Attachment 112865 Details for Bug 154359 – file.diff

[patch] file.diff

file.diff (text/plain), 44.15 KB, created by R.Mahmatkhanov on 2011-01-28 18:20:09 UTC

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Creator: R.Mahmatkhanov

Created: 2011-01-28 18:20:09 UTC

Size: 44.15 KB

patch

obsolete

>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 <bsd.port.pre.mk>
> 
>@@ -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
>+%%PORTDOCS%%%%EXAMPLESDIR%%/flane.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/flane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/flane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/form.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/form.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formbig.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formbig.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formbox.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formbox.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formbox.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formopls.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formopls.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/formopls.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/furan.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/furan.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/furan.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/glucose.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/glucose.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/glycerol.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/glycerol.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/glycerol.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/graphite.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/graphite.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/helix.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/helix.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/helix.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/heme.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/heme.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/hexane.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/hexane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/hexane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/hexanes.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/hexanes.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/hexanes.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/imidazole.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/imidazole.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/imidazole.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/imine.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/imine.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/imine.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/indole.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/indole.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/lactam.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/lactam.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/lipid.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/lipid.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/lj38.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/lj38.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.pdb
>+%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.seq
>+%%PORTDOCS%%%%EXAMPLESDIR%%/melittin.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/membrane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/membrane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/meohbox.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/meohbox.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/meohbox.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/methane.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/methane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/methane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/methanol.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/methanol.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/mgwater.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/mgwater.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/mm3.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/mm3.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nacl.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nacl.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nada.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nada.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/naphthalene.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/naphthalene.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/naphthalene.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/naphthax.frac
>+%%PORTDOCS%%%%EXAMPLESDIR%%/naphthax.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/naphthax.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nitrogen.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nitrogen.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nitrogen.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nma.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nma.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nma.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nmabox.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nmabox.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nmabox.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nmf.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nmf.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nstilbene.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nstilbene.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/nstilbene.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octane.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octane2.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octane2.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octane2.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octene.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/octene.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/palmitate.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/palmitate.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/palmitate.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pentane.frac
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pentane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pentane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/peptide.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/peptide.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/peptide.make
>+%%PORTDOCS%%%%EXAMPLESDIR%%/peptide.pdb
>+%%PORTDOCS%%%%EXAMPLESDIR%%/peptide.seq
>+%%PORTDOCS%%%%EXAMPLESDIR%%/peptide.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/phenanth.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/phenanth.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/photo.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/photo.seq
>+%%PORTDOCS%%%%EXAMPLESDIR%%/photo.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pol3.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pol3.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/polyala.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/polyala.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/propane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/propane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/propellane.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/propellane.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/propellane.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/propyne.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/propyne.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pyridine.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pyridine.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pyridine.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pyrrole.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pyrrole.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/pyrrole.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/retinoic.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/retinoic.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/skunk.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/skunk.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/spc.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/spc.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/sterol.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/sterol.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/styrene.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/styrene.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/styrene.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/terphenyl.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/terphenyl.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tfe.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tfe.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thiadiene.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thiadiene.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thiadiene.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thiophene.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thiophene.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thiophene.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thr.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thr.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/thr.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip3f.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip3f.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip3p.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip3p.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip4f.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip4f.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip4p.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip4p.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip5p.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/tip5p.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/trpcage.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/trpcage.pdb
>+%%PORTDOCS%%%%EXAMPLESDIR%%/trpcage.seq
>+%%PORTDOCS%%%%EXAMPLESDIR%%/trpcage.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/ubiquitin.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/ubiquitin.pdb
>+%%PORTDOCS%%%%EXAMPLESDIR%%/ubiquitin.seq
>+%%PORTDOCS%%%%EXAMPLESDIR%%/ubiquitin.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/ubiquitin2.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/ubiquitin2.seq
>+%%PORTDOCS%%%%EXAMPLESDIR%%/ubiquitin2.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/urea.frac
>+%%PORTDOCS%%%%EXAMPLESDIR%%/urea.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/urea.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/water.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/water.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/water.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterball.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterball.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterbig.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterbig.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterbox.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterbox.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterbox.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterdot.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterdot.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterdot.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterglobe.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterglobe.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterhuge.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterhuge.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterslab.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterslab.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/waterslab.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/watersmall.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/watersmall.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/watersmall.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/watertiny.dyn
>+%%PORTDOCS%%%%EXAMPLESDIR%%/watertiny.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/watertiny.xyz
>+%%PORTDOCS%%%%EXAMPLESDIR%%/white.int
>+%%PORTDOCS%%%%EXAMPLESDIR%%/white.key
>+%%PORTDOCS%%%%EXAMPLESDIR%%/white.xyz
>+%%PORTDOCS%%%%DATADIR%%/bench/0README
> %%PORTDOCS%%%%DATADIR%%/bench/bench1.key
> %%PORTDOCS%%%%DATADIR%%/bench/bench1.run
> %%PORTDOCS%%%%DATADIR%%/bench/bench1.xyz
>@@ -138,6 +450,14 @@
> %%PORTDOCS%%%%DATADIR%%/bench/bench5.log
> %%PORTDOCS%%%%DATADIR%%/bench/bench5.run
> %%PORTDOCS%%%%DATADIR%%/bench/bench5.xyz
>+%%PORTDOCS%%%%DATADIR%%/bench/bench6.key
>+%%PORTDOCS%%%%DATADIR%%/bench/bench6.log
>+%%PORTDOCS%%%%DATADIR%%/bench/bench6.run
>+%%PORTDOCS%%%%DATADIR%%/bench/bench6.xyz
>+%%PORTDOCS%%%%DATADIR%%/bench/bench7.key
>+%%PORTDOCS%%%%DATADIR%%/bench/bench7.log
>+%%PORTDOCS%%%%DATADIR%%/bench/bench7.run
>+%%PORTDOCS%%%%DATADIR%%/bench/bench7.xyz
> %%PORTDOCS%%%%DATADIR%%/bench/results-2.3
> %%PORTDOCS%%%%DATADIR%%/bench/results-2.4
> %%PORTDOCS%%%%DATADIR%%/bench/results-2.9
>@@ -151,17 +471,24 @@
> %%PORTDOCS%%%%DATADIR%%/bench/results-4.0
> %%PORTDOCS%%%%DATADIR%%/bench/results-4.1
> %%PORTDOCS%%%%DATADIR%%/bench/results-4.2
>-%%DATADIR%%/params/README
>+%%PORTDOCS%%%%DATADIR%%/bench/results-4.3
>+%%PORTDOCS%%%%DATADIR%%/bench/results-5.0
>+%%PORTDOCS%%%%DATADIR%%/bench/results-5.1
>+%%DATADIR%%/params/0README
>+%%DATADIR%%/params/amber02.prm
> %%DATADIR%%/params/amber94.prm
> %%DATADIR%%/params/amber96.prm
> %%DATADIR%%/params/amber98.prm
> %%DATADIR%%/params/amber99.prm
>-%%DATADIR%%/params/amoeba.prm
>-%%DATADIR%%/params/amoebapro.prm
>+%%DATADIR%%/params/amber99sb.prm
>+%%DATADIR%%/params/amoeba04.prm
>+%%DATADIR%%/params/amoeba09.prm
>+%%DATADIR%%/params/amoebabio09.prm
>+%%DATADIR%%/params/amoebapro04.prm
> %%DATADIR%%/params/charmm19.prm
>-%%DATADIR%%/params/charmm27.prm
>+%%DATADIR%%/params/charmm22.prm
>+%%DATADIR%%/params/charmm22cmap.prm
> %%DATADIR%%/params/dang.prm
>-%%DATADIR%%/params/dudek.prm
> %%DATADIR%%/params/hoch.prm
> %%DATADIR%%/params/mm2.prm
> %%DATADIR%%/params/mm3.prm
>@@ -169,303 +496,80 @@
> %%DATADIR%%/params/oplsaa.prm
> %%DATADIR%%/params/oplsaal.prm
> %%DATADIR%%/params/oplsua.prm
>-%%DATADIR%%/params/smooth.prm
> %%DATADIR%%/params/smoothaa.prm
>+%%DATADIR%%/params/smoothua.prm
>+%%DATADIR%%/params/tiny.prm
> %%DATADIR%%/params/water.prm
>-%%WITH_VIEWER%%%%DATADIR%%/rasmol/rasmol.hlp
>-%%PORTDOCS%%%%DATADIR%%/test/README
>-%%PORTDOCS%%%%DATADIR%%/test/alkane.key
>-%%PORTDOCS%%%%DATADIR%%/test/alkane.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/amoeba.key
>-%%PORTDOCS%%%%DATADIR%%/test/amoeba.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/arach.int
>-%%PORTDOCS%%%%DATADIR%%/test/arach.key
>-%%PORTDOCS%%%%DATADIR%%/test/arach.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/azulene.int
>-%%PORTDOCS%%%%DATADIR%%/test/azulene.key
>-%%PORTDOCS%%%%DATADIR%%/test/azulene.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/bdna.int
>-%%PORTDOCS%%%%DATADIR%%/test/bdna.key
>-%%PORTDOCS%%%%DATADIR%%/test/bdna.make
>-%%PORTDOCS%%%%DATADIR%%/test/bdna.seq
>-%%PORTDOCS%%%%DATADIR%%/test/bdna.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/bearing.key
>-%%PORTDOCS%%%%DATADIR%%/test/bearing.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/bearing2.key
>-%%PORTDOCS%%%%DATADIR%%/test/bearing2.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/benzene.int
>-%%PORTDOCS%%%%DATADIR%%/test/benzene.key
>-%%PORTDOCS%%%%DATADIR%%/test/benzene.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/bowl.int
>-%%PORTDOCS%%%%DATADIR%%/test/bowl.key
>-%%PORTDOCS%%%%DATADIR%%/test/bowl.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/bowl2.key
>-%%PORTDOCS%%%%DATADIR%%/test/bowl2.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/bowl3.key
>-%%PORTDOCS%%%%DATADIR%%/test/bowl3.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/bucky.int
>-%%PORTDOCS%%%%DATADIR%%/test/bucky.key
>-%%PORTDOCS%%%%DATADIR%%/test/bucky.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/butane.int
>-%%PORTDOCS%%%%DATADIR%%/test/butane.key
>-%%PORTDOCS%%%%DATADIR%%/test/butane.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/butane2.int
>-%%PORTDOCS%%%%DATADIR%%/test/butane2.key
>-%%PORTDOCS%%%%DATADIR%%/test/butane2.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/butanes.dyn
>-%%PORTDOCS%%%%DATADIR%%/test/butanes.key
>-%%PORTDOCS%%%%DATADIR%%/test/butanes.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/butanex.key
>-%%PORTDOCS%%%%DATADIR%%/test/butanex.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/butopls.int
>-%%PORTDOCS%%%%DATADIR%%/test/butopls.key
>-%%PORTDOCS%%%%DATADIR%%/test/butopls.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/butopls2.int
>-%%PORTDOCS%%%%DATADIR%%/test/butopls2.key
>-%%PORTDOCS%%%%DATADIR%%/test/butopls2.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/c5.key
>-%%PORTDOCS%%%%DATADIR%%/test/c5.seq
>-%%PORTDOCS%%%%DATADIR%%/test/c5.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/c7a.key
>-%%PORTDOCS%%%%DATADIR%%/test/c7a.seq
>-%%PORTDOCS%%%%DATADIR%%/test/c7a.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/c7e.key
>-%%PORTDOCS%%%%DATADIR%%/test/c7e.seq
>-%%PORTDOCS%%%%DATADIR%%/test/c7e.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/calmodulin.key
>-%%PORTDOCS%%%%DATADIR%%/test/calmodulin.pdb
>-%%PORTDOCS%%%%DATADIR%%/test/calmodulin.seq
>-%%PORTDOCS%%%%DATADIR%%/test/calmodulin.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/copper.key
>-%%PORTDOCS%%%%DATADIR%%/test/copper.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/cpentene.key
>-%%PORTDOCS%%%%DATADIR%%/test/cpentene.xyz
>+%%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.seq
>-%%PORTDOCS%%%%DATADIR%%/test/crambin.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/crambinx.key
>-%%PORTDOCS%%%%DATADIR%%/test/crambinx.ray
>-%%PORTDOCS%%%%DATADIR%%/test/crambinx.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/crown.int
>-%%PORTDOCS%%%%DATADIR%%/test/crown.key
>-%%PORTDOCS%%%%DATADIR%%/test/crown.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/cychept.int
>-%%PORTDOCS%%%%DATADIR%%/test/cychept.key
>-%%PORTDOCS%%%%DATADIR%%/test/cychept.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/cyclo.int
>-%%PORTDOCS%%%%DATADIR%%/test/cyclo.key
>-%%PORTDOCS%%%%DATADIR%%/test/cyclo.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/cyclo2.int
>-%%PORTDOCS%%%%DATADIR%%/test/cyclo2.key
>-%%PORTDOCS%%%%DATADIR%%/test/cyclo2.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/dang.key
>-%%PORTDOCS%%%%DATADIR%%/test/dang.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/diamond.key
>-%%PORTDOCS%%%%DATADIR%%/test/diamond.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/diene.int
>-%%PORTDOCS%%%%DATADIR%%/test/diene.key
>-%%PORTDOCS%%%%DATADIR%%/test/diene.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/dimethane.key
>-%%PORTDOCS%%%%DATADIR%%/test/dimethane.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/enkephalin.int
>+%%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.make
>-%%PORTDOCS%%%%DATADIR%%/test/enkephalin.seq
>-%%PORTDOCS%%%%DATADIR%%/test/enkephalin.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/ermer.int
>-%%PORTDOCS%%%%DATADIR%%/test/ermer.key
>-%%PORTDOCS%%%%DATADIR%%/test/ermer.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/ester.key
>-%%PORTDOCS%%%%DATADIR%%/test/ester.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/ethane.int
>-%%PORTDOCS%%%%DATADIR%%/test/ethane.key
>-%%PORTDOCS%%%%DATADIR%%/test/ethane.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/ethanol.int
>-%%PORTDOCS%%%%DATADIR%%/test/ethanol.key
>-%%PORTDOCS%%%%DATADIR%%/test/ethanol.xyz
>-%%PORTDOCS%%%%DATADIR%%/test/ethylene.int
>-%%PORTDOCS%%%%DATADIR%%/test/ethylene.key
>-%%PORTDOCS%%%%DATADIR%%/test/ethylene.xyz
>-%%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

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Attachments on bug 154359: 112865