From 5f0f9b3c0ad6c53d2c567c4cca6f3555b1805ecf Mon Sep 17 00:00:00 2001 From: Martin Wilke Date: Sat, 23 Dec 2006 21:45:17 +0000 Subject: - Update to 5.1.2 - Update maintainer mail adresse PR: ports/107118 Submitted by: M. L. Dodson (maintainer) --- biology/nab/Makefile | 45 ++-- biology/nab/distinfo | 6 +- biology/nab/files/config.h | 36 +-- biology/nab/files/patch-Makefile | 59 +++-- biology/nab/files/patch-configure | 11 + biology/nab/files/patch-examples:program_7.nab | 19 -- biology/nab/files/patch-src:wc_helix.nab | 11 + biology/nab/files/patch-src_Makefile | 8 +- biology/nab/files/patch-suppose_Makefile | 10 + biology/nab/pkg-descr | 5 +- biology/nab/pkg-plist | 334 ++++++++++++++----------- 11 files changed, 308 insertions(+), 236 deletions(-) create mode 100644 biology/nab/files/patch-configure delete mode 100644 biology/nab/files/patch-examples:program_7.nab create mode 100644 biology/nab/files/patch-src:wc_helix.nab create mode 100644 biology/nab/files/patch-suppose_Makefile (limited to 'biology') diff --git a/biology/nab/Makefile b/biology/nab/Makefile index ceac0e54df55..3df071abe00c 100644 --- a/biology/nab/Makefile +++ b/biology/nab/Makefile @@ -1,18 +1,16 @@ # New ports collection Makefile for: nab # Date created: Sept. 10, 2000 -# Whom: M. L. Dodson +# Whom: M. L. Dodson # # $FreeBSD$ # PORTNAME= nab -PORTVERSION= 5.0 -PORTREVISION= 1 +PORTVERSION= 5.1.2 CATEGORIES= biology -MASTER_SITES= http://www.scripps.edu/case/ \ - http://siegfried.utmb.edu/bdodson/ +MASTER_SITES= http://www.scripps.edu/mb/case/ -MAINTAINER= bdodson@scms.utmb.edu +MAINTAINER= mldodson@houston.rr.com COMMENT= A language for macromolecules BUILD_DEPENDS= ucpp:${PORTSDIR}/devel/ucpp @@ -21,35 +19,46 @@ RUN_DEPENDS= ucpp:${PORTSDIR}/devel/ucpp ONLY_FOR_ARCHS= i386 MAKE_ENV+= NABHOME=${WRKSRC} ARCH= PATH=${WRKSRC}/bin:${PATH} \ - CFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}" + CFLAGS="${CFLAGS}" OCFLAGS="${CFLAGS}" FFLAGS="${FFLAGS}" MAN1= nab.1 SUB_FILES= pkg-message -BINARIES= matextract matmul teLeap tss_main \ - matgen nab transform tss_next \ - matmerge nab2c tss_init +BINARIES= matmerge nab2c teLeap tss_main \ + matextract matmul transform tss_next \ + matgen nab tss_init -LIBRARIES= cifparse.a libnab.a libsym.a +LIBRARIES= cifparse.a libnab.a libsym.a -INCS= defreal.h nab.h nabcode.h nabtypes.h +INCS= defreal.h nab.h nabcode.h nabtypes.h -post-extract: +do-configure: @${CP} ${FILESDIR}/config.h ${WRKSRC} post-patch: @${RM} -f ${WRKSRC}/examples/circle.c @${RM} -f ${WRKSRC}/reslib/conf.lib.orig + @${RM} -f ${WRKSRC}/examples/program_7.nab.orig -pre-install: +do-build: + @cd ${WRKSRC} && \ + ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} install + @cd ${WRKSRC}/test && \ + ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} test + @cd ${WRKSRC}/nss && \ + ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} test + +build-general-version: @cd ${WRKSRC}/src && \ ${SETENV} ${MAKE_ENV} ${MAKE} ${MAKE_FLAGS} ${MAKEFILE} ${MAKE_ARGS} beforerealinstall -do-install: +do-install: build-general-version ${MKDIR} ${DATADIR}/bin ${DATADIR}/include ${DATADIR}/lib cd ${WRKSRC}/test && ${RM} -f d01.pdb gbrna.pdb.lpdb rembed.out + cd ${WRKSRC}/examples && ${RM} -f gcg10.pdb.save + cd ${WRKSRC}/leap/parm && ${RM} -f leap.log .if !defined(NOPORTDOCS) - cd ${WRKSRC} && (${TAR} cf - benchmarks examples test peptide suppose | \ + cd ${WRKSRC} && (${TAR} cf - benchmarks examples test | \ (cd ${DATADIR}; ${TAR} xf -)) ${MKDIR} ${DOCSDIR} ${INSTALL_DATA} ${WRKSRC}/doc/NAB.pdf ${DOCSDIR} @@ -72,11 +81,9 @@ do-install: ${INSTALL_DATA} ${WRKSRC}/lib/${f} ${PREFIX}/lib cd ${DATADIR}/lib && ${LN} -sf ${PREFIX}/lib/${f} . .endfor -.for f in blas.a lapack.a +.for f in blas.a lapack.a f2c.a ${INSTALL_DATA} ${WRKSRC}/lib/${f} ${DATADIR}/lib .endfor - -post-install: @${CAT} ${PKGMESSAGE} .include diff --git a/biology/nab/distinfo b/biology/nab/distinfo index 21d1a03b3167..16cf8d035e82 100644 --- a/biology/nab/distinfo +++ b/biology/nab/distinfo @@ -1,3 +1,3 @@ -MD5 (nab-5.0.tar.gz) = dfcde2ddaa833f4dc24d53c87b842cf9 -SHA256 (nab-5.0.tar.gz) = e7aaf3a870f22bc6d4125cdee92e7ad19042fbbc7e8fd1dba58528d91d4e7ffe -SIZE (nab-5.0.tar.gz) = 5853573 +MD5 (nab-5.1.2.tar.gz) = fc87da8a7f19832cfb4e88e6ac2b9a7f +SHA256 (nab-5.1.2.tar.gz) = 207579b78d08efa3c64796efc56b019ff2a41c035373d35d241af80ee812d625 +SIZE (nab-5.1.2.tar.gz) = 9886440 diff --git a/biology/nab/files/config.h b/biology/nab/files/config.h index 7dd5649fc85d..a3e4889166b3 100644 --- a/biology/nab/files/config.h +++ b/biology/nab/files/config.h @@ -1,4 +1,4 @@ -# NAB configuration file, created with: ./configure +# NAB configuration file, created with: ./configure -p4 -static gcc ############################################################################### @@ -19,14 +19,14 @@ INCDIR=$(NABHOME)/include # NAB programs simply by including them on the command line; libraries # included in FLIBS are always searched.) -FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a -lg2c +FLIBS= $(LIBDIR)/libsym.a $(LIBDIR)/lapack.a $(LIBDIR)/blas.a $(LIBDIR)/f2c.a -static ############################################################################### # (3) Modify any of the following if you need to change, e.g. to use gcc # rather than cc, etc. -SHELL= /bin/sh +SHELL=/bin/sh # Set the C compiler, etc. @@ -37,32 +37,36 @@ SHELL= /bin/sh # so LEX=flex is necessary. In general, gcc seems to need # flex. -CC?= cc -CFLAGS?= -OCFLAGS=${CFLAGS} -NABFLAGS?= +NABFLAGS= LEX= flex YACC= yacc -AR= ar -RANLIB= ranlib +AR= ar +RANLIB= ranlib # Set the C-preprocessor. Code for a small preprocessor is in # uccp-1.3; it gets installed as $(NABHOME)/bin/ucpp; -# this should generally *not* be changed. +# this can generally be used (maybe not on 64-bit machines like altix). -CPP= ucpp -l +CPP= /usr/local/bin/ucpp -l -# If you are going to use the Fortran lapack and blas libraries, you need +# If you are going to link in Fortran routines, you need # to set the compiler information here. (Also, add the appropriate entries # to the FLIBS variable, above.) - -FC?=f77 -FFLAGS?= -FOPTFLAGS=${FFLAGS} +# +#FC=f77 +#FFLAGS?=$(FFLAGS) +#FOPTFLAGS?=$(FFLAGS) FREEFORMAT_FLAG=-ffree-form + +# These variables control whether we will use compiled versions of BLAS +# and LAPACK (which are generally slower), or whether those libraries are +# already available (presumably in an optimized form). + LAPACK=install BLAS=install +F2C=install +UCPP= # For Windows/cygwin, set SFX to ".exe"; for Unix/Linux leave it empty: diff --git a/biology/nab/files/patch-Makefile b/biology/nab/files/patch-Makefile index d754d329ca56..3fe19a6cd21f 100644 --- a/biology/nab/files/patch-Makefile +++ b/biology/nab/files/patch-Makefile @@ -1,29 +1,49 @@ ---- Makefile.orig Thu Apr 7 20:18:20 2005 -+++ Makefile Mon Apr 25 13:37:39 2005 -@@ -2,42 +2,39 @@ +--- Makefile.orig Mon Aug 21 11:16:05 2006 ++++ Makefile Fri Dec 15 16:06:57 2006 +@@ -2,31 +2,32 @@ include config.h -+all: install test ++all: install + install: -mkdir $(BINDIR) $(LIBDIR) $(INCDIR) -- (cd ucpp-1.3; make install ) +- (cd ucpp-1.3; make $(UCPP) ) - (cd byacc; make install ) -- (cd lapack; make $(LAPACK) ) -- (cd blas; make $(BLAS) ) +- +-# here are the Fortran versions: +-# (cd lapack; make $(LAPACK) ) +-# (cd blas; make $(BLAS) ) +- +-# here are the C versions: +- (cd clapack; make $(LAPACK) ) +- (cd cblas; make $(BLAS) ) +- (cd f2c; make $(F2C) ) +- - (cd cifparse; make install ) - (cd src; make install ) - (cd nss; make install ) - (cd tleap; make install ) -+ (cd lapack; env NABHOME=.. make $(LAPACK) ) -+ (cd blas; env NABHOME=.. make $(BLAS) ) ++ (cd clapack; env NABHOME=.. make $(LAPACK) ) ++ (cd cblas; env NABHOME=.. make $(BLAS) ) ++ (cd f2c; env NABHOME=.. make $(F2C) ) + (cd cifparse; env NABHOME=.. make install ) + (cd src; env NABHOME=.. make install ) + (cd nss; env NABHOME=.. make install ) + (cd tleap; env NABHOME=.. make install ) ++# (cd peptide && \ ++# env NABHOME=.. ../bin/nab $(CFLAGS) -o peptide peptide.nab ) ++# cp -p peptide/README doc/README-peptide ++# mv peptide/peptide bin ++# @echo ++# @echo "Ignore conflicting types warnings" ++# @echo ++# (cd suppose; env NABHOME=.. make all ) ++# cp -p suppose/suppose.1 doc ++# mv suppose/suppose suppose/PCA_suppose bin @echo - @echo "completed installation of NAB version 5" +- @echo "completed installation of NAB version 5" ++ @echo "completed installation of NAB version 5.1" @echo clean: @@ -32,20 +52,13 @@ (cd cifparse; make clean ) (cd src; make clean ) (cd nss; make clean ) - (cd tleap; make clean ) - (cd lapack; make clean ) - (cd blas; make clean ) -- -+ - uninstall: clean -- (cd ucpp-1.3; make uninstall ) - (cd cifparse; make uninstall ) - (cd src; make uninstall ) - (cd nss; make uninstall ) - (cd tleap; make uninstall ) - -/bin/rm config.h - -rm -rf $(BINDIR) $(LIBDIR) $(INCDIR) +@@ -34,10 +35,12 @@ + (cd cblas; make clean ) + (cd clapack; make clean ) + (cd f2c; make clean ) - ++ (cd suppose; make clean ) ++ (cd peptide && rm -f peptide.c peptide ) + # note: "make test" needs to follow "make", since it is very hard to # tell if the compiler is completely "made" or not. diff --git a/biology/nab/files/patch-configure b/biology/nab/files/patch-configure new file mode 100644 index 000000000000..412974c8fcfa --- /dev/null +++ b/biology/nab/files/patch-configure @@ -0,0 +1,11 @@ +--- configure.orig Mon Aug 21 11:18:10 2006 ++++ configure Fri Aug 25 22:30:10 2006 +@@ -61,7 +61,7 @@ + p4='no' + gotolib='no' + compiler='gcc' +-processor=`/bin/uname -p` ++processor=`/usr/bin/uname -p` + static='no' + + while [ $# -gt 0 ]; do diff --git a/biology/nab/files/patch-examples:program_7.nab b/biology/nab/files/patch-examples:program_7.nab deleted file mode 100644 index 4e6455533df4..000000000000 --- a/biology/nab/files/patch-examples:program_7.nab +++ /dev/null @@ -1,19 +0,0 @@ -*** examples/program_7.nab Wed Mar 10 18:57:51 1999 ---- examples/program_7.nab Sun Jun 2 13:40:36 2002 -*************** -*** 9,15 **** - cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" ); - - m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb", -! "dna", 2.25, -4.96, 36.0, 4.38, "" ); - - b = newbounds(m, ""); - allocate xyz[ 4*m.natoms ]; ---- 9,15 ---- - cseq = wc_complement( "acgtacgt", "dna.amber94.rlb", "dna" ); - - m = wc_helix( seq, "dna.amber94.rlb", "dna", cseq, "dna.amber94.rlb", -! "dna", 2.25, -4.96, 36.0, 3.38, "" ); - - b = newbounds(m, ""); - allocate xyz[ 4*m.natoms ]; diff --git a/biology/nab/files/patch-src:wc_helix.nab b/biology/nab/files/patch-src:wc_helix.nab new file mode 100644 index 000000000000..960c76b2341e --- /dev/null +++ b/biology/nab/files/patch-src:wc_helix.nab @@ -0,0 +1,11 @@ +--- src/wc_helix.nab.orig Thu Apr 7 20:17:27 2005 ++++ src/wc_helix.nab Fri Sep 15 09:22:13 2006 +@@ -25,6 +25,8 @@ + + loup["g"] = "G"; loup["a"] = "A"; + loup["t"] = "T"; loup["c"] = "C"; ++ loup["G"] = "G"; loup["A"] = "A"; ++ loup["T"] = "T"; loup["C"] = "C"; + + has_s = 1; has_a = 1; + if( sreslib == "" ) sreslib_use = "all_nucleic94.lib"; diff --git a/biology/nab/files/patch-src_Makefile b/biology/nab/files/patch-src_Makefile index 32a56f228ba4..70f7c1b799f1 100644 --- a/biology/nab/files/patch-src_Makefile +++ b/biology/nab/files/patch-src_Makefile @@ -1,6 +1,6 @@ ---- src/Makefile.orig Fri Apr 8 03:17:27 2005 -+++ src/Makefile Sat Apr 30 00:02:37 2005 -@@ -181,6 +181,14 @@ +--- src/Makefile.orig Fri Aug 11 17:38:10 2006 ++++ src/Makefile Fri Dec 15 17:01:39 2006 +@@ -189,6 +189,14 @@ cp defreal.h $(INCDIR) cp nab.h $(INCDIR) @@ -9,7 +9,7 @@ + -DINCDIR='"$(PREFIX)/include"' \ + -DLIBDIR='"$(PREFIX)/share/nab/lib"' \ + $(CFLAGS) -DCC='"$(CC)"' -DCPP='"$(CPP)"' \ -+ -DFLIBS='"$(PREFIX)/share/nab/lib/libsym.a $(PREFIX)/share/nab/lib/lapack.a $(PREFIX)/share/nab/lib/blas.a -lg2c"' \ ++ -DFLIBS='"$(PREFIX)/share/nab/lib/libsym.a $(PREFIX)/share/nab/lib/lapack.a $(PREFIX)/share/nab/lib/blas.a $(PREFIX)/share/nab/lib/f2c.a"' \ + -static -o ../bin/nab${SFX} nab.c + uninstall: clean diff --git a/biology/nab/files/patch-suppose_Makefile b/biology/nab/files/patch-suppose_Makefile new file mode 100644 index 000000000000..9317b951a30c --- /dev/null +++ b/biology/nab/files/patch-suppose_Makefile @@ -0,0 +1,10 @@ +--- suppose/Makefile.orig Thu Apr 7 20:18:34 2005 ++++ suppose/Makefile Sat Aug 26 08:49:50 2006 +@@ -1,5 +1,7 @@ + include ../config.h + ++all: suppose$(SFX) PCA_suppose$(SFX) ++ + suppose$(SFX): suppose.nab + nab -o suppose$(SFX) suppose.nab + diff --git a/biology/nab/pkg-descr b/biology/nab/pkg-descr index 0d61ae35a96a..2c37138e877a 100644 --- a/biology/nab/pkg-descr +++ b/biology/nab/pkg-descr @@ -18,6 +18,5 @@ Please send comments and suggestions to Tom Macke you find the program useful, please send us a note outlining your applications. -This port to FreeBSD by M. L. Dodson, Univ. of Texas Medical -Branch, Galveston -bdodson@scms.utmb.edu +This port to FreeBSD by M. L. Dodson, Active Site Dynamics +mldodson@houston.rr.com diff --git a/biology/nab/pkg-plist b/biology/nab/pkg-plist index 0570ee87a8ee..c7291dd51d1a 100644 --- a/biology/nab/pkg-plist +++ b/biology/nab/pkg-plist @@ -17,21 +17,47 @@ lib/cifparse.a lib/libnab.a lib/libsym.a %%PORTDOCS%%%%DOCSDIR%%/NAB.pdf -%%PORTDOCS%%%%DATADIR%%/benchmarks/gbrna.nab -%%PORTDOCS%%%%DATADIR%%/benchmarks/gbrna.out.check -%%PORTDOCS%%%%DATADIR%%/benchmarks/gcn4_md.nab -%%PORTDOCS%%%%DATADIR%%/benchmarks/gcn4_nr.nab -%%PORTDOCS%%%%DATADIR%%/benchmarks/gcn4p1.mc.pdb -%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.inpcrd -%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.nab -%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.out.check -%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.pdb -%%PORTDOCS%%%%DATADIR%%/benchmarks/mb.prmtop -%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.md1.x -%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.nab -%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.out.check -%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.pdb -%%PORTDOCS%%%%DATADIR%%/benchmarks/p450.prmtop +%%DATADIR%%/benchmarks/1akd.mc.pdb +%%DATADIR%%/benchmarks/1akd.mc.x +%%DATADIR%%/benchmarks/1akd.top +%%DATADIR%%/benchmarks/README +%%DATADIR%%/benchmarks/bench_amber +%%DATADIR%%/benchmarks/bench_cg.nab +%%DATADIR%%/benchmarks/bench_md.nab +%%DATADIR%%/benchmarks/bench_nr.nab +%%DATADIR%%/benchmarks/cox2.inpcrd +%%DATADIR%%/benchmarks/cox2.nab +%%DATADIR%%/benchmarks/cox2.pdb +%%DATADIR%%/benchmarks/cox2.prmtop +%%DATADIR%%/benchmarks/gact3.mc.pdb +%%DATADIR%%/benchmarks/gact3.mc.x +%%DATADIR%%/benchmarks/gact3.top +%%DATADIR%%/benchmarks/gact4.mc.pdb +%%DATADIR%%/benchmarks/gact4.mc.x +%%DATADIR%%/benchmarks/gact4.top +%%DATADIR%%/benchmarks/gbrna.nab +%%DATADIR%%/benchmarks/gbrna.out.check +%%DATADIR%%/benchmarks/gcn4_md.nab +%%DATADIR%%/benchmarks/gcn4_nr.nab +%%DATADIR%%/benchmarks/gcn4dna.mc.pdb +%%DATADIR%%/benchmarks/gcn4dna.mc.x +%%DATADIR%%/benchmarks/gcn4dna.top +%%DATADIR%%/benchmarks/gcn4p1.mc.pdb +%%DATADIR%%/benchmarks/gcn4p1.mc.x +%%DATADIR%%/benchmarks/gcn4p1.top +%%DATADIR%%/benchmarks/halfam0.mc.pdb +%%DATADIR%%/benchmarks/halfam0.mc.x +%%DATADIR%%/benchmarks/halfam0.top +%%DATADIR%%/benchmarks/mb.inpcrd +%%DATADIR%%/benchmarks/mb.nab +%%DATADIR%%/benchmarks/mb.out.check +%%DATADIR%%/benchmarks/mb.pdb +%%DATADIR%%/benchmarks/mb.prmtop +%%DATADIR%%/benchmarks/p450.mc.pdb +%%DATADIR%%/benchmarks/p450.mc.x +%%DATADIR%%/benchmarks/p450.nab +%%DATADIR%%/benchmarks/p450.out.check +%%DATADIR%%/benchmarks/p450.top %%DATADIR%%/bin/matextract %%DATADIR%%/bin/matgen %%DATADIR%%/bin/matmerge @@ -43,6 +69,7 @@ lib/libsym.a %%DATADIR%%/bin/tss_init %%DATADIR%%/bin/tss_main %%DATADIR%%/bin/tss_next +%%DATADIR%%/config.h %%DATADIR%%/coords %%DATADIR%%/dgdb/adna.basepair.db %%DATADIR%%/dgdb/adna.nucleotide.db @@ -249,45 +276,44 @@ lib/libsym.a %%DATADIR%%/dgdb/zdna.basepair.db %%DATADIR%%/dgdb/zdna.nucleotide.db %%DATADIR%%/dgdb/zdna.stack.db -%%PORTDOCS%%%%DATADIR%%/examples/ADE.pdb -%%PORTDOCS%%%%DATADIR%%/examples/Makefile -%%PORTDOCS%%%%DATADIR%%/examples/README -%%PORTDOCS%%%%DATADIR%%/examples/THY.pdb -%%PORTDOCS%%%%DATADIR%%/examples/acgtacgt.pdb -%%PORTDOCS%%%%DATADIR%%/examples/aua.triad.min.pdb -%%PORTDOCS%%%%DATADIR%%/examples/cgc.triad.min.pdb -%%PORTDOCS%%%%DATADIR%%/examples/gcg.triad.min.pdb -%%PORTDOCS%%%%DATADIR%%/examples/gcg10.pdb -%%PORTDOCS%%%%DATADIR%%/examples/gcg10.pdb.save -%%PORTDOCS%%%%DATADIR%%/examples/getbase.nab -%%PORTDOCS%%%%DATADIR%%/examples/mme_typical_calling_sequence.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_1.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_10.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_11.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_12.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_13.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_14.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_2.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_2.ref -%%PORTDOCS%%%%DATADIR%%/examples/program_3.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_4.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_4.ref -%%PORTDOCS%%%%DATADIR%%/examples/program_5.ata.in -%%PORTDOCS%%%%DATADIR%%/examples/program_5.cgc.in -%%PORTDOCS%%%%DATADIR%%/examples/program_5.gcg.in -%%PORTDOCS%%%%DATADIR%%/examples/program_5.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_5.tat.in -%%PORTDOCS%%%%DATADIR%%/examples/program_6.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_7.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_7.nab.orig -%%PORTDOCS%%%%DATADIR%%/examples/program_8.nab -%%PORTDOCS%%%%DATADIR%%/examples/program_9.nab -%%PORTDOCS%%%%DATADIR%%/examples/rna_pseudoknot.pdb -%%PORTDOCS%%%%DATADIR%%/examples/spline.nab -%%PORTDOCS%%%%DATADIR%%/examples/tat.triad.min.pdb -%%PORTDOCS%%%%DATADIR%%/examples/test.pdb -%%PORTDOCS%%%%DATADIR%%/examples/test.sup.pdb -%%PORTDOCS%%%%DATADIR%%/examples/toto.dat +%%DATADIR%%/examples/ADE.pdb +%%DATADIR%%/examples/Makefile +%%DATADIR%%/examples/README +%%DATADIR%%/examples/THY.pdb +%%DATADIR%%/examples/acgtacgt.pdb +%%DATADIR%%/examples/ata.triad.min.pdb +%%DATADIR%%/examples/aua.triad.min.pdb +%%DATADIR%%/examples/cgc.triad.min.pdb +%%DATADIR%%/examples/gcg.triad.min.pdb +%%DATADIR%%/examples/gcg10.pdb +%%DATADIR%%/examples/getbase.nab +%%DATADIR%%/examples/mme_typical_calling_sequence.nab +%%DATADIR%%/examples/program_1.nab +%%DATADIR%%/examples/program_10.nab +%%DATADIR%%/examples/program_11.nab +%%DATADIR%%/examples/program_12.nab +%%DATADIR%%/examples/program_13.nab +%%DATADIR%%/examples/program_14.nab +%%DATADIR%%/examples/program_2.nab +%%DATADIR%%/examples/program_2.ref +%%DATADIR%%/examples/program_3.nab +%%DATADIR%%/examples/program_4.nab +%%DATADIR%%/examples/program_4.ref +%%DATADIR%%/examples/program_5.ata.in +%%DATADIR%%/examples/program_5.cgc.in +%%DATADIR%%/examples/program_5.gcg.in +%%DATADIR%%/examples/program_5.nab +%%DATADIR%%/examples/program_5.tat.in +%%DATADIR%%/examples/program_6.nab +%%DATADIR%%/examples/program_7.nab +%%DATADIR%%/examples/program_8.nab +%%DATADIR%%/examples/program_9.nab +%%DATADIR%%/examples/rna_pseudoknot.pdb +%%DATADIR%%/examples/spline.nab +%%DATADIR%%/examples/tat.triad.min.pdb +%%DATADIR%%/examples/test.pdb +%%DATADIR%%/examples/test.sup.pdb +%%DATADIR%%/examples/toto.dat %%DATADIR%%/fd_data/abdna.dat %%DATADIR%%/fd_data/abdna.dat.old %%DATADIR%%/fd_data/adna.dat @@ -303,6 +329,7 @@ lib/libsym.a %%DATADIR%%/leap/cmd/leaprc.ff02 %%DATADIR%%/leap/cmd/leaprc.ff02EP %%DATADIR%%/leap/cmd/leaprc.ff03 +%%DATADIR%%/leap/cmd/leaprc.ff03ua %%DATADIR%%/leap/cmd/leaprc.ff84 %%DATADIR%%/leap/cmd/leaprc.ff86 %%DATADIR%%/leap/cmd/leaprc.ff94 @@ -310,6 +337,9 @@ lib/libsym.a %%DATADIR%%/leap/cmd/leaprc.ff96 %%DATADIR%%/leap/cmd/leaprc.ff98 %%DATADIR%%/leap/cmd/leaprc.ff99 +%%DATADIR%%/leap/cmd/leaprc.ff99SB +%%DATADIR%%/leap/cmd/leaprc.ffAM1 +%%DATADIR%%/leap/cmd/leaprc.ffPM3 %%DATADIR%%/leap/cmd/leaprc.gaff %%DATADIR%%/leap/cmd/leaprc.glycam04 %%DATADIR%%/leap/cmd/leaprc.glycam04EP @@ -330,6 +360,8 @@ lib/libsym.a %%DATADIR%%/leap/lib/all_amino91.lib %%DATADIR%%/leap/lib/all_amino94.lib %%DATADIR%%/leap/lib/all_amino94.nmr.lib +%%DATADIR%%/leap/lib/all_aminoAM1.lib +%%DATADIR%%/leap/lib/all_aminoPM3.lib %%DATADIR%%/leap/lib/all_aminoct02.lib %%DATADIR%%/leap/lib/all_aminoct02EP.lib %%DATADIR%%/leap/lib/all_aminoct91.lib @@ -350,6 +382,7 @@ lib/libsym.a %%DATADIR%%/leap/lib/ff02EP.cmd %%DATADIR%%/leap/lib/ff03.cmd %%DATADIR%%/leap/lib/ff03.log +%%DATADIR%%/leap/lib/ff03ua.cmd %%DATADIR%%/leap/lib/ff91.cmd %%DATADIR%%/leap/lib/ff94.cmd %%DATADIR%%/leap/lib/glycam91.cmd @@ -366,19 +399,28 @@ lib/libsym.a %%DATADIR%%/leap/lib/solvents.cmd %%DATADIR%%/leap/lib/solvents.lib %%DATADIR%%/leap/lib/spcebox.off +%%DATADIR%%/leap/lib/spcfwbox.off %%DATADIR%%/leap/lib/tip3pbox.off %%DATADIR%%/leap/lib/tip4pbox.off %%DATADIR%%/leap/lib/tip4pewbox.off +%%DATADIR%%/leap/lib/uni_amino03.lib +%%DATADIR%%/leap/lib/uni_aminoct03.lib +%%DATADIR%%/leap/lib/uni_aminont03.lib %%DATADIR%%/leap/parm/frcmod.chcl3 %%DATADIR%%/leap/parm/frcmod.constph %%DATADIR%%/leap/parm/frcmod.dc4 %%DATADIR%%/leap/parm/frcmod.ff03 +%%DATADIR%%/leap/parm/frcmod.ff03ua +%%DATADIR%%/leap/parm/frcmod.ff99SB +%%DATADIR%%/leap/parm/frcmod.ff99SP %%DATADIR%%/leap/parm/frcmod.meoh %%DATADIR%%/leap/parm/frcmod.mod_phipsi.1 %%DATADIR%%/leap/parm/frcmod.mod_phipsi.2 %%DATADIR%%/leap/parm/frcmod.nma %%DATADIR%%/leap/parm/frcmod.pol3 +%%DATADIR%%/leap/parm/frcmod.qspcfw %%DATADIR%%/leap/parm/frcmod.spce +%%DATADIR%%/leap/parm/frcmod.spcfw %%DATADIR%%/leap/parm/frcmod.tip4p %%DATADIR%%/leap/parm/frcmod.tip4pew %%DATADIR%%/leap/parm/frcmod.tip5p @@ -386,7 +428,6 @@ lib/libsym.a %%DATADIR%%/leap/parm/gaff.dat %%DATADIR%%/leap/parm/glycam04.dat %%DATADIR%%/leap/parm/glycam04EP.dat -%%DATADIR%%/leap/parm/leap.log %%DATADIR%%/leap/parm/nucgen.dat %%DATADIR%%/leap/parm/opls.info %%DATADIR%%/leap/parm/opls_parm.dat @@ -398,6 +439,8 @@ lib/libsym.a %%DATADIR%%/leap/parm/parm98.dat %%DATADIR%%/leap/parm/parm99.dat %%DATADIR%%/leap/parm/parm99EP.dat +%%DATADIR%%/leap/parm/parmAM1.dat +%%DATADIR%%/leap/parm/parmPM3.dat %%DATADIR%%/leap/parm/toyrna.dat %%DATADIR%%/leap/prep/all.in %%DATADIR%%/leap/prep/all_amino02.in @@ -430,15 +473,17 @@ lib/libsym.a %%DATADIR%%/leap/prep/protein.amberua.in %%DATADIR%%/leap/prep/toyrna.in %%DATADIR%%/leap/prep/uni.in +%%DATADIR%%/leap/prep/uni_amino03.in +%%DATADIR%%/leap/prep/uni_aminoct03.in +%%DATADIR%%/leap/prep/uni_aminont03.in %%DATADIR%%/leap/prep/unict.in %%DATADIR%%/leap/prep/unint.in %%DATADIR%%/lib/blas.a %%DATADIR%%/lib/cifparse.a +%%DATADIR%%/lib/f2c.a %%DATADIR%%/lib/lapack.a %%DATADIR%%/lib/libnab.a %%DATADIR%%/lib/libsym.a -%%PORTDOCS%%%%DATADIR%%/peptide/README -%%PORTDOCS%%%%DATADIR%%/peptide/peptide.nab %%DATADIR%%/reslib/adna.std.rlb %%DATADIR%%/reslib/adna.std/adna.std.bnd %%DATADIR%%/reslib/adna.std/adna.std.pdb @@ -559,93 +604,87 @@ lib/libsym.a %%DATADIR%%/reslib/rna.amberua/rna.amberua.chi %%DATADIR%%/reslib/rna.amberua/rna.amberua.pdb %%DATADIR%%/reslib/rna.amberua/rna.amberua.qr -%%PORTDOCS%%%%DATADIR%%/suppose/Makefile -%%PORTDOCS%%%%DATADIR%%/suppose/PCA_suppose.nab -%%PORTDOCS%%%%DATADIR%%/suppose/ccmath.h -%%PORTDOCS%%%%DATADIR%%/suppose/eigen.c -%%PORTDOCS%%%%DATADIR%%/suppose/housev.c -%%PORTDOCS%%%%DATADIR%%/suppose/matutl.h -%%PORTDOCS%%%%DATADIR%%/suppose/qrevec.c -%%PORTDOCS%%%%DATADIR%%/suppose/suppose.1 -%%PORTDOCS%%%%DATADIR%%/suppose/suppose.nab -%%PORTDOCS%%%%DATADIR%%/suppose/trnm.c -%%PORTDOCS%%%%DATADIR%%/test/2.pdb -%%PORTDOCS%%%%DATADIR%%/test/5pti.obs -%%PORTDOCS%%%%DATADIR%%/test/5pti.pdb -%%PORTDOCS%%%%DATADIR%%/test/5pti.shifts.check -%%PORTDOCS%%%%DATADIR%%/test/Makefile -%%PORTDOCS%%%%DATADIR%%/test/asp.nab -%%PORTDOCS%%%%DATADIR%%/test/asp.out.check -%%PORTDOCS%%%%DATADIR%%/test/asp.pdb -%%PORTDOCS%%%%DATADIR%%/test/asp.top -%%PORTDOCS%%%%DATADIR%%/test/crambin.nab -%%PORTDOCS%%%%DATADIR%%/test/crambin.out.check -%%PORTDOCS%%%%DATADIR%%/test/crambin.pdb -%%PORTDOCS%%%%DATADIR%%/test/crambin.top -%%PORTDOCS%%%%DATADIR%%/test/crambin.x -%%PORTDOCS%%%%DATADIR%%/test/d01.lin.check -%%PORTDOCS%%%%DATADIR%%/test/d01.pdb.check -%%PORTDOCS%%%%DATADIR%%/test/dg_gyrate.nab -%%PORTDOCS%%%%DATADIR%%/test/dg_gyrate.out.check -%%PORTDOCS%%%%DATADIR%%/test/dg_gyrate2.nab -%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.ambpdb -%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.nab -%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.out.check -%%PORTDOCS%%%%DATADIR%%/test/dhfrndpmtx.prmtop -%%PORTDOCS%%%%DATADIR%%/test/dna.circle.nab -%%PORTDOCS%%%%DATADIR%%/test/duplex.in -%%PORTDOCS%%%%DATADIR%%/test/duplex.nab -%%PORTDOCS%%%%DATADIR%%/test/fd.nab -%%PORTDOCS%%%%DATADIR%%/test/fd.pdb.check -%%PORTDOCS%%%%DATADIR%%/test/gbrna.nab -%%PORTDOCS%%%%DATADIR%%/test/gbrna.out.check -%%PORTDOCS%%%%DATADIR%%/test/gbrna.pdb -%%PORTDOCS%%%%DATADIR%%/test/gbrna.prmtop -%%PORTDOCS%%%%DATADIR%%/test/gbrna_long.nab -%%PORTDOCS%%%%DATADIR%%/test/gbrna_long.out.check -%%PORTDOCS%%%%DATADIR%%/test/gbtrx.nab -%%PORTDOCS%%%%DATADIR%%/test/gbtrx.out.check -%%PORTDOCS%%%%DATADIR%%/test/get_pep_info.nab -%%PORTDOCS%%%%DATADIR%%/test/get_ring_info.nab -%%PORTDOCS%%%%DATADIR%%/test/get_sugar_info.nab -%%PORTDOCS%%%%DATADIR%%/test/getresid_from_pdb.nab -%%PORTDOCS%%%%DATADIR%%/test/hash.in -%%PORTDOCS%%%%DATADIR%%/test/hash.nab -%%PORTDOCS%%%%DATADIR%%/test/hash.out.check -%%PORTDOCS%%%%DATADIR%%/test/ico.sym -%%PORTDOCS%%%%DATADIR%%/test/ico.sym.out.check -%%PORTDOCS%%%%DATADIR%%/test/ltest.nab -%%PORTDOCS%%%%DATADIR%%/test/ltest.out.check -%%PORTDOCS%%%%DATADIR%%/test/mm_plus_dg.nab -%%PORTDOCS%%%%DATADIR%%/test/pointplane.nab -%%PORTDOCS%%%%DATADIR%%/test/prm.nab -%%PORTDOCS%%%%DATADIR%%/test/prm.out.check -%%PORTDOCS%%%%DATADIR%%/test/prmtop -%%PORTDOCS%%%%DATADIR%%/test/prmtop.gb2 -%%PORTDOCS%%%%DATADIR%%/test/pseudoknot.nab -%%PORTDOCS%%%%DATADIR%%/test/rattle_md.nab -%%PORTDOCS%%%%DATADIR%%/test/rattle_md.out.check -%%PORTDOCS%%%%DATADIR%%/test/rattle_min.nab -%%PORTDOCS%%%%DATADIR%%/test/rattle_min.out.check -%%PORTDOCS%%%%DATADIR%%/test/read_obs_shifts.nab -%%PORTDOCS%%%%DATADIR%%/test/ref.out.check -%%PORTDOCS%%%%DATADIR%%/test/reflexive.nab -%%PORTDOCS%%%%DATADIR%%/test/rembed.nab -%%PORTDOCS%%%%DATADIR%%/test/rembed.out.check -%%PORTDOCS%%%%DATADIR%%/test/sbcoil.nab -%%PORTDOCS%%%%DATADIR%%/test/shifts.h -%%PORTDOCS%%%%DATADIR%%/test/shifts.nab -%%PORTDOCS%%%%DATADIR%%/test/swap_shifts.nab -%%PORTDOCS%%%%DATADIR%%/test/tbv.60.com.pdb.check -%%PORTDOCS%%%%DATADIR%%/test/tbv.com.pdb -%%PORTDOCS%%%%DATADIR%%/test/tprmtop.check -%%PORTDOCS%%%%DATADIR%%/test/trxox.2.4ns.pdb -%%PORTDOCS%%%%DATADIR%%/test/trxox.2.4ns.x -%%PORTDOCS%%%%DATADIR%%/test/vizgrad.nab -%%PORTDOCS%%%%DATADIR%%/test/vizgrad.pdb -%%PORTDOCS%%%%DATADIR%%/test/vizgrad.prm -%%PORTDOCS%%%%DATADIR%%/test/write_sander_inp.nab -%%DATADIR%%/config.h +%%DATADIR%%/test/2.pdb +%%DATADIR%%/test/5pti.obs +%%DATADIR%%/test/5pti.pdb +%%DATADIR%%/test/5pti.shifts.check +%%DATADIR%%/test/Makefile +%%DATADIR%%/test/asp.nab +%%DATADIR%%/test/asp.out.check +%%DATADIR%%/test/asp.pdb +%%DATADIR%%/test/asp.top +%%DATADIR%%/test/aspnb.nab +%%DATADIR%%/test/aspnb.out.check +%%DATADIR%%/test/cif.nab +%%DATADIR%%/test/crambin.nab +%%DATADIR%%/test/crambin.out.check +%%DATADIR%%/test/crambin.pdb +%%DATADIR%%/test/crambin.top +%%DATADIR%%/test/crambin.x +%%DATADIR%%/test/d01.lin.check +%%DATADIR%%/test/d01.pdb.check +%%DATADIR%%/test/dg_gyrate.nab +%%DATADIR%%/test/dg_gyrate.out.check +%%DATADIR%%/test/dg_gyrate2.nab +%%DATADIR%%/test/dhfrndpmtx.ambpdb +%%DATADIR%%/test/dhfrndpmtx.nab +%%DATADIR%%/test/dhfrndpmtx.out.check +%%DATADIR%%/test/dhfrndpmtx.prmtop +%%DATADIR%%/test/dna.circle.nab +%%DATADIR%%/test/duplex.in +%%DATADIR%%/test/duplex.nab +%%DATADIR%%/test/fd.nab +%%DATADIR%%/test/fd.pdb.check +%%DATADIR%%/test/gbrna.cif.check +%%DATADIR%%/test/gbrna.nab +%%DATADIR%%/test/gbrna.out.check +%%DATADIR%%/test/gbrna.pdb +%%DATADIR%%/test/gbrna.prmtop +%%DATADIR%%/test/gbrna_long.nab +%%DATADIR%%/test/gbrna_long.out.check +%%DATADIR%%/test/gbtrx.nab +%%DATADIR%%/test/gbtrx.out.check +%%DATADIR%%/test/get_pep_info.nab +%%DATADIR%%/test/get_ring_info.nab +%%DATADIR%%/test/get_sugar_info.nab +%%DATADIR%%/test/getresid_from_pdb.nab +%%DATADIR%%/test/hash.in +%%DATADIR%%/test/hash.nab +%%DATADIR%%/test/hash.out.check +%%DATADIR%%/test/ico.sym +%%DATADIR%%/test/ico.sym.out.check +%%DATADIR%%/test/ltest.nab +%%DATADIR%%/test/ltest.out.check +%%DATADIR%%/test/mm_plus_dg.nab +%%DATADIR%%/test/pointplane.nab +%%DATADIR%%/test/prm.nab +%%DATADIR%%/test/prm.out.check +%%DATADIR%%/test/prmtop +%%DATADIR%%/test/prmtop.gb2 +%%DATADIR%%/test/pseudoknot.nab +%%DATADIR%%/test/rattle_md.nab +%%DATADIR%%/test/rattle_md.out.check +%%DATADIR%%/test/rattle_min.nab +%%DATADIR%%/test/rattle_min.out.check +%%DATADIR%%/test/read_obs_shifts.nab +%%DATADIR%%/test/ref.out.check +%%DATADIR%%/test/reflexive.nab +%%DATADIR%%/test/rembed.nab +%%DATADIR%%/test/rembed.out.check +%%DATADIR%%/test/sbcoil.nab +%%DATADIR%%/test/shifts.h +%%DATADIR%%/test/shifts.nab +%%DATADIR%%/test/swap_shifts.nab +%%DATADIR%%/test/tbv.60.com.pdb.check +%%DATADIR%%/test/tbv.com.pdb +%%DATADIR%%/test/tprmtop.check +%%DATADIR%%/test/trxox.2.4ns.pdb +%%DATADIR%%/test/trxox.2.4ns.x +%%DATADIR%%/test/vizgrad.nab +%%DATADIR%%/test/vizgrad.pdb +%%DATADIR%%/test/vizgrad.prm +%%DATADIR%%/test/write_sander_inp.nab +@dirrm %%DATADIR%%/test @dirrm %%DATADIR%%/reslib/rna.amberua @dirrm %%DATADIR%%/reslib/rna.amber94 @dirrm %%DATADIR%%/reslib/protein.opls @@ -668,14 +707,11 @@ lib/libsym.a @dirrm %%DATADIR%%/leap @dirrm %%DATADIR%%/include @dirrm %%DATADIR%%/fd_data +@dirrm %%DATADIR%%/examples @dirrm %%DATADIR%%/dgdb/stacking @dirrm %%DATADIR%%/dgdb/basepairs @dirrm %%DATADIR%%/dgdb @dirrm %%DATADIR%%/bin -%%PORTDOCS%%@dirrm %%DATADIR%%/benchmarks -%%PORTDOCS%%@dirrm %%DATADIR%%/examples -%%PORTDOCS%%@dirrm %%DATADIR%%/peptide -%%PORTDOCS%%@dirrm %%DATADIR%%/suppose -%%PORTDOCS%%@dirrm %%DATADIR%%/test +@dirrm %%DATADIR%%/benchmarks @dirrm %%DATADIR%% %%PORTDOCS%%@dirrm %%DOCSDIR%% -- cgit v1.2.3