Upgrade tinker to the latest revision

PR: 33425 Submitted by: maintainer
svn path=/head/; revision=53339
2002-01-19 15:15:16 +00:00 · 2002-01-19 15:15:16 +00:00 · ec822f7631 · 2021-03-31 03:12:20 +00:00
commit ec822f7631
parent e4eecb83b6
5 changed files with 101 additions and 64 deletions
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@ -7,6 +7,7 @@

 PORTNAME=	tinker
 PORTVERSION=	3.9
+PORTREVISION=	1
 CATEGORIES=	biology
 MASTER_SITES=	ftp://dasher.wustl.edu/pub/
 DISTNAME=	${PORTNAME}
@ -28,7 +29,7 @@ pre-fetch:
 	@${ECHO_MSG} If you get a CHECKSUM mismatch, try doing a \'make distclean\' first.
 	@${ECHO_MSG} ""

-.if defined(WANT_VIEWER)
+.if defined(WITH_VIEWER)
 .if ${XFREE86_VERSION} == 3
 BUILD_DEPENDS+=	imake:${PORTSDIR}/devel/imake
 .elif ${XFREE86_VERSION} == 4
@ -42,7 +43,7 @@ post-build:
 pre-extract:
 	@${ECHO} ""
 	@${ECHO} If you would like to also build
-	@${ECHO} the molecular viewer, define WANT_VIEWER.
+	@${ECHO} the molecular viewer, define WITH_VIEWER.
 	@${ECHO} ""
 .endif

@ -114,7 +115,7 @@ ${PREFIX}/share/tinker/bench
 	@${INSTALL_DATA} ${WRKDIR}/tinker/test/* ${PREFIX}/share/tinker/test
 .endif

-.if defined(WANT_VIEWER)
+.if defined(WITH_VIEWER)
 	@${MKDIR} ${PREFIX}/share/tinker/rasmol
 	@${INSTALL_PROGRAM} ${WRKDIR}/tinker/rasmol/tview-* ${PREFIX}/bin
 	@${INSTALL_SCRIPT} ${FILESDIR}/tview ${PREFIX}/bin
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@ -1 +1 @@
-MD5 (tinker.tar.gz) = a48fc15fe668f8e41d0cc3316a582928
+MD5 (tinker.tar.gz) = e6f34c61cc40f107fbbcf4b0c7dae5a5
--- a/biology/tinker/files/patch-aa
+++ b/biology/tinker/files/patch-aa
@ -1,5 +1,5 @@
--- ../make/Makefile.orig	Sat Jul 21 10:04:48 2001
-+++ ../make/Makefile	Wed Sep  5 13:51:19 2001
+--- ../make/Makefile.orig	Tue Nov 13 10:16:27 2001
+++ ../make/Makefile	Mon Dec 31 15:33:40 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  ##
 #################################################################
-@@ -494,11 +512,13 @@
+@@ -497,11 +515,13 @@
            xyzpdb.x \
            xyzsybyl.x
 
@ -84,7 +84,7 @@
 
 all:	${EXEFILES}
 
-@@ -509,57 +529,57 @@
+@@ -512,58 +532,58 @@
 	cat *.i *.f > tinker.txt
 
 rename:
@ -104,6 +104,7 @@
 -	mv  minimize.x   $(BINDIR)/minimize
 -	mv  minirot.x    $(BINDIR)/minirot
 -	mv  minrigid.x   $(BINDIR)/minrigid
+-	mv  monte.x      $(BINDIR)/monte
 -	mv  newton.x     $(BINDIR)/newton
 -	mv  newtrot.x    $(BINDIR)/newtrot
 -	mv  nucleic.x    $(BINDIR)/nucleic
@ -155,6 +156,7 @@
 +	${INSTALL_PROGRAM}  minimize.x   $(BINDIR)/minimize
 +	${INSTALL_PROGRAM}  minirot.x    $(BINDIR)/minirot
 +	${INSTALL_PROGRAM}  minrigid.x   $(BINDIR)/minrigid
+	${INSTALL_PROGRAM}  monte.x      $(BINDIR)/monte
 +	${INSTALL_PROGRAM}  newton.x     $(BINDIR)/newton
 +	${INSTALL_PROGRAM}  newtrot.x    $(BINDIR)/newtrot
 +	${INSTALL_PROGRAM}  nucleic.x    $(BINDIR)/nucleic
@ -193,13 +195,3 @@
 
 remove_links:
 	rm -f $(LINKDIR)/alchemy
-@@ -682,8 +702,8 @@
-         bspline.o \
-         calendar.o \
-         center.o \
-        chkxyz.o \
-         cholesky.o \
-+        chkxyz.o \
-         clock.o \
-         cluster.o \
-         column.o \
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@ -14,6 +14,7 @@ bin/intxyz
 bin/minimize
 bin/minirot
 bin/minrigid
+bin/monte
 bin/newton
 bin/newtrot
 bin/nucleic
@ -139,19 +140,18 @@ bin/xyzsybyl
 %%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/charmm.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
-%%PORTDOCS%%share/tinker/params/mm3pro.prm
-%%PORTDOCS%%share/tinker/params/opls.prm
-%%PORTDOCS%%share/tinker/params/oplsaa.prm
-%%PORTDOCS%%share/tinker/params/smooth.prm
-%%PORTDOCS%%share/tinker/params/smoothaa.prm
-%%PORTDOCS%%share/tinker/params/water.prm
+share/tinker/params/README
+share/tinker/params/amber.prm
+share/tinker/params/charmm.prm
+share/tinker/params/hoch.prm
+share/tinker/params/mm2.prm
+share/tinker/params/mm3.prm
+share/tinker/params/mm3pro.prm
+share/tinker/params/opls.prm
+share/tinker/params/oplsaa.prm
+share/tinker/params/smooth.prm
+share/tinker/params/smoothaa.prm
+share/tinker/params/water.prm
 %%PORTDOCS%%share/tinker/test/README
 %%PORTDOCS%%share/tinker/test/ala20.key
 %%PORTDOCS%%share/tinker/test/ala20.xyz
@ -182,6 +182,9 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/bowl2.xyz
 %%PORTDOCS%%share/tinker/test/bowl3.key
 %%PORTDOCS%%share/tinker/test/bowl3.xyz
+%%PORTDOCS%%share/tinker/test/bucky.int
+%%PORTDOCS%%share/tinker/test/bucky.key
+%%PORTDOCS%%share/tinker/test/bucky.xyz
 %%PORTDOCS%%share/tinker/test/butane.int
 %%PORTDOCS%%share/tinker/test/butane.key
 %%PORTDOCS%%share/tinker/test/butane.xyz
@ -202,12 +205,12 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/c5.key
 %%PORTDOCS%%share/tinker/test/c5.seq
 %%PORTDOCS%%share/tinker/test/c5.xyz
-%%PORTDOCS%%share/tinker/test/c7ax.key
-%%PORTDOCS%%share/tinker/test/c7ax.seq
-%%PORTDOCS%%share/tinker/test/c7ax.xyz
-%%PORTDOCS%%share/tinker/test/c7eq.key
-%%PORTDOCS%%share/tinker/test/c7eq.seq
-%%PORTDOCS%%share/tinker/test/c7eq.xyz
+%%PORTDOCS%%share/tinker/test/c7a.key
+%%PORTDOCS%%share/tinker/test/c7a.seq
+%%PORTDOCS%%share/tinker/test/c7a.xyz
+%%PORTDOCS%%share/tinker/test/c7e.key
+%%PORTDOCS%%share/tinker/test/c7e.seq
+%%PORTDOCS%%share/tinker/test/c7e.xyz
 %%PORTDOCS%%share/tinker/test/calmodulin.key
 %%PORTDOCS%%share/tinker/test/calmodulin.pdb
 %%PORTDOCS%%share/tinker/test/calmodulin.seq
@ -245,6 +248,9 @@ bin/xyzsybyl
 %%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.xyz
 %%PORTDOCS%%share/tinker/test/enkephalin.int
 %%PORTDOCS%%share/tinker/test/enkephalin.key
 %%PORTDOCS%%share/tinker/test/enkephalin.make
@ -271,6 +277,7 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/form.xyz
 %%PORTDOCS%%share/tinker/test/formbig.key
 %%PORTDOCS%%share/tinker/test/formbig.xyz
+%%PORTDOCS%%share/tinker/test/formbox.dyn
 %%PORTDOCS%%share/tinker/test/formbox.key
 %%PORTDOCS%%share/tinker/test/formbox.xyz
 %%PORTDOCS%%share/tinker/test/furan.int
@ -292,6 +299,7 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/hexanes.key
 %%PORTDOCS%%share/tinker/test/hexanes.run
 %%PORTDOCS%%share/tinker/test/hexanes.xyz
+%%PORTDOCS%%share/tinker/test/hexanex.xyz
 %%PORTDOCS%%share/tinker/test/imidazole.int
 %%PORTDOCS%%share/tinker/test/imidazole.key
 %%PORTDOCS%%share/tinker/test/imidazole.xyz
@ -300,10 +308,14 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/imine.xyz
 %%PORTDOCS%%share/tinker/test/lactam.key
 %%PORTDOCS%%share/tinker/test/lactam.xyz
+%%PORTDOCS%%share/tinker/test/lipid.key
+%%PORTDOCS%%share/tinker/test/lipid.xyz
 %%PORTDOCS%%share/tinker/test/melittin.key
 %%PORTDOCS%%share/tinker/test/melittin.pdb
 %%PORTDOCS%%share/tinker/test/melittin.seq
 %%PORTDOCS%%share/tinker/test/melittin.xyz
+%%PORTDOCS%%share/tinker/test/membrane.key
+%%PORTDOCS%%share/tinker/test/membrane.xyz
 %%PORTDOCS%%share/tinker/test/methane.int
 %%PORTDOCS%%share/tinker/test/methane.key
 %%PORTDOCS%%share/tinker/test/methane.xyz
@ -314,6 +326,9 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/naphthalene.int
 %%PORTDOCS%%share/tinker/test/naphthalene.key
 %%PORTDOCS%%share/tinker/test/naphthalene.xyz
+%%PORTDOCS%%share/tinker/test/nitrogen.dyn
+%%PORTDOCS%%share/tinker/test/nitrogen.key
+%%PORTDOCS%%share/tinker/test/nitrogen.xyz
 %%PORTDOCS%%share/tinker/test/nma.int
 %%PORTDOCS%%share/tinker/test/nma.key
 %%PORTDOCS%%share/tinker/test/nma.xyz
@ -342,6 +357,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/peptide.xyz
 %%PORTDOCS%%share/tinker/test/phenanth.key
 %%PORTDOCS%%share/tinker/test/phenanth.xyz
+%%PORTDOCS%%share/tinker/test/pol3.key
+%%PORTDOCS%%share/tinker/test/pol3.xyz
 %%PORTDOCS%%share/tinker/test/propane.key
 %%PORTDOCS%%share/tinker/test/propane.ray
 %%PORTDOCS%%share/tinker/test/propane.xyz
@ -358,6 +375,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/pyrrole.xyz
 %%PORTDOCS%%share/tinker/test/retinoic.key
 %%PORTDOCS%%share/tinker/test/retinoic.xyz
+%%PORTDOCS%%share/tinker/test/skunk.key
+%%PORTDOCS%%share/tinker/test/skunk.xyz
 %%PORTDOCS%%share/tinker/test/sterol.key
 %%PORTDOCS%%share/tinker/test/sterol.xyz
 %%PORTDOCS%%share/tinker/test/styrene.int
@ -394,13 +413,16 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/watersmall.dyn
 %%PORTDOCS%%share/tinker/test/watersmall.key
 %%PORTDOCS%%share/tinker/test/watersmall.xyz
+%%PORTDOCS%%share/tinker/test/watertiny.dyn
+%%PORTDOCS%%share/tinker/test/watertiny.key
+%%PORTDOCS%%share/tinker/test/watertiny.xyz
 %%PORTDOCS%%share/tinker/test/white.int
 %%PORTDOCS%%share/tinker/test/white.key
 %%PORTDOCS%%share/tinker/test/white.xyz
-%%PORTDOCS%%share/tinker/tinker.txt
+share/tinker/tinker.txt
 %%PORTDOCS%%@dirrm share/doc/tinker
 %%PORTDOCS%%@dirrm share/examples/tinker
 %%PORTDOCS%%@dirrm share/tinker/bench
-%%PORTDOCS%%@dirrm share/tinker/params
+@dirrm share/tinker/params
 %%PORTDOCS%%@dirrm share/tinker/test
-%%PORTDOCS%%@dirrm share/tinker
+@dirrm share/tinker
--- a/biology/tinker/pkg-plist.viewer
+++ b/biology/tinker/pkg-plist.viewer
@ -14,6 +14,7 @@ bin/intxyz
 bin/minimize
 bin/minirot
 bin/minrigid
+bin/monte
 bin/newton
 bin/newtrot
 bin/nucleic
@ -143,20 +144,19 @@ bin/xyzsybyl
 %%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/charmm.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
-%%PORTDOCS%%share/tinker/params/mm3pro.prm
-%%PORTDOCS%%share/tinker/params/opls.prm
-%%PORTDOCS%%share/tinker/params/oplsaa.prm
-%%PORTDOCS%%share/tinker/params/smooth.prm
-%%PORTDOCS%%share/tinker/params/smoothaa.prm
-%%PORTDOCS%%share/tinker/params/water.prm
-%%PORTDOCS%%share/tinker/rasmol/rasmol.hlp
+share/tinker/params/README
+share/tinker/params/amber.prm
+share/tinker/params/charmm.prm
+share/tinker/params/hoch.prm
+share/tinker/params/mm2.prm
+share/tinker/params/mm3.prm
+share/tinker/params/mm3pro.prm
+share/tinker/params/opls.prm
+share/tinker/params/oplsaa.prm
+share/tinker/params/smooth.prm
+share/tinker/params/smoothaa.prm
+share/tinker/params/water.prm
+share/tinker/rasmol/rasmol.hlp
 %%PORTDOCS%%share/tinker/test/README
 %%PORTDOCS%%share/tinker/test/ala20.key
 %%PORTDOCS%%share/tinker/test/ala20.xyz
@ -187,6 +187,9 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/bowl2.xyz
 %%PORTDOCS%%share/tinker/test/bowl3.key
 %%PORTDOCS%%share/tinker/test/bowl3.xyz
+%%PORTDOCS%%share/tinker/test/bucky.int
+%%PORTDOCS%%share/tinker/test/bucky.key
+%%PORTDOCS%%share/tinker/test/bucky.xyz
 %%PORTDOCS%%share/tinker/test/butane.int
 %%PORTDOCS%%share/tinker/test/butane.key
 %%PORTDOCS%%share/tinker/test/butane.xyz
@ -207,12 +210,12 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/c5.key
 %%PORTDOCS%%share/tinker/test/c5.seq
 %%PORTDOCS%%share/tinker/test/c5.xyz
-%%PORTDOCS%%share/tinker/test/c7ax.key
-%%PORTDOCS%%share/tinker/test/c7ax.seq
-%%PORTDOCS%%share/tinker/test/c7ax.xyz
-%%PORTDOCS%%share/tinker/test/c7eq.key
-%%PORTDOCS%%share/tinker/test/c7eq.seq
-%%PORTDOCS%%share/tinker/test/c7eq.xyz
+%%PORTDOCS%%share/tinker/test/c7a.key
+%%PORTDOCS%%share/tinker/test/c7a.seq
+%%PORTDOCS%%share/tinker/test/c7a.xyz
+%%PORTDOCS%%share/tinker/test/c7e.key
+%%PORTDOCS%%share/tinker/test/c7e.seq
+%%PORTDOCS%%share/tinker/test/c7e.xyz
 %%PORTDOCS%%share/tinker/test/calmodulin.key
 %%PORTDOCS%%share/tinker/test/calmodulin.pdb
 %%PORTDOCS%%share/tinker/test/calmodulin.seq
@ -250,6 +253,9 @@ bin/xyzsybyl
 %%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.xyz
 %%PORTDOCS%%share/tinker/test/enkephalin.int
 %%PORTDOCS%%share/tinker/test/enkephalin.key
 %%PORTDOCS%%share/tinker/test/enkephalin.make
@ -276,6 +282,7 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/form.xyz
 %%PORTDOCS%%share/tinker/test/formbig.key
 %%PORTDOCS%%share/tinker/test/formbig.xyz
+%%PORTDOCS%%share/tinker/test/formbox.dyn
 %%PORTDOCS%%share/tinker/test/formbox.key
 %%PORTDOCS%%share/tinker/test/formbox.xyz
 %%PORTDOCS%%share/tinker/test/furan.int
@ -297,6 +304,7 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/hexanes.key
 %%PORTDOCS%%share/tinker/test/hexanes.run
 %%PORTDOCS%%share/tinker/test/hexanes.xyz
+%%PORTDOCS%%share/tinker/test/hexanex.xyz
 %%PORTDOCS%%share/tinker/test/imidazole.int
 %%PORTDOCS%%share/tinker/test/imidazole.key
 %%PORTDOCS%%share/tinker/test/imidazole.xyz
@ -305,10 +313,14 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/imine.xyz
 %%PORTDOCS%%share/tinker/test/lactam.key
 %%PORTDOCS%%share/tinker/test/lactam.xyz
+%%PORTDOCS%%share/tinker/test/lipid.key
+%%PORTDOCS%%share/tinker/test/lipid.xyz
 %%PORTDOCS%%share/tinker/test/melittin.key
 %%PORTDOCS%%share/tinker/test/melittin.pdb
 %%PORTDOCS%%share/tinker/test/melittin.seq
 %%PORTDOCS%%share/tinker/test/melittin.xyz
+%%PORTDOCS%%share/tinker/test/membrane.key
+%%PORTDOCS%%share/tinker/test/membrane.xyz
 %%PORTDOCS%%share/tinker/test/methane.int
 %%PORTDOCS%%share/tinker/test/methane.key
 %%PORTDOCS%%share/tinker/test/methane.xyz
@ -319,6 +331,9 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/naphthalene.int
 %%PORTDOCS%%share/tinker/test/naphthalene.key
 %%PORTDOCS%%share/tinker/test/naphthalene.xyz
+%%PORTDOCS%%share/tinker/test/nitrogen.dyn
+%%PORTDOCS%%share/tinker/test/nitrogen.key
+%%PORTDOCS%%share/tinker/test/nitrogen.xyz
 %%PORTDOCS%%share/tinker/test/nma.int
 %%PORTDOCS%%share/tinker/test/nma.key
 %%PORTDOCS%%share/tinker/test/nma.xyz
@ -347,6 +362,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/peptide.xyz
 %%PORTDOCS%%share/tinker/test/phenanth.key
 %%PORTDOCS%%share/tinker/test/phenanth.xyz
+%%PORTDOCS%%share/tinker/test/pol3.key
+%%PORTDOCS%%share/tinker/test/pol3.xyz
 %%PORTDOCS%%share/tinker/test/propane.key
 %%PORTDOCS%%share/tinker/test/propane.ray
 %%PORTDOCS%%share/tinker/test/propane.xyz
@ -363,6 +380,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/pyrrole.xyz
 %%PORTDOCS%%share/tinker/test/retinoic.key
 %%PORTDOCS%%share/tinker/test/retinoic.xyz
+%%PORTDOCS%%share/tinker/test/skunk.key
+%%PORTDOCS%%share/tinker/test/skunk.xyz
 %%PORTDOCS%%share/tinker/test/sterol.key
 %%PORTDOCS%%share/tinker/test/sterol.xyz
 %%PORTDOCS%%share/tinker/test/styrene.int
@ -399,14 +418,17 @@ bin/xyzsybyl
 %%PORTDOCS%%share/tinker/test/watersmall.dyn
 %%PORTDOCS%%share/tinker/test/watersmall.key
 %%PORTDOCS%%share/tinker/test/watersmall.xyz
+%%PORTDOCS%%share/tinker/test/watertiny.dyn
+%%PORTDOCS%%share/tinker/test/watertiny.key
+%%PORTDOCS%%share/tinker/test/watertiny.xyz
 %%PORTDOCS%%share/tinker/test/white.int
 %%PORTDOCS%%share/tinker/test/white.key
 %%PORTDOCS%%share/tinker/test/white.xyz
-%%PORTDOCS%%share/tinker/tinker.txt
+share/tinker/tinker.txt
 %%PORTDOCS%%@dirrm share/doc/tinker
 %%PORTDOCS%%@dirrm share/examples/tinker
 %%PORTDOCS%%@dirrm share/tinker/bench
-%%PORTDOCS%%@dirrm share/tinker/params
-%%PORTDOCS%%@dirrm share/tinker/rasmol
+@dirrm share/tinker/params
+@dirrm share/tinker/rasmol
 %%PORTDOCS%%@dirrm share/tinker/test
-%%PORTDOCS%%@dirrm share/tinker
+@dirrm share/tinker