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authorMaho Nakata <maho@FreeBSD.org>2003-07-25 02:48:05 +0000
committerMaho Nakata <maho@FreeBSD.org>2003-07-25 02:48:05 +0000
commitd0d6c6466b95b9f6755eb4c20a3b57f529af3d8a (patch)
treec9d76964cba31624d1ffd92f95ba53e605a25461 /biology/tinker
parent6a34ed389f6e091a65babc5156ab01e57d2a6328 (diff)
downloadports-d0d6c6466b95b9f6755eb4c20a3b57f529af3d8a.tar.gz
ports-d0d6c6466b95b9f6755eb4c20a3b57f529af3d8a.zip
Notes
Diffstat (limited to 'biology/tinker')
-rw-r--r--biology/tinker/Makefile17
-rw-r--r--biology/tinker/distinfo2
-rw-r--r--biology/tinker/files/patch-aa32
-rw-r--r--biology/tinker/files/patch-openend.f14
-rw-r--r--biology/tinker/pkg-plist37
5 files changed, 69 insertions, 33 deletions
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