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Code Issues Releases Activity

biology/tinker: Update 7.1.3 -> 8.4.4; Move to science/

Browse Source 
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
This commit is contained in:
Yuri Victorovich 2018-10-07 00:19:22 +00:00
parent 52e1a26ea3
commit 377565226d
Notes: svn2git 2021-03-31 03:12:20 +00:00 
svn path=/head/; revision=481406
19 changed files with 524 additions and 962 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
MOVED
View File

@ -10566,3 +10566,4 @@ math/arpack-ng-mpich|math/arpack-ng|2018-10-04|math/arpack-ng-mpich slave port i
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

1
biology/Makefile
View File

@ -131,7 +131,6 @@
SUBDIR += tRNAscan-SE
SUBDIR += t_coffee
SUBDIR += tabixpp
SUBDIR += tinker
SUBDIR += treepuzzle
SUBDIR += trimadap
SUBDIR += trimmomatic

67
biology/tinker/Makefile
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@ -1,67 +0,0 @@
# Created by: Glenn Johnson
# $FreeBSD$
PORTNAME= tinker
PORTVERSION= 7.1.3
PORTREVISION= 5
CATEGORIES= biology
MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/
MAINTAINER= ports@FreeBSD.org
COMMENT= General purpose molecular modelling package
LICENSE= tinker
LICENSE_NAME= TINKER license agreement
LICENSE_FILE= ${WRKSRC}/doc/license.txt
LICENSE_PERMS= auto-accept
RESTRICTED= author requests no distribution except from his FTP site
OPTIONS_DEFINE= OPTIMIZED_FFLAGS DOCS EXAMPLES
OPTIMIZED_FFLAGS_DESC= compilation optimizations
WRKSRC= ${WRKDIR}/${PORTNAME}
BUILD_WRKSRC= ${WRKSRC}/source
INSTALL_WRKSRC= ${WRKSRC}/source
USES= fortran
MAKE_ENV= HAVE_G2C=yes
MAKEFILE= ${WRKSRC}/make/Makefile
ALL_TARGET= all
INSTALL_TARGET= rename
EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx
SUB_FILES= pkg-message
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS}
FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations
.if (${ARCH} == "i386")
FFLAGS+= -mfancy-math-387 -malign-double
.endif # i386
.endif
pre-build:
@${RM} ${BUILD_WRKSRC}/*.c
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)
post-install-DOCS-on:
${MKDIR} ${STAGEDIR}${DOCSDIR}
(cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf *.txt ${STAGEDIR}${DOCSDIR})
post-install-EXAMPLES-on:
${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
(cd ${WRKSRC}/example && ${INSTALL_DATA} \
0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \
${STAGEDIR}${EXAMPLESDIR})
.include <bsd.port.mk>

2
biology/tinker/distinfo
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@ -1,2 +0,0 @@
SHA256 (tinker-7.1.3.tar.gz) = c221459ac1ac423ed8c99c7ba67eaab09821c970333cd2841efb20ccbfd59095
SIZE (tinker-7.1.3.tar.gz) = 28655947

5
biology/tinker/files/patch-bench__bench1.run
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@ -1,5 +0,0 @@
--- bench/bench1.run.orig 2015-05-08 20:57:45 UTC
+++ bench/bench1.run
@@ -1 +1 @@
-../bin/timer bench1 100 y
+timer bench1 1 y

5
biology/tinker/files/patch-bench__bench2.run
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@ -1,5 +0,0 @@
--- bench/bench2.run.orig 2015-05-08 20:57:45 UTC
+++ bench/bench2.run
@@ -1 +1 @@
-../bin/timer bench2 1000 y
+timer bench2 1 y

5
biology/tinker/files/patch-bench__bench3.run
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@ -1,5 +0,0 @@
--- bench/bench3.run.orig Wed Sep 5 14:00:09 2001
+++ bench/bench3.run Wed Sep 5 14:01:27 2001
@@ -1 +1 @@
-time ../bin/vibrate bench3 0
+time vibrate bench3 0

5
biology/tinker/files/patch-bench__bench4.run
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@ -1,5 +0,0 @@
--- bench/bench4.run.orig 2014-12-16 05:17:53.000000000 +0200
+++ bench/bench4.run 2014-12-28 18:56:02.000000000 +0200
@@ -1 +1 @@
-time ../bin/dynamic bench4 1000 1.0 10.0 2 298.0
+time dynamic bench4 1000 1.0 10.0 2 298.0

5
biology/tinker/files/patch-bench__bench5.run
View File

@ -1,5 +0,0 @@
--- bench/bench5.run.orig 2014-12-16 05:17:53.000000000 +0200
+++ bench/bench5.run 2014-12-28 18:58:45.000000000 +0200
@@ -1 +1 @@
-time ../bin/dynamic bench5 1000 1.0 10.0 2 298.0
+time dynamic bench5 1000 1.0 10.0 2 298.0

235
biology/tinker/files/patch-make__Makefile
View File

@ -1,235 +0,0 @@
--- 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
-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:
- mv alchemy.x $(BINDIR)/alchemy
- mv analyze.x $(BINDIR)/analyze
- mv anneal.x $(BINDIR)/anneal
- mv archive.x $(BINDIR)/archive
- mv bar.x $(BINDIR)/bar
- mv correlate.x $(BINDIR)/correlate
- mv crystal.x $(BINDIR)/crystal
- mv diffuse.x $(BINDIR)/diffuse
- mv distgeom.x $(BINDIR)/distgeom
- mv document.x $(BINDIR)/document
- mv dynamic.x $(BINDIR)/dynamic
- mv gda.x $(BINDIR)/gda
- mv intedit.x $(BINDIR)/intedit
- mv intxyz.x $(BINDIR)/intxyz
- mv minimize.x $(BINDIR)/minimize
- mv minirot.x $(BINDIR)/minirot
- mv minrigid.x $(BINDIR)/minrigid
- mv molxyz.x $(BINDIR)/molxyz
- mv monte.x $(BINDIR)/monte
- mv newton.x $(BINDIR)/newton
- mv newtrot.x $(BINDIR)/newtrot
- mv nucleic.x $(BINDIR)/nucleic
- mv optimize.x $(BINDIR)/optimize
- mv optirot.x $(BINDIR)/optirot
- mv optrigid.x $(BINDIR)/optrigid
- mv path.x $(BINDIR)/path
- mv pdbxyz.x $(BINDIR)/pdbxyz
- mv polarize.x $(BINDIR)/polarize
- mv poledit.x $(BINDIR)/poledit
- mv potential.x $(BINDIR)/potential
- mv prmedit.x $(BINDIR)/prmedit
- mv protein.x $(BINDIR)/protein
- mv pss.x $(BINDIR)/pss
- mv pssrigid.x $(BINDIR)/pssrigid
- mv pssrot.x $(BINDIR)/pssrot
- mv radial.x $(BINDIR)/radial
- mv saddle.x $(BINDIR)/saddle
- mv scan.x $(BINDIR)/scan
- mv sniffer.x $(BINDIR)/sniffer
- 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
- mv testpol.x $(BINDIR)/testpol
- mv testrot.x $(BINDIR)/testrot
- mv timer.x $(BINDIR)/timer
- mv timerot.x $(BINDIR)/timerot
- mv torsfit.x $(BINDIR)/torsfit
- mv valence.x $(BINDIR)/valence
- mv vibbig.x $(BINDIR)/vibbig
- mv vibrate.x $(BINDIR)/vibrate
- mv vibrot.x $(BINDIR)/vibrot
- mv xtalfit.x $(BINDIR)/xtalfit
- mv xtalmin.x $(BINDIR)/xtalmin
- mv xyzedit.x $(BINDIR)/xyzedit
- mv xyzint.x $(BINDIR)/xyzint
- 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} anneal.x $(BINDIR)/anneal
+ ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive
+ ${BSD_INSTALL_PROGRAM} bar.x $(BINDIR)/bar
+ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate
+ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal
+ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse
+ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom
+ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document
+ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic
+ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda
+ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit
+ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz
+ ${BSD_INSTALL_PROGRAM} minimize.x $(BINDIR)/minimize
+ ${BSD_INSTALL_PROGRAM} minirot.x $(BINDIR)/minirot
+ ${BSD_INSTALL_PROGRAM} minrigid.x $(BINDIR)/minrigid
+ ${BSD_INSTALL_PROGRAM} molxyz.x $(BINDIR)/molxyz
+ ${BSD_INSTALL_PROGRAM} monte.x $(BINDIR)/monte
+ ${BSD_INSTALL_PROGRAM} newton.x $(BINDIR)/newton
+ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot
+ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic
+ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize
+ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot
+ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid
+ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path
+ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz
+ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize
+ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit
+ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential
+ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit
+ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein
+ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss
+ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid
+ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot
+ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial
+ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle
+ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan
+ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer
+ ${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
+ ${BSD_INSTALL_PROGRAM} testpol.x $(BINDIR)/testpol
+ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot
+ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer
+ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot
+ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit
+ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence
+ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig
+ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate
+ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot
+ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit
+ ${BSD_INSTALL_PROGRAM} xtalmin.x $(BINDIR)/xtalmin
+ ${BSD_INSTALL_PROGRAM} xyzedit.x $(BINDIR)/xyzedit
+ ${BSD_INSTALL_PROGRAM} xyzint.x $(BINDIR)/xyzint
+ ${BSD_INSTALL_PROGRAM} xyzpdb.x $(BINDIR)/xyzpdb
+ ${BSD_INSTALL_PROGRAM} xyzsybyl.x $(BINDIR)/xyzsybyl
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

631
biology/tinker/pkg-plist
View File

@ -1,631 +0,0 @@
bin/alchemy
bin/analyze_t
bin/anneal
bin/archive
bin/bar
bin/correlate
bin/crystal
bin/diffuse
bin/distgeom
bin/document
bin/dynamic
bin/gda
bin/intedit
bin/intxyz
bin/minimize
bin/minirot
bin/minrigid
bin/molxyz
bin/monte
bin/newton
bin/newtrot
bin/nucleic
bin/optimize
bin/optirot
bin/optrigid
bin/path
bin/pdbxyz
bin/polarize
bin/poledit
bin/potential
bin/prmedit
bin/protein
bin/pss
bin/pssrigid
bin/pssrot
bin/radial
bin/saddle
bin/scan
bin/sniffer
bin/spacefill
bin/spectrum
bin/superpose
bin/sybylxyz
bin/testgrad
bin/testhess
bin/testpair
bin/testpol
bin/testrot
bin/timer
bin/timerot
bin/torsfit
bin/valence
bin/vibbig
bin/vibrate
bin/vibrot
bin/xtalfit
bin/xtalmin
bin/xyzedit
bin/xyzint
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
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/aspirin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/arach.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/azulene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.make
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bdna.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bearing2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzamidine.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzamidine.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzbox.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzbox.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/benzene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/book.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/book.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bowl3.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/bucky.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butane2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanes.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butanex.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/butopls2.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c5.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7a.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.int
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/c7e.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cage.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cage.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/calmodulin.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cawater.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.make
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.pdb
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.seq
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cln025.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/copper.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.key
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/cpentene.xyz
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.dyn
%%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.key
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%%DATADIR%%/test/ifabp.key
%%DATADIR%%/test/ifabp.log
%%DATADIR%%/test/ifabp.run
%%DATADIR%%/test/ifabp.xyz
%%DATADIR%%/test/nitrogen.arc
%%DATADIR%%/test/nitrogen.key
%%DATADIR%%/test/nitrogen.log
%%DATADIR%%/test/nitrogen.run
%%DATADIR%%/test/nitrogen.xyz
%%DATADIR%%/test/salt.cell
%%DATADIR%%/test/salt.key
%%DATADIR%%/test/salt.log
%%DATADIR%%/test/salt.run
%%DATADIR%%/test/tetraala.dat
%%DATADIR%%/test/tetraala.key
%%DATADIR%%/test/tetraala.log
%%DATADIR%%/test/tetraala.run
%%DATADIR%%/test/water.key
%%DATADIR%%/test/water.log
%%DATADIR%%/test/water.pot
%%DATADIR%%/test/water.run
%%DATADIR%%/test/water.xyz

1
science/Makefile
View File

@ -276,6 +276,7 @@
SUBDIR += szip
SUBDIR += teem
SUBDIR += tfel
SUBDIR += tinker
SUBDIR += triqs
SUBDIR += udunits
SUBDIR += v_sim

77
science/tinker/Makefile Normal file
View File

@ -0,0 +1,77 @@
# Created by: Glenn Johnson
# $FreeBSD$
PORTNAME= tinker
DISTVERSION= 8.4.4
CATEGORIES= science
MASTER_SITES= https://dasher.wustl.edu/tinker/downloads/
MAINTAINER= yuri@FreeBSD.org
COMMENT= General purpose molecular modelling package
LICENSE= TINKER
LICENSE_NAME= TINKER license agreement
LICENSE_FILE= ${WRKSRC}/doc/license.pdf
LICENSE_PERMS= auto-accept # internal academic purposes only, no commercial use
OPTIONS_DEFINE= OPTIMIZED_FFLAGS DOCS EXAMPLES
OPTIMIZED_FFLAGS_DESC= compilation optimizations
WRKSRC= ${WRKDIR}/${PORTNAME}
BUILD_WRKSRC= ${WRKSRC}/source
INSTALL_WRKSRC= ${WRKSRC}/source
LIB_DEPENDS= libfftw3.so:math/fftw3
USES= fortran gmake
MAKE_ENV= HAVE_G2C=yes
MAKE_ARGS= RANLIB=ranlib BINDIR=${STAGEDIR}${PREFIX}/bin
MAKEFILE= ${WRKSRC}/make/Makefile
EXTRACT_AFTER_ARGS=--exclude fftw --exclude windows --exclude macosx
SUB_FILES= pkg-message
BINARY_ALIAS= gfortran=gfortran${GCC_DEFAULT}
PORTDOCS= *
PORTEXAMPLES= *
.include <bsd.port.options.mk>
.if ${PORT_OPTIONS:MOPTIMIZED_FFLAGS}
FFLAGS+= -O3 -ffast-math -finline-functions -fomit-frame-pointer -funroll-loops -fexpensive-optimizations
.if (${ARCH} == "i386")
FFLAGS+= -mfancy-math-387 -malign-double
.endif # i386
.endif
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}/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 ${STAGEDIR}${DOCSDIR}
post-install-EXAMPLES-on:
@${MKDIR} ${STAGEDIR}${EXAMPLESDIR}
cd ${WRKSRC}/example && ${INSTALL_DATA} \
0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \
${STAGEDIR}${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>

3
science/tinker/distinfo Normal file
View File

@ -0,0 +1,3 @@
TIMESTAMP = 1538861663
SHA256 (tinker-8.4.4.tar.gz) = c263298383bcd5a72f281d25640f7be2e9c465e08c1a61c3c3de59b6bb828da6
SIZE (tinker-8.4.4.tar.gz) = 35549655

255
science/tinker/files/patch-make_Makefile Normal file
View File

@ -0,0 +1,255 @@
--- make/Makefile.orig 2018-10-06 22:01:02 UTC
+++ make/Makefile
@@ -754,130 +754,130 @@ listing:
cat *.f *.c > tinker.txt
rename_bin:
- mv alchemy.x $(BINDIR)/alchemy
- mv analyze.x $(BINDIR)/analyze
- mv anneal.x $(BINDIR)/anneal
- mv archive.x $(BINDIR)/archive
- mv bar.x $(BINDIR)/bar
- mv correlate.x $(BINDIR)/correlate
- mv crystal.x $(BINDIR)/crystal
- mv diffuse.x $(BINDIR)/diffuse
- mv distgeom.x $(BINDIR)/distgeom
- mv document.x $(BINDIR)/document
- mv dynamic.x $(BINDIR)/dynamic
- mv gda.x $(BINDIR)/gda
- mv intedit.x $(BINDIR)/intedit
- mv intxyz.x $(BINDIR)/intxyz
- 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
- mv newtrot.x $(BINDIR)/newtrot
- mv nucleic.x $(BINDIR)/nucleic
- mv optimize.x $(BINDIR)/optimize
- mv optirot.x $(BINDIR)/optirot
- mv optrigid.x $(BINDIR)/optrigid
- mv path.x $(BINDIR)/path
- mv pdbxyz.x $(BINDIR)/pdbxyz
- mv polarize.x $(BINDIR)/polarize
- mv poledit.x $(BINDIR)/poledit
- mv potential.x $(BINDIR)/potential
- mv prmedit.x $(BINDIR)/prmedit
- mv protein.x $(BINDIR)/protein
- mv pss.x $(BINDIR)/pss
- mv pssrigid.x $(BINDIR)/pssrigid
- mv pssrot.x $(BINDIR)/pssrot
- mv radial.x $(BINDIR)/radial
- mv saddle.x $(BINDIR)/saddle
- mv scan.x $(BINDIR)/scan
- mv sniffer.x $(BINDIR)/sniffer
- mv spacefill.x $(BINDIR)/spacefill
- mv spectrum.x $(BINDIR)/spectrum
- mv superpose.x $(BINDIR)/superpose
- mv testgrad.x $(BINDIR)/testgrad
- mv testhess.x $(BINDIR)/testhess
- mv testpair.x $(BINDIR)/testpair
- mv testpol.x $(BINDIR)/testpol
- mv testrot.x $(BINDIR)/testrot
- mv timer.x $(BINDIR)/timer
- mv timerot.x $(BINDIR)/timerot
- mv torsfit.x $(BINDIR)/torsfit
- mv valence.x $(BINDIR)/valence
- mv vibbig.x $(BINDIR)/vibbig
- mv vibrate.x $(BINDIR)/vibrate
- mv vibrot.x $(BINDIR)/vibrot
- mv xtalfit.x $(BINDIR)/xtalfit
- 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
+ ${BSD_INSTALL_PROGRAM} alchemy.x $(BINDIR)/alchemy
+ ${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
+ ${BSD_INSTALL_PROGRAM} correlate.x $(BINDIR)/correlate
+ ${BSD_INSTALL_PROGRAM} crystal.x $(BINDIR)/crystal
+ ${BSD_INSTALL_PROGRAM} diffuse.x $(BINDIR)/diffuse
+ ${BSD_INSTALL_PROGRAM} distgeom.x $(BINDIR)/distgeom
+ ${BSD_INSTALL_PROGRAM} document.x $(BINDIR)/document
+ ${BSD_INSTALL_PROGRAM} dynamic.x $(BINDIR)/dynamic
+ ${BSD_INSTALL_PROGRAM} gda.x $(BINDIR)/gda
+ ${BSD_INSTALL_PROGRAM} intedit.x $(BINDIR)/intedit
+ ${BSD_INSTALL_PROGRAM} intxyz.x $(BINDIR)/intxyz
+ ${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
+ ${BSD_INSTALL_PROGRAM} newtrot.x $(BINDIR)/newtrot
+ ${BSD_INSTALL_PROGRAM} nucleic.x $(BINDIR)/nucleic
+ ${BSD_INSTALL_PROGRAM} optimize.x $(BINDIR)/optimize
+ ${BSD_INSTALL_PROGRAM} optirot.x $(BINDIR)/optirot
+ ${BSD_INSTALL_PROGRAM} optrigid.x $(BINDIR)/optrigid
+ ${BSD_INSTALL_PROGRAM} path.x $(BINDIR)/path
+ ${BSD_INSTALL_PROGRAM} pdbxyz.x $(BINDIR)/pdbxyz
+ ${BSD_INSTALL_PROGRAM} polarize.x $(BINDIR)/polarize
+ ${BSD_INSTALL_PROGRAM} poledit.x $(BINDIR)/poledit
+ ${BSD_INSTALL_PROGRAM} potential.x $(BINDIR)/potential
+ ${BSD_INSTALL_PROGRAM} prmedit.x $(BINDIR)/prmedit
+ ${BSD_INSTALL_PROGRAM} protein.x $(BINDIR)/protein
+ ${BSD_INSTALL_PROGRAM} pss.x $(BINDIR)/pss
+ ${BSD_INSTALL_PROGRAM} pssrigid.x $(BINDIR)/pssrigid
+ ${BSD_INSTALL_PROGRAM} pssrot.x $(BINDIR)/pssrot
+ ${BSD_INSTALL_PROGRAM} radial.x $(BINDIR)/radial
+ ${BSD_INSTALL_PROGRAM} saddle.x $(BINDIR)/saddle
+ ${BSD_INSTALL_PROGRAM} scan.x $(BINDIR)/scan
+ ${BSD_INSTALL_PROGRAM} sniffer.x $(BINDIR)/sniffer
+ ${BSD_INSTALL_PROGRAM} spacefill.x $(BINDIR)/spacefill
+ ${BSD_INSTALL_PROGRAM} spectrum.x $(BINDIR)/spectrum
+ ${BSD_INSTALL_PROGRAM} superpose.x $(BINDIR)/superpose
+ ${BSD_INSTALL_PROGRAM} testgrad.x $(BINDIR)/testgrad
+ ${BSD_INSTALL_PROGRAM} testhess.x $(BINDIR)/testhess
+ ${BSD_INSTALL_PROGRAM} testpair.x $(BINDIR)/testpair
+ ${BSD_INSTALL_PROGRAM} testpol.x $(BINDIR)/testpol
+ ${BSD_INSTALL_PROGRAM} testrot.x $(BINDIR)/testrot
+ ${BSD_INSTALL_PROGRAM} timer.x $(BINDIR)/timer
+ ${BSD_INSTALL_PROGRAM} timerot.x $(BINDIR)/timerot
+ ${BSD_INSTALL_PROGRAM} torsfit.x $(BINDIR)/torsfit
+ ${BSD_INSTALL_PROGRAM} valence.x $(BINDIR)/valence
+ ${BSD_INSTALL_PROGRAM} vibbig.x $(BINDIR)/vibbig
+ ${BSD_INSTALL_PROGRAM} vibrate.x $(BINDIR)/vibrate
+ ${BSD_INSTALL_PROGRAM} vibrot.x $(BINDIR)/vibrot
+ ${BSD_INSTALL_PROGRAM} xtalfit.x $(BINDIR)/xtalfit
+ ${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
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

0
biology/tinker/files/patch-source_openend.f → science/tinker/files/patch-source_openend.f
View File

0
biology/tinker/files/pkg-message.in → science/tinker/files/pkg-message.in
View File

2
biology/tinker/pkg-descr → science/tinker/pkg-descr
View File

@ -13,4 +13,4 @@ is set too large that tinker programs will abort and core dump.
For more information about Tinker see:
WWW: http://dasher.wustl.edu/tinker/
WWW: https://dasher.wustl.edu/tinker/

186
science/tinker/pkg-plist Normal file
View File

@ -0,0 +1,186 @@
bin/alchemy
bin/analyze
bin/anneal
bin/archive
bin/bar
bin/correlate
bin/crystal
bin/diffuse
bin/distgeom
bin/document
bin/dynamic
bin/gda
bin/intedit
bin/intxyz
bin/minimize
bin/minirot
bin/minrigid
bin/mol2xyz
bin/molxyz
bin/monte
bin/newton
bin/newtrot
bin/nucleic
bin/optimize
bin/optirot
bin/optrigid
bin/path
bin/pdbxyz
bin/polarize
bin/poledit
bin/potential
bin/prmedit
bin/protein
bin/pss
bin/pssrigid
bin/pssrot
bin/radial
bin/saddle
bin/scan
bin/sniffer
bin/spacefill
bin/spectrum
bin/superpose
bin/testgrad
bin/testhess
bin/testpair
bin/testpol
bin/testrot
bin/timer
bin/timerot
bin/torsfit
bin/valence
bin/vibbig
bin/vibrate
bin/vibrot
bin/xtalfit
bin/xtalmin
bin/xyzedit
bin/xyzint
bin/xyzmol2
bin/xyzpdb
%%DATADIR%%/params/0README
%%DATADIR%%/params/amber94.prm
%%DATADIR%%/params/amber96.prm
%%DATADIR%%/params/amber98.prm
%%DATADIR%%/params/amber99.prm
%%DATADIR%%/params/amber99sb.prm
%%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
%%DATADIR%%/params/charmm22.prm
%%DATADIR%%/params/charmm22cmap.prm
%%DATADIR%%/params/dang.prm
%%DATADIR%%/params/hoch.prm
%%DATADIR%%/params/iwater.prm
%%DATADIR%%/params/mm2.prm
%%DATADIR%%/params/mm3.prm
%%DATADIR%%/params/mm3pro.prm
%%DATADIR%%/params/mmff.prm
%%DATADIR%%/params/oplsaa.prm
%%DATADIR%%/params/oplsaal.prm
%%DATADIR%%/params/oplsua.prm
%%DATADIR%%/params/smoothaa.prm
%%DATADIR%%/params/smoothua.prm
%%DATADIR%%/params/tiny.prm
%%DATADIR%%/params/water03.prm
%%DATADIR%%/params/water14.prm
%%DATADIR%%/test/0README
%%DATADIR%%/test/anion.dat
%%DATADIR%%/test/anion.dyn0
%%DATADIR%%/test/anion.key
%%DATADIR%%/test/anion.log
%%DATADIR%%/test/anion.run
%%DATADIR%%/test/anion.xyz
%%DATADIR%%/test/argon.1st
%%DATADIR%%/test/argon.key
%%DATADIR%%/test/argon.log
%%DATADIR%%/test/argon.run
%%DATADIR%%/test/cluster.dat
%%DATADIR%%/test/cluster.key
%%DATADIR%%/test/cluster.log
%%DATADIR%%/test/cluster.run
%%DATADIR%%/test/cluster.xyz
%%DATADIR%%/test/crambin.key
%%DATADIR%%/test/crambin.log
%%DATADIR%%/test/crambin.pdb
%%DATADIR%%/test/crambin.run
%%DATADIR%%/test/cyclohex.boat
%%DATADIR%%/test/cyclohex.chair
%%DATADIR%%/test/cyclohex.key
%%DATADIR%%/test/cyclohex.log
%%DATADIR%%/test/cyclohex.run
%%DATADIR%%/test/dhfr.dyn
%%DATADIR%%/test/dhfr.key
%%DATADIR%%/test/dhfr.log
%%DATADIR%%/test/dhfr.run
%%DATADIR%%/test/dhfr.xyz
%%DATADIR%%/test/dialanine.key
%%DATADIR%%/test/dialanine.log
%%DATADIR%%/test/dialanine.run
%%DATADIR%%/test/dialanine.xyz
%%DATADIR%%/test/enkephalin.dat
%%DATADIR%%/test/enkephalin.key
%%DATADIR%%/test/enkephalin.log
%%DATADIR%%/test/enkephalin.run
%%DATADIR%%/test/ethanol.000
%%DATADIR%%/test/ethanol.020
%%DATADIR%%/test/ethanol.040
%%DATADIR%%/test/ethanol.060
%%DATADIR%%/test/ethanol.080
%%DATADIR%%/test/ethanol.100
%%DATADIR%%/test/ethanol.120
%%DATADIR%%/test/ethanol.140
%%DATADIR%%/test/ethanol.160
%%DATADIR%%/test/ethanol.180
%%DATADIR%%/test/ethanol.dat
%%DATADIR%%/test/ethanol.key
%%DATADIR%%/test/ethanol.log
%%DATADIR%%/test/ethanol.run
%%DATADIR%%/test/ethanol.xyz
%%DATADIR%%/test/formamide.cell
%%DATADIR%%/test/formamide.dat
%%DATADIR%%/test/formamide.key
%%DATADIR%%/test/formamide.log
%%DATADIR%%/test/formamide.run
%%DATADIR%%/test/gpcr.blk
%%DATADIR%%/test/gpcr.key
%%DATADIR%%/test/gpcr.log
%%DATADIR%%/test/gpcr.run
%%DATADIR%%/test/gpcr.xyz
%%DATADIR%%/test/helix.1st
%%DATADIR%%/test/helix.key
%%DATADIR%%/test/helix.log
%%DATADIR%%/test/helix.run
%%DATADIR%%/test/ice.key
%%DATADIR%%/test/ice.log
%%DATADIR%%/test/ice.run
%%DATADIR%%/test/ice.xyz
%%DATADIR%%/test/ifabp.dat
%%DATADIR%%/test/ifabp.key
%%DATADIR%%/test/ifabp.log
%%DATADIR%%/test/ifabp.run
%%DATADIR%%/test/ifabp.xyz
%%DATADIR%%/test/nitrogen.arc
%%DATADIR%%/test/nitrogen.key
%%DATADIR%%/test/nitrogen.log
%%DATADIR%%/test/nitrogen.run
%%DATADIR%%/test/nitrogen.xyz
%%DATADIR%%/test/salt.cell
%%DATADIR%%/test/salt.key
%%DATADIR%%/test/salt.log
%%DATADIR%%/test/salt.run
%%DATADIR%%/test/tetraala.dat
%%DATADIR%%/test/tetraala.key
%%DATADIR%%/test/tetraala.log
%%DATADIR%%/test/tetraala.run
%%DATADIR%%/test/water.key
%%DATADIR%%/test/water.log
%%DATADIR%%/test/water.pot
%%DATADIR%%/test/water.run
%%DATADIR%%/test/water.xyz