Index: head/biology/tinker/Makefile =================================================================== --- head/biology/tinker/Makefile (revision 315139) +++ head/biology/tinker/Makefile (revision 315140) @@ -1,74 +1,68 @@ # Created by: Glenn Johnson # $FreeBSD$ PORTNAME= tinker -PORTVERSION= 6.1.01 +PORTVERSION= 6.2.01 CATEGORIES= biology MASTER_SITES= http://dasher.wustl.edu/tinker/downloads/ MAINTAINER= ports@FreeBSD.org COMMENT= A general purpose molecular modelling package RESTRICTED= author requests no distribution except from his FTP site -OPTIONS_DEFINE= OPTIMIZED_FFLAGS DATA DOCS EXAMPLES -OPTIONS_DEFAULT=DATA +OPTIONS_DEFINE= OPTIMIZED_FFLAGS DOCS EXAMPLES OPTIMIZED_FFLAGS_DESC= compilation optimizations WRKSRC= ${WRKDIR}/${PORTNAME} BUILD_WRKSRC= ${WRKSRC}/source INSTALL_WRKSRC= ${WRKSRC}/source USE_FORTRAN= yes MAKE_ENV= HAVE_G2C=yes MAKEFILE= ${WRKSRC}/make/Makefile ALL_TARGET= all listing INSTALL_TARGET= rename MAKE_JOBS_SAFE= yes SUB_FILES= pkg-message -DOCS= 0README *.pdf *.txt -SAMPLES= 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz -BENCHES= 0README *.dyn0 *.log *.key *.run *.xyz results* .include .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 -.if empty(PORT_OPTIONS:MDATA) -NOPORTDATA= yes -.endif - post-extract: @${CHMOD} -R u+w ${WRKSRC} post-install: @${MKDIR} ${DATADIR} - ${INSTALL_DATA} ${INSTALL_WRKSRC}/tinker.txt ${DATADIR} - @${MKDIR} ${DATADIR}/params - ${INSTALL_DATA} ${WRKSRC}/params/* ${DATADIR}/params -.if ${PORT_OPTIONS:MDATA} + (cd ${INSTALL_WRKSRC} && ${INSTALL_DATA} tinker.txt ${DATADIR}) @${MKDIR} ${DATADIR}/bench - ${INSTALL_DATA} ${BENCHES:S|^|${WRKSRC}/bench/|} ${DATADIR}/bench + (cd ${WRKSRC}/bench && ${INSTALL_DATA} \ + 0README *.dyn0 *.log *.key *.run *.xyz results* \ + ${DATADIR}/bench) + @${MKDIR} ${DATADIR}/params + (cd ${WRKSRC}/params && ${INSTALL_DATA} * ${DATADIR}/params) @${MKDIR} ${DATADIR}/test - ${INSTALL_DATA} ${WRKSRC}/test/* ${DATADIR}/test -.endif + (cd ${WRKSRC}/test && ${INSTALL_DATA} * ${DATADIR}/test) .if ${PORT_OPTIONS:MDOCS} @${MKDIR} ${DOCSDIR} - ${INSTALL_DATA} ${DOCS:S|^|${WRKSRC}/doc/|} ${DOCSDIR} + (cd ${WRKSRC}/doc && ${INSTALL_DATA} 0README *.pdf *.txt ${DOCSDIR}) .endif .if ${PORT_OPTIONS:MEXAMPLES} @${MKDIR} ${EXAMPLESDIR} - ${INSTALL_DATA} ${SAMPLES:S|^|${WRKSRC}/example/|} ${EXAMPLESDIR} + (cd ${WRKSRC}/example && ${INSTALL_DATA} \ + 0README *.make *.dyn *.int *.frac *.key *.seq *.pdb *.xyz \ + ${EXAMPLESDIR}) .endif @${ECHO_CMD} @${CAT} ${PKGMESSAGE} @${ECHO_CMD} .include Index: head/biology/tinker/distinfo =================================================================== --- head/biology/tinker/distinfo (revision 315139) +++ head/biology/tinker/distinfo (revision 315140) @@ -1,2 +1,2 @@ -SHA256 (tinker-6.1.01.tar.gz) = fa287c381fd866822b19396fa152406b8463421f0a27902867cdbbf6b67233e4 -SIZE (tinker-6.1.01.tar.gz) = 19478639 +SHA256 (tinker-6.2.01.tar.gz) = a19fd7e1b5afa7b55245b50f3358c43ae88efd664185ca32506e5ee9d504c88d +SIZE (tinker-6.2.01.tar.gz) = 19561083 Index: head/biology/tinker/files/patch-make__Makefile =================================================================== --- head/biology/tinker/files/patch-make__Makefile (revision 315139) +++ head/biology/tinker/files/patch-make__Makefile (revision 315140) @@ -1,211 +1,202 @@ --- make/Makefile.orig 2012-06-29 14:51:42.000000000 +0900 +++ make/Makefile 2012-11-10 00:12:19.000000000 +0900 -@@ -9,8 +9,8 @@ - ## - ## 1. make all Build all the TINKER executables - ## 2. make rename Move the executables to BINDIR --## 3. make remove_links Create soft links in LINKDIR --## 4. make create_links Remove soft links from LINKDIR -+## 3. make remove_links Remove soft links in LINKDIR -+## 4. make create_links Create soft links from LINKDIR - ## 6. make listing Concatenate source to tinker.txt - ## 5. make clean Delete objects and executables - ## @@ -30,9 +30,9 @@ ## LINKDIR Linked Copies of TINKER Executables ## -TINKERDIR = /Users/ponder/tinker -BINDIR = $(TINKERDIR)/bin -LINKDIR = /usr/local/bin +TINKERDIR = ${WRKDIR} +BINDIR = ${PREFIX}/bin +#LINKDIR = /usr/local/bin #################################################################### ## Known Machine Types; Uncomment One of the Following Sections ## @@ -40,6 +40,20 @@ #################################################################### ## +## Machine: IntelPC / FreeBSD +## CPU Type: Intel, AMD, Cyrix +## Oper Sys: FreeBSD 4.2 +## Compiler: f77 , aka g77 +## + +F77 = ${FC} +LIBS = +F77FLAGS = -c ${FFLAGS} +LINKFLAGS = ${LDFLAGS} +OPTFLAGS = +LIBFLAGS = -rcuv + +## ## Machine: Generic Linux ## CPU Type: Intel x86 Compatible ## Oper Sys: Fedora Core @@ -104,12 +118,12 @@ ## Parallel: OpenMP ## -F77 = /opt/intel/bin/ifort -LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3 -F77FLAGS = -c -axSSSE3 -assume cc_omp -OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp -LIBFLAGS = -crusv -LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4 +#F77 = /opt/intel/bin/ifort +#LIBS = -L$(TINKERDIR)/fftw/lib -lfftw3_omp -lfftw3 +#F77FLAGS = -c -axSSSE3 -assume cc_omp +#OPTFLAGS = -O3 -no-ipo -no-prec-div -openmp +#LIBFLAGS = -crusv +#LINKFLAGS = $(OPTFLAGS) -static-intel -mmacosx-version-min=10.4 ## ## Machine: Macintosh -@@ -592,6 +606,8 @@ +@@ -595,6 +609,8 @@ xyzpdb.x \ xyzsybyl.x +.SUFFIXES: .x + .f.o: ${F77} ${F77FLAGS} ${OPTFLAGS} $*.f -@@ -601,8 +617,8 @@ +@@ -604,8 +620,8 @@ server.o: ${F77} ${F77FLAGS} ${OPTFLAGS} server.f -%.x: %.o libtinker.a - ${F77} ${LINKFLAGS} -o $@ $^ ${LIBS}; strip $@ +.o.x: libtinker.a + ${F77} ${LINKFLAGS} -o $@ $< libtinker.a ${LIBS} all: ${EXEFILES} -@@ -613,65 +629,65 @@ +@@ -616,66 +632,66 @@ cat *.i *.f *.c > tinker.txt rename: - mv alchemy.x $(BINDIR)/alchemy - mv analyze.x $(BINDIR)/analyze - mv anneal.x $(BINDIR)/anneal - mv archive.x $(BINDIR)/archive - 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 + ${BSD_INSTALL_PROGRAM} anneal.x $(BINDIR)/anneal + ${BSD_INSTALL_PROGRAM} archive.x $(BINDIR)/archive + ${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 Index: head/biology/tinker/files/pkg-message.in =================================================================== --- head/biology/tinker/files/pkg-message.in (revision 315139) +++ head/biology/tinker/files/pkg-message.in (revision 315140) @@ -1,6 +1,6 @@ ********************************************************** The author requests that you return a license form to him if you find Tinker to be useful. See %%DOCSDIR%% for license forms. -**********************************************************" +********************************************************** Index: head/biology/tinker/pkg-plist =================================================================== --- head/biology/tinker/pkg-plist (revision 315139) +++ head/biology/tinker/pkg-plist (revision 315140) @@ -1,602 +1,613 @@ bin/alchemy bin/analyze bin/anneal bin/archive 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%%/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.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambin.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crambinx.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.int %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/crown.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.int %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cychept.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.int %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.int %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cyclo2.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/cycprop.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dang.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.int %%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.make %%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/deltorphin.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.pdb %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.seq %%PORTEXAMPLES%%%%EXAMPLESDIR%%/dhfr2.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/diamond.xyz %%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.int %%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.key %%PORTEXAMPLES%%%%EXAMPLESDIR%%/diene.xyz 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