Date: Thu, 6 Sep 2001 10:11:49 -0500 (CDT) From: Glenn Johnson <gjohnson@srrc.ars.usda.gov> To: FreeBSD-gnats-submit@freebsd.org Subject: ports/30398: update of ports/biology/tinker Message-ID: <200109061511.f86FBns99430@node7.cluster.srrc.usda.gov>
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>Number: 30398
>Category: ports
>Synopsis: update of ports/biology/tinker
>Confidential: no
>Severity: non-critical
>Priority: medium
>Responsible: freebsd-ports
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: maintainer-update
>Submitter-Id: current-users
>Arrival-Date: Thu Sep 06 08:20:01 PDT 2001
>Closed-Date:
>Last-Modified:
>Originator: Glenn Johnson
>Release: FreeBSD 4.4-RC i386
>Organization:
USDA, ARS, SRRC
>Environment:
System: FreeBSD node7.cluster.srrc.usda.gov 4.4-RC FreeBSD 4.4-RC #4: Tue Sep 4 16:55:10 CDT 2001 root@node7.cluster.srrc.usda.gov:/usr/obj/usr/src/sys/CLUSTER-UP i386
>Description:
The enclosed patch updates the biology/tinker port from 3.8 to
3.9
>How-To-Repeat:
>Fix:
Apply the enclosed patch to ports/biology/tinker. Note that
files/patch-ag has been removed.
diff -ruN tinker.old/Makefile tinker/Makefile
--- tinker.old/Makefile Wed Sep 5 13:42:06 2001
+++ tinker/Makefile Thu Sep 6 09:52:38 2001
@@ -6,8 +6,7 @@
#
PORTNAME= tinker
-PORTVERSION= 3.8
-PORTREVISION= 1
+PORTVERSION= 3.9
CATEGORIES= biology
MASTER_SITES= ftp://dasher.wustl.edu/pub/
DISTNAME= ${PORTNAME}
@@ -24,14 +23,19 @@
RESTRICTED= author requests no distribution except from his FTP site
+pre-fetch:
+ @${ECHO} ""
+ @${ECHO} If you get a CHECKSUM mismatch, try doing a \'make distclean\' first.
+ @${ECHO} ""
+
.if defined(WANT_VIEWER)
.if ${XFREE86_VERSION} == 3
-BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake
+BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake
.elif ${XFREE86_VERSION} == 4
-BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake-4
+BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake-4
.endif
-PLIST= ${PKGDIR}/pkg-plist.viewer
-USE_XLIB= yes
+PLIST= ${PKGDIR}/pkg-plist.viewer
+USE_XLIB= yes
post-build:
${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer
.else
@@ -65,8 +69,12 @@
${PREFIX}/share/doc/tinker
${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.txt \
${PREFIX}/share/doc/tinker
+ ${INSTALL_DATA} ${WRKDIR}/tinker/doc/release* \
+${PREFIX}/share/doc/tinker
${INSTALL_DATA} ${WRKDIR}/tinker/example/README \
${PREFIX}/share/examples/tinker
+ ${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \
+${PREFIX}/share/examples/tinker
${INSTALL_DATA} ${WRKDIR}/tinker/example/*.1st \
${PREFIX}/share/examples/tinker
${INSTALL_DATA} ${WRKDIR}/tinker/example/*.boat \
@@ -87,29 +95,31 @@
${PREFIX}/share/examples/tinker
${INSTALL_DATA} ${WRKDIR}/tinker/example/*.xyz \
${PREFIX}/share/examples/tinker
- ${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/clean.make \
-${PREFIX}/share/examples/tinker
${INSTALL_SCRIPT} ${WRKDIR}/tinker/example/*.run \
${PREFIX}/share/examples/tinker
+ ${INSTALL_DATA} ${WRKDIR}/tinker/bench/README \
+${PREFIX}/share/tinker/bench
${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.dyn0 \
${PREFIX}/share/tinker/bench
${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.log \
${PREFIX}/share/tinker/bench
${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.key \
${PREFIX}/share/tinker/bench
+ ${INSTALL_SCRIPT} ${WRKDIR}/tinker/bench/*.run \
+${PREFIX}/share/tinker/bench
${INSTALL_DATA} ${WRKDIR}/tinker/bench/*.xyz \
${PREFIX}/share/tinker/bench
${INSTALL_DATA} ${WRKDIR}/tinker/bench/results* \
${PREFIX}/share/tinker/bench
- ${INSTALL_SCRIPT} ${WRKDIR}/tinker/bench/*.run \
-${PREFIX}/share/tinker/bench
${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${PREFIX}/share/tinker/test
.endif
.if defined(WANT_VIEWER)
${MKDIR} ${PREFIX}/share/tinker/rasmol
${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin
- ${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp ${PREFIX}/share/tinker/rasmol
+ ${INSTALL_SCRIPT} ${FILESDIR}/tview ${PREFIX}/bin
+ ${INSTALL_DATA} ${WRKDIR}/tinker/rasmol/rasmol.hlp \
+ ${PREFIX}/share/tinker/rasmol
.endif
diff -ruN tinker.old/distinfo tinker/distinfo
--- tinker.old/distinfo Wed Sep 5 13:42:06 2001
+++ tinker/distinfo Wed Sep 5 13:45:34 2001
@@ -1 +1 @@
-MD5 (tinker.tar.gz) = 11e66fb5452e2153a2ced410ea9acadb
+MD5 (tinker.tar.gz) = a48fc15fe668f8e41d0cc3316a582928
diff -ruN tinker.old/files/patch-aa tinker/files/patch-aa
--- tinker.old/files/patch-aa Wed Sep 5 13:42:06 2001
+++ tinker/files/patch-aa Wed Sep 5 13:53:03 2001
@@ -1,5 +1,5 @@
---- ../make/Makefile.orig Mon Jan 15 12:39:52 2001
-+++ ../make/Makefile Thu Apr 19 14:39:26 2001
+--- ../make/Makefile.orig Sat Jul 21 10:04:48 2001
++++ ../make/Makefile Wed Sep 5 13:51:19 2001
@@ -9,8 +9,8 @@
##
## 1. make all Build all the TINKER executables
@@ -68,7 +68,7 @@
#################################################################
## Should not be Necessary to Change Things Below this Point ##
#################################################################
-@@ -486,11 +504,13 @@
+@@ -494,11 +512,13 @@
xyzpdb.x \
xyzsybyl.x
@@ -84,7 +84,7 @@
all: ${EXEFILES}
-@@ -501,56 +521,56 @@
+@@ -509,57 +529,57 @@
cat *.i *.f > tinker.txt
rename:
@@ -112,6 +112,7 @@
- mv optrigid.x $(BINDIR)/optrigid
- mv path.x $(BINDIR)/path
- mv pdbxyz.x $(BINDIR)/pdbxyz
+- mv polarize.x $(BINDIR)/polarize
- mv protein.x $(BINDIR)/protein
- mv pss.x $(BINDIR)/pss
- mv pssrigid.x $(BINDIR)/pssrigid
@@ -162,6 +163,7 @@
+ ${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} protein.x $(BINDIR)/protein
+ ${INSTALL_PROGRAM} pss.x $(BINDIR)/pss
+ ${INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid
@@ -191,7 +193,7 @@
remove_links:
rm -f $(LINKDIR)/alchemy
-@@ -671,8 +691,8 @@
+@@ -682,8 +702,8 @@
bspline.o \
calendar.o \
center.o \
diff -ruN tinker.old/files/patch-ag tinker/files/patch-ag
--- tinker.old/files/patch-ag Wed Sep 5 13:42:06 2001
+++ tinker/files/patch-ag Wed Dec 31 18:00:00 1969
@@ -1,11 +0,0 @@
---- sizes.i.orig Fri Jan 12 11:43:06 2001
-+++ sizes.i Fri Jan 12 11:43:38 2001
-@@ -52,7 +52,7 @@
- integer maxvar,maxopt,maxhess,maxlight,maxvib,maxgeo,maxcell
- integer maxring,maxfix,maxbio,maxres,maxamino,maxnuc,maxbnd
- integer maxang,maxtors,maxpi,maxpib,maxpit
-- parameter (maxatm=10000)
-+ parameter (maxatm=2500)
- parameter (maxval=4)
- parameter (maxgrp=100)
- parameter (maxtyp=1000)
diff -ruN tinker.old/files/patch-ah tinker/files/patch-ah
--- tinker.old/files/patch-ah Wed Sep 5 13:42:06 2001
+++ tinker/files/patch-ah Wed Sep 5 13:57:50 2001
@@ -1,5 +1,5 @@
---- ../bench/bench-1.run.orig Tue Jan 9 14:28:53 2001
-+++ ../bench/bench-1.run Tue Jan 9 14:29:19 2001
+--- ../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 bench-1 1 y
-+timer bench-1 1 y
+-../bin/timer bench1 1 y
++timer bench1 1 y
diff -ruN tinker.old/files/patch-ai tinker/files/patch-ai
--- tinker.old/files/patch-ai Wed Sep 5 13:42:06 2001
+++ tinker/files/patch-ai Wed Sep 5 13:59:04 2001
@@ -1,5 +1,5 @@
---- ../bench/bench-2.run.orig Tue Jan 9 14:29:26 2001
-+++ ../bench/bench-2.run Tue Jan 9 14:29:33 2001
+--- ../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 bench-2 1 y
-+timer bench-2 1 y
+-../bin/timer bench2 1 y
++timer bench2 1 y
diff -ruN tinker.old/files/patch-aj tinker/files/patch-aj
--- tinker.old/files/patch-aj Wed Sep 5 13:42:06 2001
+++ tinker/files/patch-aj Wed Sep 5 14:01:40 2001
@@ -1,5 +1,5 @@
---- ../bench/bench-3.run.orig Tue Jan 9 14:29:40 2001
-+++ ../bench/bench-3.run Tue Jan 9 14:29:53 2001
+--- ../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 bench-3 0
-+time vibrate bench-3 0
+-time ../bin/vibrate bench3 0
++time vibrate bench3 0
diff -ruN tinker.old/files/patch-ak tinker/files/patch-ak
--- tinker.old/files/patch-ak Wed Sep 5 13:42:06 2001
+++ tinker/files/patch-ak Wed Sep 5 14:02:29 2001
@@ -1,7 +1,7 @@
---- ../bench/bench-4.run.orig Tue Jan 9 14:29:59 2001
-+++ ../bench/bench-4.run Tue Jan 9 14:30:14 2001
+--- ../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 bench-4.dyn0 bench-4.dyn
--time ../bin/dynamic bench-4 1000 1.0 10.0 2 298.0
-+time dynamic bench-4 1000 1.0 10.0 2 298.0
- rm bench-4.dyn
+ 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 -ruN tinker.old/files/patch-al tinker/files/patch-al
--- tinker.old/files/patch-al Wed Sep 5 13:42:06 2001
+++ tinker/files/patch-al Wed Sep 5 14:03:17 2001
@@ -1,7 +1,7 @@
---- ../bench/bench-5.run.orig Tue Jan 9 14:30:18 2001
-+++ ../bench/bench-5.run Tue Jan 9 14:30:29 2001
+--- ../bench/bench5.run.orig Tue Jul 24 14:02:20 2001
++++ ../bench/bench5.run Wed Sep 5 14:03:07 2001
@@ -1,3 +1,3 @@
- cp bench-5.dyn0 bench-5.dyn
--time ../bin/dynamic bench-5 100 1.0 10.0 2 298.0
-+time dynamic bench-5 100 1.0 10.0 2 298.0
- rm bench-5.dyn
+ 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
+ rm bench5.dyn
diff -ruN tinker.old/files/tview tinker/files/tview
--- tinker.old/files/tview Wed Dec 31 18:00:00 1969
+++ tinker/files/tview Wed Sep 5 16:08:44 2001
@@ -0,0 +1,21 @@
+#!/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 -ruN tinker.old/pkg-plist tinker/pkg-plist
--- tinker.old/pkg-plist Wed Sep 5 13:42:06 2001
+++ tinker/pkg-plist Wed Sep 5 15:27:36 2001
@@ -22,6 +22,7 @@
bin/optrigid
bin/path
bin/pdbxyz
+bin/polarize
bin/protein
bin/pss
bin/pssrigid
@@ -49,7 +50,6 @@
bin/xyzpdb
bin/xyzsybyl
%%PORTDOCS%%share/doc/tinker/README
-%%PORTDOCS%%share/doc/tinker/announce.txt
%%PORTDOCS%%share/doc/tinker/guide.pdf
%%PORTDOCS%%share/doc/tinker/guide.ps.gz
%%PORTDOCS%%share/doc/tinker/guide.txt
@@ -58,6 +58,11 @@
%%PORTDOCS%%share/doc/tinker/license.txt
%%PORTDOCS%%share/doc/tinker/logo.pdf
%%PORTDOCS%%share/doc/tinker/logo.ps.gz
+%%PORTDOCS%%share/doc/tinker/release-3.2
+%%PORTDOCS%%share/doc/tinker/release-3.6
+%%PORTDOCS%%share/doc/tinker/release-3.7
+%%PORTDOCS%%share/doc/tinker/release-3.8
+%%PORTDOCS%%share/doc/tinker/release-3.9
%%PORTDOCS%%share/doc/tinker/summary.pdf
%%PORTDOCS%%share/doc/tinker/summary.ps
%%PORTDOCS%%share/doc/tinker/summary.txt
@@ -104,24 +109,26 @@
%%PORTDOCS%%share/examples/tinker/salt.key
%%PORTDOCS%%share/examples/tinker/salt.log
%%PORTDOCS%%share/examples/tinker/salt.run
-%%PORTDOCS%%share/tinker/bench/bench-1.key
-%%PORTDOCS%%share/tinker/bench/bench-1.run
-%%PORTDOCS%%share/tinker/bench/bench-1.xyz
-%%PORTDOCS%%share/tinker/bench/bench-2.key
-%%PORTDOCS%%share/tinker/bench/bench-2.run
-%%PORTDOCS%%share/tinker/bench/bench-2.xyz
-%%PORTDOCS%%share/tinker/bench/bench-3.key
-%%PORTDOCS%%share/tinker/bench/bench-3.run
-%%PORTDOCS%%share/tinker/bench/bench-3.xyz
-%%PORTDOCS%%share/tinker/bench/bench-4.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-4.key
-%%PORTDOCS%%share/tinker/bench/bench-4.log
-%%PORTDOCS%%share/tinker/bench/bench-4.run
-%%PORTDOCS%%share/tinker/bench/bench-4.xyz
-%%PORTDOCS%%share/tinker/bench/bench-5.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-5.key
-%%PORTDOCS%%share/tinker/bench/bench-5.run
-%%PORTDOCS%%share/tinker/bench/bench-5.xyz
+%%PORTDOCS%%share/tinker/bench/README
+%%PORTDOCS%%share/tinker/bench/bench1.key
+%%PORTDOCS%%share/tinker/bench/bench1.run
+%%PORTDOCS%%share/tinker/bench/bench1.xyz
+%%PORTDOCS%%share/tinker/bench/bench2.key
+%%PORTDOCS%%share/tinker/bench/bench2.run
+%%PORTDOCS%%share/tinker/bench/bench2.xyz
+%%PORTDOCS%%share/tinker/bench/bench3.key
+%%PORTDOCS%%share/tinker/bench/bench3.run
+%%PORTDOCS%%share/tinker/bench/bench3.xyz
+%%PORTDOCS%%share/tinker/bench/bench4.dyn0
+%%PORTDOCS%%share/tinker/bench/bench4.key
+%%PORTDOCS%%share/tinker/bench/bench4.log
+%%PORTDOCS%%share/tinker/bench/bench4.run
+%%PORTDOCS%%share/tinker/bench/bench4.xyz
+%%PORTDOCS%%share/tinker/bench/bench5.dyn0
+%%PORTDOCS%%share/tinker/bench/bench5.key
+%%PORTDOCS%%share/tinker/bench/bench5.log
+%%PORTDOCS%%share/tinker/bench/bench5.run
+%%PORTDOCS%%share/tinker/bench/bench5.xyz
%%PORTDOCS%%share/tinker/bench/results-2.3
%%PORTDOCS%%share/tinker/bench/results-2.4
%%PORTDOCS%%share/tinker/bench/results-2.9
@@ -131,11 +138,11 @@
%%PORTDOCS%%share/tinker/bench/results-3.5
%%PORTDOCS%%share/tinker/bench/results-3.7
%%PORTDOCS%%share/tinker/bench/results-3.8
+%%PORTDOCS%%share/tinker/bench/results-3.9
%%PORTDOCS%%share/tinker/params/README
%%PORTDOCS%%share/tinker/params/amber.prm
-%%PORTDOCS%%share/tinker/params/amberN.prm
%%PORTDOCS%%share/tinker/params/charmm.prm
-%%PORTDOCS%%share/tinker/params/emr.prm
+%%PORTDOCS%%share/tinker/params/dudek.prm
%%PORTDOCS%%share/tinker/params/hoch.prm
%%PORTDOCS%%share/tinker/params/mm2.prm
%%PORTDOCS%%share/tinker/params/mm3.prm
@@ -144,7 +151,6 @@
%%PORTDOCS%%share/tinker/params/oplsaa.prm
%%PORTDOCS%%share/tinker/params/smooth.prm
%%PORTDOCS%%share/tinker/params/smoothaa.prm
-%%PORTDOCS%%share/tinker/params/tinker.prm
%%PORTDOCS%%share/tinker/params/water.prm
%%PORTDOCS%%share/tinker/test/README
%%PORTDOCS%%share/tinker/test/ala20.key
@@ -163,10 +169,8 @@
%%PORTDOCS%%share/tinker/test/bdna.seq
%%PORTDOCS%%share/tinker/test/bdna.xyz
%%PORTDOCS%%share/tinker/test/bearing.key
-%%PORTDOCS%%share/tinker/test/bearing.pdb
%%PORTDOCS%%share/tinker/test/bearing.xyz
%%PORTDOCS%%share/tinker/test/bearing2.key
-%%PORTDOCS%%share/tinker/test/bearing2.pdb
%%PORTDOCS%%share/tinker/test/bearing2.xyz
%%PORTDOCS%%share/tinker/test/benzene.int
%%PORTDOCS%%share/tinker/test/benzene.key
@@ -208,10 +212,11 @@
%%PORTDOCS%%share/tinker/test/calmodulin.pdb
%%PORTDOCS%%share/tinker/test/calmodulin.seq
%%PORTDOCS%%share/tinker/test/calmodulin.xyz
+%%PORTDOCS%%share/tinker/test/copper.key
+%%PORTDOCS%%share/tinker/test/copper.xyz
%%PORTDOCS%%share/tinker/test/cpentene.key
%%PORTDOCS%%share/tinker/test/cpentene.xyz
%%PORTDOCS%%share/tinker/test/crambin.key
-%%PORTDOCS%%share/tinker/test/crambin.min
%%PORTDOCS%%share/tinker/test/crambin.pdb
%%PORTDOCS%%share/tinker/test/crambin.seq
%%PORTDOCS%%share/tinker/test/crambin.super
@@ -231,15 +236,15 @@
%%PORTDOCS%%share/tinker/test/cyclo2.int
%%PORTDOCS%%share/tinker/test/cyclo2.key
%%PORTDOCS%%share/tinker/test/cyclo2.xyz
+%%PORTDOCS%%share/tinker/test/dang.key
+%%PORTDOCS%%share/tinker/test/dang.xyz
+%%PORTDOCS%%share/tinker/test/diamond.key
+%%PORTDOCS%%share/tinker/test/diamond.xyz
%%PORTDOCS%%share/tinker/test/diene.int
%%PORTDOCS%%share/tinker/test/diene.key
%%PORTDOCS%%share/tinker/test/diene.xyz
%%PORTDOCS%%share/tinker/test/dimethane.key
%%PORTDOCS%%share/tinker/test/dimethane.xyz
-%%PORTDOCS%%share/tinker/test/diwater.key
-%%PORTDOCS%%share/tinker/test/diwater.lin
-%%PORTDOCS%%share/tinker/test/diwater.min
-%%PORTDOCS%%share/tinker/test/diwater.xyz
%%PORTDOCS%%share/tinker/test/enkephalin.int
%%PORTDOCS%%share/tinker/test/enkephalin.key
%%PORTDOCS%%share/tinker/test/enkephalin.make
@@ -273,8 +278,13 @@
%%PORTDOCS%%share/tinker/test/furan.xyz
%%PORTDOCS%%share/tinker/test/glucose.key
%%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/graphite.key
+%%PORTDOCS%%share/tinker/test/graphite.xyz
+%%PORTDOCS%%share/tinker/test/helix.dyn
%%PORTDOCS%%share/tinker/test/helix.key
%%PORTDOCS%%share/tinker/test/helix.xyz
+%%PORTDOCS%%share/tinker/test/heme.key
+%%PORTDOCS%%share/tinker/test/heme.xyz
%%PORTDOCS%%share/tinker/test/hexane.int
%%PORTDOCS%%share/tinker/test/hexane.key
%%PORTDOCS%%share/tinker/test/hexane.xyz
@@ -301,6 +311,7 @@
%%PORTDOCS%%share/tinker/test/methanol.xyz
%%PORTDOCS%%share/tinker/test/nacl.key
%%PORTDOCS%%share/tinker/test/nacl.xyz
+%%PORTDOCS%%share/tinker/test/naphthalene.int
%%PORTDOCS%%share/tinker/test/naphthalene.key
%%PORTDOCS%%share/tinker/test/naphthalene.xyz
%%PORTDOCS%%share/tinker/test/nma.int
@@ -320,21 +331,17 @@
%%PORTDOCS%%share/tinker/test/octane2.xyz
%%PORTDOCS%%share/tinker/test/octene.key
%%PORTDOCS%%share/tinker/test/octene.xyz
+%%PORTDOCS%%share/tinker/test/palmitate.int
%%PORTDOCS%%share/tinker/test/palmitate.key
%%PORTDOCS%%share/tinker/test/palmitate.xyz
%%PORTDOCS%%share/tinker/test/peptide.int
%%PORTDOCS%%share/tinker/test/peptide.key
%%PORTDOCS%%share/tinker/test/peptide.make
-%%PORTDOCS%%share/tinker/test/peptide.min
%%PORTDOCS%%share/tinker/test/peptide.pdb
%%PORTDOCS%%share/tinker/test/peptide.seq
%%PORTDOCS%%share/tinker/test/peptide.xyz
%%PORTDOCS%%share/tinker/test/phenanth.key
%%PORTDOCS%%share/tinker/test/phenanth.xyz
-%%PORTDOCS%%share/tinker/test/photo.key
-%%PORTDOCS%%share/tinker/test/photo.pdb
-%%PORTDOCS%%share/tinker/test/photo.seq
-%%PORTDOCS%%share/tinker/test/photo.xyz
%%PORTDOCS%%share/tinker/test/propane.key
%%PORTDOCS%%share/tinker/test/propane.ray
%%PORTDOCS%%share/tinker/test/propane.xyz
@@ -365,6 +372,10 @@
%%PORTDOCS%%share/tinker/test/thr.int
%%PORTDOCS%%share/tinker/test/thr.key
%%PORTDOCS%%share/tinker/test/thr.xyz
+%%PORTDOCS%%share/tinker/test/tip3p.key
+%%PORTDOCS%%share/tinker/test/tip3p.xyz
+%%PORTDOCS%%share/tinker/test/tip4p.key
+%%PORTDOCS%%share/tinker/test/tip4p.xyz
%%PORTDOCS%%share/tinker/test/tip5p.key
%%PORTDOCS%%share/tinker/test/tip5p.xyz
%%PORTDOCS%%share/tinker/test/water.int
diff -ruN tinker.old/pkg-plist.viewer tinker/pkg-plist.viewer
--- tinker.old/pkg-plist.viewer Wed Sep 5 13:42:06 2001
+++ tinker/pkg-plist.viewer Wed Sep 5 15:55:18 2001
@@ -22,6 +22,7 @@
bin/optrigid
bin/path
bin/pdbxyz
+bin/polarize
bin/protein
bin/pss
bin/pssrigid
@@ -40,6 +41,7 @@
bin/testrot
bin/timer
bin/timerot
+bin/tview
bin/tview-8
bin/tview-16
bin/tview-32
@@ -52,7 +54,6 @@
bin/xyzpdb
bin/xyzsybyl
%%PORTDOCS%%share/doc/tinker/README
-%%PORTDOCS%%share/doc/tinker/announce.txt
%%PORTDOCS%%share/doc/tinker/guide.pdf
%%PORTDOCS%%share/doc/tinker/guide.ps.gz
%%PORTDOCS%%share/doc/tinker/guide.txt
@@ -61,6 +62,11 @@
%%PORTDOCS%%share/doc/tinker/license.txt
%%PORTDOCS%%share/doc/tinker/logo.pdf
%%PORTDOCS%%share/doc/tinker/logo.ps.gz
+%%PORTDOCS%%share/doc/tinker/release-3.2
+%%PORTDOCS%%share/doc/tinker/release-3.6
+%%PORTDOCS%%share/doc/tinker/release-3.7
+%%PORTDOCS%%share/doc/tinker/release-3.8
+%%PORTDOCS%%share/doc/tinker/release-3.9
%%PORTDOCS%%share/doc/tinker/summary.pdf
%%PORTDOCS%%share/doc/tinker/summary.ps
%%PORTDOCS%%share/doc/tinker/summary.txt
@@ -107,24 +113,26 @@
%%PORTDOCS%%share/examples/tinker/salt.key
%%PORTDOCS%%share/examples/tinker/salt.log
%%PORTDOCS%%share/examples/tinker/salt.run
-%%PORTDOCS%%share/tinker/bench/bench-1.key
-%%PORTDOCS%%share/tinker/bench/bench-1.run
-%%PORTDOCS%%share/tinker/bench/bench-1.xyz
-%%PORTDOCS%%share/tinker/bench/bench-2.key
-%%PORTDOCS%%share/tinker/bench/bench-2.run
-%%PORTDOCS%%share/tinker/bench/bench-2.xyz
-%%PORTDOCS%%share/tinker/bench/bench-3.key
-%%PORTDOCS%%share/tinker/bench/bench-3.run
-%%PORTDOCS%%share/tinker/bench/bench-3.xyz
-%%PORTDOCS%%share/tinker/bench/bench-4.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-4.key
-%%PORTDOCS%%share/tinker/bench/bench-4.log
-%%PORTDOCS%%share/tinker/bench/bench-4.run
-%%PORTDOCS%%share/tinker/bench/bench-4.xyz
-%%PORTDOCS%%share/tinker/bench/bench-5.dyn0
-%%PORTDOCS%%share/tinker/bench/bench-5.key
-%%PORTDOCS%%share/tinker/bench/bench-5.run
-%%PORTDOCS%%share/tinker/bench/bench-5.xyz
+%%PORTDOCS%%share/tinker/bench/README
+%%PORTDOCS%%share/tinker/bench/bench1.key
+%%PORTDOCS%%share/tinker/bench/bench1.run
+%%PORTDOCS%%share/tinker/bench/bench1.xyz
+%%PORTDOCS%%share/tinker/bench/bench2.key
+%%PORTDOCS%%share/tinker/bench/bench2.run
+%%PORTDOCS%%share/tinker/bench/bench2.xyz
+%%PORTDOCS%%share/tinker/bench/bench3.key
+%%PORTDOCS%%share/tinker/bench/bench3.run
+%%PORTDOCS%%share/tinker/bench/bench3.xyz
+%%PORTDOCS%%share/tinker/bench/bench4.dyn0
+%%PORTDOCS%%share/tinker/bench/bench4.key
+%%PORTDOCS%%share/tinker/bench/bench4.log
+%%PORTDOCS%%share/tinker/bench/bench4.run
+%%PORTDOCS%%share/tinker/bench/bench4.xyz
+%%PORTDOCS%%share/tinker/bench/bench5.dyn0
+%%PORTDOCS%%share/tinker/bench/bench5.key
+%%PORTDOCS%%share/tinker/bench/bench5.log
+%%PORTDOCS%%share/tinker/bench/bench5.run
+%%PORTDOCS%%share/tinker/bench/bench5.xyz
%%PORTDOCS%%share/tinker/bench/results-2.3
%%PORTDOCS%%share/tinker/bench/results-2.4
%%PORTDOCS%%share/tinker/bench/results-2.9
@@ -134,11 +142,11 @@
%%PORTDOCS%%share/tinker/bench/results-3.5
%%PORTDOCS%%share/tinker/bench/results-3.7
%%PORTDOCS%%share/tinker/bench/results-3.8
+%%PORTDOCS%%share/tinker/bench/results-3.9
%%PORTDOCS%%share/tinker/params/README
%%PORTDOCS%%share/tinker/params/amber.prm
-%%PORTDOCS%%share/tinker/params/amberN.prm
%%PORTDOCS%%share/tinker/params/charmm.prm
-%%PORTDOCS%%share/tinker/params/emr.prm
+%%PORTDOCS%%share/tinker/params/dudek.prm
%%PORTDOCS%%share/tinker/params/hoch.prm
%%PORTDOCS%%share/tinker/params/mm2.prm
%%PORTDOCS%%share/tinker/params/mm3.prm
@@ -147,7 +155,6 @@
%%PORTDOCS%%share/tinker/params/oplsaa.prm
%%PORTDOCS%%share/tinker/params/smooth.prm
%%PORTDOCS%%share/tinker/params/smoothaa.prm
-%%PORTDOCS%%share/tinker/params/tinker.prm
%%PORTDOCS%%share/tinker/params/water.prm
%%PORTDOCS%%share/tinker/rasmol/rasmol.hlp
%%PORTDOCS%%share/tinker/test/README
@@ -167,10 +174,8 @@
%%PORTDOCS%%share/tinker/test/bdna.seq
%%PORTDOCS%%share/tinker/test/bdna.xyz
%%PORTDOCS%%share/tinker/test/bearing.key
-%%PORTDOCS%%share/tinker/test/bearing.pdb
%%PORTDOCS%%share/tinker/test/bearing.xyz
%%PORTDOCS%%share/tinker/test/bearing2.key
-%%PORTDOCS%%share/tinker/test/bearing2.pdb
%%PORTDOCS%%share/tinker/test/bearing2.xyz
%%PORTDOCS%%share/tinker/test/benzene.int
%%PORTDOCS%%share/tinker/test/benzene.key
@@ -212,10 +217,11 @@
%%PORTDOCS%%share/tinker/test/calmodulin.pdb
%%PORTDOCS%%share/tinker/test/calmodulin.seq
%%PORTDOCS%%share/tinker/test/calmodulin.xyz
+%%PORTDOCS%%share/tinker/test/copper.key
+%%PORTDOCS%%share/tinker/test/copper.xyz
%%PORTDOCS%%share/tinker/test/cpentene.key
%%PORTDOCS%%share/tinker/test/cpentene.xyz
%%PORTDOCS%%share/tinker/test/crambin.key
-%%PORTDOCS%%share/tinker/test/crambin.min
%%PORTDOCS%%share/tinker/test/crambin.pdb
%%PORTDOCS%%share/tinker/test/crambin.seq
%%PORTDOCS%%share/tinker/test/crambin.super
@@ -235,15 +241,15 @@
%%PORTDOCS%%share/tinker/test/cyclo2.int
%%PORTDOCS%%share/tinker/test/cyclo2.key
%%PORTDOCS%%share/tinker/test/cyclo2.xyz
+%%PORTDOCS%%share/tinker/test/dang.key
+%%PORTDOCS%%share/tinker/test/dang.xyz
+%%PORTDOCS%%share/tinker/test/diamond.key
+%%PORTDOCS%%share/tinker/test/diamond.xyz
%%PORTDOCS%%share/tinker/test/diene.int
%%PORTDOCS%%share/tinker/test/diene.key
%%PORTDOCS%%share/tinker/test/diene.xyz
%%PORTDOCS%%share/tinker/test/dimethane.key
%%PORTDOCS%%share/tinker/test/dimethane.xyz
-%%PORTDOCS%%share/tinker/test/diwater.key
-%%PORTDOCS%%share/tinker/test/diwater.lin
-%%PORTDOCS%%share/tinker/test/diwater.min
-%%PORTDOCS%%share/tinker/test/diwater.xyz
%%PORTDOCS%%share/tinker/test/enkephalin.int
%%PORTDOCS%%share/tinker/test/enkephalin.key
%%PORTDOCS%%share/tinker/test/enkephalin.make
@@ -277,8 +283,13 @@
%%PORTDOCS%%share/tinker/test/furan.xyz
%%PORTDOCS%%share/tinker/test/glucose.key
%%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/graphite.key
+%%PORTDOCS%%share/tinker/test/graphite.xyz
+%%PORTDOCS%%share/tinker/test/helix.dyn
%%PORTDOCS%%share/tinker/test/helix.key
%%PORTDOCS%%share/tinker/test/helix.xyz
+%%PORTDOCS%%share/tinker/test/heme.key
+%%PORTDOCS%%share/tinker/test/heme.xyz
%%PORTDOCS%%share/tinker/test/hexane.int
%%PORTDOCS%%share/tinker/test/hexane.key
%%PORTDOCS%%share/tinker/test/hexane.xyz
@@ -305,6 +316,7 @@
%%PORTDOCS%%share/tinker/test/methanol.xyz
%%PORTDOCS%%share/tinker/test/nacl.key
%%PORTDOCS%%share/tinker/test/nacl.xyz
+%%PORTDOCS%%share/tinker/test/naphthalene.int
%%PORTDOCS%%share/tinker/test/naphthalene.key
%%PORTDOCS%%share/tinker/test/naphthalene.xyz
%%PORTDOCS%%share/tinker/test/nma.int
@@ -324,21 +336,17 @@
%%PORTDOCS%%share/tinker/test/octane2.xyz
%%PORTDOCS%%share/tinker/test/octene.key
%%PORTDOCS%%share/tinker/test/octene.xyz
+%%PORTDOCS%%share/tinker/test/palmitate.int
%%PORTDOCS%%share/tinker/test/palmitate.key
%%PORTDOCS%%share/tinker/test/palmitate.xyz
%%PORTDOCS%%share/tinker/test/peptide.int
%%PORTDOCS%%share/tinker/test/peptide.key
%%PORTDOCS%%share/tinker/test/peptide.make
-%%PORTDOCS%%share/tinker/test/peptide.min
%%PORTDOCS%%share/tinker/test/peptide.pdb
%%PORTDOCS%%share/tinker/test/peptide.seq
%%PORTDOCS%%share/tinker/test/peptide.xyz
%%PORTDOCS%%share/tinker/test/phenanth.key
%%PORTDOCS%%share/tinker/test/phenanth.xyz
-%%PORTDOCS%%share/tinker/test/photo.key
-%%PORTDOCS%%share/tinker/test/photo.pdb
-%%PORTDOCS%%share/tinker/test/photo.seq
-%%PORTDOCS%%share/tinker/test/photo.xyz
%%PORTDOCS%%share/tinker/test/propane.key
%%PORTDOCS%%share/tinker/test/propane.ray
%%PORTDOCS%%share/tinker/test/propane.xyz
@@ -369,6 +377,10 @@
%%PORTDOCS%%share/tinker/test/thr.int
%%PORTDOCS%%share/tinker/test/thr.key
%%PORTDOCS%%share/tinker/test/thr.xyz
+%%PORTDOCS%%share/tinker/test/tip3p.key
+%%PORTDOCS%%share/tinker/test/tip3p.xyz
+%%PORTDOCS%%share/tinker/test/tip4p.key
+%%PORTDOCS%%share/tinker/test/tip4p.xyz
%%PORTDOCS%%share/tinker/test/tip5p.key
%%PORTDOCS%%share/tinker/test/tip5p.xyz
%%PORTDOCS%%share/tinker/test/water.int
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