diff -ruNa tinker.orig/Makefile tinker/Makefile --- tinker.orig/Makefile 2011-01-22 00:34:14.000000000 +0300 +++ tinker/Makefile 2011-01-27 16:15:59.000000000 +0300 @@ -6,14 +6,9 @@ # PORTNAME= tinker -PORTVERSION= 4.2.20040908 -PORTREVISION= 5 +PORTVERSION= 5.1.09 CATEGORIES= biology -MASTER_SITES= ftp://ftp.tu-chemnitz.de/.SAN0/pub/FreeBSD/ports/distfiles/RESTRICTED/${PORTNAME}-${PORTVERSION}/\ - ftp://ftp.tw.freebsd.org/pub/ports/distfiles/${PORTNAME}-${PORTVERSION}/ \ - ftp://ftp.uvsq.fr/pub/FreeBSD/ports/distfiles/RESTRICTED/${PORTNAME}-${PORTVERSION}/ -DISTNAME= ${PORTNAME} -DIST_SUBDIR= ${PORTNAME}-${PORTVERSION} +MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/ MAINTAINER= ports@FreeBSD.org COMMENT= A general purpose molecular modelling package @@ -27,10 +22,9 @@ INSTALL_TARGET= rename RESTRICTED= author requests no distribution except from his FTP site -DOCS= README *.pdf *.txt release* -SAMPLES= README clean.make *.1st *.boat *.cell *.chair *.dat *.dyn0 \ - *.key *.log *.pdb *.run *.xyz -BENCHES= README *.dyn0 *.log *.key *.run *.xyz results* +DOCS= 0README *.pdf *.txt announce/release* +SAMPLES= 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.run *.xyz +BENCHES= 0README *.dyn0 *.log *.key *.run *.xyz results* .include @@ -43,21 +37,6 @@ .endif # i386 .endif -.if defined(WITH_VIEWER) -BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake -USE_XORG= x11 xext xi -PLIST_SUB+= WITH_VIEWER="" -post-build: - @${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer -.else -PLIST_SUB+= WITH_VIEWER="@comment " -pre-extract: - @${ECHO_MSG} "" - @${ECHO_MSG} If you would like to also build - @${ECHO_MSG} the molecular viewer, define WITH_VIEWER. - @${ECHO_MSG} "" -.endif - pre-everything:: .if !defined(WITH_OPTIMIZED_FLAGS) @${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes." @@ -85,13 +64,6 @@ @${INSTALL_DATA} ${BENCHES:S|^|${WRKDIR}/tinker/bench/|} ${DATADIR}/bench @${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${DATADIR}/test .endif -.if defined(WITH_VIEWER) - @${MKDIR} ${DATADIR}/rasmol - @${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin - @${INSTALL_SCRIPT} ${FILESDIR}/tview ${PREFIX}/bin - @${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp \ - ${DATADIR}/rasmol -.endif @${ECHO_MSG} "" @${ECHO_MSG} " **********************************************************" @${ECHO_MSG} " The author requests that you return a license form " diff -ruNa tinker.orig/distinfo tinker/distinfo --- tinker.orig/distinfo 2005-11-24 03:04:00.000000000 +0300 +++ tinker/distinfo 2011-01-22 00:48:58.000000000 +0300 @@ -1,3 +1,2 @@ -MD5 (tinker-4.2.20040908/tinker.tar.gz) = 5618d8a373896f00e452b137200223fd -SHA256 (tinker-4.2.20040908/tinker.tar.gz) = ad0cc9782dabdb0cce490fe26508761a36078e741f019090cbaa3e6cacf71055 -SIZE (tinker-4.2.20040908/tinker.tar.gz) = 8177555 +SHA256 (tinker-5.1.09.tar.gz) = 61765adfe260e3f3083243542dac49d38141191d5d6580e9a66a29c31d5a3183 +SIZE (tinker-5.1.09.tar.gz) = 14071638 diff -ruNa tinker.orig/files/patch-aa tinker/files/patch-aa --- tinker.orig/files/patch-aa 2007-01-12 15:21:21.000000000 +0300 +++ tinker/files/patch-aa 2011-01-22 01:13:57.000000000 +0300 @@ -1,5 +1,5 @@ ---- ../make/Makefile.orig Thu Aug 19 17:37:44 2004 -+++ ../make/Makefile Thu Aug 19 22:52:41 2004 +--- ../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 @@ -15,7 +15,7 @@ ## LINKDIR Linked Copies of TINKER Executables ## --TINKERDIR = /user/ponder/tinker +-TINKERDIR = /Users/ponder/tinker -BINDIR = $(TINKERDIR)/bin -LINKDIR = /usr/local/bin +TINKERDIR = ${WRKDIR} @@ -24,11 +24,10 @@ #################################################################### ## Known Machine Types; Uncomment One of the Following Sections ## -@@ -122,6 +122,20 @@ - #LIBFLAGS = -crusv - #LINKFLAGS = +@@ -40,6 +40,20 @@ + #################################################################### -+## + ## +## Machine: IntelPC / FreeBSD +## CPU Type: Intel, AMD, Cyrix +## Oper Sys: FreeBSD 4.2 @@ -42,10 +41,30 @@ +OPTFLAGS = +LIBFLAGS = -rcuv + - ################################################################# - ## Should not be Necessary to Change Things Below this Point ## - ################################################################# -@@ -529,11 +543,13 @@ ++## + ## 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 @@ -54,6 +73,10 @@ .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 @@ -61,7 +84,7 @@ all: ${EXEFILES} -@@ -544,59 +560,59 @@ +@@ -608,63 +624,63 @@ cat *.i *.f > tinker.txt rename: @@ -91,6 +114,8 @@ - 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 @@ -106,10 +131,12 @@ - mv sybylxyz.x $(BINDIR)/sybylxyz - mv testgrad.x $(BINDIR)/testgrad - mv testhess.x $(BINDIR)/testhess -- mv testlight.x $(BINDIR)/testlight +- 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 @@ -144,6 +171,8 @@ + ${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 @@ -159,10 +188,12 @@ + ${INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz + ${INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad + ${INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess -+ ${INSTALL_PROGRAM} testlight.x $(BINDIR)/testlight ++ ${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 diff -ruNa tinker.orig/files/patch-al tinker/files/patch-al --- tinker.orig/files/patch-al 2001-09-13 05:13:52.000000000 +0400 +++ tinker/files/patch-al 2011-01-26 23:37:53.000000000 +0300 @@ -1,7 +1,7 @@ ---- ../bench/bench5.run.orig Tue Jul 24 14:02:20 2001 -+++ ../bench/bench5.run Wed Sep 5 14:03:07 2001 +--- ../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 100 1.0 10.0 2 298.0 -+time dynamic bench5 100 1.0 10.0 2 298.0 +-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 -ruNa tinker.orig/files/tview tinker/files/tview --- tinker.orig/files/tview 2001-09-13 05:13:52.000000000 +0400 +++ tinker/files/tview 1970-01-01 03:00:00.000000000 +0300 @@ -1,21 +0,0 @@ -#!/bin/sh - -# Determine if X is running -if [ -z $DISPLAY ]; then - echo You must be running X for this. -else -# Try to determine the color depth of the X server - - DEPTH=`xwininfo -root | grep Depth | awk '{print $2}'` - - if [ $DEPTH = 24 -o $DEPTH = 32 ]; then - PROGRAM=tview-32 - elif [ $DEPTH = 16 ]; then - PROGRAM=tview-16 - elif [ $DEPTH = 8 ]; then - PROGRAM=tview-8 - else - echo Can not determine color depth of Display $DISPLAY - fi - exec $PROGRAM $@ -fi diff -ruNa tinker.orig/pkg-plist tinker/pkg-plist --- tinker.orig/pkg-plist 2004-08-20 02:24:21.000000000 +0400 +++ tinker/pkg-plist 2011-01-27 16:11:30.000000000 +0300 @@ -24,6 +24,8 @@ bin/path bin/pdbxyz bin/polarize +bin/poledit +bin/potential bin/prmedit bin/protein bin/pss @@ -39,14 +41,12 @@ bin/sybylxyz bin/testgrad bin/testhess -bin/testlight +bin/testpair bin/testrot bin/timer bin/timerot -%%WITH_VIEWER%%bin/tview -%%WITH_VIEWER%%bin/tview-8 -%%WITH_VIEWER%%bin/tview-16 -%%WITH_VIEWER%%bin/tview-32 +bin/valence +bin/vibbig bin/vibrate bin/vibrot bin/xtalfit @@ -55,7 +55,7 @@ bin/xyzint bin/xyzpdb bin/xyzsybyl -%%PORTDOCS%%%%DOCSDIR%%/README +%%PORTDOCS%%%%DOCSDIR%%/0README %%PORTDOCS%%%%DOCSDIR%%/ffe-guide.pdf %%PORTDOCS%%%%DOCSDIR%%/guide.pdf %%PORTDOCS%%%%DOCSDIR%%/guide.txt @@ -71,54 +71,366 @@ %%PORTDOCS%%%%DOCSDIR%%/release-4.2 %%PORTDOCS%%%%DOCSDIR%%/summary.pdf %%PORTDOCS%%%%DOCSDIR%%/summary.txt -%%PORTDOCS%%share/examples/tinker/README -%%PORTDOCS%%share/examples/tinker/anion.dat -%%PORTDOCS%%share/examples/tinker/anion.dyn0 -%%PORTDOCS%%share/examples/tinker/anion.key -%%PORTDOCS%%share/examples/tinker/anion.log -%%PORTDOCS%%share/examples/tinker/anion.run -%%PORTDOCS%%share/examples/tinker/anion.xyz -%%PORTDOCS%%share/examples/tinker/argon.1st -%%PORTDOCS%%share/examples/tinker/argon.key -%%PORTDOCS%%share/examples/tinker/argon.log -%%PORTDOCS%%share/examples/tinker/argon.run -%%PORTDOCS%%share/examples/tinker/clean.make -%%PORTDOCS%%share/examples/tinker/cluster.dat -%%PORTDOCS%%share/examples/tinker/cluster.key -%%PORTDOCS%%share/examples/tinker/cluster.log -%%PORTDOCS%%share/examples/tinker/cluster.run -%%PORTDOCS%%share/examples/tinker/cluster.xyz -%%PORTDOCS%%share/examples/tinker/crambin.key -%%PORTDOCS%%share/examples/tinker/crambin.log -%%PORTDOCS%%share/examples/tinker/crambin.pdb -%%PORTDOCS%%share/examples/tinker/crambin.run -%%PORTDOCS%%share/examples/tinker/cyclohex.boat -%%PORTDOCS%%share/examples/tinker/cyclohex.chair -%%PORTDOCS%%share/examples/tinker/cyclohex.key -%%PORTDOCS%%share/examples/tinker/cyclohex.log -%%PORTDOCS%%share/examples/tinker/cyclohex.run -%%PORTDOCS%%share/examples/tinker/dialanine.key -%%PORTDOCS%%share/examples/tinker/dialanine.log -%%PORTDOCS%%share/examples/tinker/dialanine.run -%%PORTDOCS%%share/examples/tinker/dialanine.xyz -%%PORTDOCS%%share/examples/tinker/enkephalin.dat -%%PORTDOCS%%share/examples/tinker/enkephalin.key -%%PORTDOCS%%share/examples/tinker/enkephalin.log -%%PORTDOCS%%share/examples/tinker/enkephalin.run -%%PORTDOCS%%share/examples/tinker/formamide.cell -%%PORTDOCS%%share/examples/tinker/formamide.dat -%%PORTDOCS%%share/examples/tinker/formamide.key -%%PORTDOCS%%share/examples/tinker/formamide.log -%%PORTDOCS%%share/examples/tinker/formamide.run -%%PORTDOCS%%share/examples/tinker/helix.1st -%%PORTDOCS%%share/examples/tinker/helix.key -%%PORTDOCS%%share/examples/tinker/helix.log -%%PORTDOCS%%share/examples/tinker/helix.run -%%PORTDOCS%%share/examples/tinker/salt.cell -%%PORTDOCS%%share/examples/tinker/salt.key -%%PORTDOCS%%share/examples/tinker/salt.log -%%PORTDOCS%%share/examples/tinker/salt.run -%%PORTDOCS%%%%DATADIR%%/bench/README +%%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 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-%%PORTDOCS%%%%DATADIR%%/test/flane.int -%%PORTDOCS%%%%DATADIR%%/test/flane.key -%%PORTDOCS%%%%DATADIR%%/test/flane.xyz -%%PORTDOCS%%%%DATADIR%%/test/form.key -%%PORTDOCS%%%%DATADIR%%/test/form.xyz -%%PORTDOCS%%%%DATADIR%%/test/formbig.key -%%PORTDOCS%%%%DATADIR%%/test/formbig.xyz -%%PORTDOCS%%%%DATADIR%%/test/formbox.dyn -%%PORTDOCS%%%%DATADIR%%/test/formbox.key -%%PORTDOCS%%%%DATADIR%%/test/formbox.xyz -%%PORTDOCS%%%%DATADIR%%/test/furan.int -%%PORTDOCS%%%%DATADIR%%/test/furan.key -%%PORTDOCS%%%%DATADIR%%/test/furan.xyz -%%PORTDOCS%%%%DATADIR%%/test/glucose.key -%%PORTDOCS%%%%DATADIR%%/test/glucose.xyz -%%PORTDOCS%%%%DATADIR%%/test/glycerol.dyn -%%PORTDOCS%%%%DATADIR%%/test/glycerol.key -%%PORTDOCS%%%%DATADIR%%/test/glycerol.xyz -%%PORTDOCS%%%%DATADIR%%/test/graphite.key -%%PORTDOCS%%%%DATADIR%%/test/graphite.xyz -%%PORTDOCS%%%%DATADIR%%/test/helix.dyn +%%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.xyz -%%PORTDOCS%%%%DATADIR%%/test/heme.key -%%PORTDOCS%%%%DATADIR%%/test/heme.xyz -%%PORTDOCS%%%%DATADIR%%/test/hexane.int -%%PORTDOCS%%%%DATADIR%%/test/hexane.key -%%PORTDOCS%%%%DATADIR%%/test/hexane.xyz -%%PORTDOCS%%%%DATADIR%%/test/hexanes.dyn -%%PORTDOCS%%%%DATADIR%%/test/hexanes.key -%%PORTDOCS%%%%DATADIR%%/test/hexanes.xyz -%%PORTDOCS%%%%DATADIR%%/test/imidazole.int -%%PORTDOCS%%%%DATADIR%%/test/imidazole.key -%%PORTDOCS%%%%DATADIR%%/test/imidazole.xyz -%%PORTDOCS%%%%DATADIR%%/test/imine.int -%%PORTDOCS%%%%DATADIR%%/test/imine.key -%%PORTDOCS%%%%DATADIR%%/test/imine.xyz -%%PORTDOCS%%%%DATADIR%%/test/lactam.key -%%PORTDOCS%%%%DATADIR%%/test/lactam.xyz -%%PORTDOCS%%%%DATADIR%%/test/lipid.key -%%PORTDOCS%%%%DATADIR%%/test/lipid.xyz -%%PORTDOCS%%%%DATADIR%%/test/melittin.key -%%PORTDOCS%%%%DATADIR%%/test/melittin.pdb -%%PORTDOCS%%%%DATADIR%%/test/melittin.seq -%%PORTDOCS%%%%DATADIR%%/test/melittin.xyz -%%PORTDOCS%%%%DATADIR%%/test/membrane.key -%%PORTDOCS%%%%DATADIR%%/test/membrane.xyz -%%PORTDOCS%%%%DATADIR%%/test/methane.int -%%PORTDOCS%%%%DATADIR%%/test/methane.key -%%PORTDOCS%%%%DATADIR%%/test/methane.xyz -%%PORTDOCS%%%%DATADIR%%/test/methanol.key -%%PORTDOCS%%%%DATADIR%%/test/methanol.xyz -%%PORTDOCS%%%%DATADIR%%/test/mm3.key -%%PORTDOCS%%%%DATADIR%%/test/mm3.xyz -%%PORTDOCS%%%%DATADIR%%/test/nacl.key -%%PORTDOCS%%%%DATADIR%%/test/nacl.xyz -%%PORTDOCS%%%%DATADIR%%/test/nada.key -%%PORTDOCS%%%%DATADIR%%/test/nada.xyz -%%PORTDOCS%%%%DATADIR%%/test/naphthalene.int -%%PORTDOCS%%%%DATADIR%%/test/naphthalene.key -%%PORTDOCS%%%%DATADIR%%/test/naphthalene.xyz -%%PORTDOCS%%%%DATADIR%%/test/nitrogen.dyn -%%PORTDOCS%%%%DATADIR%%/test/nitrogen.key -%%PORTDOCS%%%%DATADIR%%/test/nitrogen.xyz -%%PORTDOCS%%%%DATADIR%%/test/nma.int -%%PORTDOCS%%%%DATADIR%%/test/nma.key -%%PORTDOCS%%%%DATADIR%%/test/nma.xyz -%%PORTDOCS%%%%DATADIR%%/test/nmabox.dyn -%%PORTDOCS%%%%DATADIR%%/test/nmabox.key -%%PORTDOCS%%%%DATADIR%%/test/nmabox.xyz -%%PORTDOCS%%%%DATADIR%%/test/nstilbene.int -%%PORTDOCS%%%%DATADIR%%/test/nstilbene.key -%%PORTDOCS%%%%DATADIR%%/test/nstilbene.xyz -%%PORTDOCS%%%%DATADIR%%/test/octane.int -%%PORTDOCS%%%%DATADIR%%/test/octane.key -%%PORTDOCS%%%%DATADIR%%/test/octane.xyz -%%PORTDOCS%%%%DATADIR%%/test/octane2.int -%%PORTDOCS%%%%DATADIR%%/test/octane2.key -%%PORTDOCS%%%%DATADIR%%/test/octane2.xyz -%%PORTDOCS%%%%DATADIR%%/test/octene.key -%%PORTDOCS%%%%DATADIR%%/test/octene.xyz -%%PORTDOCS%%%%DATADIR%%/test/palmitate.int -%%PORTDOCS%%%%DATADIR%%/test/palmitate.key -%%PORTDOCS%%%%DATADIR%%/test/palmitate.xyz -%%PORTDOCS%%%%DATADIR%%/test/peptide.int -%%PORTDOCS%%%%DATADIR%%/test/peptide.key -%%PORTDOCS%%%%DATADIR%%/test/peptide.make -%%PORTDOCS%%%%DATADIR%%/test/peptide.pdb -%%PORTDOCS%%%%DATADIR%%/test/peptide.seq -%%PORTDOCS%%%%DATADIR%%/test/peptide.xyz -%%PORTDOCS%%%%DATADIR%%/test/phenanth.key -%%PORTDOCS%%%%DATADIR%%/test/phenanth.xyz -%%PORTDOCS%%%%DATADIR%%/test/photo.key -%%PORTDOCS%%%%DATADIR%%/test/photo.pdb -%%PORTDOCS%%%%DATADIR%%/test/photo.seq -%%PORTDOCS%%%%DATADIR%%/test/photo.xyz -%%PORTDOCS%%%%DATADIR%%/test/pol3.key -%%PORTDOCS%%%%DATADIR%%/test/pol3.xyz -%%PORTDOCS%%%%DATADIR%%/test/polyala.key -%%PORTDOCS%%%%DATADIR%%/test/polyala.xyz -%%PORTDOCS%%%%DATADIR%%/test/propane.key -%%PORTDOCS%%%%DATADIR%%/test/propane.ray -%%PORTDOCS%%%%DATADIR%%/test/propane.xyz -%%PORTDOCS%%%%DATADIR%%/test/propellane.int -%%PORTDOCS%%%%DATADIR%%/test/propellane.key -%%PORTDOCS%%%%DATADIR%%/test/propellane.xyz -%%PORTDOCS%%%%DATADIR%%/test/propyne.key -%%PORTDOCS%%%%DATADIR%%/test/propyne.xyz -%%PORTDOCS%%%%DATADIR%%/test/pyridine.int -%%PORTDOCS%%%%DATADIR%%/test/pyridine.key -%%PORTDOCS%%%%DATADIR%%/test/pyridine.xyz -%%PORTDOCS%%%%DATADIR%%/test/pyrrole.int -%%PORTDOCS%%%%DATADIR%%/test/pyrrole.key -%%PORTDOCS%%%%DATADIR%%/test/pyrrole.xyz -%%PORTDOCS%%%%DATADIR%%/test/retinoic.key -%%PORTDOCS%%%%DATADIR%%/test/retinoic.xyz -%%PORTDOCS%%%%DATADIR%%/test/skunk.key -%%PORTDOCS%%%%DATADIR%%/test/skunk.xyz -%%PORTDOCS%%%%DATADIR%%/test/spc.key -%%PORTDOCS%%%%DATADIR%%/test/spc.xyz -%%PORTDOCS%%%%DATADIR%%/test/sterol.key -%%PORTDOCS%%%%DATADIR%%/test/sterol.xyz -%%PORTDOCS%%%%DATADIR%%/test/styrene.int -%%PORTDOCS%%%%DATADIR%%/test/styrene.key -%%PORTDOCS%%%%DATADIR%%/test/styrene.xyz -%%PORTDOCS%%%%DATADIR%%/test/terphenyl.key -%%PORTDOCS%%%%DATADIR%%/test/terphenyl.xyz -%%PORTDOCS%%%%DATADIR%%/test/tfe.key -%%PORTDOCS%%%%DATADIR%%/test/tfe.xyz -%%PORTDOCS%%%%DATADIR%%/test/thiadiene.int -%%PORTDOCS%%%%DATADIR%%/test/thiadiene.key -%%PORTDOCS%%%%DATADIR%%/test/thiadiene.xyz -%%PORTDOCS%%%%DATADIR%%/test/thiophene.int -%%PORTDOCS%%%%DATADIR%%/test/thiophene.key -%%PORTDOCS%%%%DATADIR%%/test/thiophene.xyz -%%PORTDOCS%%%%DATADIR%%/test/thr.int -%%PORTDOCS%%%%DATADIR%%/test/thr.key -%%PORTDOCS%%%%DATADIR%%/test/thr.xyz -%%PORTDOCS%%%%DATADIR%%/test/tip3f.key -%%PORTDOCS%%%%DATADIR%%/test/tip3f.xyz -%%PORTDOCS%%%%DATADIR%%/test/tip3p.key -%%PORTDOCS%%%%DATADIR%%/test/tip3p.xyz -%%PORTDOCS%%%%DATADIR%%/test/tip4f.key -%%PORTDOCS%%%%DATADIR%%/test/tip4f.xyz -%%PORTDOCS%%%%DATADIR%%/test/tip4p.key -%%PORTDOCS%%%%DATADIR%%/test/tip4p.xyz -%%PORTDOCS%%%%DATADIR%%/test/tip5p.key -%%PORTDOCS%%%%DATADIR%%/test/tip5p.xyz -%%PORTDOCS%%%%DATADIR%%/test/trpcage.key -%%PORTDOCS%%%%DATADIR%%/test/trpcage.pdb -%%PORTDOCS%%%%DATADIR%%/test/trpcage.seq -%%PORTDOCS%%%%DATADIR%%/test/trpcage.xyz -%%PORTDOCS%%%%DATADIR%%/test/water.int +%%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 -%%PORTDOCS%%%%DATADIR%%/test/waterbig.key -%%PORTDOCS%%%%DATADIR%%/test/waterbig.xyz -%%PORTDOCS%%%%DATADIR%%/test/waterbox.dyn -%%PORTDOCS%%%%DATADIR%%/test/waterbox.key -%%PORTDOCS%%%%DATADIR%%/test/waterbox.xyz -%%PORTDOCS%%%%DATADIR%%/test/waterdot.dyn -%%PORTDOCS%%%%DATADIR%%/test/waterdot.key -%%PORTDOCS%%%%DATADIR%%/test/waterdot.xyz -%%PORTDOCS%%%%DATADIR%%/test/waterhuge.key -%%PORTDOCS%%%%DATADIR%%/test/waterhuge.xyz -%%PORTDOCS%%%%DATADIR%%/test/watersmall.dyn -%%PORTDOCS%%%%DATADIR%%/test/watersmall.key -%%PORTDOCS%%%%DATADIR%%/test/watersmall.xyz -%%PORTDOCS%%%%DATADIR%%/test/watertiny.dyn -%%PORTDOCS%%%%DATADIR%%/test/watertiny.key -%%PORTDOCS%%%%DATADIR%%/test/watertiny.xyz -%%PORTDOCS%%%%DATADIR%%/test/white.int -%%PORTDOCS%%%%DATADIR%%/test/white.key -%%PORTDOCS%%%%DATADIR%%/test/white.xyz %%DATADIR%%/tinker.txt -%%PORTDOCS%%@dirrm %%DOCSDIR%% -%%PORTDOCS%%@dirrm share/examples/tinker -%%PORTDOCS%%@dirrm %%DATADIR%%/bench -@dirrm %%DATADIR%%/params -%%WITH_VIEWER%%@dirrm %%DATADIR%%/rasmol %%PORTDOCS%%@dirrm %%DATADIR%%/test +@dirrm %%DATADIR%%/params +%%PORTDOCS%%@dirrm %%DATADIR%%/bench @dirrm %%DATADIR%% +%%PORTDOCS%%@dirrm %%EXAMPLESDIR%% +%%PORTDOCS%%@dirrm %%DOCSDIR%% diff -ruNa tinker.orig/scripts/build_viewer tinker/scripts/build_viewer --- tinker.orig/scripts/build_viewer 2001-01-24 20:58:44.000000000 +0300 +++ tinker/scripts/build_viewer 1970-01-01 03:00:00.000000000 +0300 @@ -1,47 +0,0 @@ -#!/bin/sh - -# This builds the molecular viewer for tinker files. It is a modified -# version of rasmol. One of the problems with rasmol is that is only -# works at one color depth. This script will build three viewers at -# different color depths, 8-bit, 16-bit, and 32-bit. The binaries are -# called tview-8, tview-16, and tview-32 respectively. - -cd ${WRKSRC}/../rasmol - -cp Imakefile Imakefile.orig - -sed s@/user/ponder@${PREFIX}/share@ Imakefile > Imakefile.temp - -sed s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-32)'@ \ - Imakefile.temp > Imakefile - -xmkmf -a - -make clean && make - -sed -e s@'DEPTHDEF = -DTHIRTYTWOBIT'@'# DEPTHDEF = -DTHIRTYTWOBIT'@ \ - -e s@'# DEPTHDEF = -DSIXTEENBIT'@'DEPTHDEF = -DSIXTEENBIT'@ \ - -e s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-16)'@ \ - Imakefile.temp > Imakefile - -xmkmf -a - -make clean && make - -sed -e s@'DEPTHDEF = -DTHIRTYTWOBIT'@'# DEPTHDEF = -DTHIRTYTWOBIT'@ \ - -e s@'# DEPTHDEF = -DEIGHTBIT'@'DEPTHDEF = -DEIGHTBIT'@ \ - -e s@'ComplexProgramTarget(rasmol)'@'ComplexProgramTarget(tview-8)'@ \ - Imakefile.temp > Imakefile - -xmkmf -a - -make clean && make - -# Restore Imakefile to original state so that rerunning this script does -# the right thing. -rm Imakefile.temp -mv Imakefile.orig Imakefile -xmkmf -a -make clean - -exit 0