From owner-freebsd-ports Sat Jun 19 20:20:13 1999 Delivered-To: freebsd-ports@freebsd.org Received: from freefall.freebsd.org (freefall.FreeBSD.ORG [204.216.27.21]) by hub.freebsd.org (Postfix) with ESMTP id 50F6A14CE5 for ; Sat, 19 Jun 1999 20:20:02 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: (from gnats@localhost) by freefall.freebsd.org (8.9.3/8.9.2) id UAA50377; Sat, 19 Jun 1999 20:20:01 -0700 (PDT) (envelope-from gnats@FreeBSD.org) Received: from mail2.lig.bellsouth.net (mail2.lig.bellsouth.net [205.152.0.56]) by hub.freebsd.org (Postfix) with ESMTP id 9F9EF14BF5 for ; Sat, 19 Jun 1999 20:13:34 -0700 (PDT) (envelope-from gljohns@bellsouth.net) Received: from gforce.johnson.home (host-209-214-148-27.msy.bellsouth.net [209.214.148.27]) by mail2.lig.bellsouth.net (8.8.8-spamdog/8.8.5) with ESMTP id XAA05312 for ; Sat, 19 Jun 1999 23:13:21 -0400 (EDT) Received: (from glenn@localhost) by gforce.johnson.home (8.9.3/8.9.3) id WAA75960; Sat, 19 Jun 1999 22:13:16 -0500 (CDT) (envelope-from glenn) Message-Id: <199906200313.WAA75960@gforce.johnson.home> Date: Sat, 19 Jun 1999 22:13:16 -0500 (CDT) From: gljohns@bellsouth.net To: FreeBSD-gnats-submit@freebsd.org X-Send-Pr-Version: 3.2 Subject: ports/12301: Update of Tinker Sender: owner-freebsd-ports@FreeBSD.ORG Precedence: bulk X-Loop: FreeBSD.org >Number: 12301 >Category: ports >Synopsis: Update of biology/tinker from 3.6 to 3.7 >Confidential: no >Severity: serious >Priority: medium >Responsible: freebsd-ports >State: open >Quarter: >Keywords: >Date-Required: >Class: change-request >Submitter-Id: current-users >Arrival-Date: Sat Jun 19 20:20:00 PDT 1999 >Closed-Date: >Last-Modified: >Originator: Glenn Johnson >Release: FreeBSD 3.2-STABLE i386 >Organization: >Environment: I have tested this with f77 in FreeBSD-3.2 and g77 from the EGCS port. >Description: This updates biology/tinker from version 3.6 to version 3.7 >How-To-Repeat: >Fix: Apply the enclosed diff to $PORTS/biology/tinker, and remove the resulting *.orig files. diff -ruN tinker.old/Makefile tinker/Makefile --- tinker.old/Makefile Fri Jun 18 21:54:27 1999 +++ tinker/Makefile Sat Jun 19 21:53:34 1999 @@ -1,5 +1,5 @@ # New ports collection makefile for: tinker -# Version required: 3.6 +# Version required: 3.7 # Date Created: 26 August 1998 # Whom: Glenn Johnson # @@ -7,7 +7,7 @@ # DISTNAME= tinker -PKGNAME= tinker-3.6 +PKGNAME= tinker-3.7 CATEGORIES= biology MASTER_SITES= ftp://dasher.wustl.edu/pub/ @@ -18,10 +18,13 @@ .if ${OSVERSION} < 400005 LIB_DEPENDS= U77:${PORTSDIR}/devel/libU77 -# If you have EGCS installed and wish to use it, do the following: +# If you wish to use g77 from EGCS, do the following: # a) comment out the LIB_DEPENDS line above and uncomment the following line -#BUILD_DEPENDS= g77:${PORTSDIR}/lang/egcs -# b) set env variable 'FC' to 'g77' before running `make' + +# BUILD_DEPENDS= g77:${PORTSDIR}/lang/egcs + +# b) set env variable 'FC' to 'g77' before running `make'; or 'make FC=g77' + .else MAKE_ENV+= HAVE_G2C=yes .endif @@ -35,11 +38,12 @@ RESTRICTED= author requests no distribution except from his FTP site post-install: + ${MKDIR} ${PREFIX}/share/tinker ${MKDIR} ${PREFIX}/share/tinker/params - ${INSTALL_DATA} ${WRKDIR}/tinker/params/* \ -${PREFIX}/share/tinker/params ${INSTALL_DATA} ${WRKDIR}/tinker/source/tinker.txt \ ${PREFIX}/share/tinker + ${INSTALL_DATA} ${WRKDIR}/tinker/params/* \ +${PREFIX}/share/tinker/params .if !defined(NOPORTDOCS) ${MKDIR} ${PREFIX}/share/tinker/doc ${MKDIR} ${PREFIX}/share/tinker/example @@ -47,6 +51,8 @@ ${MKDIR} ${PREFIX}/share/tinker/test ${INSTALL_DATA} ${WRKDIR}/tinker/doc/README \ ${PREFIX}/share/tinker/doc + ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.pdf \ +${PREFIX}/share/tinker/doc ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.ps \ ${PREFIX}/share/tinker/doc ${INSTALL_DATA} ${WRKDIR}/tinker/doc/*.Z \ @@ -96,7 +102,7 @@ @${ECHO} "" @${ECHO} " **********************************************************" @${ECHO} " The author requests that you return a license form " - @${ECHO} " to him if you find Tinker to be useful. " + @${ECHO} " to him if you find Tinker to be useful. " @${ECHO} " " @${ECHO} " See ${PREFIX}/share/tinker/doc for license forms. " @${ECHO} " **********************************************************" diff -ruN tinker.old/README.html tinker/README.html --- tinker.old/README.html Fri Jun 18 21:54:27 1999 +++ tinker/README.html Sat Jun 19 21:50:10 1999 @@ -3,7 +3,7 @@

The FreeBSD Ports Collection ("biology/tinker")

-

You are now in the directory for the port "biology/tinker" (package name "tinker-3.6"). +

You are now in the directory for the port "biology/tinker" (package name "tinker-3.7").

This is the one-line description for this port: @@ -18,9 +18,9 @@ a summary on how to use the ports collection.

-This port requires package(s) "libU77-2.6" to build. +This port requires package(s) "" to build.

-This port requires package(s) "libU77-2.6" to run. +This port requires package(s) "" to run.

Go up one level diff -ruN tinker.old/files/md5 tinker/files/md5 --- tinker.old/files/md5 Fri Jun 18 21:54:27 1999 +++ tinker/files/md5 Sat Jun 19 21:50:10 1999 @@ -1 +1 @@ -MD5 (tinker.tar.gz) = 9b21715ee725eddbcd750a1d0f5836b4 +MD5 (tinker.tar.gz) = 00a14152f016a0e2f0abc1e459d1a792 diff -ruN tinker.old/patches/patch-aa tinker/patches/patch-aa --- tinker.old/patches/patch-aa Fri Jun 18 21:54:27 1999 +++ tinker/patches/patch-aa Sat Jun 19 21:50:10 1999 @@ -1,225 +1,191 @@ -*** ../make/Makefile.orig Sat Apr 11 11:38:14 1998 ---- ../make/Makefile Sat May 22 15:08:09 1999 -*************** -*** 9,16 **** - ## - ## 1. make all Build all the TINKER executables - ## 2. make rename Move the executables to BINDIR -! ## 3. make remove_links Create soft links in LINKDIR -! ## 4. make create_links Remove soft links from LINKDIR - ## 6. make listing Concatenate source to tinker.txt - ## 5. make clean Delete objects and executables - ## ---- 9,16 ---- - ## - ## 1. make all Build all the TINKER executables - ## 2. make rename Move the executables to BINDIR -! ## 3. make remove_links Remove soft links in LINKDIR -! ## 4. make create_links Create soft links from LINKDIR - ## 6. make listing Concatenate source to tinker.txt - ## 5. make clean Delete objects and executables - ## -*************** -*** 30,38 **** - ## LINKDIR Linked Copies of TINKER Executables - ## - -! TINKERDIR = /user/ponder/tinker -! BINDIR = $(TINKERDIR)/bin -! LINKDIR = /usr/local/bin - - #################################################################### - ## Known Machine Types; Uncomment One of the Following Sections ## ---- 30,38 ---- - ## LINKDIR Linked Copies of TINKER Executables - ## - -! TINKERDIR = ${WRKDIR} -! BINDIR = ${PREFIX}/bin -! #LINKDIR = /usr/local/bin - - #################################################################### - ## Known Machine Types; Uncomment One of the Following Sections ## -*************** -*** 45,57 **** - ## Compiler: DEC Fortran 77/90, V4.1 - ## - -! F77 = /usr/bin/f77 -! RM = /sbin/rm -! LIBS = -! F77FLAGS = -c -! OPTFLAGS = -fast -tune host -! LIBFLAGS = -rlv -! LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched - - ## - ## Machine: Silicon Graphics ---- 45,57 ---- - ## Compiler: DEC Fortran 77/90, V4.1 - ## - -! #F77 = /usr/bin/f77 -! #RM = /sbin/rm -! #LIBS = -! #F77FLAGS = -c -! #OPTFLAGS = -fast -tune host -! #LIBFLAGS = -rlv -! #LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched - - ## - ## Machine: Silicon Graphics -*************** -*** 104,109 **** ---- 104,141 ---- - #diagq.o: - # ${F77} ${F77FLAGS} -ffast-math diagq.f - -+ ## -+ ## Machine: IntelPC -+ ## CPU Type: Pentium Pro -+ ## Oper Sys: FreeBSD 3.0 -+ ## Compiler: f77(f2c/gcc version 2.7.2.1) || egcs g77 -+ ## -+ -+ F77 = ${FC} -+ RM = /bin/rm -+ -+ .if ${FC}==f77 -+ .if !defined(HAVE_G2C) -+ LIBS = -lU77 -+ .else -+ LIBS = -lg2c -+ .endif -+ F77FLAGS = -NL400 -c -+ LINKFLAGS = -L${PREFIX}/lib -+ .elseif ${FC}==g77 -+ LIBS= -+ F77FLAGS = -Wno-globals -fno-globals -c -+ LINKFLAGS = -+ .endif -+ -+ OPTFLAGS = ${FFLAGS} -ffast-math -+ .if ${MACHINE_ARCH} == "i386" -+ OPTFLAGS+= -malign-double -+ .endif -+ LIBFLAGS = -rcuv -+ diagq.o: -+ ${F77} ${F77FLAGS} -ffast-math diagq.f -+ - ################################################################# - ## Should not be Necessary to Change Things Below this Point ## - ################################################################# -*************** -*** 766,771 **** ---- 798,804 ---- - volume2.o \ - writeout.o \ - xyzatm.o -+ ranlib libtinker.a - - alchemy.x: - ${F77} ${LINKFLAGS} -o alchemy.x alchemy.o libtinker.a ${LIBS} -*************** -*** 857,906 **** - ${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS} - - rename: -! mv alchemy.x $(BINDIR)/alchemy -! mv analyze.x $(BINDIR)/analyze -! mv anneal.x $(BINDIR)/anneal -! mv archive.x $(BINDIR)/archive -! mv correlate.x $(BINDIR)/correlate -! mv crystal.x $(BINDIR)/crystal -! mv distgeom.x $(BINDIR)/distgeom -! mv document.x $(BINDIR)/document -! mv dynamic.x $(BINDIR)/dynamic -! mv gda.x $(BINDIR)/gda -! mv intedit.x $(BINDIR)/intedit -! mv intxyz.x $(BINDIR)/intxyz -! mv minimize.x $(BINDIR)/minimize -! mv minirot.x $(BINDIR)/minirot -! mv newton.x $(BINDIR)/newton -! mv newtrot.x $(BINDIR)/newtrot -! mv optimize.x $(BINDIR)/optimize -! mv optirot.x $(BINDIR)/optirot -! mv optrigid.x $(BINDIR)/optrigid -! mv path.x $(BINDIR)/path -! mv pdbxyz.x $(BINDIR)/pdbxyz -! mv protein.x $(BINDIR)/protein -! mv pss.x $(BINDIR)/pss -! mv pssrigid.x $(BINDIR)/pssrigid -! mv pssrot.x $(BINDIR)/pssrot -! mv saddle.x $(BINDIR)/saddle -! mv sniffer.x $(BINDIR)/sniffer -! mv spacefill.x $(BINDIR)/spacefill -! mv superpose.x $(BINDIR)/superpose -! mv sybylxyz.x $(BINDIR)/sybylxyz -! mv testgrad.x $(BINDIR)/testgrad -! mv testhess.x $(BINDIR)/testhess -! mv testlight.x $(BINDIR)/testlight -! mv testrot.x $(BINDIR)/testrot -! mv timer.x $(BINDIR)/timer -! mv timerot.x $(BINDIR)/timerot -! mv vibrate.x $(BINDIR)/vibrate -! mv vibrot.x $(BINDIR)/vibrot -! mv xtalfit.x $(BINDIR)/xtalfit -! mv xtalmin.x $(BINDIR)/xtalmin -! mv xyzedit.x $(BINDIR)/xyzedit -! mv xyzint.x $(BINDIR)/xyzint -! mv xyzpdb.x $(BINDIR)/xyzpdb -! mv xyzsybyl.x $(BINDIR)/xyzsybyl - - remove_links: - rm -f $(LINKDIR)/alchemy ---- 890,939 ---- - ${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS} - - rename: -! ${INSTALL} -s alchemy.x $(BINDIR)/alchemy -! ${INSTALL} -s analyze.x $(BINDIR)/analyze -! ${INSTALL} -s anneal.x $(BINDIR)/anneal -! ${INSTALL} -s archive.x $(BINDIR)/archive -! ${INSTALL} -s correlate.x $(BINDIR)/correlate -! ${INSTALL} -s crystal.x $(BINDIR)/crystal -! ${INSTALL} -s distgeom.x $(BINDIR)/distgeom -! ${INSTALL} -s document.x $(BINDIR)/document -! ${INSTALL} -s dynamic.x $(BINDIR)/dynamic -! ${INSTALL} -s gda.x $(BINDIR)/gda -! ${INSTALL} -s intedit.x $(BINDIR)/intedit -! ${INSTALL} -s intxyz.x $(BINDIR)/intxyz -! ${INSTALL} -s minimize.x $(BINDIR)/minimize -! ${INSTALL} -s minirot.x $(BINDIR)/minirot -! ${INSTALL} -s newton.x $(BINDIR)/newton -! ${INSTALL} -s newtrot.x $(BINDIR)/newtrot -! ${INSTALL} -s optimize.x $(BINDIR)/optimize -! ${INSTALL} -s optirot.x $(BINDIR)/optirot -! ${INSTALL} -s optrigid.x $(BINDIR)/optrigid -! ${INSTALL} -s path.x $(BINDIR)/path -! ${INSTALL} -s pdbxyz.x $(BINDIR)/pdbxyz -! ${INSTALL} -s protein.x $(BINDIR)/protein -! ${INSTALL} -s pss.x $(BINDIR)/pss -! ${INSTALL} -s pssrigid.x $(BINDIR)/pssrigid -! ${INSTALL} -s pssrot.x $(BINDIR)/pssrot -! ${INSTALL} -s saddle.x $(BINDIR)/saddle -! ${INSTALL} -s sniffer.x $(BINDIR)/sniffer -! ${INSTALL} -s spacefill.x $(BINDIR)/spacefill -! ${INSTALL} -s superpose.x $(BINDIR)/superpose -! ${INSTALL} -s sybylxyz.x $(BINDIR)/sybylxyz -! ${INSTALL} -s testgrad.x $(BINDIR)/testgrad -! ${INSTALL} -s testhess.x $(BINDIR)/testhess -! ${INSTALL} -s testlight.x $(BINDIR)/testlight -! ${INSTALL} -s testrot.x $(BINDIR)/testrot -! ${INSTALL} -s timer.x $(BINDIR)/timer -! ${INSTALL} -s timerot.x $(BINDIR)/timerot -! ${INSTALL} -s vibrate.x $(BINDIR)/vibrate -! ${INSTALL} -s vibrot.x $(BINDIR)/vibrot -! ${INSTALL} -s xtalfit.x $(BINDIR)/xtalfit -! ${INSTALL} -s xtalmin.x $(BINDIR)/xtalmin -! ${INSTALL} -s xyzedit.x $(BINDIR)/xyzedit -! ${INSTALL} -s xyzint.x $(BINDIR)/xyzint -! ${INSTALL} -s xyzpdb.x $(BINDIR)/xyzpdb -! ${INSTALL} -s xyzsybyl.x $(BINDIR)/xyzsybyl - - remove_links: - rm -f $(LINKDIR)/alchemy +--- ../make/Makefile.orig Mon Jun 14 10:23:04 1999 ++++ ../make/Makefile Sat Jun 19 14:15:27 1999 +@@ -9,8 +9,8 @@ + ## + ## 1. make all Build all the TINKER executables + ## 2. make rename Move the executables to BINDIR +-## 3. make remove_links Create soft links in LINKDIR +-## 4. make create_links Remove soft links from LINKDIR ++## 3. make remove_links Remove soft links in LINKDIR ++## 4. make create_links Create soft links from LINKDIR + ## 6. make listing Concatenate source to tinker.txt + ## 5. make clean Delete objects and executables + ## +@@ -30,9 +30,9 @@ + ## LINKDIR Linked Copies of TINKER Executables + ## + +-TINKERDIR = /user/ponder/tinker +-BINDIR = $(TINKERDIR)/bin +-LINKDIR = /usr/local/bin ++TINKERDIR = ${WRKDIR} ++BINDIR = ${PREFIX}/bin ++#LINKDIR = /usr/local/bin + + #################################################################### + ## Known Machine Types; Uncomment One of the Following Sections ## +@@ -45,13 +45,13 @@ + ## Compiler: DEC Fortran 77/90, V4.1 + ## + +-F77 = /usr/bin/f77 +-RM = /sbin/rm +-LIBS = +-F77FLAGS = -c +-OPTFLAGS = -fast -tune host +-LIBFLAGS = -rlv +-LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched ++#F77 = /usr/bin/f77 ++#RM = /sbin/rm ++#LIBS = ++#F77FLAGS = -c ++#OPTFLAGS = -fast -tune host ++#LIBFLAGS = -rlv ++#LINKFLAGS = -fast -non_shared -om -WL,-om_no_inst_sched + + ## + ## Machine: Silicon Graphics +@@ -104,6 +104,38 @@ + #diagq.o: + # ${F77} ${F77FLAGS} -ffast-math diagq.f + ++## ++## Machine: IntelPC ++## CPU Type: Pentium Pro ++## Oper Sys: FreeBSD 3.0 ++## Compiler: f77(f2c/gcc version 2.7.2.1) || egcs g77 ++## ++ ++F77 = ${FC} ++RM = /bin/rm ++ ++.if ${FC}==f77 ++.if !defined(HAVE_G2C) ++LIBS = -lU77 ++.else ++LIBS = -lg2c ++.endif ++F77FLAGS = -NL400 -c ++LINKFLAGS = -L${PREFIX}/lib ++.elseif ${FC}==g77 ++LIBS= ++F77FLAGS = -Wno-globals -fno-globals -c ++LINKFLAGS = ++.endif ++ ++OPTFLAGS = ${FFLAGS} -ffast-math ++.if ${MACHINE_ARCH} == "i386" ++OPTFLAGS+= -malign-double ++.endif ++LIBFLAGS = -rcuv ++diagq.o: ++ ${F77} ${F77FLAGS} -ffast-math diagq.f ++ + ################################################################# + ## Should not be Necessary to Change Things Below this Point ## + ################################################################# +@@ -765,6 +797,7 @@ + volume2.o \ + writeout.o \ + xyzatm.o ++ ranlib libtinker.a + + alchemy.x: + ${F77} ${LINKFLAGS} -o alchemy.x alchemy.o libtinker.a ${LIBS} +@@ -858,51 +891,51 @@ + ${F77} ${LINKFLAGS} -o xyzsybyl.x xyzsybyl.o libtinker.a ${LIBS} + + rename: +- mv alchemy.x $(BINDIR)/alchemy +- mv analyze.x $(BINDIR)/analyze +- mv anneal.x $(BINDIR)/anneal +- mv archive.x $(BINDIR)/archive +- mv correlate.x $(BINDIR)/correlate +- mv crystal.x $(BINDIR)/crystal +- mv distgeom.x $(BINDIR)/distgeom +- mv document.x $(BINDIR)/document +- mv dynamic.x $(BINDIR)/dynamic +- mv gda.x $(BINDIR)/gda +- mv intedit.x $(BINDIR)/intedit +- mv intxyz.x $(BINDIR)/intxyz +- mv minimize.x $(BINDIR)/minimize +- mv minirot.x $(BINDIR)/minirot +- mv newton.x $(BINDIR)/newton +- mv newtrot.x $(BINDIR)/newtrot +- mv optimize.x $(BINDIR)/optimize +- mv optirot.x $(BINDIR)/optirot +- mv optrigid.x $(BINDIR)/optrigid +- mv path.x $(BINDIR)/path +- mv pdbxyz.x $(BINDIR)/pdbxyz +- mv protein.x $(BINDIR)/protein +- mv pss.x $(BINDIR)/pss +- mv pssrigid.x $(BINDIR)/pssrigid +- mv pssrot.x $(BINDIR)/pssrot +- mv saddle.x $(BINDIR)/saddle +- mv scan.x $(BINDIR)/scan +- mv sniffer.x $(BINDIR)/sniffer +- mv spacefill.x $(BINDIR)/spacefill +- mv superpose.x $(BINDIR)/superpose +- mv sybylxyz.x $(BINDIR)/sybylxyz +- mv testgrad.x $(BINDIR)/testgrad +- mv testhess.x $(BINDIR)/testhess +- mv testlight.x $(BINDIR)/testlight +- mv testrot.x $(BINDIR)/testrot +- mv timer.x $(BINDIR)/timer +- mv timerot.x $(BINDIR)/timerot +- mv vibrate.x $(BINDIR)/vibrate +- mv vibrot.x $(BINDIR)/vibrot +- mv xtalfit.x $(BINDIR)/xtalfit +- mv xtalmin.x $(BINDIR)/xtalmin +- mv xyzedit.x $(BINDIR)/xyzedit +- mv xyzint.x $(BINDIR)/xyzint +- mv xyzpdb.x $(BINDIR)/xyzpdb +- mv xyzsybyl.x $(BINDIR)/xyzsybyl ++ ${INSTALL} -s alchemy.x $(BINDIR)/alchemy ++ ${INSTALL} -s analyze.x $(BINDIR)/analyze ++ ${INSTALL} -s anneal.x $(BINDIR)/anneal ++ ${INSTALL} -s archive.x $(BINDIR)/archive ++ ${INSTALL} -s correlate.x $(BINDIR)/correlate ++ ${INSTALL} -s crystal.x $(BINDIR)/crystal ++ ${INSTALL} -s distgeom.x $(BINDIR)/distgeom ++ ${INSTALL} -s document.x $(BINDIR)/document ++ ${INSTALL} -s dynamic.x $(BINDIR)/dynamic ++ ${INSTALL} -s gda.x $(BINDIR)/gda ++ ${INSTALL} -s intedit.x $(BINDIR)/intedit ++ ${INSTALL} -s intxyz.x $(BINDIR)/intxyz ++ ${INSTALL} -s minimize.x $(BINDIR)/minimize ++ ${INSTALL} -s minirot.x $(BINDIR)/minirot ++ ${INSTALL} -s newton.x $(BINDIR)/newton ++ ${INSTALL} -s newtrot.x $(BINDIR)/newtrot ++ ${INSTALL} -s optimize.x $(BINDIR)/optimize ++ ${INSTALL} -s optirot.x $(BINDIR)/optirot ++ ${INSTALL} -s optrigid.x $(BINDIR)/optrigid ++ ${INSTALL} -s path.x $(BINDIR)/path ++ ${INSTALL} -s pdbxyz.x $(BINDIR)/pdbxyz ++ ${INSTALL} -s protein.x $(BINDIR)/protein ++ ${INSTALL} -s pss.x $(BINDIR)/pss ++ ${INSTALL} -s pssrigid.x $(BINDIR)/pssrigid ++ ${INSTALL} -s pssrot.x $(BINDIR)/pssrot ++ ${INSTALL} -s saddle.x $(BINDIR)/saddle ++ ${INSTALL} -s scan.x $(BINDIR)/scan ++ ${INSTALL} -s sniffer.x $(BINDIR)/sniffer ++ ${INSTALL} -s spacefill.x $(BINDIR)/spacefill ++ ${INSTALL} -s superpose.x $(BINDIR)/superpose ++ ${INSTALL} -s sybylxyz.x $(BINDIR)/sybylxyz ++ ${INSTALL} -s testgrad.x $(BINDIR)/testgrad ++ ${INSTALL} -s testhess.x $(BINDIR)/testhess ++ ${INSTALL} -s testlight.x $(BINDIR)/testlight ++ ${INSTALL} -s testrot.x $(BINDIR)/testrot ++ ${INSTALL} -s timer.x $(BINDIR)/timer ++ ${INSTALL} -s timerot.x $(BINDIR)/timerot ++ ${INSTALL} -s vibrate.x $(BINDIR)/vibrate ++ ${INSTALL} -s vibrot.x $(BINDIR)/vibrot ++ ${INSTALL} -s xtalfit.x $(BINDIR)/xtalfit ++ ${INSTALL} -s xtalmin.x $(BINDIR)/xtalmin ++ ${INSTALL} -s xyzedit.x $(BINDIR)/xyzedit ++ ${INSTALL} -s xyzint.x $(BINDIR)/xyzint ++ ${INSTALL} -s xyzpdb.x $(BINDIR)/xyzpdb ++ ${INSTALL} -s xyzsybyl.x $(BINDIR)/xyzsybyl + + remove_links: + rm -f $(LINKDIR)/alchemy diff -ruN tinker.old/patches/patch-ab tinker/patches/patch-ab --- tinker.old/patches/patch-ab Fri Jun 18 21:54:27 1999 +++ tinker/patches/patch-ab Sat Jun 19 21:50:10 1999 @@ -1,19 +1,12 @@ -*** ../doc/license.txt.orig Fri Aug 28 23:47:07 1998 ---- ../doc/license.txt Fri Aug 28 23:49:13 1998 -*************** -*** 1,7 **** -! TINKER ­ Software Tools for Molecular Design - - Version 3.6 February 1998 -! Copyright © 1990-1998 Jay William Ponder - - TINKER is a modular program package for molecular mechanics- - based potential energy calculations, molecular dynamics ---- 1,7 ---- -! TINKER -- Software Tools for Molecular Design - - Version 3.6 February 1998 -! Copyright 1990-1998 Jay William Ponder - - TINKER is a modular program package for molecular mechanics- - based potential energy calculations, molecular dynamics +--- ../doc/license.txt.orig Wed Jun 16 13:54:43 1999 ++++ ../doc/license.txt Sat Jun 19 14:19:18 1999 +@@ -1,7 +1,7 @@ +- TINKER ­ Software Tools for Molecular Design ++ TINKER - Software Tools for Molecular Design + + Version 3.7 June 1999 +- Copyright © 1990-1999 Jay William Ponder ++ Copyright (c) 1990-1999 Jay William Ponder + + TINKER is a modular program package for molecular mechanics- + based potential energy calculations, molecular dynamics diff -ruN tinker.old/patches/patch-ac tinker/patches/patch-ac --- tinker.old/patches/patch-ac Fri Jun 18 21:54:27 1999 +++ tinker/patches/patch-ac Sat Jun 19 21:50:10 1999 @@ -7,7 +7,7 @@ Jay Ponder Lab, Dept. of Biochemistry & Molecular Biophysics, --- 1,4 ---- -! TINKER -- Software Tools for Molecular Design +! TINKER - Software Tools for Molecular Design Jay Ponder Lab, Dept. of Biochemistry & Molecular Biophysics, diff -ruN tinker.old/pkg/DESCR tinker/pkg/DESCR --- tinker.old/pkg/DESCR Fri Jun 18 21:54:27 1999 +++ tinker/pkg/DESCR Sat Jun 19 21:50:10 1999 @@ -1,10 +1,11 @@ Tinker is a set of small programs for doing general purpose molecular modeling. Tools are included for energy minimizations, geometry -calculations, and molecular analysis calculations. Tools for -converting coordinate sets are also provided. +calculations, and molecular analysis calculations. Tools for converting +coordinate sets are also provided. Tinker employs several force fields and minimizaation techniques. -Simulated annealing and molecular dynamics can be performed with -Tinker. +Simulated annealing and molecular dynamics can be performed with Tinker. + +For more information about Tinker see: WWW: http://dasher.wustl.edu/tinker/ diff -ruN tinker.old/pkg/PLIST tinker/pkg/PLIST --- tinker.old/pkg/PLIST Fri Jun 18 21:54:27 1999 +++ tinker/pkg/PLIST Sat Jun 19 21:50:10 1999 @@ -47,23 +47,26 @@ share/tinker/params/charmm.prm share/tinker/params/emr.prm share/tinker/params/hoch.prm -share/tinker/params/merck.prm share/tinker/params/mm2.prm share/tinker/params/mm3.prm share/tinker/params/mm3pro.prm -share/tinker/params/mmffpro.prm share/tinker/params/opls.prm share/tinker/params/oplsaa.prm share/tinker/params/smooth.prm +share/tinker/params/smoothaa.prm share/tinker/params/tinker.prm share/tinker/params/water.prm share/tinker/doc/README +share/tinker/doc/guide.pdf share/tinker/doc/guide.ps.Z share/tinker/doc/guide.txt +share/tinker/doc/license.pdf share/tinker/doc/license.ps share/tinker/doc/license.txt +share/tinker/doc/logo-bind.ps.Z share/tinker/doc/logo.ps.Z share/tinker/doc/spine.ps +share/tinker/doc/summary.pdf share/tinker/doc/summary.ps share/tinker/doc/summary.txt share/tinker/tinker.txt @@ -116,6 +119,11 @@ share/tinker/example/formamide.key share/tinker/example/formamide.log share/tinker/example/formamide.run +share/tinker/example/helix.in1 +share/tinker/example/helix.key +share/tinker/example/helix.log +share/tinker/example/helix.run +share/tinker/example/helix.xyz share/tinker/bench/crambin.input share/tinker/bench/crambin.key share/tinker/bench/crambin.run @@ -131,6 +139,7 @@ share/tinker/bench/results-3.2 share/tinker/bench/results-3.4 share/tinker/bench/results-3.5 +share/tinker/bench/results-3.7 share/tinker/bench/water.dyn0 share/tinker/bench/water.input share/tinker/bench/water.key @@ -148,15 +157,17 @@ share/tinker/test/annulene3.xyz share/tinker/test/arach.int share/tinker/test/arach.key -share/tinker/test/arach.xmol share/tinker/test/arach.xyz share/tinker/test/azulene.int share/tinker/test/azulene.key share/tinker/test/azulene.xyz -share/tinker/test/bearing.big share/tinker/test/bearing.key share/tinker/test/bearing.pdb share/tinker/test/bearing.xyz +share/tinker/test/bearing2.key +share/tinker/test/bearing2.pdb +share/tinker/test/c5.key +share/tinker/test/bearing2.xyz share/tinker/test/benzene.int share/tinker/test/benzene.key share/tinker/test/benzene.xyz @@ -177,29 +188,29 @@ share/tinker/test/butopls2.int share/tinker/test/butopls2.key share/tinker/test/butopls2.xyz -share/tinker/test/c5.int -share/tinker/test/c5.key +share/tinker/test/c5.seq share/tinker/test/c5.xyz -share/tinker/test/c7ax.int share/tinker/test/c7ax.key +share/tinker/test/c7ax.seq share/tinker/test/c7ax.xyz -share/tinker/test/c7eq.int share/tinker/test/c7eq.key +share/tinker/test/c7eq.seq share/tinker/test/c7eq.xyz share/tinker/test/cpentene.key share/tinker/test/cpentene.xyz -share/tinker/test/crambin.int share/tinker/test/crambin.key share/tinker/test/crambin.pdb share/tinker/test/crambin.seq share/tinker/test/crambin.xyz share/tinker/test/crambinx.key +share/tinker/test/crambinx.ray share/tinker/test/crambinx.xyz share/tinker/test/crown.int share/tinker/test/crown.key share/tinker/test/crown.xyz share/tinker/test/cychept.int share/tinker/test/cychept.key +share/tinker/test/cychept.pdb share/tinker/test/cychept.xyz share/tinker/test/cyclo.int share/tinker/test/cyclo.key @@ -207,25 +218,28 @@ share/tinker/test/cyclo2.int share/tinker/test/cyclo2.key share/tinker/test/cyclo2.xyz -share/tinker/test/nma.int share/tinker/test/diene.int share/tinker/test/diene.key share/tinker/test/diene.xyz share/tinker/test/dimethane.key share/tinker/test/dimethane.xyz share/tinker/test/diwater.key -share/tinker/test/diwater.lin +share/tinker/test/diwater.min share/tinker/test/diwater.xyz share/tinker/test/enkephalin.int share/tinker/test/enkephalin.key share/tinker/test/enkephalin.make share/tinker/test/enkephalin.pdb +share/tinker/test/enkephalin.run share/tinker/test/enkephalin.seq share/tinker/test/enkephalin.xyz share/tinker/test/ermer.int share/tinker/test/ermer.key share/tinker/test/ermer.xyz +share/tinker/test/ester.key +share/tinker/test/ester.xyz share/tinker/test/ethane.int +share/tinker/test/nma.int share/tinker/test/ethane.key share/tinker/test/ethane.xyz share/tinker/test/ethylene.int @@ -234,6 +248,8 @@ share/tinker/test/flane.int share/tinker/test/flane.key share/tinker/test/flane.xyz +share/tinker/test/formamide.key +share/tinker/test/formamide.xyz share/tinker/test/furan.int share/tinker/test/furan.key share/tinker/test/furan.xyz @@ -280,10 +296,6 @@ share/tinker/test/peptide.xyz share/tinker/test/phenanth.key share/tinker/test/phenanth.xyz -share/tinker/test/photo.key -share/tinker/test/photo.pdb -share/tinker/test/photo.seq -share/tinker/test/photo.xyz share/tinker/test/propellane.int share/tinker/test/propellane.key share/tinker/test/propellane.xyz >Release-Note: >Audit-Trail: >Unformatted: To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message