Date: Sun, 7 Oct 2018 00:19:22 +0000 (UTC) From: Yuri Victorovich <yuri@FreeBSD.org> To: ports-committers@freebsd.org, svn-ports-all@freebsd.org, svn-ports-head@freebsd.org Subject: svn commit: r481406 - in head: . biology biology/tinker science science/tinker science/tinker/files Message-ID: <201810070019.w970JMDs085094@repo.freebsd.org>
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Author: yuri Date: Sun Oct 7 00:19:22 2018 New Revision: 481406 URL: https://svnweb.freebsd.org/changeset/ports/481406 Log: biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/ Port changes: * Take maintainership * Implement the 'benchmarks' target, and stop installing benchmarks * Add USES=gmake * Update license * Change MASTER_SITES and WWW to https * Silence some commands Added: head/science/tinker/ - copied from r481405, head/biology/tinker/ head/science/tinker/files/patch-make_Makefile - copied, changed from r481405, head/biology/tinker/files/patch-make__Makefile Deleted: head/biology/tinker/ head/science/tinker/files/patch-bench__bench1.run head/science/tinker/files/patch-bench__bench2.run head/science/tinker/files/patch-bench__bench3.run head/science/tinker/files/patch-bench__bench4.run head/science/tinker/files/patch-bench__bench5.run head/science/tinker/files/patch-make__Makefile Modified: head/MOVED head/biology/Makefile head/science/Makefile head/science/tinker/Makefile head/science/tinker/distinfo head/science/tinker/pkg-descr head/science/tinker/pkg-plist Modified: head/MOVED ============================================================================== --- head/MOVED Sat Oct 6 23:27:37 2018 (r481405) +++ head/MOVED Sun Oct 7 00:19:22 2018 (r481406) @@ -10566,3 +10566,4 @@ math/arpack-ng-mpich|math/arpack-ng|2018-10-04|math/ar editors/latexila|editors/gnome-latex|2018-10-05|Project was renamed math/arpack|math/arpack-ng|2018-10-06|math/arpack is the old, unmaintained version, math/arpack-ng should be used instead net-p2p/libtorrent-rasterbar-python|net-p2p/py-libtorrent-rasterbar|2018-10-06|Rename to the canonical name for a python port +biology/tinker|science/tinker|2018-10-06|Move to proper category Modified: head/biology/Makefile ============================================================================== --- head/biology/Makefile Sat Oct 6 23:27:37 2018 (r481405) +++ head/biology/Makefile Sun Oct 7 00:19:22 2018 (r481406) @@ -131,7 +131,6 @@ SUBDIR += tRNAscan-SE SUBDIR += t_coffee SUBDIR += tabixpp - SUBDIR += tinker SUBDIR += treepuzzle SUBDIR += trimadap SUBDIR += trimmomatic Modified: head/science/Makefile ============================================================================== --- head/science/Makefile Sat Oct 6 23:27:37 2018 (r481405) +++ head/science/Makefile Sun Oct 7 00:19:22 2018 (r481406) @@ -276,6 +276,7 @@ SUBDIR += szip SUBDIR += teem SUBDIR += tfel + SUBDIR += tinker SUBDIR += triqs SUBDIR += udunits SUBDIR += v_sim Modified: head/science/tinker/Makefile ============================================================================== --- head/biology/tinker/Makefile Sat Oct 6 23:27:37 2018 (r481405) +++ head/science/tinker/Makefile Sun Oct 7 00:19:22 2018 (r481406) @@ -2,21 +2,18 @@ # $FreeBSD$ PORTNAME= tinker -PORTVERSION= 7.1.3 -PORTREVISION= 5 -CATEGORIES= biology -MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/ +DISTVERSION= 8.4.4 +CATEGORIES= science +MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/ -MAINTAINER= ports@FreeBSD.org +MAINTAINER= yuri@FreeBSD.org COMMENT= General purpose molecular modelling package -LICENSE= tinker +LICENSE= TINKER LICENSE_NAME= TINKER license agreement -LICENSE_FILE= ${WRKSRC}/doc/license.txt -LICENSE_PERMS= auto-accept +LICENSE_FILE= ${WRKSRC}/doc/license.pdf +LICENSE_PERMS= auto-accept # internal academic purposes only, no commercial use -RESTRICTED= author requests no distribution except from his FTP site - OPTIONS_DEFINE= OPTIMIZED_FFLAGS DOCS EXAMPLES OPTIMIZED_FFLAGS_DESC= compilation optimizations @@ -24,15 +21,21 @@ WRKSRC= ${WRKDIR}/${PORTNAME} BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source -USES= fortran +LIB_DEPENDS= libfftw3.so:math/fftw3 + +USES= fortran gmake MAKE_ENV= HAVE_G2C=yes +MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin MAKEFILE= ${WRKSRC}/make/Makefile -ALL_TARGET= all -INSTALL_TARGET= rename EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx SUB_FILES= pkg-message +BINARY_ALIAS= gfortran=gfortran${GCC_DEFAULT} + +PORTDOCS= * +PORTEXAMPLES= * + .include <bsd.port.options.mk> .if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS} @@ -42,26 +45,33 @@ FFLAGS+= -mfancy-math-387 -malign-double .endif # i386 .endif -pre-build: +post-extract: @${RM} ${BUILD_WRKSRC}/*.c + @${RM} ${WRKSRC}/other/eopbend.orig +post-patch: + @${REINPLACE_CMD} -i '' 's|\.\./bin/|${STAGEDIR}${PREFIX}/bin/|' ${BUILD_WRKSRC}/../bench/bench*.run + post-install: - ${MKDIR} ${STAGEDIR}${DATADIR} - ${MKDIR} ${STAGEDIR}${DATADIR}/bench - (cd ${WRKSRC}/bench && ${INSTALL_DATA} \ - 0README *.log *.key *.run *.xyz results* \ - ${STAGEDIR}${DATADIR}/bench) - ${MKDIR} ${STAGEDIR}${DATADIR}/params - (cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params) - ${MKDIR} ${STAGEDIR}${DATADIR}/test - (cd ${WRKSRC}/test && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/test) + @${MKDIR} ${STAGEDIR}${DATADIR} + @${MKDIR} ${STAGEDIR}${DATADIR}/params + cd ${WRKSRC}/params && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/params + @${MKDIR} ${STAGEDIR}${DATADIR}/test + cd ${WRKSRC}/test && ${INSTALL_DATA} * ${STAGEDIR}${DATADIR}/test + post-install-DOCS-on: - ${MKDIR} ${STAGEDIR}${DOCSDIR} - (cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf *.txt ${STAGEDIR}${DOCSDIR}) + @${MKDIR} ${STAGEDIR}${DOCSDIR} + cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf ${STAGEDIR}${DOCSDIR} + post-install-EXAMPLES-on: - ${MKDIR} ${STAGEDIR}${EXAMPLESDIR} - (cd ${WRKSRC}/example && ${INSTALL_DATA} \ + @${MKDIR} ${STAGEDIR}${EXAMPLESDIR} + cd ${WRKSRC}/example && ${INSTALL_DATA} \ 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \ - ${STAGEDIR}${EXAMPLESDIR}) + ${STAGEDIR}${EXAMPLESDIR} + +benchmarks: stage +.for n in 1 2 3 4 5 6 7 8 9 + @cd ${BUILD_WRKSRC}/../bench && ./bench${n}.run +.endfor .include <bsd.port.mk> Modified: head/science/tinker/distinfo ============================================================================== --- head/biology/tinker/distinfo Sat Oct 6 23:27:37 2018 (r481405) +++ head/science/tinker/distinfo Sun Oct 7 00:19:22 2018 (r481406) @@ -1,2 +1,3 @@ -SHA256 (tinker-7.1.3.tar.gz) = c221459ac1ac423ed8c99c7ba67eaab09821c970333cd2841efb20ccbfd59095 -SIZE (tinker-7.1.3.tar.gz) = 28655947 +TIMESTAMP = 1538861663 +SHA256 (tinker-8.4.4.tar.gz) = c263298383bcd5a72f281d25640f7be2e9c465e08c1a61c3c3de59b6bb828da6 +SIZE (tinker-8.4.4.tar.gz) = 35549655 Copied and modified: head/science/tinker/files/patch-make_Makefile (from r481405, head/biology/tinker/files/patch-make__Makefile) ============================================================================== --- head/biology/tinker/files/patch-make__Makefile Sat Oct 6 23:27:37 2018 (r481405, copy source) +++ head/science/tinker/files/patch-make_Makefile Sun Oct 7 00:19:22 2018 (r481406) @@ -1,99 +1,9 @@ ---- make/Makefile.orig 2015-05-18 16:58:50.748044000 +0800 -+++ make/Makefile 2015-05-18 17:07:06.767545000 +0800 -@@ -33,9 +33,9 @@ - ## BINDIR Hard Copies of TINKER Executables - ## LINKDIR Linked Copies of TINKER Executables +--- make/Makefile.orig 2018-10-06 22:01:02 UTC ++++ make/Makefile +@@ -754,130 +754,130 @@ listing: + cat *.f *.c > tinker.txt --TINKERDIR = $(HOME)/tinker --BINDIR = $(TINKERDIR)/bin --LINKDIR = /usr/local/bin -+TINKERDIR = ${WRKDIR} -+BINDIR = ${DESTDIR}${PREFIX}/bin -+#LINKDIR = /usr/local/bin - - #################################################################### - ## Known Machine Types; Uncomment One of the Following Sections ## -@@ -46,26 +46,26 @@ - ## CPU Type: Intel x86 Compatible - ## Compiler: GNU gfortran - --#F77 = gfortran --#LIBS = --#F77FLAGS = -c --#OPTFLAGS = -O3 -ffast-math --#LIBFLAGS = -crusv --#RANLIB = ranlib -c --#LINKFLAGS = $(OPTFLAGS) -static-libgcc -+F77 = ${FC} -+LIBS = -+F77FLAGS = -c ${FFLAGS} -+OPTFLAGS = -+LIBFLAGS = -crusv -+RANLIB = ranlib -+LINKFLAGS = ${LDFLAGS} - - ## Machine: Generic Linux or Macintosh - ## CPU Type: Intel x86 Compatible - ## Compiler: GNU gfortran - ## Parallel: OpenMP - --F77 = gfortran --LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3 --F77FLAGS = -c --OPTFLAGS = -O3 -ffast-math -fopenmp --LIBFLAGS = -crusv --RANLIB = ranlib -c --LINKFLAGS = $(OPTFLAGS) -static-libgcc -+#F77 = gfortran -+#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_threads -lfftw3 -+#F77FLAGS = -c -+#OPTFLAGS = -O3 -ffast-math -fopenmp -+#LIBFLAGS = -crusv -+#RANLIB = ranlib -c -+#LINKFLAGS = $(OPTFLAGS) -static-libgcc - - ## Machine: Generic Linux - ## CPU Type: Intel x86 Compatible (also AMD) -@@ -106,7 +106,7 @@ - #LIBFLAGS = -crusv - #RANLIB = ranlib -c - #LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.6 \ -- -Wl,-stack_size,0x10000000 -+# -Wl,-stack_size,0x10000000 - - ## Machine: Macintosh - ## CPU Type: Intel Xeon -@@ -710,92 +710,88 @@ - xyzpdb.x \ - xyzsybyl.x - --%.o: %.f -- ${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ -+.SUFFIXES: .x - --%.o: %.c -- ${CC} ${CFLAGS} ${INCLUDEDIR} ${OPTFLAGS} $< -+.f.o: -+ ${F77} ${F77FLAGS} ${OPTFLAGS} $< -o $@ - --%.x: %.o libtinker.a -- ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ -+.o.x: libtinker.a -+ ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} - - all: ${EXEFILES} - --install: -- rename -- - clean: - rm -f *.o *.mod *.a *.x - - listing: -- cat *.i *.f *.c > tinker.txt -+ cat *.i *.f > tinker.txt - - rename: + rename_bin: - mv alchemy.x $(BINDIR)/alchemy - mv analyze.x $(BINDIR)/analyze - mv anneal.x $(BINDIR)/anneal @@ -111,6 +21,7 @@ - mv minimize.x $(BINDIR)/minimize - mv minirot.x $(BINDIR)/minirot - mv minrigid.x $(BINDIR)/minrigid +- mv mol2xyz.x $(BINDIR)/mol2xyz - mv molxyz.x $(BINDIR)/molxyz - mv monte.x $(BINDIR)/monte - mv newton.x $(BINDIR)/newton @@ -136,7 +47,6 @@ - mv spacefill.x $(BINDIR)/spacefill - mv spectrum.x $(BINDIR)/spectrum - mv superpose.x $(BINDIR)/superpose -- mv sybylxyz.x $(BINDIR)/sybylxyz - mv testgrad.x $(BINDIR)/testgrad - mv testhess.x $(BINDIR)/testhess - mv testpair.x $(BINDIR)/testpair @@ -153,10 +63,10 @@ - mv xtalmin.x $(BINDIR)/xtalmin - mv xyzedit.x $(BINDIR)/xyzedit - mv xyzint.x $(BINDIR)/xyzint +- mv xyzmol2.x $(BINDIR)/xyzmol2 - mv xyzpdb.x $(BINDIR)/xyzpdb -- mv xyzsybyl.x $(BINDIR)/xyzsybyl + ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy -+ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze_t ++ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze + ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal + ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive + ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar @@ -172,6 +82,7 @@ + ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize + ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot + ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid ++ ${BSD_INSTALL_PROGRAM} mol2xyz.x $(BINDIR)/mol2xyz + ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz + ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte + ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton @@ -197,7 +108,6 @@ + ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill + ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum + ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose -+ ${BSD_INSTALL_PROGRAM} sybylxyz.x $(BINDIR)/sybylxyz + ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad + ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess + ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair @@ -214,22 +124,132 @@ + ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin + ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit + ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint ++ ${BSD_INSTALL_PROGRAM} xyzmol2.x $(BINDIR)/xyzmol2 + ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb -+ ${BSD_INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl + rename_exe: +- mv alchemy.x $(BINDIR)/alchemy.exe +- mv analyze.x $(BINDIR)/analyze.exe +- mv anneal.x $(BINDIR)/anneal.exe +- mv archive.x $(BINDIR)/archive.exe +- mv bar.x $(BINDIR)/bar.exe +- mv correlate.x $(BINDIR)/correlate.exe +- mv crystal.x $(BINDIR)/crystal.exe +- mv diffuse.x $(BINDIR)/diffuse.exe +- mv distgeom.x $(BINDIR)/distgeom.exe +- mv document.x $(BINDIR)/document.exe +- mv dynamic.x $(BINDIR)/dynamic.exe +- mv gda.x $(BINDIR)/gda.exe +- mv intedit.x $(BINDIR)/intedit.exe +- mv intxyz.x $(BINDIR)/intxyz.exe +- mv minimize.x $(BINDIR)/minimize.exe +- mv minirot.x $(BINDIR)/minirot.exe +- mv minrigid.x $(BINDIR)/minrigid.exe +- mv mol2xyz.x $(BINDIR)/mol2xyz.exe +- mv molxyz.x $(BINDIR)/molxyz.exe +- mv monte.x $(BINDIR)/monte.exe +- mv newton.x $(BINDIR)/newton.exe +- mv newtrot.x $(BINDIR)/newtrot.exe +- mv nucleic.x $(BINDIR)/nucleic.exe +- mv optimize.x $(BINDIR)/optimize.exe +- mv optirot.x $(BINDIR)/optirot.exe +- mv optrigid.x $(BINDIR)/optrigid.exe +- mv path.x $(BINDIR)/path.exe +- mv pdbxyz.x $(BINDIR)/pdbxyz.exe +- mv polarize.x $(BINDIR)/polarize.exe +- mv poledit.x $(BINDIR)/poledit.exe +- mv potential.x $(BINDIR)/potential.exe +- mv prmedit.x $(BINDIR)/prmedit.exe +- mv protein.x $(BINDIR)/protein.exe +- mv pss.x $(BINDIR)/pss.exe +- mv pssrigid.x $(BINDIR)/pssrigid.exe +- mv pssrot.x $(BINDIR)/pssrot.exe +- mv radial.x $(BINDIR)/radial.exe +- mv saddle.x $(BINDIR)/saddle.exe +- mv scan.x $(BINDIR)/scan.exe +- mv sniffer.x $(BINDIR)/sniffer.exe +- mv spacefill.x $(BINDIR)/spacefill.exe +- mv spectrum.x $(BINDIR)/spectrum.exe +- mv superpose.x $(BINDIR)/superpose.exe +- mv testgrad.x $(BINDIR)/testgrad.exe +- mv testhess.x $(BINDIR)/testhess.exe +- mv testpair.x $(BINDIR)/testpair.exe +- mv testpol.x $(BINDIR)/testpol.exe +- mv testrot.x $(BINDIR)/testrot.exe +- mv timer.x $(BINDIR)/timer.exe +- mv timerot.x $(BINDIR)/timerot.exe +- mv torsfit.x $(BINDIR)/torsfit.exe +- mv valence.x $(BINDIR)/valence.exe +- mv vibbig.x $(BINDIR)/vibbig.exe +- mv vibrate.x $(BINDIR)/vibrate.exe +- mv vibrot.x $(BINDIR)/vibrot.exe +- mv xtalfit.x $(BINDIR)/xtalfit.exe +- mv xtalmin.x $(BINDIR)/xtalmin.exe +- mv xyzedit.x $(BINDIR)/xyzedit.exe +- mv xyzint.x $(BINDIR)/xyzint.exe +- mv xyzmol2.x $(BINDIR)/xyzmol2.exe +- mv xyzpdb.x $(BINDIR)/xyzpdb.exe ++ ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy.exe ++ ${BSD_INSTALL_PROGRAM} analyze.x $(BINDIR)/analyze.exe ++ ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal.exe ++ ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive.exe ++ ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar.exe ++ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate.exe ++ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal.exe ++ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse.exe ++ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom.exe ++ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document.exe ++ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic.exe ++ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda.exe ++ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit.exe ++ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz.exe ++ ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize.exe ++ ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot.exe ++ ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid.exe ++ ${BSD_INSTALL_PROGRAM} mol2xyz.x $(BINDIR)/mol2xyz.exe ++ ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz.exe ++ ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte.exe ++ ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton.exe ++ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot.exe ++ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic.exe ++ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize.exe ++ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot.exe ++ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid.exe ++ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path.exe ++ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz.exe ++ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize.exe ++ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit.exe ++ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential.exe ++ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit.exe ++ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein.exe ++ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss.exe ++ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid.exe ++ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot.exe ++ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial.exe ++ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle.exe ++ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan.exe ++ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer.exe ++ ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill.exe ++ ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum.exe ++ ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose.exe ++ ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad.exe ++ ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess.exe ++ ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair.exe ++ ${BSD_INSTALL_PROGRAM} testpol.x $(BINDIR)/testpol.exe ++ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot.exe ++ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer.exe ++ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot.exe ++ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit.exe ++ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence.exe ++ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig.exe ++ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate.exe ++ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot.exe ++ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit.exe ++ ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin.exe ++ ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit.exe ++ ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint.exe ++ ${BSD_INSTALL_PROGRAM} xyzmol2.x $(BINDIR)/xyzmol2.exe ++ ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb.exe + remove_links: rm -f $(LINKDIR)/alchemy -- rm -f $(LINKDIR)/analyze -+ rm -f $(LINKDIR)/analyze_t - rm -f $(LINKDIR)/anneal - rm -f $(LINKDIR)/archive - rm -f $(LINKDIR)/bar -@@ -858,7 +854,7 @@ - - create_links: - ln -s $(BINDIR)/alchemy $(LINKDIR)/alchemy -- ln -s $(BINDIR)/analyze $(LINKDIR)/analyze -+ ln -s $(BINDIR)/analyze_t $(LINKDIR)/analyze_t - ln -s $(BINDIR)/anneal $(LINKDIR)/anneal - ln -s $(BINDIR)/archive $(LINKDIR)/archive - ln -s $(BINDIR)/bar $(LINKDIR)/bar Modified: head/science/tinker/pkg-descr ============================================================================== --- head/biology/tinker/pkg-descr Sat Oct 6 23:27:37 2018 (r481405) +++ head/science/tinker/pkg-descr Sun Oct 7 00:19:22 2018 (r481406) @@ -13,4 +13,4 @@ is set too large that tinker programs will abort and c For more information about Tinker see: -WWW: http://dasher.wustl.edu/tinker/ +WWW: https://dasher.wustl.edu/tinker/ Modified: head/science/tinker/pkg-plist ============================================================================== --- head/biology/tinker/pkg-plist Sat Oct 6 23:27:37 2018 (r481405) +++ head/science/tinker/pkg-plist Sun Oct 7 00:19:22 2018 (r481406) @@ -1,5 +1,5 @@ bin/alchemy -bin/analyze_t +bin/analyze bin/anneal bin/archive bin/bar @@ -15,6 +15,7 @@ bin/intxyz bin/minimize bin/minirot bin/minrigid +bin/mol2xyz bin/molxyz bin/monte bin/newton @@ -40,7 +41,6 @@ bin/sniffer bin/spacefill bin/spectrum bin/superpose -bin/sybylxyz bin/testgrad bin/testhess bin/testpair @@ -57,455 +57,8 @@ bin/xtalfit bin/xtalmin bin/xyzedit bin/xyzint +bin/xyzmol2 bin/xyzpdb -bin/xyzsybyl -%%PORTDOCS%%%%DOCSDIR%%/0README -%%PORTDOCS%%%%DOCSDIR%%/ffe-guide.pdf -%%PORTDOCS%%%%DOCSDIR%%/guide.pdf -%%PORTDOCS%%%%DOCSDIR%%/license.pdf -%%PORTDOCS%%%%DOCSDIR%%/license.txt -%%PORTDOCS%%%%DOCSDIR%%/summary.pdf -%%PORTDOCS%%%%DOCSDIR%%/summary.txt -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/0README -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.int -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.seq -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alatet.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/alkane.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ammonia.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/amoeba.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/anthracene.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/anthracene.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aspirin.key 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-%%PORTEXAMPLES%%%%EXAMPLESDIR%%/trpcage.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.pdb -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.seq -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.seq -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/ubiquitin2.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.frac -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/urea.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.int -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/water.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterball.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterball.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbig.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbig.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.dyn -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterbox.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.dyn -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterdot.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterglobe.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterglobe.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterhuge.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterhuge.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.dyn -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/waterslab.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.dyn -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watersmall.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.dyn -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/watertiny.xyz -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.int -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.key -%%PORTEXAMPLES%%%%EXAMPLESDIR%%/white.xyz -%%DATADIR%%/bench/0README -%%DATADIR%%/bench/bench1.key -%%DATADIR%%/bench/bench1.run -%%DATADIR%%/bench/bench1.xyz -%%DATADIR%%/bench/bench2.key -%%DATADIR%%/bench/bench2.run -%%DATADIR%%/bench/bench2.xyz -%%DATADIR%%/bench/bench3.key -%%DATADIR%%/bench/bench3.log -%%DATADIR%%/bench/bench3.run -%%DATADIR%%/bench/bench3.xyz -%%DATADIR%%/bench/bench4.key -%%DATADIR%%/bench/bench4.log -%%DATADIR%%/bench/bench4.run -%%DATADIR%%/bench/bench4.xyz -%%DATADIR%%/bench/bench5.key -%%DATADIR%%/bench/bench5.log -%%DATADIR%%/bench/bench5.run -%%DATADIR%%/bench/bench5.xyz -%%DATADIR%%/bench/bench6.key -%%DATADIR%%/bench/bench6.log -%%DATADIR%%/bench/bench6.run -%%DATADIR%%/bench/bench6.xyz -%%DATADIR%%/bench/bench7.key -%%DATADIR%%/bench/bench7.log -%%DATADIR%%/bench/bench7.run -%%DATADIR%%/bench/bench7.xyz -%%DATADIR%%/bench/bench8.key -%%DATADIR%%/bench/bench8.log -%%DATADIR%%/bench/bench8.run -%%DATADIR%%/bench/bench8.xyz -%%DATADIR%%/bench/bench9.key -%%DATADIR%%/bench/bench9.log -%%DATADIR%%/bench/bench9.run -%%DATADIR%%/bench/bench9.xyz -%%DATADIR%%/bench/results-2.3 -%%DATADIR%%/bench/results-2.4 -%%DATADIR%%/bench/results-2.9 -%%DATADIR%%/bench/results-3.1 -%%DATADIR%%/bench/results-3.2 -%%DATADIR%%/bench/results-3.4 -%%DATADIR%%/bench/results-3.5 -%%DATADIR%%/bench/results-3.7 -%%DATADIR%%/bench/results-3.8 -%%DATADIR%%/bench/results-3.9 -%%DATADIR%%/bench/results-4.0 -%%DATADIR%%/bench/results-4.1 -%%DATADIR%%/bench/results-4.2 -%%DATADIR%%/bench/results-4.3 -%%DATADIR%%/bench/results-5.0 -%%DATADIR%%/bench/results-5.1 -%%DATADIR%%/bench/results-6.0 -%%DATADIR%%/bench/results-6.2 -%%DATADIR%%/bench/results-6.3 -%%DATADIR%%/bench/results-7.0 %%DATADIR%%/params/0README %%DATADIR%%/params/amber94.prm %%DATADIR%%/params/amber96.prm @@ -515,6 +68,8 @@ bin/xyzsybyl %%DATADIR%%/params/amoeba04.prm %%DATADIR%%/params/amoeba09.prm %%DATADIR%%/params/amoebabio09.prm +%%DATADIR%%/params/amoebabio18.prm +%%DATADIR%%/params/amoebanuc17.prm %%DATADIR%%/params/amoebapro04.prm %%DATADIR%%/params/amoebapro13.prm %%DATADIR%%/params/charmm19.prm
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