ports/154359: [UPDATE] biology/tinker: update to 5.1.09
Ruslan Mahmatkhanov
cvs-src at yandex.ru
Fri Jan 28 18:20:10 UTC 2011
>Number: 154359
>Category: ports
>Synopsis: [UPDATE] biology/tinker: update to 5.1.09
>Confidential: no
>Severity: non-critical
>Priority: low
>Responsible: freebsd-ports-bugs
>State: open
>Quarter:
>Keywords:
>Date-Required:
>Class: update
>Submitter-Id: current-users
>Arrival-Date: Fri Jan 28 18:20:09 UTC 2011
>Closed-Date:
>Last-Modified:
>Originator: Ruslan Mahmatkhanov
>Release: 8.2-PRERELEASE
>Organization:
>Environment:
8.2-PRERELEASE i386
>Description:
- update to 5.1.09
- remove stale mirrors
- remove WITH_VIEWER Makefile option and related files, because gui support was dropped upstream
- remove md5
It was reported to work fine by Joseph Maxwell <jaymax36 at gmail dot com>, who originally requested this update there:
http://lists.freebsd.org/pipermail/freebsd-ports/2011-January/065487.html
>How-To-Repeat:
>Fix:
Patch attached with submission follows:
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 at 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
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@@ -138,6 +450,14 @@
%%PORTDOCS%%%%DATADIR%%/bench/bench5.log
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@@ -151,17 +471,24 @@
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-%%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
- at dirrm %%DATADIR%%/params
-%%WITH_VIEWER%%@dirrm %%DATADIR%%/rasmol
%%PORTDOCS%%@dirrm %%DATADIR%%/test
+ at 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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