diff options
| -rw-r--r-- | LEGAL | 1 | ||||
| -rw-r--r-- | biology/tinker/Makefile | 17 | ||||
| -rw-r--r-- | biology/tinker/distinfo | 2 | ||||
| -rw-r--r-- | biology/tinker/files/patch-aa | 32 | ||||
| -rw-r--r-- | biology/tinker/files/patch-openend.f | 14 | ||||
| -rw-r--r-- | biology/tinker/pkg-plist | 37 |
6 files changed, 70 insertions, 33 deletions
@@ -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 |