6 files changed, 70 insertions, 33 deletions

diff --git a/LEGAL b/LEGAL
index 48a7930e6b55..7fd4de89edf1 100644
--- a/LEGAL
+++ b/LEGAL
@@ -277,6 +277,7 @@ su2-1.3.tar.gz		ports/sysutils/su2	Don't sell for profit.
 swing11.tar.Z		ports/java/jfc		Don't distribute without
 						value-added application.
 timidity-*		ports/audio/timidity	Uses copyrighted patches.
+tinker-*		ports/biology/tinker	Distribution is prohibited
 tkman-1.7.3.tar.Z	ports/misc/tkman	Restrictive copyright
 tkman-2.*		ports/misc/tkman	Don't sell for profit.
 tuc-*			ports/converters/tuc	Author does not allow
diff --git a/biology/tinker/Makefile b/biology/tinker/Makefile
index 1ff1a6f3b76d..5e2ac7488d26 100644
--- a/biology/tinker/Makefile
+++ b/biology/tinker/Makefile
@@ -11,7 +11,7 @@ CATEGORIES=	biology
 MASTER_SITES=	ftp://dasher.wustl.edu/pub/
 DISTNAME=	${PORTNAME}
 
-MAINTAINER=	gjohnson@srrc.ars.usda.gov
+MAINTAINER=	ports@FreeBSD.org
 COMMENT=	A general purpose molecular modelling package
 
 MAKE_ENV+=	HAVE_G2C=yes INSTALL_PROGRAM="${INSTALL_PROGRAM}"
@@ -23,6 +23,8 @@ ALL_TARGET=	all listing
 INSTALL_TARGET=	rename
 
 RESTRICTED=	author requests no distribution except from his FTP site
+NO_CDROM=	${RESTRICTED}
+NO_PACKAGE=	${RESTRICTED}
 
 .include <bsd.port.pre.mk>
 
@@ -34,6 +36,19 @@ BUILD_DEPENDS+=	imake:${PORTSDIR}/devel/imake-4
 .endif
 PLIST=		${PKGDIR}/pkg-plist.viewer
 USE_XLIB=	yes
+
+.if defined(WITH_OPTIMIZED_FLAGS)
+CFLAGS+=        -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations
+.if (${MACHINE_ARCH} == "i386")
+CFLAGS+=        -mfancy-math-387 -malign-double
+.endif # i386
+.endif
+
+pre-everything::
+.if !defined(WITH_OPTIMIZED_FLAGS)
+	@${ECHO_MSG} "You can optimize by setting WITH_OPTIMIZED_FLAGS=yes."
+.endif
+
 post-build:
 	@${SETENV} ${SCRIPTS_ENV} ${SH} ${SCRIPTDIR}/build_viewer
 .else
diff --git a/biology/tinker/distinfo b/biology/tinker/distinfo
index e0a0bfe8ec0a..0614da22b696 100644
--- a/biology/tinker/distinfo
+++ b/biology/tinker/distinfo
@@ -1 +1 @@
-MD5 (tinker.tar.gz) = e6f34c61cc40f107fbbcf4b0c7dae5a5
+MD5 (tinker.tar.gz) = 571224cc0de71099b59de74b3dca648d
diff --git a/biology/tinker/files/patch-aa b/biology/tinker/files/patch-aa
index 6f83ecacd6dd..7f4270289c43 100644
--- a/biology/tinker/files/patch-aa
+++ b/biology/tinker/files/patch-aa
@@ -1,5 +1,5 @@
---- ../make/Makefile.orig	Wed Nov 14 01:16:27 2001
-+++ ../make/Makefile	Sat Jul 19 12:22:51 2003
+--- ../make/Makefile.orig	Sat Apr 19 03:32:36 2003
++++ ../make/Makefile	Fri Jul 25 11:33:40 2003
 @@ -9,8 +9,8 @@
  ##
  ##   1. make all              Build all the TINKER executables
@@ -24,26 +24,26 @@
  
  ####################################################################
  ##  Known Machine Types; Uncomment One of the Following Sections  ##
-@@ -87,12 +87,12 @@
- ##  Compiler: GNU g77
+@@ -101,12 +101,12 @@
+ ##  Compiler: Intel Fortran
  ##
  
--F77 = /usr/bin/g77
+-F77 = /usr/intel/compiler70/ia32/bin/ifc
 -LIBS =
 -F77FLAGS = -c
--OPTFLAGS = -O3 -ffast-math
+-OPTFLAGS = -O2 -cm -w
 -LIBFLAGS = -crusv
--LINKFLAGS =
-+#F77 = /usr/bin/g77
+-LINKFLAGS = -Vaxlib
++#F77 = /usr/intel/compiler70/ia32/bin/ifc
 +#LIBS =
 +#F77FLAGS = -c
-+#OPTFLAGS = -O3 -ffast-math
++#OPTFLAGS = -O2 -cm -w
 +#LIBFLAGS = -crusv
-+#LINKFLAGS =
++#LINKFLAGS = -Vaxlib
  
  ##
  ##  Machine:  IntelPC / Linux
-@@ -108,6 +108,24 @@
+@@ -122,6 +122,20 @@
  #LIBFLAGS = -crusv
  #LINKFLAGS =
  
@@ -58,17 +58,13 @@
 +LIBS =
 +F77FLAGS = -Wno-globals -fno-globals -c -w
 +LINKFLAGS =
-+
-+OPTFLAGS = ${FFLAGS} -ffast-math
-+.if ${MACHINE_ARCH} == "i386"
-+OPTFLAGS += -malign-double
-+.endif
++OPTFLAGS = ${FFLAGS}
 +LIBFLAGS = -rcuv
 +
  #################################################################
  ##  Should not be Necessary to Change Things Below this Point  ##
  #################################################################
-@@ -497,11 +515,13 @@
+@@ -522,11 +536,13 @@
             xyzpdb.x \
             xyzsybyl.x
  
@@ -84,7 +80,7 @@
  
  all:	${EXEFILES}
  
-@@ -512,58 +532,58 @@
+@@ -537,58 +553,58 @@
  	cat *.i *.f > tinker.txt
  
  rename:
diff --git a/biology/tinker/files/patch-openend.f b/biology/tinker/files/patch-openend.f
index a34260872792..ad2afdc47adf 100644
--- a/biology/tinker/files/patch-openend.f
+++ b/biology/tinker/files/patch-openend.f
@@ -1,6 +1,14 @@
---- openend.f.orig	Tue Dec 18 12:28:54 2001
-+++ openend.f	Sat Jul 19 12:30:57 2003
-@@ -33,7 +33,7 @@
+
+$FreeBSD$
+
+--- openend.f.orig	Fri Apr 18 13:31:51 2003
++++ openend.f	Mon Jul 21 13:36:11 2003
+@@ -29,11 +29,11 @@
+ c
+ c     standard Fortran 90, unavailable in some Fortran 77 compilers
+ c
+-      open (unit=iunit,file=name,status='old',position='append')
++c     open (unit=iunit,file=name,status='old',position='append')
  c
  c     common extension supported by many Fortran 77 compilers
  c
diff --git a/biology/tinker/pkg-plist b/biology/tinker/pkg-plist
index ed19ce608489..3a5deee9f83c 100644
--- a/biology/tinker/pkg-plist
+++ b/biology/tinker/pkg-plist
@@ -13,6 +13,8 @@ bin/intedit
 bin/intxyz
 bin/minimize
 bin/minirot
+bin/minrigid
+bin/monte
 bin/newton
 bin/newtrot
 bin/nucleic
@@ -43,8 +45,6 @@ bin/timerot
 bin/vibrate
 bin/vibrot
 bin/xtalfit
-bin/vibrot
-bin/xtalfit
 bin/xtalmin
 bin/xyzedit
 bin/xyzint
@@ -57,6 +57,8 @@ bin/xyzsybyl
 %%PORTDOCS%%share/doc/tinker/license.pdf
 %%PORTDOCS%%share/doc/tinker/license.ps
 %%PORTDOCS%%share/doc/tinker/license.txt
+%%PORTDOCS%%share/doc/tinker/logo-bind.pdf
+%%PORTDOCS%%share/doc/tinker/logo-bind.ps.gz
 %%PORTDOCS%%share/doc/tinker/logo.pdf
 %%PORTDOCS%%share/doc/tinker/logo.ps.gz
 %%PORTDOCS%%share/doc/tinker/release-3.2
@@ -64,6 +66,7 @@ bin/xyzsybyl
 %%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/release-4.0
 %%PORTDOCS%%share/doc/tinker/summary.pdf
 %%PORTDOCS%%share/doc/tinker/summary.ps
 %%PORTDOCS%%share/doc/tinker/summary.txt
@@ -140,15 +143,21 @@ 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/bench/results-4.0
 share/tinker/params/README
-share/tinker/params/amber.prm
-share/tinker/params/charmm.prm
+share/tinker/params/amber94.prm
+share/tinker/params/amber96.prm
+share/tinker/params/amber98.prm
+share/tinker/params/amoeba.prm
+share/tinker/params/charmm19.prm
+share/tinker/params/charmm27.prm
+share/tinker/params/dudek.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/oplsua.prm
 share/tinker/params/smooth.prm
 share/tinker/params/smoothaa.prm
 share/tinker/params/water.prm
@@ -157,6 +166,8 @@ share/tinker/params/water.prm
 %%PORTDOCS%%share/tinker/test/ala20.xyz
 %%PORTDOCS%%share/tinker/test/alkane.key
 %%PORTDOCS%%share/tinker/test/alkane.xyz
+%%PORTDOCS%%share/tinker/test/amoeba.key
+%%PORTDOCS%%share/tinker/test/amoeba.xyz
 %%PORTDOCS%%share/tinker/test/arach.int
 %%PORTDOCS%%share/tinker/test/arach.key
 %%PORTDOCS%%share/tinker/test/arach.xyz
@@ -222,7 +233,6 @@ share/tinker/params/water.prm
 %%PORTDOCS%%share/tinker/test/crambin.key
 %%PORTDOCS%%share/tinker/test/crambin.pdb
 %%PORTDOCS%%share/tinker/test/crambin.seq
-%%PORTDOCS%%share/tinker/test/crambin.super
 %%PORTDOCS%%share/tinker/test/crambin.xyz
 %%PORTDOCS%%share/tinker/test/crambinx.key
 %%PORTDOCS%%share/tinker/test/crambinx.ray
@@ -248,9 +258,6 @@ share/tinker/params/water.prm
 %%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
@@ -285,6 +292,9 @@ share/tinker/params/water.prm
 %%PORTDOCS%%share/tinker/test/furan.xyz
 %%PORTDOCS%%share/tinker/test/glucose.key
 %%PORTDOCS%%share/tinker/test/glucose.xyz
+%%PORTDOCS%%share/tinker/test/glycerol.dyn
+%%PORTDOCS%%share/tinker/test/glycerol.key
+%%PORTDOCS%%share/tinker/test/glycerol.xyz
 %%PORTDOCS%%share/tinker/test/graphite.key
 %%PORTDOCS%%share/tinker/test/graphite.xyz
 %%PORTDOCS%%share/tinker/test/helix.dyn
@@ -299,7 +309,6 @@ share/tinker/params/water.prm
 %%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
@@ -357,6 +366,10 @@ share/tinker/params/water.prm
 %%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/pol3.key
 %%PORTDOCS%%share/tinker/test/pol3.xyz
 %%PORTDOCS%%share/tinker/test/propane.key
@@ -397,6 +410,10 @@ share/tinker/params/water.prm
 %%PORTDOCS%%share/tinker/test/tip4p.xyz
 %%PORTDOCS%%share/tinker/test/tip5p.key
 %%PORTDOCS%%share/tinker/test/tip5p.xyz
+%%PORTDOCS%%share/tinker/test/trpcage.key
+%%PORTDOCS%%share/tinker/test/trpcage.pdb
+%%PORTDOCS%%share/tinker/test/trpcage.seq
+%%PORTDOCS%%share/tinker/test/trpcage.xyz
 %%PORTDOCS%%share/tinker/test/water.int
 %%PORTDOCS%%share/tinker/test/water.key
 %%PORTDOCS%%share/tinker/test/water.xyz