From owner-freebsd-ports Thu Sep 6 8:20:39 2001 Delivered-To: freebsd-ports@hub.freebsd.org Received: from freefall.freebsd.org (freefall.freebsd.org [216.136.204.21]) by hub.freebsd.org (Postfix) with ESMTP id BC87D37B40B for ; Thu, 6 Sep 2001 08:20:01 -0700 (PDT) Received: (from gnats@localhost) by freefall.freebsd.org (8.11.4/8.11.4) id f86FK1D16872; Thu, 6 Sep 2001 08:20:01 -0700 (PDT) (envelope-from gnats) Received: from symbion.srrc.usda.gov (symbion.srrc.usda.gov [199.133.86.40]) by hub.freebsd.org (Postfix) with ESMTP id 84A7F37B406 for ; Thu, 6 Sep 2001 08:11:51 -0700 (PDT) Received: from node7.cluster.srrc.usda.gov (node7.cluster.srrc.usda.gov [192.168.1.7]) by symbion.srrc.usda.gov (8.11.6/8.11.6) with ESMTP id f86FBo707541 for ; Thu, 6 Sep 2001 10:11:50 -0500 (CDT) (envelope-from gjohnson@srrc.ars.usda.gov) Received: (from glenn@localhost) by node7.cluster.srrc.usda.gov (8.11.6/8.11.6) id f86FBns99430; Thu, 6 Sep 2001 10:11:49 -0500 (CDT) (envelope-from glenn) Message-Id: <200109061511.f86FBns99430@node7.cluster.srrc.usda.gov> Date: Thu, 6 Sep 2001 10:11:49 -0500 (CDT) From: Glenn Johnson Reply-To: Glenn Johnson To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.113 Subject: ports/30398: update of ports/biology/tinker Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk List-ID: List-Archive: (Web Archive) List-Help: (List Instructions) List-Subscribe: List-Unsubscribe: X-Loop: FreeBSD.org >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 >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to 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