tinker/files/patch-bench__bench3.run 1970-01-01 09:00:00.000000000 +0900 +++ biology/tinker/files/patch-bench__bench3.run 2012-07-26 14:38:51.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/files/patch-bench__bench4.run biology/tinker/files/patch-bench__bench4.run --- /usr/ports/biology/tinker/files/patch-bench__bench4.run 1970-01-01 09:00:00.000000000 +0900 +++ biology/tinker/files/patch-bench__bench4.run 2012-07-26 14:39:20.000000000 +0900 @@ -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 diff -urN /usr/ports/biology/tinker/files/patch-bench__bench5.run biology/tinker/files/patch-bench__bench5.run --- /usr/ports/biology/tinker/files/patch-bench__bench5.run 1970-01-01 09:00:00.000000000 +0900 +++ biology/tinker/files/patch-bench__bench5.run 2012-07-26 14:39:39.000000000 +0900 @@ -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 diff -urN /usr/ports/biology/tinker/files/patch-make__Makefile biology/tinker/files/patch-make__Makefile --- /usr/ports/biology/tinker/files/patch-make__Makefile 1970-01-01 09:00:00.000000000 +0900 +++ biology/tinker/files/patch-make__Makefile 2012-07-26 15:17:26.000000000 +0900 @@ -0,0 +1,209 @@ +--- make/Makefile.orig 2011-11-06 05:29:19.000000000 +0900 ++++ make/Makefile 2011-11-23 05:37:09.000000000 +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 ${FFLAGS} ++LINKFLAGS = ++OPTFLAGS = ++LIBFLAGS = -rcuv ++ ++## + ## Machine: Generic Linux + ## CPU Type: Intel x86 Compatible + ## Oper Sys: Fedora Core +@@ -104,12 +118,12 @@ + ## Parallel: OpenMP + ## + +-F77 = /opt/intel/bin/ifort +-LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -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_threads -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 +@@ -587,6 +601,8 @@ + 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}; strip $@ ++.o.x: libtinker.a ++ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} + + all: ${EXEFILES} + +@@ -608,64 +624,64 @@ + 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 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} 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 -urN /usr/ports/biology/tinker/files/patch-openend.f biology/tinker/files/patch-openend.f --- /usr/ports/biology/tinker/files/patch-openend.f 2003-07-25 11:48:05.000000000 +0900 +++ biology/tinker/files/patch-openend.f 2012-07-26 14:40:22.000000000 +0900 @@ -1,8 +1,8 @@ $FreeBSD: ports/biology/tinker/files/patch-openend.f,v 1.2 2003/07/25 02:48:05 maho Exp $ ---- 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 -urN /usr/ports/biology/tinker/files/pkg-message.in biology/tinker/files/pkg-message.in --- /usr/ports/biology/tinker/files/pkg-message.in 1970-01-01 09:00:00.000000000 +0900 +++ biology/tinker/files/pkg-message.in 2012-07-26 14:34:04.000000000 +0900 @@ -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 -urN /usr/ports/biology/tinker/pkg-plist biology/tinker/pkg-plist --- /usr/ports/biology/tinker/pkg-plist 2011-01-31 20:45:44.000000000 +0900 +++ biology/tinker/pkg-plist 2012-07-26 14:54:44.000000000 +0900 @@ -45,6 +45,7 @@ bin/testrot bin/timer bin/timerot +bin/torsfit bin/valence bin/vibbig bin/vibrate @@ -61,421 +62,415 @@ %%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 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%%DATADIR%%/params/0README -%%DATADIR%%/params/amber02.prm %%DATADIR%%/params/amber94.prm %%DATADIR%%/params/amber96.prm %%DATADIR%%/params/amber98.prm @@ -500,76 +495,91 @@ %%DATADIR%%/params/smoothua.prm %%DATADIR%%/params/tiny.prm %%DATADIR%%/params/water.prm -%%PORTDOCS%%%%DATADIR%%/test/0README -%%PORTDOCS%%%%DATADIR%%/test/anion.dat -%%PORTDOCS%%%%DATADIR%%/test/anion.dyn0 -%%PORTDOCS%%%%DATADIR%%/test/anion.key -%%PORTDOCS%%%%DATADIR%%/test/anion.log -%%PORTDOCS%%%%DATADIR%%/test/anion.run -%%PORTDOCS%%%%DATADIR%%/test/anion.xyz -%%PORTDOCS%%%%DATADIR%%/test/argon.1st -%%PORTDOCS%%%%DATADIR%%/test/argon.key -%%PORTDOCS%%%%DATADIR%%/test/argon.log -%%PORTDOCS%%%%DATADIR%%/test/argon.run -%%PORTDOCS%%%%DATADIR%%/test/clean.make -%%PORTDOCS%%%%DATADIR%%/test/cluster.dat -%%PORTDOCS%%%%DATADIR%%/test/cluster.key -%%PORTDOCS%%%%DATADIR%%/test/cluster.log -%%PORTDOCS%%%%DATADIR%%/test/cluster.run -%%PORTDOCS%%%%DATADIR%%/test/cluster.xyz -%%PORTDOCS%%%%DATADIR%%/test/crambin.key -%%PORTDOCS%%%%DATADIR%%/test/crambin.log -%%PORTDOCS%%%%DATADIR%%/test/crambin.pdb -%%PORTDOCS%%%%DATADIR%%/test/crambin.run -%%PORTDOCS%%%%DATADIR%%/test/cyclohex.boat -%%PORTDOCS%%%%DATADIR%%/test/cyclohex.chair -%%PORTDOCS%%%%DATADIR%%/test/cyclohex.key -%%PORTDOCS%%%%DATADIR%%/test/cyclohex.log -%%PORTDOCS%%%%DATADIR%%/test/cyclohex.run -%%PORTDOCS%%%%DATADIR%%/test/dhfr.dyn -%%PORTDOCS%%%%DATADIR%%/test/dhfr.key -%%PORTDOCS%%%%DATADIR%%/test/dhfr.log -%%PORTDOCS%%%%DATADIR%%/test/dhfr.run -%%PORTDOCS%%%%DATADIR%%/test/dhfr.xyz -%%PORTDOCS%%%%DATADIR%%/test/dialanine.key -%%PORTDOCS%%%%DATADIR%%/test/dialanine.log -%%PORTDOCS%%%%DATADIR%%/test/dialanine.run -%%PORTDOCS%%%%DATADIR%%/test/dialanine.xyz -%%PORTDOCS%%%%DATADIR%%/test/enkephalin.dat -%%PORTDOCS%%%%DATADIR%%/test/enkephalin.key -%%PORTDOCS%%%%DATADIR%%/test/enkephalin.log -%%PORTDOCS%%%%DATADIR%%/test/enkephalin.run -%%PORTDOCS%%%%DATADIR%%/test/formamide.cell -%%PORTDOCS%%%%DATADIR%%/test/formamide.dat -%%PORTDOCS%%%%DATADIR%%/test/formamide.key -%%PORTDOCS%%%%DATADIR%%/test/formamide.log -%%PORTDOCS%%%%DATADIR%%/test/formamide.run -%%PORTDOCS%%%%DATADIR%%/test/gpcr.blk -%%PORTDOCS%%%%DATADIR%%/test/gpcr.key -%%PORTDOCS%%%%DATADIR%%/test/gpcr.log -%%PORTDOCS%%%%DATADIR%%/test/gpcr.run -%%PORTDOCS%%%%DATADIR%%/test/gpcr.xyz -%%PORTDOCS%%%%DATADIR%%/test/helix.1st -%%PORTDOCS%%%%DATADIR%%/test/helix.key -%%PORTDOCS%%%%DATADIR%%/test/helix.log -%%PORTDOCS%%%%DATADIR%%/test/helix.run -%%PORTDOCS%%%%DATADIR%%/test/salt.cell -%%PORTDOCS%%%%DATADIR%%/test/salt.key -%%PORTDOCS%%%%DATADIR%%/test/salt.log -%%PORTDOCS%%%%DATADIR%%/test/salt.run -%%PORTDOCS%%%%DATADIR%%/test/tetraala.dat -%%PORTDOCS%%%%DATADIR%%/test/tetraala.key -%%PORTDOCS%%%%DATADIR%%/test/tetraala.log -%%PORTDOCS%%%%DATADIR%%/test/tetraala.run -%%PORTDOCS%%%%DATADIR%%/test/water.key -%%PORTDOCS%%%%DATADIR%%/test/water.log -%%PORTDOCS%%%%DATADIR%%/test/water.pot -%%PORTDOCS%%%%DATADIR%%/test/water.run -%%PORTDOCS%%%%DATADIR%%/test/water.xyz +%%PORTDATA%%%%DATADIR%%/test/0README +%%PORTDATA%%%%DATADIR%%/test/anion.dat +%%PORTDATA%%%%DATADIR%%/test/anion.dyn0 +%%PORTDATA%%%%DATADIR%%/test/anion.key +%%PORTDATA%%%%DATADIR%%/test/anion.log +%%PORTDATA%%%%DATADIR%%/test/anion.run +%%PORTDATA%%%%DATADIR%%/test/anion.xyz +%%PORTDATA%%%%DATADIR%%/test/argon.1st +%%PORTDATA%%%%DATADIR%%/test/argon.key +%%PORTDATA%%%%DATADIR%%/test/argon.log +%%PORTDATA%%%%DATADIR%%/test/argon.run +%%PORTDATA%%%%DATADIR%%/test/clean.make +%%PORTDATA%%%%DATADIR%%/test/cluster.dat +%%PORTDATA%%%%DATADIR%%/test/cluster.key +%%PORTDATA%%%%DATADIR%%/test/cluster.log +%%PORTDATA%%%%DATADIR%%/test/cluster.run +%%PORTDATA%%%%DATADIR%%/test/cluster.xyz +%%PORTDATA%%%%DATADIR%%/test/crambin.key +%%PORTDATA%%%%DATADIR%%/test/crambin.log +%%PORTDATA%%%%DATADIR%%/test/crambin.pdb +%%PORTDATA%%%%DATADIR%%/test/crambin.run +%%PORTDATA%%%%DATADIR%%/test/cyclohex.boat +%%PORTDATA%%%%DATADIR%%/test/cyclohex.chair +%%PORTDATA%%%%DATADIR%%/test/cyclohex.key +%%PORTDATA%%%%DATADIR%%/test/cyclohex.log +%%PORTDATA%%%%DATADIR%%/test/cyclohex.run +%%PORTDATA%%%%DATADIR%%/test/dhfr.dyn +%%PORTDATA%%%%DATADIR%%/test/dhfr.key +%%PORTDATA%%%%DATADIR%%/test/dhfr.log +%%PORTDATA%%%%DATADIR%%/test/dhfr.run +%%PORTDATA%%%%DATADIR%%/test/dhfr.xyz +%%PORTDATA%%%%DATADIR%%/test/dialanine.key +%%PORTDATA%%%%DATADIR%%/test/dialanine.log +%%PORTDATA%%%%DATADIR%%/test/dialanine.run +%%PORTDATA%%%%DATADIR%%/test/dialanine.xyz +%%PORTDATA%%%%DATADIR%%/test/enkephalin.dat +%%PORTDATA%%%%DATADIR%%/test/enkephalin.key +%%PORTDATA%%%%DATADIR%%/test/enkephalin.log +%%PORTDATA%%%%DATADIR%%/test/enkephalin.run +%%PORTDATA%%%%DATADIR%%/test/ethanol.000 +%%PORTDATA%%%%DATADIR%%/test/ethanol.020 +%%PORTDATA%%%%DATADIR%%/test/ethanol.040 +%%PORTDATA%%%%DATADIR%%/test/ethanol.060 +%%PORTDATA%%%%DATADIR%%/test/ethanol.080 +%%PORTDATA%%%%DATADIR%%/test/ethanol.100 +%%PORTDATA%%%%DATADIR%%/test/ethanol.120 +%%PORTDATA%%%%DATADIR%%/test/ethanol.140 +%%PORTDATA%%%%DATADIR%%/test/ethanol.160 +%%PORTDATA%%%%DATADIR%%/test/ethanol.180 +%%PORTDATA%%%%DATADIR%%/test/ethanol.dat +%%PORTDATA%%%%DATADIR%%/test/ethanol.key +%%PORTDATA%%%%DATADIR%%/test/ethanol.log +%%PORTDATA%%%%DATADIR%%/test/ethanol.run +%%PORTDATA%%%%DATADIR%%/test/ethanol.xyz +%%PORTDATA%%%%DATADIR%%/test/formamide.cell +%%PORTDATA%%%%DATADIR%%/test/formamide.dat +%%PORTDATA%%%%DATADIR%%/test/formamide.key +%%PORTDATA%%%%DATADIR%%/test/formamide.log +%%PORTDATA%%%%DATADIR%%/test/formamide.run +%%PORTDATA%%%%DATADIR%%/test/gpcr.blk +%%PORTDATA%%%%DATADIR%%/test/gpcr.key +%%PORTDATA%%%%DATADIR%%/test/gpcr.log +%%PORTDATA%%%%DATADIR%%/test/gpcr.run +%%PORTDATA%%%%DATADIR%%/test/gpcr.xyz +%%PORTDATA%%%%DATADIR%%/test/helix.1st +%%PORTDATA%%%%DATADIR%%/test/helix.key +%%PORTDATA%%%%DATADIR%%/test/helix.log +%%PORTDATA%%%%DATADIR%%/test/helix.run +%%PORTDATA%%%%DATADIR%%/test/salt.cell +%%PORTDATA%%%%DATADIR%%/test/salt.key +%%PORTDATA%%%%DATADIR%%/test/salt.log +%%PORTDATA%%%%DATADIR%%/test/salt.run +%%PORTDATA%%%%DATADIR%%/test/tetraala.dat +%%PORTDATA%%%%DATADIR%%/test/tetraala.key +%%PORTDATA%%%%DATADIR%%/test/tetraala.log +%%PORTDATA%%%%DATADIR%%/test/tetraala.run +%%PORTDATA%%%%DATADIR%%/test/water.key +%%PORTDATA%%%%DATADIR%%/test/water.log +%%PORTDATA%%%%DATADIR%%/test/water.pot +%%PORTDATA%%%%DATADIR%%/test/water.run +%%PORTDATA%%%%DATADIR%%/test/water.xyz %%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%% >Release-Note: >Audit-Trail: >Unformatted:
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