FreeBSD Bugzilla – Attachment 128075 Details for
Bug 171971
biology/tinker: Update to version 6.0.01
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[patch]
file.diff
file.diff (text/plain), 67.33 KB, created by
tkato432
on 2012-09-25 19:10:13 UTC
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Description:
file.diff
Filename:
MIME Type:
Creator:
tkato432
Created:
2012-09-25 19:10:13 UTC
Size:
67.33 KB
patch
obsolete
>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 >-%%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 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>+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ether.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/etherbox.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/etherbox.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/etherbox.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethylene.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethylene.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ethylene.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/flane.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/flane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/flane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/form.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/form.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbig.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbig.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbox.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbox.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formbox.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formopls.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formopls.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/formopls.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/furan.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/furan.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/furan.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glucose.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glucose.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glycerol.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glycerol.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/glycerol.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/graphite.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/graphite.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/helix.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/helix.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/helix.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/heme.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/heme.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexane.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexanes.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexanes.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/hexanes.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imidazole.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imidazole.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imidazole.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imine.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imine.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/imine.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/indole.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/indole.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lactam.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lactam.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lipid.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lipid.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lj38.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/lj38.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.pdb >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.seq >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/melittin.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/membrane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/meohbox.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methanol.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/methanol.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgwater.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mgwater.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mm3.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/mm3.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nacl.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nacl.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nada.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nada.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthalene.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthalene.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthalene.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthax.frac >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthax.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/naphthax.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrile.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrile.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrogen.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrogen.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nitrogen.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nma.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nma.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nma.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmabox.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmabox.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmabox.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmf.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nmf.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nstilbene.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nstilbene.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/nstilbene.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane2.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane2.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octane2.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octene.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octene.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/octene.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/palmitate.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/palmitate.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/palmitate.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pentane.frac >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pentane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pentane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.make >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.pdb >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.seq >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/peptide.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/phenanth.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/phenanth.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.pdb >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.seq >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/photo.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pol3.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pol3.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/polyala.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/polyala.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propellane.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propellane.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propellane.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propyne.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/propyne.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyridine.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyridine.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyridine.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyrrole.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyrrole.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/pyrrole.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/retinoic.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/retinoic.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skunk.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/skunk.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/spc.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/spc.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sterol.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/sterol.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/styrene.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/styrene.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/styrene.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/terphenyl.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/terphenyl.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tfe.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tfe.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiadiene.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiadiene.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiadiene.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiophene.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiophene.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thiophene.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thr.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thr.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/thr.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3f.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3f.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3p.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip3p.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4f.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4f.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip4p.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/tip5p.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.pdb >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.seq >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.pdb >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.seq >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.seq >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.frac >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterball.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterball.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbig.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbig.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterglobe.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterglobe.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterhuge.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterhuge.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.dyn >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.xyz >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.int >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.key >+%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.xyz >+%%PORTDATA%%%%DATADIR%%/bench/0README >+%%PORTDATA%%%%DATADIR%%/bench/bench1.key >+%%PORTDATA%%%%DATADIR%%/bench/bench1.run >+%%PORTDATA%%%%DATADIR%%/bench/bench1.xyz >+%%PORTDATA%%%%DATADIR%%/bench/bench2.key >+%%PORTDATA%%%%DATADIR%%/bench/bench2.run >+%%PORTDATA%%%%DATADIR%%/bench/bench2.xyz >+%%PORTDATA%%%%DATADIR%%/bench/bench3.key >+%%PORTDATA%%%%DATADIR%%/bench/bench3.run >+%%PORTDATA%%%%DATADIR%%/bench/bench3.xyz >+%%PORTDATA%%%%DATADIR%%/bench/bench4.dyn0 >+%%PORTDATA%%%%DATADIR%%/bench/bench4.key >+%%PORTDATA%%%%DATADIR%%/bench/bench4.log >+%%PORTDATA%%%%DATADIR%%/bench/bench4.run >+%%PORTDATA%%%%DATADIR%%/bench/bench4.xyz >+%%PORTDATA%%%%DATADIR%%/bench/bench5.dyn0 >+%%PORTDATA%%%%DATADIR%%/bench/bench5.key >+%%PORTDATA%%%%DATADIR%%/bench/bench5.log >+%%PORTDATA%%%%DATADIR%%/bench/bench5.run >+%%PORTDATA%%%%DATADIR%%/bench/bench5.xyz >+%%PORTDATA%%%%DATADIR%%/bench/bench6.key >+%%PORTDATA%%%%DATADIR%%/bench/bench6.log >+%%PORTDATA%%%%DATADIR%%/bench/bench6.run >+%%PORTDATA%%%%DATADIR%%/bench/bench6.xyz >+%%PORTDATA%%%%DATADIR%%/bench/bench7.key >+%%PORTDATA%%%%DATADIR%%/bench/bench7.log >+%%PORTDATA%%%%DATADIR%%/bench/bench7.run >+%%PORTDATA%%%%DATADIR%%/bench/bench7.xyz >+%%PORTDATA%%%%DATADIR%%/bench/results-2.3 >+%%PORTDATA%%%%DATADIR%%/bench/results-2.4 >+%%PORTDATA%%%%DATADIR%%/bench/results-2.9 >+%%PORTDATA%%%%DATADIR%%/bench/results-3.1 >+%%PORTDATA%%%%DATADIR%%/bench/results-3.2 >+%%PORTDATA%%%%DATADIR%%/bench/results-3.4 >+%%PORTDATA%%%%DATADIR%%/bench/results-3.5 >+%%PORTDATA%%%%DATADIR%%/bench/results-3.7 >+%%PORTDATA%%%%DATADIR%%/bench/results-3.8 >+%%PORTDATA%%%%DATADIR%%/bench/results-3.9 >+%%PORTDATA%%%%DATADIR%%/bench/results-4.0 >+%%PORTDATA%%%%DATADIR%%/bench/results-4.1 >+%%PORTDATA%%%%DATADIR%%/bench/results-4.2 >+%%PORTDATA%%%%DATADIR%%/bench/results-4.3 >+%%PORTDATA%%%%DATADIR%%/bench/results-5.0 >+%%PORTDATA%%%%DATADIR%%/bench/results-5.1 >+%%PORTDATA%%%%DATADIR%%/bench/results-6.0 > %%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%%
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