From dfd533edaacdf98679630eda21b8aa4fbcb798cd Mon Sep 17 00:00:00 2001 From: Mario Sergio Fujikawa Ferreira Date: Thu, 13 Sep 2001 01:13:52 +0000 Subject: [PATCH] Update to 3.9 PR: 30398 Submitted by: MAINTAINER --- biology/tinker/Makefile | 24 +++++++--- biology/tinker/distinfo | 2 +- biology/tinker/files/patch-aa | 12 ++--- biology/tinker/files/patch-ag | 11 ----- biology/tinker/files/patch-ah | 8 ++-- biology/tinker/files/patch-ai | 8 ++-- biology/tinker/files/patch-aj | 8 ++-- biology/tinker/files/patch-ak | 12 ++--- biology/tinker/files/patch-al | 12 ++--- biology/tinker/files/tview | 21 +++++++++ biology/tinker/pkg-plist | 79 ++++++++++++++++++-------------- biology/tinker/pkg-plist.viewer | 80 +++++++++++++++++++-------------- 12 files changed, 161 insertions(+), 116 deletions(-) delete mode 100644 biology/tinker/files/patch-ag create mode 100644 biology/tinker/files/tview diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile index 98cf283d0b09..8430abc675ae 100644 --- a/biology/tinker/Makefile +++ b/biology/tinker/Makefile @@ -6,8 +6,7 @@ # PORTNAME= tinker -PORTVERSION= 3.8 -PORTREVISION= 1 +PORTVERSION= 3.9 CATEGORIES= biology MASTER_SITES= ftp://dasher.wustl.edu/pub/ DISTNAME= ${PORTNAME} @@ -24,6 +23,11 @@ INSTALL_TARGET= rename RESTRICTED= author requests no distribution except from his FTP site +pre-fetch: + @${ECHO_MSG} "" + @${ECHO_MSG} If you get a CHECKSUM mismatch, try doing a \'make distclean\' first. + @${ECHO_MSG} "" + .if defined(WANT_VIEWER) .if ${XFREE86_VERSION} == 3 BUILD_DEPENDS+= imake:${PORTSDIR}/devel/imake @@ -64,8 +68,12 @@ ${PREFIX}/share/doc/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.ps \ ${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 @@ -86,22 +94,22 @@ ${PREFIX}/share/examples/tinker ${INSTALL_DATA} ${WRKDIR}/tinker/example/*.pdb \ ${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 @@ -109,7 +117,9 @@ ${PREFIX}/share/tinker/bench .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 --git a/biology/tinker/distinfo b/biology/tinker/distinfo index a22df5355677..3d11520fdd4f 100644 --- a/biology/tinker/distinfo +++ b/biology/tinker/distinfo @@ -1 +1 @@ -MD5 (tinker.tar.gz) = 11e66fb5452e2153a2ced410ea9acadb +MD5 (tinker.tar.gz) = a48fc15fe668f8e41d0cc3316a582928 diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa index c12a46cb6f62..e9cf0c948aaf 100644 --- a/biology/tinker/files/patch-aa +++ b/biology/tinker/files/patch-aa @@ -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 --git a/biology/tinker/files/patch-ag b/biology/tinker/files/patch-ag deleted file mode 100644 index a1084876fe7d..000000000000 --- a/biology/tinker/files/patch-ag +++ /dev/null @@ -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 --git a/biology/tinker/files/patch-ah b/biology/tinker/files/patch-ah index c3f23dd2e057..12bd7c9ac00d 100644 --- a/biology/tinker/files/patch-ah +++ b/biology/tinker/files/patch-ah @@ -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 --git a/biology/tinker/files/patch-ai b/biology/tinker/files/patch-ai index 643cc82de1ed..e5a6559bb29f 100644 --- a/biology/tinker/files/patch-ai +++ b/biology/tinker/files/patch-ai @@ -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 --git a/biology/tinker/files/patch-aj b/biology/tinker/files/patch-aj index 1f36c30fe172..3e18d09b5071 100644 --- a/biology/tinker/files/patch-aj +++ b/biology/tinker/files/patch-aj @@ -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 --git a/biology/tinker/files/patch-ak b/biology/tinker/files/patch-ak index d0549d42829d..9a415fcd0f32 100644 --- a/biology/tinker/files/patch-ak +++ b/biology/tinker/files/patch-ak @@ -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 --git a/biology/tinker/files/patch-al b/biology/tinker/files/patch-al index 8127254d2daa..e85fd419c12f 100644 --- a/biology/tinker/files/patch-al +++ b/biology/tinker/files/patch-al @@ -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 --git a/biology/tinker/files/tview b/biology/tinker/files/tview new file mode 100644 index 000000000000..834dd72ba166 --- /dev/null +++ b/biology/tinker/files/tview @@ -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 --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist index afba39f57dc1..fab9edbff2ef 100644 --- a/biology/tinker/pkg-plist +++ b/biology/tinker/pkg-plist @@ -22,6 +22,7 @@ bin/optirot bin/optrigid bin/path bin/pdbxyz +bin/polarize bin/protein bin/pss bin/pssrigid @@ -49,7 +50,6 @@ bin/xyzint 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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 --git a/biology/tinker/pkg-plist.viewer b/biology/tinker/pkg-plist.viewer index d1d741483e17..851a2eccc975 100644 --- a/biology/tinker/pkg-plist.viewer +++ b/biology/tinker/pkg-plist.viewer @@ -22,6 +22,7 @@ bin/optirot bin/optrigid bin/path bin/pdbxyz +bin/polarize bin/protein bin/pss bin/pssrigid @@ -40,6 +41,7 @@ bin/testlight bin/testrot bin/timer bin/timerot +bin/tview bin/tview-8 bin/tview-16 bin/tview-32 @@ -52,7 +54,6 @@ bin/xyzint 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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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 @@ bin/xyzsybyl %%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